A Biogeographic Assessment off North/Central California:

To Support the Joint Management Plan Review for 

Cordell Bank, Gulf of the Farallones, and Monterey Bay

National Marine Sanctuaries: Phase I -

Marine Fishes, Birds and Mammals

Prepared by NOAA's Center for Coastal Monitoring and Assessment - Biogeography Team

National Centers for Coastal Ocean Science

December 2003

__________________________________________________________________________________________________________________________________________

A Biogeographic Assessment off North/Central California:

To Support the Joint Management Plan Review for 

Cordell Bank, Gulf of the Farallones, and Monterey Bay

National Marine Sanctuaries: Phase I -

Marine Fishes, Birds and Mammals

Prepared by NOAA's Center for Coastal Monitoring and Assessment - Biogeography Team

National Centers for Coastal Ocean Science
ABOUT THIS DOCUMENT

In the spring of 2001, NOAA’s National Marine Sanctuary Program (NMSP) and National Centers for Coastal Ocean Science (NCCOS), launched a 24-month effort to assess biogeographic patterns of selected marine species found within and adjacent to 

the boundaries of three west coast National Marine Sanctuaries. These sanctuaries, Monterey Bay, Gulf of the Farallones, and Cordell Bank, are conducting a joint review process to update sanctuary management plans. To support this review, NCCOS’s 

Biogeography Program is leading a partnership effort to conduct a robust analytical assessment to define important biological areas and time periods within, and adjacent to, current sanctuary boundaries. The assessment was based on a synthesis of 

many data sets that were provided by project partners. This document represents the results of the first of two phases of the assessment. Phase I provides data, analytical results, a description of ecosystems and their linkages, identifies data gaps, and 

suggests future activities to be addressed in Phase II.

Phase I of the biogeographic assessment was formulated around three integrated study components: 1) an Ecological Linkages Report, 2) biogeographic analyses, and 3) development of Geographical Information System (GIS) data for incorporation into 

NMSP’s Marine Information System (MarIS). The majority of the results from the assessment are presented as a suite of GIS maps to visually display species biogeographic patterns across the study area. The body of this document provides examples 

of the entire suite of digital map products found on the CD-ROM located on the back cover of this document. The spatial data and additional information, such as digital species distribution maps, and additional details on analytical methodologies are also 

presented on the CD-ROM. An HTML version of the CD-ROM can be found on the Biogeography Program website: http://biogeo.nos.noaa.gov/products/canms_cd/.

Results of the assessment are being used to assist the NMSP in addressing issues such as evaluating potential modification of sanctuary boundaries, and changes in management strategies or administration, based on the principles of biogeography. The 

progress of the biogeographic assessment for Central and Northern California National Marine Sanctuaries can be followed by consulting NCCOS’s Biogeography Program web site: http://biogeo.nos.noaa.gov/projects/assess/ca_nms/.

For questions and comments, please contact:

Dr. Mark E. Monaco, Biogeography Team Leader

NOAA/NCCOS/CCMA

1305 East West Highway, N/SCI1

Silver Spring, MD 20910

p. 301-713-3028 x 160

f. 301-713-4384

mark.monaco@noaa.gov

or

Mr. Charles E. Alexander, National Programs Branch Chief

NOAA/NMSP

1305 East West Highway, 

Silver Spring, MD 20910

p. 301-713-3125 x 147

f. 301-713-0404

charles.alexander@noaa.gov

Citation:

NOAA National Centers for Coastal Ocean Science (NCCOS) 2003. A Biogeographic Assessment off North/Central 

California: To Support the Joint Management Plan Review for Cordell Bank, Gulf of the Farallones, and Monterey 

Bay National Marine Sanctuaries: Phase I - Marine Fishes, Birds and Mammals. Prepared by NCCOS’s Biogeography Team in cooperation with the National Marine Sanctuary Program. Silver Spring, MD 145 pp. 

David Ainley, H.T. Harvey and Associates

Satie Airamé, National Marine Sanctuary Program

Charles Alexander, National Marine Sanctuary Program

Lisa Ballance, Southwest Fisheries Science Center

Maria Brown, National Marine Sanctuary Program

Erica Burton, National Marine Sanctuary Program

Kenneth Buja, National Centers for Coastal Ocean Science

Chris Caldow, National Centers for Coastal Ocean Science

Janet Casey, R.G. Ford Consulting Company

John Christensen, National Centers for Coastal Ocean Science

Lawrence Claflin, National Centers for Coastal Ocean Science

Randall Clark, National Centers for Coastal Ocean Science

Michael Coyne, National Centers for Coastal Ocean Science

Andrew DeVogelaere, National Marine Sanctuary Program

William Douros, National Marine Sanctuary Program

R. Glenn Ford, R.G. Ford Consulting Company

Steve Gaines, University of California Santa Barbara

Tracy Gill, National Centers for Coastal Ocean Science

Jamison Higgins, National Centers for Coastal Ocean Science

Dan Howard, National Marine Sanctuary Program

Olaf Jensen, National Centers for Coastal Ocean Science

Carol Keiper, Oikonos

Matthew Kendall, National Centers for Coastal Ocean Science

Kevin McMahon, National Centers for Coastal Ocean Science

Mark Monaco, National Centers for Coastal Ocean Science

Wendy Morrison, National Centers for Coastal Ocean Science

Sean Morton, National Marine Sanctuary Program

Jan Roletto, National Marine Sanctuary Program

Larry Spear, H.T. Harvey and Associates 

Lynn Takata, National Centers for Coastal Ocean Science

Mitchell Tartt, National Marine Sanctuary Program

Christine Taylor, National Marine Sanctuary Program

Ed Ueber, National Marine Sanctuary Program

Jeannette Waddell, National Centers for Coastal Ocean Science

Anne Walton, National Marine Sanctuary Program

Wendy Williams, R.G. Ford Consulting Co.

Project Team

Cover Photo by Kip Evans

i
TABLE OF CONTENTS

About This Document ................................................................................................. i Section 3 Integration of Analyses................................................................................ 129 Table 8. Average frequency of occurrence of fish species assemblages (percent 

Table of Contents ....................................................................................................... ii Introduction.............................................................................................................. 129 occurrence calculated for each species and then averaged for each fish

Introduction................................................................................................................. 1 Data and Analyses .................................................................................................. 129 assemblage) for each 1999 midwater site group. Number of trawls in each 

 The Study Area..................................................................................................... 1 Analytical Map Products .......................................................................................... 130 site group is provided in the first row. Bold numbers represent influential

 Study Objectives .................................................................................................. 1 References .............................................................................................................. 136 species assemblages within that site group.................................................... 32

Section 1 Synopsis of Ecological Linkages Report................................................ 6 Section 4 Data Sources and Gaps ............................................................................... 138 Table 9. Example data matrix for calculating bathymetry SI values for subadult 

 Introduction........................................................................................................... 6 Introduction.............................................................................................................. 138 bocaccio taken in NMFS trawl samples (Rubec et al., 1999). ........................ 36

 National Marine Sanctuaries of Central and Northern California ........................ 6 Conclusions and Recommendations for Future Activities ....................................... 138 Table 10. Example presence/absence information and SI calculation from scientific

 Geographic Setting of the Study Area .................................................................. 6 References .............................................................................................................. 139 literature. ........................................................................................................ 36

 Ocean Currents .................................................................................................... 6 Section 5 Summary of Biogeographic Assessment .................................................. 140 Table 11. Marine bird species used in this analysis........................................................ 46

 Oceanographic Seasons ...................................................................................... 7 Background ............................................................................................................. 140 Table 12. Summary of at-sea survey data sets used in the analyses............................. 47

 Natural Perturbations ........................................................................................... 7 Biogeographic Assessment off North/Central California.......................................... 140 Table 13. Summary of combined data set effort by ocean season............................... . 48

 Ecosystems .......................................................................................................... 7 Ecological Linkages Report..................................................................................... 140 Table 14. Assignment of warm, cold and neutral periods, based on surface water 

 Biogeography ...................................................................................................... 8 Biogeographic Analyses .......................................................................................... 141 temperatures off Cental California .................................................................. 50

 Conclusions.......................................................................................................... 9 Integration of Analyses ............................................................................................ 142 Table 15. Life history and management information for selected marine birds off 

 References ........................................................................................................... 9 Data Sources and Gaps .......................................................................................... 143 north/central California.................................................................................... 84

Section 2 Biogeographic Analyses ........................................................................ 10 Phase II Biogeographic Assessment....................................................................... 143 Table 16. A summary of temporal and spatial patterns in the at-sea survey data

 Introduction......................................................................................................... 10 CD-ROM.................................................................................................................. 143 (1980-2001) of selected marine birds off north/central California. .................. 85

 Assessment Process ......................................................................................... 10 Concluding Comments ............................................................................................ 143 Table 17. Important at-sea areas for marine birds off north/central California, 

 References ......................................................................................................... 10 References .............................................................................................................. 143 based on biomass, density and diversity.. ...................................................... 86

Section 2.1 Biogeography of Fishes....................................................................... 12 Section 6 Phase II Biogeographic Assessment.......................................................... 144 Table 18. Major marine bird colonies along the central California coast . ...................... 87

 Introduction......................................................................................................... 12 Acknowledgments......................................................................................................... 145 Table 19. Three most important variables (of nine investigated) having independent

 Subsection 2.1.1 Assemblage Analyses ........................................................ 13 effects in explaining the variance in density of 25 selected marine bird 

 Introduction......................................................................................................... 13 species. .......................................................................................................... 88

 Review of Relevant Literature ............................................................................ 13 Table 20. Effects of ocean season and ENSO events on the abundance of 26 

 Introduction to Clustering ................................................................................... 14 marine bird species off central California between 1985 and 2002, as List of Tables Section Summary ............................................................................................... 33 determined through multiple regression analyses.. ........................................ 88 Table 1. Site group results for recreational data. The numbers of trip/location References ......................................................................................................... 34 Table 21. A summary of changes in marine bird occurrence patterns, as a response combinations associated with each group as well as average depth, ± stan- Subsection 2.1.2 Habitat Suitability Modeling............................................... 35 to warm and cold ocean anomalies, as determined by visual comparison of dard deviation, are provided. Different letters signify a significant difference Introduction......................................................................................................... 35 species’ maps during the 1997-1998 El Niño event and the using Tukey’s pairwise comparison on log adjusted depth with overall Data and Analyses ............................................................................................. 35 1999-2000 La Niña event................................................................................ 89 alpha set at 0.001. .......................................................................................... 24 Analytical Map Products ..................................................................................... 36 Table 22. Marine mammal species included in this assessment and map types Table 2. Average frequency of occurrence of fish species assemblages (percent Section Summary ............................................................................................... 44 developed for them (Phase I and Phase II) .................................................... 92 occurrence calculated for each species and then averaged for each fish Reviews.............................................................................................................. 44 Table 23. Summary of at-sea data sets used in the preliminary marine mammal assemblage) for each recreational site group. Numbers in bold represent Reviewers........................................................................................................... 44 analyses.......................................................................................................... 93 influential species assemblages within that site group. .................................. 24 References ......................................................................................................... 45 Table 24. Summary of combined data set effort for mammals, by ocean season.. ........ 93 Table 3. Site group results for shelf trawl data. The numbers of trawls associated with Section 2.2 Biogeography of Marine Birds ............................................................ 46 Table 25. Preliminary life history and management information for selected marine each group as well as average depth ± standard deviation are provided. Introduction......................................................................................................... 46 mammals off north/central California.. .......................................................... 123 Different letters signify a significant difference using Tukey’s pairwise Data and Analyses ............................................................................................ 46 Table 26. Summary statistics and parameter estimates for spatial models..................130 comparison on log adjusted depth with overall alpha set at 0.001. ................ 26 Analytical Map Products ..................................................................................... 50 Table 27. Matrix of data sets and their associated characteristics that were used or Table 4. Average frequency of occurrence of fish species assemblages (percent Section Summary ............................................................................................... 84 referenced in the biogeographic assessment. ............................................. 138 occurrence calculated for each species and then averaged for each fish Major Section Contributors................................................................................. 89 assemblage) for each shelf site group. Numbers in bold represent Reviewers........................................................................................................... 89 List of Figures influential species assemblages within that site group. .................................. 27 Personal Communications ................................................................................. 89 Figure 1. Project flow diagram showing steps to complete Biogeographic Table 5. Site group results for slope trawl data. The numbers of trawls associated with References ......................................................................................................... 90 Assessment Phase 1........................................................................................ 1 each group as well as average depth ± standard deviation are provided. Section 2.3 Biogeography of Marine Mammals..................................................... 92 Figure 2. Locator map of entire study area from Point Arena to Point Sal. National Different letters signify a significant difference using Tukey’s pairwise Introduction......................................................................................................... 92 Marine Sanctuary boundaries shown in red..................................................... 2 comparison on log adjusted depth with overall alpha set at 0.001. ................ 28 Data and Analyses ............................................................................................. 92 Figure 3. Detailed locator map of northern study area from Bodega Head to Table 6. Average frequency of occurrence of fish species assemblages (percent Analytical Map Products ..................................................................................... 94 Pescadero Point. National Marine Sanctuary boundaries shown in occurrence calculated for each species and then averaged for each fish Section Summary ............................................................................................. 123 red............. ....................................................................................................... 3 assemblage) for each slope site group. Bold numbers represent influential Discussion ........................................................................................................ 125 Figure 4. Detailed locator map of central study area from Pescadero Point to Pfeiffer species assemblages within that site group.................................................... 29 Major Section Contributors............................................................................... 125 Point. National Marine Sanctuary boundaries shown in red. ........................... 4 Table 7. Average frequency of occurrence of fish species assemblages (percent Reviewers......................................................................................................... 125 Figure 5. Detailed locator map of southern study area from Pfeiffer Point to occurrence calculated for each species and then averaged for each fish Personal Communications ................................................................................126 Point Sal. National Marine Sanctuary boundaries shown in red. ..................... 5 assemblage) for each 1998 midwater site group. Number of trawls in each References ........................................................................................................126 Figure 6. Biogeographic assessment process ............................................................... 10 site group is provided in the first row. Bold numbers represent influential Figure 7. 3-D image of bathymetric relief within and adjacent to the sanctuaries.......... 11 species assemblages within that site group.................................................... 31

ii
TABLE OF CONTENTS

Figure 8. Biogeographic approach to fish analysis ........................................................ 12 Figure 23. Location of site groups for NMFS slope trawls. Lines showing the 50, Figure 51. Rhinoceros auklet, seasonal density, high use areas and breeding

Figure 9. Hypothetical example of the methods used to determine species assemblag- 100, 200 and 2,000 depth contours are provided. .......................................... 29 colonies........................................................................................................... 69

es, site groups, and the interaction between species assemblages and Figure 24. Species assemblage results for the midwater trawls utilizing all data from Figure 52. Marine bird density, by season and for all seasons........................................ 71

 site groups...................................................................................................... 15 1986 to 2001. Assemblages are named for the most influential species in Figure 53. Marine bird biomass, by season and for all seasons. .................................... 72

Figure 10. Standard deviation of bathymetry calculated for a 1 km radius around each each group. Non-italicized species were consistently placed into the same Figure 54. Marine bird diversity, by season and for all seasons...................................... 73

cell. Results are presented in standard deviations above or below species assemblage >80% of the time; italicized species tended to roam Figure 55. Major marine bird breeding colonies. . ........................................................... 75

 the mean. ....................................................................................................... 16 into other assemblages with random sampling.............................................. 30 Figure 56. Density in warm, cold, and neutral periods: 1980-2001. ...............................

Figure 11. Species richness of individual NMFS shelf and slope trawls. ...................... . 17 Figure 25. Species assemblage results for the midwater trawls conducted in 1998. AsFigure 12. Mean species richness of NMFS shelf and slope trawls for 5’ grid cells. The semblages are named for the most influential species in each group. Nondeviation is shown as an overlay to provide an indication of the variability italicized species were consistently placed into the same species assemblage 

 in results for each grid cell. ............................................................................. 18 >80% of the time; italicized species tended to roam into other 

Figure 13. Species diversity of individual NMFS shelf and slope trawls. . ...................... 19 assemblages with random sampling............................................................... 31

Figure 14. Mean species diversity of NMFS shelf and slope trawls for 5’ grid cells. The Figure 26. Location of site groups for NMFS 1998 midwater trawls. Lines showing 

deviation is shown as an overlay to provide an indication of the the 50, 100, 200, and 2,000 depth contours are provided. ............................ 31

 variability in results for each grid cell. ............................................................. 20 Figure 27. Species assemblage results for the midwater trawls conducted in 1999. AsFigure 15. Species richness of rockfish from individual NMFS shelf and slope trawls.... 21 semblages are named for the most influential species in each group. NonFigure 16.The relationship between depth and rockfish richness showing mean rockfish italicized species were consistently placed into the same species assemblage 

richness (for 10 meter depth intervals between 50-1,300 meters). >80% of the time; italicized species tended to roam into other 

 The relationship was fit with a smoothing spline, lambda = 1,000,000. .......... 21 assemblages with random sampling............................................................... 32

Figure 17. NMFS shelf and slope trawls with the highest species diversity, species rich- Figure 28. Location of site groups for NMFS 1999 midwater trawls. Lines showing

ness, and rockfish richness are mapped. The underlying map illustrates the the 50, 100, 200, and 2,000 depth contours are provided. ............................ 32

bathymetric complexity of the study area and can be used to identify Figure 29. Overlap between the three data sets that analyzed demersal fish: CDF&G

 the shelf break. ............................................................................................... 22 recreational (yellow), NMFS shelf (green), and NMFS slope (orange). .......... 33

Figure 18.Species assemblage results for the recreational data. Assemblages are named Figure 30. Species habitat suitability modeling approach. .............................................. 35

for the most influential species in each group. Assemblages are arranged Figure 31. Polynomial regression curve fit with mean log abundance by categorical 

from shallow to deep, unless they are influential at all or none of the depths. bathymetric class for subadult bocaccio. ........................................................ 35

The assemblages that were not influential at any depth were composed of Figure 32. Bathymetric map for the north/central California study area. Red lines

relatively rare species, making depth associations indiscernible given the indicate National Marine Sanctuary boundaries. . .......................................... 37

methodology for defining “influential” assemblages. Non-italicized species Figure 33. Substrate types for the north/central California marine region....................... 38

were consistently placed into the same species assemblage >80% of the Figure 34. Potential distribution of habitat suitability for adult and subadult bocaccio. 

time; italicized species tended to roam into other assemblages with Map inset contains validation statistics. SI values for bathymetry and 

 random sampling. ........................................................................................... 23 substrate are graphically displayed below the map. ....................................... 39

Figure 19. Location of CDF&G recreational fishing data in 2.5 minute grids which are Figure 35. Potential distribution of habitat suitability for adult and subadult Dover sole. 

color coded according to the average depth of the fishing trips within the grid Map inset contains validation statistics. SI values for bathymetry 

cell. Lines showing the 50, 100, 200, and 2,000 depth contours and substrate are displayed below the maps. ................................................ 40

 are provided. ................................................................................................... 25 Figure 36. Potential distribution of habitat suitability for adult dungeness crab. Map inset 

Figure 20. Species assemblage results for the shelf trawls. Assemblages are named contains validation statistics. SI values for bathymetry and substrate 

for the most influential species in each group. Assemblages are arranged are graphically displayed below the map. ....................................................... 41

from shallow to deep, unless they are influential at all or none of the depths. Figure 37. Areas of groundfish potential hot spots based on mean fish species HSI

The assemblages that were not influential at any depth were composed of models and overlap of predicted highly suitable habitats. .............................. 42

relatively rare species, making depth associations indiscernible given the Figure 38. Areas of potential habitat importance based on mean HSI models for

methodology for defining “influential” assemblages. Non-italicized species selected species assemblages. ...................................................................... 43

were consistently placed into the same species assemblage >80% of the time; Figure 39. Spatial extent of data sets used in the marine bird analysis:

italicized species tended to roam into other assemblages with random ship-based surveys. ....................................................................................... 47

 sampling. ....................................................................................................... 26 Figure 40. Spatial extent of data sets used in the analysis: aerial surveys. .................... 48

Figure 21.Location of site groups for NMFS shelf trawls. Lines showing the 50, 100, Figure 41. Total survey effort for marine bird analyses.................................................... 49

 200, and 2,000 depth contours are provided. ................................................. 27 Figure 42. Western and Clark’s grebes, seasonal density and high use areas............... 51

Figure 22. Species assemblage results for the slope trawls. Assemblages are named Figure 43. Northern fulmar, seasonal density and high use areas. ................................. 53

for the most influential species in each group. Assemblages are arranged Figure 44. Sooty shearwater, seasonal density and high use areas. .............................. 55

from shallow to deep, unless they are influential at all or none of the depths. Figure 45. Ashy storm-petrel, seasonal density, high use areas, and breeding colonies.57

The assemblages that were not influential at any depth were composed of Figure 46. Leach’s storm-petrel, seasonal density, high use areas, and 

relatively rare species, making depth associations indiscernible given the breeding colonies............................................................................................ 59

methodology for defining “influential” assemblages. Non-italicized species Figure 47. Scoters, seasonal density and high use areas............................................... 61

were consistently placed into the same species assemblage >80% of the time; Figure 48. Brown pelican, seasonal density and high use areas. ................................... 63

italicized species tended to roam into other assemblages with random Figure 49. Black-legged kittiwake, seasonal density and high use areas. ...................... 65

 sampling.......................................................................................................... 28 Figure 50. Common murre, seasonal density, high use areas and breeding colonies. .. 67

76

Figure 57. Biomass in warm, cold and neutral periods: 1980-2001. ............................... 78

Figure 58. Diversity in warm, cold and neutral periods: 1980-2001. ............................... 80

Figure 59. Density during El Niño and La Niña events, 1997-2000. ............................... 82

Figure 60. El Niño/La Niña Event changes, as an example of regime shift effects......... 83

Figure 61. Total at-sea survey effort for marine mammal analysis. ................................. 94

Figure 62. Maps for southern sea otter: rangewide count and linear density, 

 fall 2001 and spring 2002............................................................................... 95

Figure 63. Map for California sea lion: haulouts and rookeries. ...................................... 96

Figure 64. Maps for California sea lion: seasonal at-sea densities, high use areas

 and rookeries. ................................................................................................. 97

Figure 65. Map for Steller sea lion: at-sea sightings and survey effort,

 rookeries and haulouts.................................................................................... 99

Figure 66. Maps for northern fur seal: seasonal at-sea densities, high use areas

 and rookery. .................................................................................................. 101

Figure 67. Map for harbor seal: at-sea sightings, survey effort and haulouts................ 103

Figure 68. Map for northern elephant seal: at-sea sightings and survey effort,

 rookeries and haulouts.................................................................................. 105

Figure 69. Maps for Dall’s porpoise: seasonal at-sea densities and high use areas..... 107

Figure 70. Maps for Pacific white-sided dolphin: seasonal at-sea densities and 

 high use areas. ............................................................................................. 109

Figure 71. Maps for Risso’s dolphin: seasonal at-sea densities and high use areas.....111

Figure 72. Maps for northern right-whale dolphin: seasonal at-sea densities and

 high use areas. ............................................................................................ 113

Figure 73. Map for blue whale: at-sea sightings and survey effort................................ 115

Figure 74. Maps for humpback whale: seasonal at-sea densities and high use areas. 117

Figure 75. Maps for gray whale: seasonal at-sea densities and high use areas........... 119

Figure 76. Maps for Dall’s porpoise: SWFSC stock assessment data: average

 group size of sightings and survey effort....................................................... 121

Figure 77. Maps for blue whale: SWFSC stock assessment data: average

 group size of sightings and survey effort....................................................... 122

Figure 78. Maps for humpback whale: SWFSC stock assessment data: average

 group size of sightings and survey effort....................................................... 122

Figure 79. Pictogram of species diversity...................................................................... 129

Figure 80. Estimated diversity (a), density (b), and hot spots (top 20%)

 (c) for marine birds........................................................................................ 131

Figure 81. Relationships between bird diversity and bathymetric variance and

 between bird density and depth. ................................................................... 131

Figure 82. Estimated diversity (a), density (b), and hot spots (top 20%) (c) for fish...... 132

Figure 83. Integration option 1, diversity hot spots (top 20%) for fish and

 marine birds. Coastal kelp bed areas are also shown. ................................. 133

Figure 84. Integration option 2, density hot spots (top 20%) for marine birds and fish.

 Coastal kelp bed areas are also shown. ....................................................... 134

Figure 85. Integration option 3, diversity and density, hot spots (top 20%) for fish

 and marine birds. Coastal kelp bed areas are also shown. .......................... 135

iii
INTRODUCTION

In the spring of 2001, NOAA’s National Marine Sanctuary 

Program (NMSP) and National Centers for Coastal Ocean 

Science (NCCOS), in consultation with the National Marine 

Fisheries Service (NMFS), launched a 24-month effort to 

define and assess biogeographic patterns of selected marine 

species found within and adjacent to the boundaries of three 

west coast National Marine Sanctuaries. These sanctuaries, 

Monterey Bay, Gulf of the Farallones, and Cordell Bank are 

conducting a joint review process to update sanctuary management plans. The management plans for these sanctuaries 

have not been updated for over ten years and the status of the 

natural resources and their management issues in and around 

the sanctuaries may have changed. In addition, significant accomplishments in research and resource assessments have 

been made within the region. Thus, it is important to incorporate 

new and expanding knowledge into the revised management 

plans for these Sanctuaries.

As part of the review process, the NMSP requires an integrated 

biogeographic assessment of the spatial and temporal distributions of marine resources off north/central California. The NMSP 

headquarters and sanctuary field personnel have partnered 

with NCCOS’s Biogeography Team to conduct this assessment. 

The biogeographic assessment includes the identification and 

characterization of important biological areas and time periods 

off the coast and addresses existing and emerging issues concerning management of biotic resources in the area. Results of 

this assessment aid the NMSP in addressing issues, such as 

potential modification of sanctuary boundaries and changes in 

management approaches based on the principles of biogeography. The publication of this document completes Phase I of 

the biogeographic assessment for the North/Central California 

National Marine Sanctuaries. The assessment and additional 

ecosystem characterization of habitats and species (e.g., estuaries) will continue over the next few years. The initial plans 

for Phase II are discussed in Section 6 of this document.

The Phase I assessment is based on biogeographic patterns 

of fishes, macroinvertebrates, marine mammals, and marine 

birds and the distribution of their habitats. The study did not 

attempt to define biogeographic patterns along the entire US 

west coast nor in very near shore environments (e.g, estuaries). 

Rather, the study area was restricted to the marine area from 

Point Arena (in the north) to Point Sal, California (in the south). 

The Assessment was based on a synthesis of data provided 

by project partners (e.g., NMFS fishery independent surveys). 

The biogeographic assessment was formulated around three 

integrated study components: 1) an Ecological Linkages Report, 2) biogeographic analyses, and 3) development of spatial 

data for incorporation into NMSP’s Marine Information System 

(MarIS). GIS-based data and additional information, such as 

the complete Ecological Linkages Report, can be found on the 

CD-ROM on the back cover of this document. To enable development and integration of these components and to support 

project management, the overall process used to conduct the 

biogeographic assessment is shown in Figure 1.

The Ecological Linkages Report is a comprehensive synthesis 

of existing information on ecological relationships between marine biota and the habitats they utilize along the West Coast. 

The report is much broader in geographic scope than the 

project study area and provides the context to understand 

overall assessment results relative to the biogeography of the 

West Coast. In addition, the report addresses near-shore and 

estuarine ecosystems while quantitative data analyses were 

conducted only for the marine waters of the National Marine 

Sanctuaries.

The biogeographic analyses component includes a suite of 

quantitative spatial and statistical analyses based on the distribution and abundance of fishes, marine birds, and marine 

mammals found in the Point Arena to Point Sal study area. The 

analytical results contributed to defining important biological 

areas throughout the region, based on visualization of species 

distribution patterns and community metrics. The results aid in 

understanding the potential implications to changes in sanctuary boundaries or management strategies relative to marine 

biogeography within and adjacent to the sanctuaries.

To enable NMSP and others to make maximum use of the spatial data generated from this study and other activities that are 

supporting the joint management plan revision process (e.g., 

economic assessments), the NMSP is developing a GIS tool. 

This GIS tool, the Marine Assessment and Resource Information System (MarIS), has been designed to facilitate the organization and analysis of spatial data to support NMSP management questions and issues within and across the sanctuaries. 

All GIS compatible data, the Ecological Linkages Report, and 

products from the biogeographic analyses component are found 

on the companion CD-ROM. The contents of the CD-ROM are 

also found on the web at http://biogeo.nos.noaa.gov/products/

canms_cd/. All of the applicable digital data will be integrated 

into MarIS.

THE STUDY AREA

The study area, shown on the locator maps, extends from Point 

Arena, in the southern portion of Mendocino county, to Point 

Sal, just south of Pismo Beach and the Nipomo Dunes area in 

Northern Santa Barbara county (Figure 2). Based on the California Department of Fish and Game’s 200-meter resolution 

bathymetry data, this map displays the locations of prominent 

bathymetric features occurring off the coast, including the continental shelf/slope interface. In support of this assessment, 

the National Geophysical Data Center, Monterey Bay Aquarium 

Research Institute, and the NMSP jointly developed the first 

high-resolution 70-meter bathymetry maps for the region. The 

highly resolved bathymetry is shown on the three regional maps 

to highlight the complexity of the seafloor and to begin outlining 

the multitude of distinct ecosystems occurring in this region 

(Figures 3-5). The Northern Region map focuses on Cordell 

Bank and Gulf of the Farallones National Marine Sanctuaries. Cordell Bank, the Farallon Islands, Bodega and Pioneer 

Canyons, and Gumdrop and Pioneer Seamounts appear as 

very clear features along the seafloor. The focus of the Central 

Region map is Monterey Bay. The most significant feature in 

this regional view is the Monterey Canyon, although the nearby 

canyons, Ascension, Año Nuevo, Cabrillo, Soquel, and Carmel, 

are also labeled. Other significant bathymetric features in this 

region include the Guide Seamount, Sur Ridge, and Shepard 

Meander. The bathymetry for most of the Southern Region 

map is less resolved than the other two, as the frequency of 

sampling was significantly less. In this area, the Sur and Lucia 

Canyons are found, as well as Santa Lucia Bank and one of 

the most prominent features in this region, the Davidson Seamount. Descriptions of the features observed in these maps, 

along with the linkages and processes operating to influence 

the distribution of associated biota, are found in the Ecological 

Linkages Report.

STUDY OBJECTIVES

Based on consultations with NMSP field and headquarters staff 

and requirements to update the sanctuary management plans, 

the following study objectives were addressed:

1. Identify and compile available priority biological and environmental data sets in the study area in order to conduct 

biogeographic analyses. 

2. Conduct marine biogeographic analyses of available data 

to define significant biological areas (i.e., “hot spots”) and time 

periods, based on species distributions, abundance, habitats, 

life stage function, and community metrics (e.g., species richness, diversity). 

3. Produce a report that describes the ecological components 

and linkages between the estuarine, coastal, and marine ecosystems of north/central California.

4. Develop GIS compatible data for integration into the 

NMSP’s Marine Information System (MarIS) to support 

Phase 1 

GIS

Analytical

Results

Digital

Products

Ecolinkage

Report

Identify

species and 

habitats of 

interest with 

sanctuaries

staff

DATA

COLLECTION

Metadata

creation

Evaluate data 

sets and 

conduct

preliminary

analyses

Revise

species and 

habitat list 

based on data 

quality and 

availability

Determine

optimal

analytical

approach

Develop Statement of 

Work and select PIs to 

write the report

Create web page for 

project information and 

product review

PIs deliver 

iterative draft 

reports for 

NOAA review

Conduct

analyses

and develop 

draft

products for 

review

Organize data and 

transfer to CD-ROM

Ecological Linkages Report

Integrate into NMSP’s

MarIS system

Conduct

review and 

revise

analytical

products

Biogeographic Analyses

GIS Data Development

Data collection and 

standardization

Interim Products

Draft

Biogeographic

Assessment

PIs

deliver

final

report

PIs develop 

presentation

of results

Project

‘Kickoff

Meetings’

with Team 

Members

Interim Product: 

Biogeographic

Assessment Atlas

Biogeographic

Assessment

Phase II

Biogeographic

Assessment

Phase I

Figure 1. Project flow diagram showing steps to complete Biogeographic Assessment Phase 1.

1
INTRODUCTION

sanctuary staff in developing and evaluating resource management scenarios.

5. Support sanctuary staff in the integration of biogeographic 

assessment products into revisions of the sanctuary management plans.

The publication of this product completes Phase I efforts to 

meet objectives 1-4. The data and analytical results from these 

objectives will be used to address objective 5 over the next year. 

This investigation synthesized many databases and information 

sources for the study area. The data and information originated 

from a wide variety of government, academic, and private institution studies that had different objectives, study areas, and 

methodologies. Thus, several criteria were used in selecting 

appropriate data sets for biogeographic analyses. For example, 

the selection process favored databases that addressed the entire study area and were conducted relatively consistently over 

time. Thus, small databases that were limited in both content 

and spatial coverage were generally not useful in developing 

the assessment. When appropriate, these types of databases 

were used to aid in the interpretation of results and to develop 

and validate species habitat suitability models.

The following sections of this document provide information 

on the data compiled, analytical approaches, and Phase I assessment results. For the three main study components, (the 

Ecological Linkages Report, biogeographic analyses, and the 

CD-ROM contents), the primary information found within each 

component is introduced, methods described, and representative or example results provided. Many of the results are 

presented as map products to easily convey the biogeographic 

distribution of species and associated habitats. In addition, a 

summary of the biogeographic assessment is found in section 

5. For more complete information (e.g., complete suite of digital 

species maps), please review and use the digital contents of 

the CD-ROM or the web version at http://biogeo.nos.noaa.gov/

products/canms_cd/.

Figure 2. Locator map of entire study area from Point Arena to Point Sal. National Marine Sanctuary boundaries shown in red.

124°W

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Figure 3. Detailed locator map of northern study area from Bodega Head to Pescadero Point. National Marine Sanctuary boundaries shown in red.

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Gulf of the Farallones

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National

Marine Sanctuary

Monterey Bay

National

Marine Sanctuary

Bodega

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Point

Reyes

Double Point

Bodega Head

Tomales Point

Tomales

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3
Figure 4. Detailed locator map of central study area from Pescadero Point to Pfeiffer Point. National Marine Sanctuary boundaries shown in red.

4

123°30'W

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Salinas River
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Monterey Bay

National

Marine Sanctuary Lopez Point

Point Piedras Blancas

3 nautical

mile line

Davidson

Seamount

Cambria

Point Sal

Area

Enlarged

Morro

Bay

Point Estero

0 10 20 30 40 50 5

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Southern Region

Lucia Cany on

Cape San Martin

Su r Canyon

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50 m

Estero

Bay

San

Luis Obispo

Bay

La Cruz

Canyon

Villa

Canyon

Mill Creek Canyon

Santa

Lucia

Bank

Pfeiffer Point

Point San Luis

Figure 5. Detailed locator map of southern study area from Pfeiffer Point to Point Sal. National Marine Sanctuary boundaries shown in red.

5
Section 1: SYNOPSIS OF ECOLOGICAL LINKAGES REPORT

INTRODUCTION

The Ecological Linkages Report complements the biogeographic analyses conducted by The National Centers for 

Coastal Ocean Science (NCCOS) by providing an overview 

of the physical and biological characteristics of the region. Key 

ecosystems and species occurring in estuarine and marine 

waters off northern and central California are highlighted and 

linkages between them discussed. In addition, this report describes biogeographic processes operating to affect species’ 

distributional patterns. The biogeographic analyses build upon 

this background to further understanding of the biogeography 

of this region. The following material is a synopsis of the report 

either excerpted or directly summarized from the completed 

document (Airamé et al., 2003) found on the companion CDROM.

NATIONAL MARINE SANCTUARIES OFF CENTRAL AND 

NORTHERN CALIFORNIA

The study area, from Point Arena to Point Sal, includes three 

national marine sanctuaries (Cordell Bank, Gulf of the Farallones, and Monterey Bay) encompassing marine and estuarine 

habitats along the central and northern coast of California. 

Together, these contiguous national marine sanctuaries include 

more than 650 km of coastline, from Bodega Bay, north of San 

Francisco, to Cambria, near San Luis Obispo, and a total area 

of approximately 18,000 km2

. 

The Gulf of the Farallones National Marine Sanctuary, established in 1981, includes an area of 3,250 km2

 off the northern 

and central California coast. The Gulf of the Farallones extends 

beyond the Sanctuary’s boundaries and is one of the broadest 

sections of the continental shelf off the U.S. West Coast. Besides the broad shelf, the major oceanographic feature that affects this coastal region is the San Francisco Bay Plume, which, 

under certain conditions, extends outwards to all areas of the 

Gulf. The Golden Gate, from which the plume emanates, lies 

midway along this section of coast. The Gulf of the Farallones 

National Marine Sanctuary itself, however, extends along the 

coast only as far south as Rocky Point, Marin County (where 

the Gulf of the Farallones National Marine Sanctuary abuts the 

Monterey Bay National Marine Sanctuary). Offshore, the Gulf 

of the Farallones National Marine Sanctuary extends farther 

south to the waters west of San Mateo County. Habitats within 

the Gulf of the Farallones National Marine Sanctuary include 

rocky shores, sandy beaches, estuaries, lagoons and bays, 

as well as the Farallon Islands and the subsurface Farallon 

Ridge. The entire stretch of the broad shelf within the physical features described above is strongly influenced by coastal 

upwelling and the San Francisco Bay Plume. The upwelled 

waters, which support tremendous phytoplankton production, 

are advected offshore into the California Current as eddies and 

jets. These productive waters stimulate growth of organisms 

at all levels of the marine food web. In periods when upwelling 

is reduced, the nutrient input from the San Francisco Plume 

becomes important. The Farallon Islands, which are protected 

as a National Wildlife Refuge, are home to the largest concentration of breeding seabirds in the contiguous United States (12 

species), as well as one of the richest assemblages of pinnipeds 

(5 species). About 163 species of marine, coastal, and estuarine 

birds and 36 species of marine mammals use the Sanctuary 

during breeding or migration. Further, great white sharks are 

attracted to marine mammal colonies on the Farallon Islands, 

Point Año Nuevo, and Año Nuevo Island. 

The Cordell Bank National Marine Sanctuary, designated in 

May 1989, includes an area of 1,362 km2 off the coast of central 

California (Figure 2: Northern Region). Cordell Bank is located 

at the edge of the continental shelf, about 80 km northwest of 

the Golden Gate Bridge and 33 km west of Point Reyes. The 

main feature of the Sanctuary is an offshore granite bank, 7 km 

wide and 15 km long. The rocky bank emerges from the soft 

sediments of the continental shelf, reaching within 37 m of the 

ocean’s surface. The base of the Bank is over 120 m deep. The 

combination of oceanographic conditions and undersea topography of Cordell Bank supports a diverse and productive marine 

ecosystem. A persistent upwelling plume projects southward 

and offshore from Point Arena and Point Reyes, transporting 

nutrients and organisms suspended in the water column into the 

bank’s relatively shallow waters. Insolation fuels primary productivity and eventually influences the entire food web through 

direct and indirect trophic linkages. This high local productivity 

supports abundant resident populations of invertebrates, fishes 

(240 species), seabirds (69 species), and marine mammals (28 

species), and attracts many migratory species.

The Monterey Bay National Marine Sanctuary, established in 

1992, is the largest of 13 marine sanctuaries administered by 

the National Marine Sanctuary Program. The Sanctuary extends from Rocky Point to Cambria Rock, encompassing nearly 

450 km of shoreline and 13,780 km2

 of ocean, extending an 

average distance of 32 km from shore. At its deepest point, the 

Sanctuary reaches a depth of 3,250 m. The Sanctuary includes 

a variety of coastal and marine habitats, such as rugged rocky 

shores, lush kelp forests, and several underwater canyons, the 

largest of which is the Monterey Submarine Canyon. North of 

Partington Point and within the Gulf of the Farallones, the continental shelf is relatively wide and shallow. South of Partington 

Point, the Sanctuary generally protects deep ocean, owing to 

the consistently narrow continental shelf that extends south to 

Point Conception. The diverse array of habitats in the Sanctuary is home to 33 marine mammals, 94 species of seabirds, 

at least 345 species of fishes, and numerous invertebrates, 

and plants.

GEOGRAPHIC SETTING OF THE STUDY AREA

The study region extends from Point Arena, a small peninsula 

on an elevated coastal plain in the southern portion of Mendocino County, to Point Sal, just south of Pismo Beach and 

the Nipomo Dunes area. The region consists of a multitude 

of diverse and important ecosystems that are very unique in 

their assemblages of marine organisms. Beginning near-shore, 

the coast of California, especially north of Point Reyes and 

south of Point Pinos, is renowned for its strikingly beautiful, 

dramatic rocky cliffs. Pocket beaches occur along the coast 

where streams and rivers deposit sediment along the shore. 

Rivers that flow over broad, flat expanses of soft sediments 

into the ocean may be strongly influenced by tides and are 

frequently associated with upland and salt marshes, sandy 

beaches, intertidal flats, and estuaries. Estuaries and lagoons 

commonly form where rivers enter the ocean, mixing fresh and 

salt water. Rocky shores, which are more resistant to erosion 

than the sandy beaches, support a complex intertidal community, influenced primarily by the semidiurnal movements of 

tides. Moving offshore, subtidal communities are strongly influenced by sediment type, nutrient input, and depth. The majority 

of the continental shelf is sandy, but rocky outcrops cover a 

portion of it, forming submerged reefs, seamounts, and other 

features. Marine algae, unable to attach to the shifting sandy 

sediments, find more secure substrate on rocky reefs. At the 

shelf break, the continental slope drops precipitously to depths 

of over 3000 m. Sediments, transported down the continental 

slope and submarine canyons, collect in broad fans at the 

base of the slope. Below the rise, the abyssal plain is relatively 

flat, broken occasionally by such features as seamounts and 

small depressions. It is this array of ecosystems, combined 

with the oceanographic processes affecting the composition 

and abundance of marine organisms in them, that make this 

such a unique area. 

OCEAN CURRENTS

The cold water California Current and comparatively warmwater Davidson Currents are major forces shaping the ecosystems in and around the study region. They affect upwelling 

and downwelling and, consequently, the amount of productivity 

6
Section 1: SYNOPSIS OF ECOLOGICAL LINKAGES REPORT

seen along the coast. Additionally, where the two converge 

at Point Conception, a barrier is created that many species 

do not cross. The species north of Point Conception, encompassing the entire study region right up through Washington 

State, are a part of the Oregonian Province, while just south 

of Point Conception, they belong to the Californian Province. 

Although many species have ranges that end at the borders 

of these biogeographic zones under normal conditions, species of the subtropical Californian Province may occasionally 

extend their ranges to central and northern California during 

unusually warm oceanographic events, such as El Niño and 

the Pacific Decadal Oscillation. Other more localized oceanographic features, such as eddies, internal waves and bores, 

are also important factors influencing the distribution and 

abundance of marine species.

OCEANOGRAPHIC SEASONS

While certain geological and biological features are evident 

along particular regions of the coast, the same oceanographic 

processes and climatic phenomena are operating throughout 

the study region. Over a 12 month time-frame, the study area 

is exposed to three distinct oceanographic periods that vary 

with respect to prominence and location of ocean currents. 

These periods, described by upwelling (March to August), wind 

relaxation (August to November), and winter storms (November 

to March), are associated with different degrees of upwelling 

or downwelling. The amount of production in surface waters 

and the ability of organisms to disperse is directly impacted 

by these processes. In response to these periods, the abundance and types of organisms present in a given region change 

throughout the year. 

NATURAL PERTURBATIONS

Longer term climatic phenomena influencing the region include: 

El Niño, Pacific Decadal Oscillation, and global warming. Off 

the coast of California, El Niño events are characterized by 

increases in ocean temperature and sea level, enhanced onshore and northward flow, and reduced coastal upwelling of 

deep, cold, nutrient-rich water. During this period, survivorship 

and reproductive success of planktivorous invertebrates and 

fishes decrease with plankton abundance. Marine mammals 

and seabirds, which depend on these organisms for food, 

suffer food shortages, leading to widespread starvation and 

decreased reproductive success. 

Every 20-30 years, the surface waters of the central and 

northern Pacific Ocean shift several degrees from the mean 

temperature. Such shifts in mean surface water temperature, 

known as the Pacific Decadal Oscillation, have been detected 

5 times during the past century, with the most recent shift in 

1998. The Pacific Decadal Oscillation impacts production in 

the eastern Pacific Ocean and, consequently, affects organism 

abundance and distribution throughout the food chain. 

Ocean waters off the coast of California have warmed considerably over the last 40 years. It is not yet clear if this warming 

is a consequence of an interdecadal climate shift or global 

warming. 

In response to these three phenomena, some species have 

shifted their geographic ranges northward, altering the composition of local assemblages. 

ECOSYSTEMS

The Land-Sea Interface

Rivers carry freshwater and sediments to bays, estuaries, and 

the ocean. Thirteen major watersheds are located along the 

central California coast. Historically, these supported large 

numbers of coho and chinook salmon, steelhead trout, and 

sturgeon. Today, many native anadromous fish stocks throughout California are in danger of extinction. General degradation 

of upland watershed and freshwater ecosystems is a major 

factor in the decline.

Two major estuaries in northern and central California are 

San Francisco Bay and Tomales Bay. Several smaller estuaries and lagoons within the region, from north to south, are 

Estero Americano, Estero de San Antonio, Bolinas Lagoon, 

Drakes/Limantour Estero, and Elkhorn Slough (National Estuarine Reserve). Estuaries and bays are vulnerable to coastal 

development, pollution, introduction of invasive species, and 

commercial and recreational fishing for species that live in 

near-shore waters. Humans have modified and transformed 

about 90% of the wetlands in California. The existence and 

health of these coastal wetlands is critical to the survival of 

organisms that depend on these habitats for survival. One of 

California’s wetland sites, Bolinas Lagoon, was designated as 

internationally important in this role under the Convention on 

Wetlands, signed in Ramsar, Iran in 1971. 

Wetlands along the central California coast are sparse, but 

those present support millions of shorebirds and waterfowl during spring and fall migrations and the winter months. Migratory 

species require consistent sources of food and shelter along 

their migration route. If the distances between wetlands are too 

large, migrating birds may become exhausted and disoriented, 

increasing mortality.

Numerous marine species use embayments, lagoons, and 

estuaries as spawning and nursery grounds. Bat rays, leopard and smoothhound sharks, midshipman, Pacific herring, 

starry flounder, staghorn sculpin, surf perch of several species, 

jacksmelt, topsmelt, and pile perch mate and bear their young 

in estuarine habitats. Shallow, coastal waters of central and 

northern California also are critical habitat for chinook and, 

especially, coho salmon as they travel en route to spawning 

grounds in autumn and winter.

Geology and other physical forces influence the structure of 

the coastline. Energetic forces of water and wind erode the 

rocky coastline, creating the dramatic rocky intertidal habitat 

characteristic of the northern and central California coast. Small 

beaches form along the northern California coast where wind 

and waves erode granite and basalt cliffs. Further sourth, erosion of soft shale and sandstone bluffs creates the broad sandy 

beaches typical of southern California.

Sandy beach and rocky intertidal habitats are divided into distinct biological zones relative to height above mean high tide. 

In part, species’ distributions are affected by their physiological tolerance to temperature, moisture, and salt. In response 

to these and other physical factors, the number of species of 

marine algae, gastropods, and fishes increases with depth in 

the intertidal zone.

Nutrients processed in marine systems are essential to communities using sandy beaches and rocky intertidal habitat. Waves 

carry and deposit plankton, macroalgae, as well as occasional 

corpses of fishes, birds, and marine mammals in the intertidal 

zone, which provide an unpredictable and patchy source of 

food. Beach wrack attracts numerous mobile organisms, including amphipods, isopods, flies, beetles, and shorebirds. The 

sporadic deposition of food from the ocean sustains intertidal 

communities in habitats that are subjected to strong physical 

forces and relatively low local production.

Marine Ecosystems

Production in subtidal habitats depends on levels of light and 

nutrients, and exposure to physical forces. Sufficient light to 

support highly productive photosynthetic communities penetrates surface waters to approximately 30 m. Kelp, which 

can grow up to 10 cm per day, is among the most productive 

of marine plants. Primary productivity in kelp forests has been 

estimated at 350 to 2,800 grams of carbon per square meter.

7
Section 1: SYNOPSIS OF ECOLOGICAL LINKAGES REPORT

Kelp provides substrate for numerous benthic and epibenthic 

invertebrates, as well as food and shelter for many fishes, 

seabirds, and marine mammals. Colonies of bryozoans grow 

on kelp fronds. Several species of snails, including purple ring 

top snail and blue top snail, feed on kelp, while kelp crabs 

cling to the underside of kelp fronds. During periods of low 

productivity, sea urchins may emerge from protective crevices 

in rocky reefs to graze on kelp. At the surface, floating kelp 

masses are important habitats for juvenile fishes, particularly 

rockfishes and kelp surfperch. Schools of blue, black, and kelp 

rockfishes and bocaccio are generally recorded in the midwater 

kelp canopy. Gopher, copper, black, and yellow rockfishes, 

lingcod, cabezon, and greenlings tend to associate with the 

bottom of the kelp fronds. In addition, the sea otter has been 

described as a “keystone species” for its role in structuring kelp 

forest communities through predation of herbivores, particularly 

sea urchins, resulting in increased kelp growth. 

Productivity from seaweeds can also have indirect effects on 

coastal food webs. Particulate and dissolved organic carbon 

that results from fragmentation and decomposition of kelps 

and other seaweeds can be consumed by suspension-feeding 

zooplankton or benthic invertebrates, providing a trophic link 

between kelps and higher-level pelagic consumers, such as 

fish. A small portion of the drift algae may be transported off 

the reef, where it can contribute to production in submarine 

canyons and the deep sea.

Productivity is reduced on rocky reefs below 30 m, where light 

levels are low and kelp is unable to flourish. However, the physical structure of rocky reefs does provide shelter for numerous 

benthic invertebrates and fishes. Shortbelly rockfish (Sebastes 

jordani), the most abundant rockfish species on the continental 

shelf and upper slope off California, are often associated with 

rocky reefs between 30-80 m depth. Various seabirds and 

marine mammals rely on shortbelly rockfish for food. Sculpin 

(Cottidae) occur in shallow water and tidepools, as well as in 

deeper water around kelp forests, rocky reefs, and sand or mud 

bottoms on the continental shelf. Lingcod (Hexigrammidae), 

commonly associated with shallow rocky reefs, also occur in 

waters as deep as 300 m.

Soft bottom habitats on the continental shelf lack the physical structure and high biological production of kelp forests 

and rocky reefs. Species that live in soft sediments on the 

continental shelf are subjected to shifting sediments through 

wave action and near bottom currents. Some species that live 

in these habitats, such as crustaceans and mollusks, secure 

themselves in tubes and burrows. Other species, such as flatfishes, are camouflaged on sandy sediments of the seafloor 

by their color and shape.

Deep submarine canyons, such as Monterey, Ascension, Pioneer and Bodega, are remnants of riverbeds that deeply incised 

the continental shelf and slope during glacial periods. Because 

they cut into the continental shelf, submarine canyons support 

deep-sea communities relatively close to shore. Canyon walls 

are often steep and rocky, providing shelter for species, such 

as rockfishes and thornyheads, which are associated with 

complex physical structures. Canyon bottoms tend to slope 

gently and accumulate finer sediments, such as silt and mud, 

providing habitat for species such as flatfishes. In addition, 

the structure of submarine canyons affects the circulation of 

near-shore waters and the concentration of organisms in the 

water column.

Submarine canyons, submerged volcanoes, and other physical 

features under high pressure often concentrate gases and fluids 

beneath the sea floor. In some areas, where the sea floor is 

weak, these gases and fluids may be forced through the sediments, creating features known as cold seeps. Most cold seeps 

are found in the deep sea (600-3000 m) under conditions of 

low light, temperature, and oxygen, and high pressure. In spite 

of these difficult conditions, numerous organisms are adapted 

to life around cold seeps. Vesicomyid clams are the dominant 

species at cold seeps off central and northern California. These 

clams support chemoautotrophic bacteria in a symbiotic relationship. The bacteria use inorganic chemical compounds 

released by the cold seeps to produce organic compounds, 

which are used by their vesicomyid clam hosts.

Deep-sea communities depend on the distribution and quantity 

of primary production in surface waters, the rate of movement 

of organic material to the bottom, and the conditions of deposition and transformation of the organic matter in the sediment. 

A portion of dead organic matter produced in surface waters 

is transported to the sea floor either through passive sinking, 

or by active transport during vertical migration of plankton. In 

the northeastern Pacific Ocean where production is particularly 

high, approximately 5-15% of the surface production eventually 

reaches the deep sea.

In a few places, extinct volcanoes or seamounts disrupt the 

monotony of the abyssal plain. Off central California, several 

seamounts (Gumdrop, Pioneer, Guide, and Davidson) are 

located near the bottom of the continental slope. Seamounts 

provide physical structures which support complex deep-sea 

communities of benthic invertebrates and some fishes.

Offshore Islands

The California coast is a tectonic subduction zone, inhibiting 

the formation of offshore islands. The few that do exist are 

extremely important sites for breeding by seabirds and pinnipeds. The largest offshore islands in the study region are 

the Farallon Islands, west of San Francisco. The Farallon 

Islands support some of the largest colonies of breeding seabirds south of Alaska. Numerous marine mammals, including 

northern elephant seals, Steller sea lions, harbor seals, and 

fur seals, haul out and breed on the Farallon Islands as well. 

Other important but much smaller breeding populations occur 

on rocks off Point Reyes, Año Nuevo Island, and on rocks off 

Big Sur. Subsurface features, e.g., the Farallon Ridge, Cordell 

Bank, and various seamounts, provide substrate and protection for diverse communities of benthic invertebrates and some 

fishes, as well.

BIOGEOGRAPHY

An understanding of biogeographic patterns and how they are 

influenced by ecological linkages enables management decisions to be placed in a spatial context relative to the distribution of marine resources. Distributions of marine species are 

determined by oceanographic phenomena, physical tolerances, 

and biological interactions. Each species responds to these 

factors in slightly different ways. Despite the physiological and 

ecological differences between species’ response, there are 

many similarities in species’ distributions, which can be used 

to define biogeographic regions. The transitions between biogeographic regions are more distinct outside the study area 

than within.

The geographic distributions of numerous marine organisms 

of the northeastern Pacific Ocean coincide with major oceanographic shifts. The biogeographic boundary at the Gulf of Alaska 

occurs at the transition between sea and land along the south 

coast of Alaska. The biogeographic transition at Vancouver 

Island corresponds to the eastern portion of the North Pacific 

Drift, which bifurcates in this region with part diverted north into 

the Gulf of Alaska and part diverted south along the western 

coast of North America as the California Current. The biogeographic transition at Point Conception corresponds to a shift in 

8
the oceanographic regime. At Point Conception, the California 

coastline turns abruptly east and the cool water moving south in 

the California Current is diverted offshore. The most significant 

biogeographic boundary in the study region occurs at Monterey 

Bay; however, other minor boundaries occur around points and 

bays along the coast.

In addition to the changes in latitudinal distributions, the diversity of species changes with depth. The changes in species 

composition and abundance are associated with physiological 

tolerances for temperature, exposure, light and nutrient input, as 

well as a wide range of biological interactions among species. At 

all latitudes, the average number of species of algae and marine 

gastropods increased with depth from high to low intertidal and 

subtidal zones. In addition, species that occur across several 

depth zones are likely to have broader latitudinal distributions 

than species that occupy a single depth zone. In contrast to the 

patterns observed for marine algae and gastropods, the average number of fish species declined with latitude and depth. 

The greatest numbers of fish species occurred south of 50

o

N 

latitude and shallower than 200 m.

For some species, the range of single individuals spans nearly 

the entire geographical distribution of the species. These species use local resources during long-distance migration, but no 

individual resource supports a resident population. Examples 

of these species include baleen whales that feed at highly 

productive sites along their migration route, and seabirds that 

use estuaries along the coast as resting and feeding sites 

during their annual migrations. For other species, the entire 

geographical range far exceeds the range of an individual. 

Many intertidal invertebrates and fishes have dispersal and 

sedentary phases during their life cycles. Examples of these 

species include barnacles, mussels, and clams that settle into 

intertidal habitats, and rockfish that settle into kelp forests or 

rocky reefs after a pelagic larval stage. 

CONCLUSIONS

Within the study region there are many distinct ecosystems 

each hosting a unique assemblage of organisms. In addition 

to describing these key ecosystems and species in the region, 

the Ecological Linkages Report provides information on linkages within and between these systems. By understanding 

the climatic, oceanographic, physical and biological influences 

operating together to shape the regional biogeography, the 

background exists for the biogeographic analyses to be interpreted. The "Biogeographic Analyses" section complements the 

synthesis of literature in the Ecological Linkages Report with a 

data driven look into the biogeographic patterns evident around 

the sanctuaries. The analyses provide a spatially explicit view 

of marine resources within the study area from which management decisions can be better enacted. It is important that the 

Section 1: SYNOPSIS OF ECOLOGICAL LINKAGES REPORT

results from the biogeographic analyses are interpreted within 

the context of the Ecological Linkages Report as it demonstrates the understanding that the patterns presented in the 

Geographical Information System are dynamic in nature due 

to the multitude of factors operating to shape them. Changes in 

any of these factors can result in changes to the biogeography 

of the region.

Annie Crawley

REFERENCE

Airamé, S., S. Gaines, and C. Caldow. 2003. Ecological Linkages: Marine and estuarine ecosystems of central and northern 

California. NOAA, National Ocean Service. Silver Spring, MD. 

163 p.

9
Section 2: BIOGEOGRAPHIC ANALYSES

INTRODUCTION

The biogeographic analyses component is the cornerstone of 

the overall assessment to support the joint management plan 

revision process. The data, analyses, and supporting information are linked using statistical and GIS tools to visualize the 

location of significant biological areas or “hot spots.” There were 

many different ways to analyze and organize the biological 

data compiled for this assessment. To efficiently support the 

management plan revision process, only a limited number of 

analytical options were selected based on reviewer’s comments 

on the Interim Product, mission of the NMSP, technical review 

meetings, and peer review workshops. These key analyses are 

presented in this document and on the CD-ROM. In addition to 

these results, spatial data and information on the companion 

CD-ROM enable NMSP staff, advisory councils, and research 

partners to conduct additional analyses not specifically addressed in this product. 

A critical step in the biogeographic analyses component was the 

extensive effort to have data, analytical approaches, and results 

peer reviewed. Initial results from the suite of analyses were 

presented to experts on marine ecosystems of north/central 

California, as well as to the originators of the data sources in 

an attempt to improve the analyses. The role of expert review 

and input has been considerable, and the contributions made 

by experts have significantly enhanced the analyses. 

ASSESSMENT PROCESS

To aid in focusing on the most important analyses, the biogeographic assessment process displayed in Figure 6 was utilized. 

This process is currently being implemented through a joint 

NMSP and NCCOS Biogeography Team effort to initiate biogeographic assessments across all sanctuaries within the next 

five years. The process is organized around development of 

biogeographical data layers, integrated analyses, and specific 

products to aid in sanctuary management plans (Kendall and 

Monaco 2003). Thus, the integration of partner’s comments 

and use of the biogeographic assessment process resulted in 

the analyses and results presented in this document.

Biogeographic data assembled for this project were derived 

from many sources (see section 4), including NOAA Fisheries, academia, state government, and data housed within the 

NMS and Biogeography Programs. The biogeographic data 

cut across various themes, such as species distributions and 

habitats, and are integrated using a common spatial framework 

in a GIS. The GIS enables a user to select particular data layers 

to be displayed, combined, and manipulated in a wide variety 

of ways to achieve specific analytical objectives (Figure 6).

The use of the GIS enabled species-specific data, such as 

distribution and abundance data or community metrics (e.g., 

species richness statistics), to be directly linked to specific 

areas or habitats they correspond to across the study area. 

The GIS also facilitated integration of multiple data types and 

sources into a common spatial and temporal framework (Gill 

et al., 2001). The following suite of map products quantitatively 

defined significant biological areas that are within or adjacent 

to existing boundaries of Cordell Bank, Gulf of the Farallones, 

and Monterey Bay National Marine Sanctuaries. The GIS-based 

products are intended to aid in evaluating current sanctuary 

boundaries relative to biological resources and habitats (Figure 7), explore options for environmental protection of existing 

NMS areas, identify additional biologically important areas, and 

evaluate alternative management strategies.

To develop this capability, a suite of analyses were conducted 

that were most appropriate in addressing NMSP natural resource management issues. The biogeographic assessment 

framework (Figure 6) aided in targeting the suite of analytical 

approaches to define biologically significant areas in support 

of the sanctuary management plan reviews. Categories of 

analysis include: temporal and spatial analysis of individual 

species’ distributions, species assemblage analyses, habitat 

suitability modeling, and community metrics within and across 

species groups. Important individual species maps were developed from a number of data sets to visualize species presence and/or abundance data within the study area by season. 

Where possible, well-established breeding colonies, rookeries, 

and high concentrations of species are displayed on the digital 

maps. The single species maps enabled various groupings of 

species within a group, such as by family (e.g. rockfish), and 

comparison of spatial patterns between groups. Analysis of 

spatial patterns resulted in information on the relationships 

between individual species, between assemblages of species, 

and of the relationship of species to specific environmental 

and habitat parameters. Furthermore, the compilation and 

integration of individual species maps were used to calculate 

community metrics, such as total richness or diversity of fish 

and marine bird species, at a specific location.

To define species assemblages, multivariate techniques were 

applied to various data sets to group organisms found at specific sampling sites. The assemblage analyses defined species 

groups across the study area. By visualizing the assemblages 

geographically, areas of overlap became apparent and group 

habitat affinities, such as depth range, were delineated.

Species habitat suitability index modeling (HSI) studies were 

undertaken for 20 fish and invertebrate species in an attempt 

to characterize areas within the study region that suffered a 

lack of sampling data, particularly in near-shore habitats. The 

integration of HSI models into a GIS provides a spatial depiction of species habitat suitability models for individual species 

by integrating information on species habitat affinities and the 

distribution of those habitats in space and time (Brown et al., 

2002; Monaco and Christensen 1997). The modeling component of the biogeographic analyses is a necessary step due to 

the incomplete distribution of sampling data across the entire 

study area. Thus, species that were representative of the assemblages described above and/or other key species were 

selected for modeling their potential distribution. The composite 

set of species habitat suitability models contributed to defining 

significant biological areas within the region.

Measures of community structure for fishes and marine birds Figure 6. Biogeographic assessment process. were calculated independently by species group, compared, 

and, where applicable, integrated. Convergence of overlapping 

spatial patterns defined significant biological areas based on 

a number of criteria (e.g., high species abundance, high species diversity). 

Thus, the biogeographic analyses component was a result of 

interpreting or visualizing the analytical results from statistical 

analyses, ecological modeling, and integration of results across 

biota and habitats. The cumulative results aided in assessing the biogeographic patterns in the study with regard to the 

distribution of individual species, species assemblages, and 

species habitat utilization patterns.

REFERENCES

Brown, S.K., K.R. Buja, S.H. Jury, M.E. Monaco, and A. Banner. 

2000. Habitat suitability index models for eight fish and inverAnalyses Integrated Analyses Data Layers and Products and Products to 

Aid Sanctuary 

Management

Study Area

Catch Data

Sightings

Bathymetry

Substrate

Temperature

Life History

Data

Species Distributions

Community Distributions

Modeled Distributions

Ecological Linkages Report

mte

syS

n iot a rm

fo In ic

hpar goe G

d te

ar g te In

Significant Biological

Areas

10
Section 2: BIOGEOGRAPHIC ANALYSES

tebrate species in Casco and Sheepscot Bays, Maine. North 

American Journal of Fisheries Management 20:408-435.

Gill, T.A., M.E. Monaco, S.K. Brown, and S.P. Orlando. 2001. 

Three GIS tools for assessing or predicting distributions of 

species, habitats, and impacts: CORA, HSM, and CA&DS. In: 

Proceedings of the first international symposium on geographic 

information systems (GIS) in fishery science. Nishida, T., Kailola, P. and Hollingworth, C.E. (Eds.). pp 404-415.

Kendall, M.S. and M.E. Monaco. 2003. Biogeography of the 

National Marine Sanctuaries: A partnership between the NOS 

Biogeography Program and the National Marine Sanctuary 

Program. January 2003. 8pp.

Monaco, M.E. and J.D. Christensen. 1997. Biogeography Program: Coupling species distributions and habitat. Pages 133-

139 in G.W. Boehlert and J.D. Schumacher, editors. Changing 

oceans and changing fisheries: Environmental data for fisheries 

research and management. National Marine Fisheries Service 

Technical Memorandum NOAA-TM-NMFS-SWRSC-239, Pacific Grove, California.

Figure 7. 3-D image of bathymetric relief within and adjacent to the sanctuaries.

11
Section 2.1: BIOGEOGRAPHY OF FISHES

Data Input:

Literature review

NMFS trawl data

GIS habitat layers

Key species used:

Representatives of local 

assemblages, or species

of economical/ecological

importance.

Analytical Approach:

Clustering of species 

assemblages, site groups, 

species diversity, and 

richness.

Analytical Approach:

Distribution maps for 

representative species 

based on habitat 

suitability indices.

Statistical validation with 

catch data.

1. Assemblage Analyses

Data Input:

NMFS shelf

NMFS slope

CDF&G recreational

NMFS midwater 

2. Habitat Suitability Modeling

Results:

Define and Interpret

Biological Hot spots. 

(e.g. assemblages of 

station/species, 

diversity, richness)

Overlay, compare, and 

combine with marine 

bird results.

Integrate into final 

report.

Results:

Define and Interpret 

Biological Hot spots.

(e.g. overlay maps of 

modeled species to 

determine locations of 

co-occurrence)

INTRODUCTION

The biogeography of fishes section is a robust 

statistical analysis of fish and a few economically 

important macro-invertebrates. A two-pronged approach was conducted to examine both fisheriesdependent and independent catch data and model 

the potential distribution and relative abundance of 

selected species (Figure 8). Analysis of fisheries 

data can be a slow process which often requires 

extensive exploratory statistical techniques to increase our understanding of the data before presenting reliable and salient results. Many data sets 

were evaluated, however, only four data sets that 

were spatially comprehensive within the study area 

were analyzed: 1) the California Department of Fish 

and Game fishery dependent recreational fishing 

trips targeting rockfish (CDF&G recreational); 2) the 

National Marine Fisheries Service fishery independent benthic trawls on the continental shelf (NMFS 

shelf trawls); 3) NMFS fishery independent benthic 

trawls on the slope (NMFS slope trawls); and 4) 

the NMFS fishery independent trawls in midwater 

(NMFS midwater trawls). Detailed information on 

these trawls is given in each respective section. 

The NMFS trawls on the continental shelf and slope 

provide information on the diverse demersal fish assemblages found on trawlable habitats between 50 

and 1280 meters depth throughout the study area. 

Pelagic fish encountered either as the trawl descended or ascended are also included with these 

analyses. The CDF&G recreational hook and line 

data complements the NMFS data sets by providing information on midwater as well as demersal 

species. The recreational data was collected over 

soft bottom and hard bottom habitats between 

5 and 200 meters depth. The NMFS midwater 

trawl data targets juvenile rockfish and provides 

information on fish and invertebrates found in the 

neritic environment during the upwelling season. 

Even though the spatial extent of this data set does not cover all four data sets, 119 species were analyzed. A complete list of fish and invertebrate species across the study area (Brown 

the entire study area, it provides a source of information on of species included in the assemblage analyses can be found et al., 2000). Thirty two species of fish and invertebrates were 

the neritic environment, which is important as juvenile habitat, on the CD-ROM. In addition, community metrics, including initially investigated through literature searches to determine if 

and as the base of the food web for marine birds, fish, and species richness, species diversity, and rockfish richness sufficient information was available to model potential distribumarine mammals. were calculated for the NMFS shelf and slope trawls and tions. The process of determining which species to include in 

the results presented spatially using GIS. However, due to the modeling procedure included consultation by the sanctuDue to time constraints, analysis of all species individually spatial and temperal limitations of available data, (i.e. NMFS ary staff, and integration of information on the economic and 

was not feasible. Instead, all four data sets were analyzed demersal trawls have no information on rocky or shallow areas ecological importance of the species as well as initial results on 

using multivariate statistics to identify species assemblages, (<50 meter) and contain trawls only for the months of June species assemblages. Of the 32 species initially investigated, 

site groups, and the location of the species assemblages in through November) areas such as Cordell Bank and the Far- there was sufficient information available to conduct HSM on 

space using a Geographic Information System (GIS). For the allon Islands are not adequately sampled. Therefore, habitat the adult and subadult stages of 14 fish species, and adult stage 

multivariate statistics, species were included in an analysis if suitability modeling (HSM) was conducted to supplement the of 4 fish and 2 invertebrate species. Habitat suitability models 

they were captured in at least 5% of the collections. Through analysis of catch data, and to model the potential distribution were either derived from an analysis of a portion of the NMFS 

trawls on the continental shelf and slope or derived from species habitat affinities described in 

the literature. Model results were validated with 

NMFS trawls on the shelf and slope (a different 

subset than that used to create the affinities) or 

CDF&G recreational catch data. Model results 

for 3 species are included in the main body of 

this document, with the models for the rest of 

the species included in the CD-ROM.

The integration of the fish and invertebrate 

analyses is shown in Section 3. For example, 

a comparison of important areas derived from 

the diversity of NMFS trawls and those derived 

from overlays of the HSM’s was conducted to 

define significant biological areas. In addition, 

aspects of the Ecological Linkages Report were 

qualitatively incorporated into the assemblage 

and HSM discussions to aid in interpretation of 

these analyses.

Figure 8. Biogeographic approach to fish analysis.

12

Biogeographic Approach to Fish Analyses
Subsection 2.1.1: ASSEMBLAGE ANALYSES

INTRODUCTION

No species exists in isolation from other species or their environment. Monitoring species individually may cause managers 

to miss important interactions (Chavez et al., 2003; Worm and 

Myers, 2003; Baraff and Loughlin, 2000; Estes et al., 1998). 

In addition, individual species' abundance may be considered 

sustainable in the context of a fishery, but still be low enough 

to influence ecosystem dynamics and health (NMFS 2001). 

There has been a growing recognition that effort needs to be 

extended toward understanding the entire ecosystem. The 

National Marine Sanctuary Program is tasked with ensuring the continued health of the ecosystems contained in the 

sanctuaries. However, important species-species interactions 

and species-habitat interactions are still not well understood. 

Abiotic (e.g., habitat preferences toward depth or sediment) 

and biotic (e.g., presence or absence of prey, predators) factors can impact the importance of an area to fish. Elucidating 

habitat characteristics that are most important to animals, and 

understanding the co-occurrence of species, is a first step in 

determining areas that should be managed as “essential” habitats. This study aids in clarifying the interactions among species 

and between broad scale habitat characteristics and species 

on the scale of the commercial and recreational fisheries. Even 

though these data sets were originally deployed to collect information necessary for setting fishing limits, these data sets can 

provide preliminary information on multi-species interactions. 

Recreational hook and line drifts covering approximately one 

kilometer, demersal trawls on the continental shelf and slope 

covering one kilometer, and fifteen minute trawls in midwater, 

were analyzed to determine species assemblages, site groupings, and the interaction between species and locations. In 

addition, analyses were completed to determine larger scale 

environmental variables that were significantly different among 

identified groups. Due to limitations of the data sets (section 

4), and the lack of results on individual species’ distributions, 

habitat suitability models (section 2.1.2) for selected species 

were completed to complement this analysis. 

The primary objective of the assemblage analysis is to define 

spatial biogeographic patterns of fishes and macro-invertebrates within the study area from Point Arena to Point Sal in 

California. The study is based on a synthesis of four primary 

databases of fish and invertebrates that were spatially comprehensive throughout the study area including: 1) the California 

Department of Fish and Game fishery dependent recreational 

fishing trips targeting rockfish (CDF&G recreational); 2) the 

National Marine Fisheries Service fishery independent benthic 

trawls on the continental shelf (NMFS shelf trawls); 3) NMFS 

fishery independent benthic trawls on the slope (NMFS slope 

trawls); and 4) the NMFS fishery independent trawls in midwater 

(NMFS midwater trawls). Detailed information on these surveys 

is given in each respective section. Databases that were limited 

in content and spatial coverage 

were not utilized in this analysis, 

but were used to help interpret 

the results. 

Five specific objectives of the 

assemblage analysis (all of 

which aim to increase our understanding of the biogeography of 

fishes and macro-invertebrates 

in relationship to their environment, as well as identify important areas or habitats within the 

study area), were as follows:

1. Identifying spatial patterns 

and hot spots in community 

metrics (diversity and richness); 

2. Determining which species tended to be caught together 

(species assemblages); 

3. Analyzing fishing locations to determine which locations 

contained similar catches (site groups); 

4. Resolving where the species assemblages were being 

caught by combining results from objectives 2 and 3 and 

then utilizing GIS to map the results; and 

5. Identifying significant relationships between site groups 

identified in objective 3 and broad scale habitat characteristics (bathymetry, bathymetric complexity, and large-scale 

habitat classification).

Community metrics can be used to determine which areas are 

important to multiple species. Experts in California have acknowledged a management need to increase our understanding 

of fish species interactions (objective 2) (Starr, 1998) and the 

interactions between fish assemblages and habitat (objective 

5) (Starr, 1998; Yoklavich et al., 2000, 2002). Studies exist that 

identify either species assemblages or site groups (see below), 

but so far none have integrated multiple data sets, provided 

the interaction between species assemblages and site groups, 

nor presented spatially explicit results. The results of these 

analyses aid in defining the region's biogeography based on 

the spatial pattern of fishes and macroinvertebrates.

REVIEW OF RELEVANT LITERATURE

Due to the economic importance of recreational and commercial 

fisheries in California, several studies have been completed 

that look at species co-occurrences or species interactions 

with their environment. NMFS publishes yearly reports on the 

status of demersal fish species by analyzing results from their 

shelf and slope trawls (Turk et al., 2001; Weinberg et al., 2002; 

Lauth, 2001; Shaw et al, 2000). Zimmerman et al. (2001) looked 

at the biomass of demersal species to determine NMFS shelf 

trawls that did not fish the bottom as intended. He then looked 

at the effect these trawls had on the 

estimates of biomass of selected 

species through time. Based on 

Zimmerman’s results, we excluded 

these abnormal “water hauls” from 

our analyses. Williams and Ralston 

(2002) analyzed data from NMFS 

shelf trawls to determine rockfish 

species assemblages. The same 

data were used in this analysis; 

however, the multivariate statistical method utilized, the spatial 

coverage employed, and the species examined were different. The 

overall conclusion from Williams and 

Ralston was that rockfish richness 

was highest at a depth of 200-250 meters, where the shelf 

and slope meet, and that depth and latitude were the main 

determinants of rockfish assemblages. Jay (1996) analyzed 

the 1977-1992 NMFS shelf trawls to determine site groups 

that contained similar catches. Using 33 species of fish, he 

identified 23 site groups, many of which contained the same 

species, but with different relative abundance. Even though 

depth and latitude showed some influence on site groups, 

overall he found little association between the site groups and 

a suite of environmental parameters. 

Gabriel and Tyler (1980) used data from the Oregon Department of Fish and Wildlife Trawl Survey and the West Coast Joint 

Agency Rockfish Survey to look for site groups from California 

to Alaska. They differentiated three large site groups: “intermediate” at less than 145 meters, “deep” between 145 and 

200 meters, and “slope” greater than 200 meters deep. They 

found that site groups were “strongly associated with depth 

contours”. Matthews and Richards (1991) compared gill net 

catches from trawlable and untrawlable areas to determine if 

untrawlable areas could be considered de-facto fish reserves. 

Even though some species overlapped, they concluded that the 

species assemblages were significantly different; suggesting 

that species assemblages determined from trawls cannot be 

extrapolated to non-trawlable habitats. 

Only a few studies have analyzed recreational hook and line 

data. For a general analysis of a species’ specific decline 

in recreational catch see Love et al. (1998), Mason (1998), 

or Wilson-Vandenberg et al. (1996). Mason (1995) analyzed 

various CDF&G recreational fishing surveys and documented 

trends in effort, fishing location, and species catch. She documented two principal rockfish assemblages and distinguished 

them by depth (less than 70 meters and greater than 70 meters). Sullivan (1995) used the CDF&G recreational fishing data 

(1987-1992) to determine site groups. His overall conclusion 

was that the rockfish management groups could be defined, 

and that both depth and latitude were important. 

Even though the neritic zone is ecologically important, little research has addressed the midwater environment. Cailliet et al. 

(1979) described fish and invertebrate species co-occurrences 

in anchovy purse seines, and midwater trawls. An extremely 

thorough report by Larson et al. (1994) looked at the NMFS 

midwater trawl results in conjunction with local environmental 

conditions to determine juvenile rockfish assemblages. Their 

results emphasize the ephemeral nature of the pelagic environment, but they were able to document two consistent spatial 

trends: 1) the rockfish are larger inshore than offshore, and 2) 

there was a north/south gradient in species composition and 

abundance. Moser et al (2000) described changes in rockfish 

larvae abundance in CalCOFI plankton tows from 1951 to 1998 

in response to adult biomass and environmental conditions. 

He concluded that over-fishing as well as decadal shifts in 

environmental conditions were affecting the stocks. 

Underwater submersibles have been used to describe fish assemblages and their interaction with habitat at spatial scales 

relevant to the fish themselves. Yoklavich et al. (2000 and 

2002) surveyed Soquel Canyon and Big Creek Ecological 

Reserve on the Big Sur coast, Field et al. (2002) looked at 

Big Creek Ecological Reserve, while Hixon et al. (1991) and 

Hixon and Tissot (1992) researched Haceta, Coquille, Daisy, 

and Stonewall Banks off the Pacific northwest. These results 

are very important to managers because they show fish and 

habitat interactions on very small scales. However, many of the 

results from these studies are not comparable with the current 

studies due to large differences in scale. Hixon et al. (1991) 

documented that the species composition observed from the 

submersibles was different than that seen in trawls. The results 

from these studies reveal the importance of habitat, especially 

rugosity, to fish species composition. 

Substantial declines in the standing stock biomass of economically important rockfish species (Ralston, 1998) prompted 

NMFS to organize a symposium to discuss the implications of 

no-take areas for rockfish in September of 1997. Eleven plenary 

papers and six case studies are available online, and cover a 

range of topics. Starr (1998) provided a thorough evaluation 

of the potential of rockfish no-take reserves. He expressed 

a management need for the identification of species assemblages. Once assemblages are identified, management can 

address actions for adequate protection of each species assemblage. Starr also suggested protecting rectangular areas 

that cover 20-50 km of the coast and extend west to the edge 

of the continental shelf. 

Mutivariate Analyses of Fisheries Dependent 

and Independent Data

13
Subsection 2.1.1: ASSEMBLAGE ANALYSES

INTRODUCTION TO CLUSTERINGThe use of multivariate analyses is gaining popularity in ecology and fisheries management (McGarigal et al., 2000; Paukert and Wittig, 2002), but can be confusing due to the availability of many statistical techniques. Therefore, this section provides a basic introduction to the principles of clustering, one form of multivariate analysis. Interested readers should reference Boesch (1977), Gauch (1982), or McGarigal et al., (2000) for more detailed information on clustering than will be provided in this brief introduction. Clustering is “a technique for optimal grouping of entities according to the resemblance of their attributes as expressed by given criteria” (Boesch, 1977) or, in short, a method that places things (sites, species, etc.) into groups. Clustering uses statistics to determine these groups, but the method also possesses aspects that are subjective and require an understanding of the ecosystem being analyzed. There are five steps to clustering, which all have some aspect of subjectivity (adapted from Sullivan, 1995): 1) the choice of data, including what data to include or remove, and how to transform and standardize that data; 2) the choice of a resemblance metric (can be based on similarity or dissimilarity); 3) the choice of clustering model; 4) the choice of number of groups (or level of similarity) and; 5) the choice of whether or not to reassign objects to more appropriate groups. The following is a more detailed description of each of these fi ve steps. The choice of data to include in the analyses can infl uence 

results in many ways. Rare species are usually removed from analyses because they can have a disproportionate infl uence 

on the resulting clusters. What is considered “rare” can vary for analyses, but typically species found in less than 5% of the trawls/catches are removed (Gauch, 1982). Additionally, the transformation and standardization of the data may affect the influence of rare and abundant species. Binary data (presence/ absence) weights all species the same, and reduces the influence of abundant species while increasing the influence of rare species (Boesch, 1977). Transformations are needed because most ecological data do not conform to the assumptions of a normal distribution and homogeneity of variances required for parametric analyses (Boesch, 1977). Transformations decrease the variation between abundant and rare species, thereby reducing the infl uence of abundant species. The clustering method dictates the way that groups are formed. The two classes of clustering are: 1) hierarchical, which show the relationship between groups in dendrograms, and 2) nonheirarchical, which do not. Hierarchical clustering may be biased because the researcher can choose the results that best match expectations (Williams and Ralston, 2002); however, it is advantageous because it clearly shows the relationship between the resulting groups. 

Within hierarchical clustering, the choice of resemblance metric (a formula that determines how similar two things are) and clustering model (a method that groups things based on their resemblance metrics) can also have an influence by adjusting the importance of abundant and rare species and changing the importance of zero values (Gauch, 1982; Boesch, 1977; McGarigal et al., 2000). Common resemblance metrics used in ecology are the Bray-Curtis, Euclidean distance, Jaccard, and Pearson correlation coefficients. Common clustering models include Ward’s minimum variance, average linkage, centroid linkage, and single linkage. Because of chaining, not all outputs from cluster analyses can be utilized. When chaining occurs, entities fuse to a few nuclear groups one at a time rather than forming new groups, and make it impossible to divide the data into meaningful smaller groups (Boesch, 1977).Hierarchical clustering results in a tree diagram, called a dendrogram, which shows the linkages between all of the entities and groups at different levels of similarity. Various objective methods, such as scree plots, are used to determine what level of similarity is important or how many groups are created. A scree plot shows the dissimilarity values plotted against the 

number of clusters such that breaks in the level of dissimilarity are revealed through the shape of the curve (McGarigal et al., 2000). Experts recommend combining this objectivity with ecological knowledge to determine clustering results that are ecologically meaningful (Boesch, 1977). The final decision when clustering is whether to reclassify entities into more appropriate groups based on some identified criterion. This step has created 

controversy because of the subjectivity introduced. For comparison, a brief introduction to another widely used form multivariate analysis, the Principal Component Analysis (PCA), is provided. PCA reduces the dimensionality of data (Gauch, 1982, McGarigal et al., 2000). One difference between the results from PCA and hierarchical clustering is that in clustering each species is ultimately assigned to one and only one group. In PCA, only species with a certain loading (i.e. level of influence) are included in a group. This means that in PCA some species are never assigned to a component, and others are assigned to more than one. This can be a drawback because often very important species that are found everywhere are never attributed to any group. In clustering methods, since every fish must be placed into a group, species which are found 

everywhere can be grouped together. At the same time, species which are only marginally associated with a group can be added to a group. For this study, an extensive exploration was conducted on the data using multiple data transformation, similarity metrics, and clustering models. Ultimately, one method was chosen, and 

the reasons behind those decisions arfollowing detailed methodology section.DETAILED METHODOLOGYTo reduce the amount of material that is retion, a detailed methodology for all four dhere, with only a brief overview provided i9 is an example of the clustering methodata. The first objective of this study was community metrics. For these analyses, and those without an abundance estimThe Shannon index (H’) was calculated and slope trawl based on the following eWhere S is the number of species, ni is thals found of species i, and n is the total (Shannon and Weaver, 1949). Richness species caught) was also enumerated for slope trawl. In addition, the rockfish richncounting the number of Sebastes and Scaught in each trawl.Due to the overlap in trawls between yearto approximately the same area each yedifficult to determine spatial trends in divediversity and mean richness were calcu(approximately 5 km by 9 km cells, althouvary with latitude) throughout the study size was utilized because it was emplo(bird, mammal, and environmental mapcomparison of results among these anaBoth clustering analyses (objectives 2 ana site by species or species by site matrix or log adjusted abundance. All species at least 5% of the trawls were included number was chosen because it is a comfisheries management (Gauch, 1982), athe number of zero values in the data adequate number of species for analysisdance data did not conform to assumptiontion and homogeneity of variances, eithe(if effort was available) or presence/absprovided) were used. No standardizatiocause correlation coefficients were used

were run to investigate multiple resemblaEuclidean Distance, Jaccard, and Pearsoand multiple clustering models (including ance, average linkage, centroid linkage

S  n 

H

∑   

n 

′ =

−  i  ln  i 

i =1  n  

n 
Subsection 2.1.1: ASSEMBLAGE ANALYSES

In order to combine these two analyses and resolve where the 

fish assemblages were being caught (objective 4), the average 

frequency of occurrence for species assemblages was calculated for each site group to determine the overlap between 

the site and species groups. By looking at the frequency of 

occurrence of species assemblages in each site group, it was 

possible to determine which species groups were influential 

in forming the site groups. Species groups were considered 

influential if, on average, species were present in 25% of the 

trawls. Since rare species had low frequency of occurrence for 

all site groups, 25% is a reasonable number when rare and 

abundant species are averaged. Spatial distribution of the site 

groups was determined by mapping the site groups in GIS.

For management purposes, it is important to understand which 

environmental characteristics influence species distributions. 

Analyses of variance (ANOVA) were conducted to determine 

if there were significant differences in bathymetry, bathymetric 

complexity, and gross sediment type between the site groups 

at the scale of this analysis. Bottom depth was measured in the 

field for each of the four data sets. Using ArcView, individual 

trawl locations were overlaid on the sediment (pp. 38) and 

bathymetric complexity (pp. 16) maps and the underlying parameters extracted. For the midwater trawl, other environmental 

conditions measured in the field, such as water temperature, 

salinity, and density, were also tested. 

Bathymetry appeared to be the overriding influence in determining fish assemblages. Attempts were made to statistically remove the influence of bathymetry from the data and 

then re-analyze the data for assemblage patterns caused by 

secondary influences. However, two general problems were 

encountered. First, the standard statistical procedure to remove the influence of bathymetry required a linear relationship 

between species abundance and bathymetry. Unfortunately, 

the relationship between species abundance and bathymetry 

was non-linear even after various transformations were tried. 

Experiments with spline-fitting were also unsuccessful. A major 

problem was the presence of zero species abundance values 

for those depths the species assemblages were not present. 

Secondly, the species abundance data were collected over 

narrow ranges of other influences, such as bathymetric complexity and substrate/sediment size. Again, the problems of 

non-linearity and zero species abundance prevented further 

conventional statistical analyses. Figure 9. Hypothetical example of the methods used to determine species assemblages, site groups, and the interaction between species assemblages and site groups.

spiny dogfish

widow rf

bocaccio

chilipepper

Dover sole

Rex sole

Site1 Site2 Site3 Site4 Site5

bocaccio 23 66 0 2 1

chilipepper 11 5 7 0 0

widow rf 15 47 0 0 0

Rex sole 1 0 55 0 23

Dover sole 0 0 43 0 21

spiny dogfish 0 4 0 44 0

spiny bocaccio chilipepper widow rf Rex sole Dover sole dogfish

Site1 23 11 15 1 0 0

Site2 66 5 47 0 0 4

Site3 0 7 0 55 43 0

Site4 2 0 0 0 0 44

Site5 1 0 0 23 21 0

Site1 Site2 Site3 Site4 Site5

Site1 1.00

Site2 0.92 1.00

Site3 -0.66 -0.61 1.00

Site4 -0.38 -0.22 -0.35 1.00

Site5 -0.65 -0.56 0.99 -0.30 1.00

Site 1

Site 2

Site 4

Site 3

Site 5

site 1, 2 site 4 site 3,5

Rockfish 100 33 33

Sp. Dogfish 50 100 0

Sole 25 0 100

Determining species assemblages, site groups, and their interaction

(example with hypothetical data)

Start with site by species or 

species by site matrices of 

abundances

Calculate Pearson 

correlation coefficients 

between species or sites

Run average means cluster 

analyses on correlations to 

determine species 

assemblages and site 

groups. Determine 

appropriate number of 

groups.

Calculate frequency of occurrence of species assemblages in site groups.

Determine which species groups were influential in forming the site groups

bocaccio chilipepper widow rf Rex sole Dover sole spiny dogfish

bocaccio 1.00

chilipepper 0.30 1.00

widow rf 1.00 0.27 1.00

Rex sole -0.52 0.07 -0.53 1.00

Dover sole -0.53 0.02 -0.54 1.00 1.00

spiny dogfish -0.29 -0.57 -0.25 -0.35 -0.35 1.00

15
ABOUT THIS MAP

Figure 10 displays bathymetric complexity derived from high 

resolution bathymetry. Bathymetric complexity is calculated for 

each cell as the standard deviation of depth for all grid cells 

within a 1 kilometer radius. The range of resulting bathymetric 

complexity is large, and the majority of cells show a low variance. Therefore, in order to visualize differences, results have 

to be displayed as standard deviations above and below the 

mean. The areas in blue are relatively flat with little slope, and 

the darker red shows the highest variance. Results highlight the 

edge between the shelf and slope areas, and create a dramatic 

visual for the canyons and seamounts. 

DATA SOURCES

Results were calculated from 3 arc second (nominally 70 x 

70 meters) bathymetry derived from NGDC and MBARI data 

sources. All available multibeam points were used in the area. 

Hydrographic survey data (echo sounder data) was eliminated 

from the interpolation if it overlapped with multibeam data. Vertical and horizontal correction was performed on all data prior to 

incorporating it into the data set. All data were triangulated and 

gridded using "The Vertical Mapper" extension with MapInfo 

6.5. Cell size varies depending on the available data for each 

area, with a minimum cell size of 70 x 70 meters. 

METHODS

Bathymetric complexity was calculated using the "neighborhood 

statistics" option in Arcview 3.2. Arcview computes a standard 

deviation from all grid cells within a 1 kilometer radius around 

each cell. The results are displayed as standard deviations 

from the mean as this scale provides the best resolution for 

visualizing the location of high slope areas.

RESULTS AND DISCUSSION

Fish species, especially some rockfish species, have a very 

strong affinity to areas with a high relief (Yoklavich et al., 2000, 

2002; Hixon et al., 1991; Hixon and Tissot, 1992; Field et al., 

2002; Starr, 1998; and Williams and Ralston, 2002). Calculating 

the variability in bathymetry for a given area can provide a rough 

estimate of bottom rugosity on a scale of km. Smaller pinnacles 

may not be distinguished at this scale, but the large physical 

characteristics, such as the edge between the continental shelf 

and slope, canyons, and seamounts, will be displayed. The 

variable depth of the continental shelf break can be estimated 

using these maps. North of Cordell Bank NMS, the break occurs 

around 300 meters, within Cordell Bank and Gulf of the Farallones NMS, it is around 200 meters depth, north of Monterey 

Bay it becomes shallower at 150 meters, and inside Monterey 

Bay and to the south, the break is as shallow as 100 meters. 

Subsection 2.1.1: ASSEMBLAGE ANALYSES

To determine the importance of bathymetric complexity to the 

formation of fish abundance, an analysis of variance was run 

to test for significant differences in bathymetric complexity 

between site groups for CDF&G recreational hook and line, 

NMFS shelf trawl, and NMFS slope trawl catches (see individual 

sections for results). 

Figure 10. Standard deviation of bathymetry calculated for a 1 km radius around each cell. Results are presented in standard 

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Bathymetric Complexity

Departure from Mean

0 10 20 40 60 80

Kilometers

-1 - 0 Std. Dev.

0 - 1 Std. Dev.

1 - 2 Std. Dev.

2 - 3 Std. Dev.

Calculated for a 1 km radius

around each grid cell

>3 Std. Dev.

50 m

20

m

0 m

2

100

0

0 m 200

10

0

00

m

m 2000 m

deviations above or below the mean.

16
Subsection 2.1.1: ASSEMBLAGE ANALYSES

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Species Richness of

Demersal Fish

Richness

0 10 20 40 60

Kilometers

19 - 33

15 - 18

Richness by Individual Trawl

3 - 14

2

10

5

00

0

0

0

20

m

m

m

0 m

ABOUT THESE MAPS

Species richness of demersal fish was calculated for NMFS 

fish trawls (shelf and slope) conducted at depths between 50 

and 1280 meters. The mean number of fish species recorded 

for trawls (± standard deviation) was 16±5. Species richness 

results are displayed for individual trawls (Figure 11), as well 

as mean richness for 5’ grid cells (Figure 12). There appear to 

be three trawl areas with consistently high species richness: 

NW of Point Año Nuevo, SW of Morro Bay, and near the center 

of Cordell Bank NMS. In addition, there are smaller clusters 

within all three national marine sanctuaries. This map can be 

used to identify hot spots of demersal fish biodiversity.

DATA SOURCES

Richness estimates were derived from 1,336 NMFS (AKFSC 

and NWFSC) shelf (pp. 26) and slope (pp. 28) trawls conducted 

between 50-1280 meters depth during June-November every 

third year from 1977-2001. For details on the trawl methods 

see Lauth (2001), Shaw et al. (2000), Turk et al. (2001), and 

Williams and Ralston (2002). All fish identified to the species 

level were included (230 species). 

METHODS

Richness is defined as the number of fish species present at 

a given location. To calculate richness, data were tabulated 

to determine the number of species caught in each trawl. Although there was a significant positive relationship between 

effort (calculated as distance fished x net width) and species 

richness (p<0.0002), this accounted for a very small percentage 

of the variability in the data set (adjusted r2

=.01). Therefore, 

raw values of species richness for each trawl were used for this 

analysis. Trawls are only possible along relatively flat bottom 

areas with a minor incline, and no data were available for rocky, 

highly sloped areas. In addition, the NMFS data did not include 

trawls conducted in water less than 50 meters deep, therefore, 

shallow water sites are not represented with these results. 

Figure 11 is useful for identifying actual trends in space, as 

well as identifying where the trawls occurred. Species richness 

results were organized into three equally sized groups representing the lowest, middle, and highest third of richness values. 

It is also useful to consider the mean richness for a small area. 

Therefore, mean richness and its deviation (how variable it is) 

was calculated for 5’ grid cells throughout the study area (Figure 

12). Cells with no deviation contained only one trawl. Cells that 

document high species richness, with low deviation, represent 

an area with consistently high species richness. Cell size was 

determined by minimizing the number of cells containing only 

one measurement yet retaining a reasonable spatial resolution 

of the cells. This also was the cell size used for integration with 

marine bird results. Species richness in cells is also presented 

in three equal sized groups as this best represents differences 

in measurements between cells and facilitates comparisons 

between maps. Since the placement of the grids is arbitrary, the 

results will in-part depend on where the grid falls. An analysis 

comparing three different grid placements was conducted. It 

was determined that the placement of the grids had minimal 

influence on the results. 

RESULTS AND DISCUSSION

The mean (± standard deviation) number of fish species recorded for a demersal trawl was 16±5, and ranged from 1 to 

33. There are large areas with high species richness directly 

west and north of Point Año Nuevo, between the 50 and 100 m 

contour lines as well as west and south of Morro Bay between 

50 and 200 M depth. There are smaller hot spots within Cordell 

Bank NMS, between 100 and 200 meters, as well as along the 

200 meter contour in four locations: north of Cordell Bank NMS, 

just north of the southern Gulf of the Farallones NMS boundary, 

north of Monterey Bay and in southern Monterey Bay (Figure 

11). For all trawls, there was a significant negative relationship 

between richness and depth, and a significant positive relationship between richness and latitude. However, neither of these 

relationships explained much of the variance (r2

=0.04, p<0.0001 

for depth; and r2=0.005, p<0.004 for latitude, N=1336). 

Many fish species are associated with near-shore areas, and 

were not included in this analysis due to the absence of NMFS 

trawls in shallow water areas. Other analyses in shallow water can provide a comparison to these results. Laidig (Pers 

Comm NMFS) has completed underwater scuba surveys to 

determine the presence of fish on kelp beds near Sonoma and 

Monterey. Average richness recorded on 43 dives in Sonoma 

was 5±3 (range of 1 to 15), and 15±4 on 9 dives in Monterey 

(range of 9 to 21). California Department of Fish and Game 

recreational fishing trips targeting rockfish (pp. 23) can also 

be used to determine approximate fish richness. Without effort 

information on angler hours, the utility of mapping richness is 

questionable. However, the mean richness recorded was 7±4 

(range of 1 to 21). The estimate of richness for near-shore 

areas from CDF&G trawls is lower than those measured with 

the NMFS shelf and slope trawl data, but the difference could 

be due to fishing method (hook and line vs. trawl) and is only 

mentioned as anecdotal validation. There was a large difference 

in the number of species observed in Sonoma and Monterey 

by Laidig, providing an example of the variability that can be 

experienced in kelp areas. Managers interested in protecting 

biodiversity of demersal fish could use this information in combination with the other assemblage analysis to address various 

management strategies. Cells with high species richness and 

low deviation could be used to identify potentially important 

areas which deserve further investigation. 

Figure 11. Species richness of individual NMFS shelf and slope trawls. 

17
Subsection 2.1.1: ASSEMBLAGE ANALYSE

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Species Richness of

Demersal Fish

Richness

0 10 20 40 60 80 100

Kilometers

18 - 25

15 - 17

8 - 14

Deviation of Richness

No Deviation

Less than Mean Deviation

Mean Richness in 5' Cells

Greater than Mean Deviation

2

1

0

0

5

0

2

0

0

0

0

m

0

m

m

m

N°53 N°63 N°73 N°83 N°93

Figure 12. Mean species richness of NMFS shelf and slope trawls for 5’ grid cells. The deviation is shown as an overlay to provide an 

indication of the variability in results for each grid cell.

S

18
ABOUT THESE MAPS

Species diversity of demersal fish was calculated for NMFS 

trawls on the shelf and slope at depths between 50 and 1280 

meters. The mean diversity recorded for trawls (± standard 

deviation) was 1.5±0.5. Species diversity results are displayed 

for individual trawls (Figure 13), as well as mean diversity for 

5’ grid cells (Figure 14). The largest cluster of high species 

diversity trawls is found 20 km north and south of the border 

between Monterey Bay NMS and Gulf of the Farallones NMS. 

Smaller clusters of high diversity values are present in the 

northwest corner of Cordell Bank NMS and to the north and 

south of the NMS boundaries in waters slightly deeper than 

the 200 meter contour line. 

DATA SOURCES

Diversity estimates were derived from 1,336 NMFS (AKFSC 

and NWFSC) shelf (pp. 26) and slope (pp. 28) trawls conducted 

between 50-1280 meters depth during June-November every 

third year from 1977-2001. For details on the trawl methods 

see Lauth (2001), Shaw et al. (2000), Turk et al. (2001), and 

Williams and Ralston (2002). All fish identified to the species 

level were included (230 species).

METHODS

Diversity reflects the distribution of species’ abundance within 

a trawl. For example, a trawl dominated by one species would 

have a low diversity, while a trawl with an even number of all 

species would have a high diversity (see Figure 78, pp. 124). 

Since diversity is dependent on the abundance of species, fish 

caught in a trawl which were not given an estimate of abundance, or were not identified to species, were eliminated from 

the analysis. The Shannon index (H’) was calculated for each 

NMFS shelf and slope trawl based on the following equation:

Where S is the number of species, ni is the number of individuals found of species i, and n is the total number of individuals (Shannon and Weaver, 1949). Although there was a 

significant positive relationship between effort (calculated as 

distance fished x net width) and species diversity (p<0.0001), 

this accounted for a very small percentage of the variability in 

the data set (adjusted r2=.06). Therefore, raw values of species 

diversity for each trawl were used for this analysis. Trawls are 

only possible along relatively flat bottom areas with a minor incline, and no data were available for rocky, highly sloped areas. 

In addition, the NMFS data did not include trawls conducted 

in water less than 50 m deep, therefore, shallow water sites 

are not represented with these results. Figure 13 is useful for 

identifying actual trends in space, as well as identifying where 

effort occurred. For this figure, species diversity results were 

Subsection 2.1.1: ASSEMBLAGE ANALYSES

divided into 3 equal sized groups representing the lowest, 

middle, and highest third of diversity values. 

It is also useful to consider the mean diversity for a small area. 

Therefore, mean diversity and its deviation (how variable it is) 

was calculated for all trawls within 5’ grid cells throughout the 

study area (Figure 14). Cells with no deviation contained only 

one trawl. Cells that document high species diversity, with low 

deviation, represent an area with consistently high species 

diversity. Cell size was determined by minimizing the number 

of cells containing only one measurement, yet retaining a reasonable spatial resolution of the cells. In addition, this was also 

the cell size used for integration with marine bird analyses (section 3). Species diversity in cells is also presented in 3 equally 

sized groups. Since the placement of the grids is arbitrary, the 

results will in-part depend on where the grid falls. An analysis 

comparing three different grid placements was conducted, and 

it was determined that the placement of the grids had minimal 

influence on the results. 

RESULTS AND DISCUSSION

The mean (± standard deviation) diversity recorded for a demersal trawl was 1.5±0.5, with range from 0.02 to 2.54. The 

largest cluster of high species diversity straddles the boundary 

between Monterey Bay NMS and Gulf of the Farallones NMS. 

Fifty-eight (13%) of the high diversity trawls are located within 

20 kilometers of this boundary. The western edge of this area 

contains consistently high diversity trawls (low deviation). A 

smaller cluster of high diversity trawls is present in the northwest corner of Cordell Bank NMS, extending approximately 6 

kilometers north of the current boundary. Within this cluster, 

95% of the trawls are classified as either medium or high 

diversity. In addition, there are two lines of trawls with high 

species diversity located slightly deeper than the 200 meter 

contour line: one north of Cordell Bank NMS to the northern 

edge of the study area, and the other from Lopez Point south 

to the southern edge of the study area. A large portion of these 

trawls are outside sanctuary boundaries. For all trawls, there 

was no significant relationship between diversity and latitude 

(r2=0.0, p=0.57, N=1336). There was a significant relationship between diversity and depth; however, it did not explain 

much of the variance in the data (r2=0.04, p<0.0001, N=1336). 

Many fish species associated with near-shore, or high relief 

areas, were not included in this analysis due to the absence of 

NMFS trawls in these areas. California Department of Fish and 

Game recreational fishing trips (pp. 23) were often located in 

near-shore or high relief areas, and can be used to determine 

approximate fish diversity over these habitats. The mean fish 

diversity recorded for recreational hook and line locations was 

1.3 ± 0.6 (range of 0 to 2.5). This estimate of diversity is similar 

to those measured with the NMFS shelf and slope trawl data; 

however, since the collection method was different, no statisti124°W

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Species Diversity of

Demersal Fish

Diversity

0 10 20 40 60

Kilometers

1.78 - 2.54

1.37 - 1.77

Diversity by Individual Trawl

0.02 - 1.36

2

1

0

0

5

0

2

0

0

0

0

m

0

m

m

m

Figure 13. Species diversity of individual NMFS shelf and slope trawls.

S  n  H ∑    n  ′ = −  i  ln  i  i =1  n   n 

19
Subsection 2.1.1: ASSEMBLAGE ANALYSES

cal comparisons can be completed and these results are only 

intended as anecdotal validation. 

Trawls with high species diversity are not necessarily trawls with 

high richness. Since diversity takes into account the number of 

fish of each species found, areas with one or two abundant species have a lower diversity than areas with less fish species, but 

an even distribution. High richness trawls are slightly shallower 

than high diversity trawls suggesting that the trawls deeper than 

200 meters have fewer species, but a more even distribution. 

The presence of a high diversity area along the boundary between Gulf of the Farallones and Monterey Bay Sanctuaries 

defines an area of biological significance for demersal fish. In 

addition, there are lines of high species diversity north and south 

of the current boundaries deeper than the 200 meter contour. 

The trawls located on top of Santa Lucia Bank had medium to 

high species diversity, and represent a large expanse of deep 

habitat not within sanctuary boundaries. This area, combined 

with existing NMS shelf and slope areas, appears important to 

groundfish as indicated by high diversity patterns. Managers 

interested in protecting biodiversity of demersal fish can use this 

information in combination with the other assemblage analysis 

results to address various management strategies.

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Species Diversity of

Demersal Fish

Diversity

0 10 20 40 60 80 100

Kilometers

1.63 - 2.27

1.39 - 1.62

0.18 - 1.38

Deviation of Diversity

No Deviation

Less than Mean Deviation

Mean Diversity in 5' Cells

Greater than Mean Deviation

2

1

0

0

5

0

2

0

0

0

0

m

0

m

m

m

Figure 14. Mean species diversity of NMFS shelf and slope trawls for 5’ grid cells. The deviation is shown as an overlay to provide an 

indication of the variability in results for each grid cell.

20
Subsection 2.1.1: ASSEMBLAGE ANALYSES

1

2

3

4

5

6

7

8

ssenhcir hsifkcor naeM

0 100200 400 600 800 1000 1200

Depth (10 meter intervals) 

ABOUT THIS MAP

Species richness of demersal rockfishes was calculated from 

NMFS shelf and slope trawls (Figure 15). The information on 

this map identifies areas with a high number of rockfish species. Values were not influenced by latitude, but were highly 

influenced by depth. The highest rockfish richness values 

were observed along the edge between the shelf and slope, 

emphasizing the importance of these areas to rockfish. Sanctuary boundaries now include more than 500 square kilometers 

of this edge area (between 200 and 300 meters depth), with 

75% of this area within Monterey Bay NMS. The area south 

of Monterey Bay NMS to the edge of the study area contains 

another 500 square kilometers of habitat between 200 and 

300 meters. 

DATA SOURCES

Data were derived from 1,336 NMFS (AKFSC and NWFSC) 

shelf (pp. 26) and slope (pp. 28) trawls conducted between 

50-1280 meters depth during June-November from 1977-2001. 

For details on the trawl methods see Lauth (2001), Shaw et al. 

(2000), Turk et al. (2001), and Williams and Ralston (2002). 

All rockfish identified to the species level were included (48 

species).

METHODS

Species richness is defined as the number of fish species 

present at a given location. To calculate rockfish richness, data 

were tabulated to determine the number of rockfish species 

Sebastes or Sebastolobus present in each trawl. There was no 

significant relationship between trawl effort (distance fished x 

net width) and species richness (N=1336, F=1.3, p=0.26), so 

raw values of species richness for each trawl were used for this 

analysis. Trawls are only possible along relatively flat bottom 

areas. No trawls were conducted over rocky, high relief areas or 

areas in water less than 50 m deep, therefore, some potentially 

important sites were not considered in these analyses.

RESULTS AND DISCUSSION

The mean (± standard deviation) number of rockfish species 

recorded for a demersal trawl was 4±3, with a range from 0 to 

14. The results show that bathymetry has a strong influence 

on rockfish species richness. The lowest rockfish richness is 

found in the shallower (but still >50 m) and deeper waters. 

A band of high rockfish richness is located around 200-300 

meters depth and parallels the edge between the continental 

shelf and slope. For all trawls, there was a significant non-linear 

relationship between richness and depth (Figure 16, F=166, 

p<0.0001), and no significant relationship between richness 

and latitude (F=2.1, p=0.15). Almost all trawls on the deep slope 

(deeper than 600 meters) contain the same two rockfish species (shortspine and longspine thornyheads). It is important to 

note that many rockfish species are associated with kelp beds 

or high relief areas which were not included in this analysis. 

Other analyses conducted in these habitats can provide a comparison to these results. Tom Laidig (pers. comm. NMFS) has 

conducted scuba surveys to determine the presence of fish on 

kelp beds near Sonoma and Monterey in California. Average 

rockfish richness recorded on 43 dives in Sonoma, between 

1983 and 1995, was 5±2 (range of 0 to 9), and 8±2 on 9 dives 

in Monterey (range of 5 to 12). California Department of Fish 

and Game recreational fishing trips targeting rockfish (pp. 23) 

can also be used to determine approximate rockfish richness. 

However, without fishing effort information, the utility of mapping 

the richness from recreational fishing data is questionable. Average rockfish richness recorded per location/trip combination 

was 6±2 (range of 0 to 12). The estimate of rockfish richness 

for near-shore areas from CDF&G trawls is similar to those 

measured with the NMFS shelf and slope trawl data, but since 

the capture method was different, these results should only be 

used as an anecdotal validation. 

The results of this analysis illustrate the importance of the edge 

between shelf and slope areas. This result supports that of Williams and Ralston (2002), who found highest rockfish richness 

between 200 to 250 meters depth using NMFS shelf data for 

California and Oregon.

Figure 15. Species richness of rockfish from individual NMFS shelf and slope trawls.

Figure 16. The relationship between depth and rockfish richness 

showing mean rockfish richness (for 10 meter depth intervals between 50-1300 meters). The relationship was fit with a smoothing 

spline, lambda = 1,000,000.

124°W

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N°53N°53

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Species Richness of

Demersal Rockfish

Richness

0 10 20 40 60

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5 - 6

3 - 4

2

Richness by Individual Trawl

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21
Subsection 2.1.1: ASSEMBLAGE ANALYSES

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Integration of Community

Metrics for Fish

Legend

0 10 20 40 60 80 100

Kilometers

Top 20% of

Diversity and Richness

Top 20% of Diversity

Top 17% of Richness

Top 17% of

Rockfish Richness

Bathymetric Complexity

Departure from Mean

-1 - 0 Std. Dev.

0 - 1 Std. Dev.

1 - 2 Std. Dev.

2 - 3 Std. Dev.

>3 Std. Dev.

50 m

20

m

0 m

2

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0

0 m 200

10

0

00

m

m 2000 m

Figure 17. NMFS shelf and slope trawls with the highest species diversity, species richness, and rockfish richness are mapped. The 

underlying map illustrates the bathymetric complexity of the study area and can be used to identify the shelf break.

ABOUT THIS MAP

The last three sections showing species diversity, species richness, and rockfish richness have provided results relevant to 

managing resources. Figure 17 illustrates the overlay of the 

top 17-20% of trawls for high species diversity, species richness, or rockfish richness. The background of the map shows 

the bathymetric complexity from page 16. The overlay of the 

points provides visual representation of the results.

DATA SOURCES

Diversity, richness, and rockfish richness estimates were derived from 1,336 NMFS (AKFSC and NWFSC) shelf (pp. 26) 

and slope (pp. 28) trawls conducted between 50-1280 meters 

depth during June-November from 1977-2001. For details on 

the trawl methods see Lauth (2001), Shaw et al. (2000), Turk 

et al. (2001), and Williams and Ralston (2002).

METHODS

Methods for calculating diversity, richness, and rockfish richness are detailed in each section. The top 20% of trawls for 

diversity were extracted and mapped. Ideally, the top 20% 

of trawls for overall species richness and rockfish richness 

would be provided; however, since richness is discrete and not 

continuous, either 17% (21+ species) or 23% (20+ species) 

could be mapped. The trawls which were within the top 20% 

for both richness and diversity are distinguished. 

RESULTS AND DISCUSSION

Richness calculates the number of fish species present in 

each trawl, while diversity takes into account the abundance 

of fish species as well. Diversity and richness are correlated 

(r2

=0.06), but trawls with high diversity are not necessarily 

trawls with high richness. Trawls which were high in overall 

richness and diversity were distinguished, and show areas 

important to demersal fish. A cluster of trawls with high diversity and high richness straddle the boundary between Gulf of 

the Farallones and Monterey Bay NMS, as well as along the 

200 meter contour north of Cordell Bank NMS. Small clusters 

of high diversity and high richness trawls are present within 

each sanctuary. Depth varied between the three community 

metrics, with high richness, rockfish richness, and diversity 

progressing from shallow to deep. The mean depth for trawls 

with the top 17% of rockfish richness was 221±87, with 43% 

of the trawls between 200 and 300 meters depth. Showing 

these trawls reemphasizes the interaction between rockfish 

richness and the edge of the continental shelf. The trawls with 

high species richness show much more variability with depth 

(mean depth 212±225 meters), but 64% of them are in water 

less than 200 meters deep. The trawls with high species diversity were deeper (mean depth 372±289 meters), with 52% of 

them greater than 300 meters depth. Overall, the trawls with 

high diversity were deeper than the trawls with high richness. 

A good example of this split by depth can be found south of 

the Monterey Bay NMS. This suggests that trawls with high 

species richness found just east of the 200 meter contour are 

dominated by a few influential species. Conversely, the areas 

of high diversity just west of the 200 meter contour might have 

one or two fewer species, but overall the species are evenly 

distributed. 

Results from the assemblage analyses were significantly tied to 

depth; therefore, maps show bands of similar sites along depth 

contours and do not delineate areas important to demersal fish. 

Conversely, the results from the community metrics do delineate hot spots. Results are limited by collection method since 

rocky, highly sloped, or shallow (less than 50 meters depth) 

areas were not sampled. Managers could use the interaction 

of the community metrics to decide on proper management 

strategies. For example, management is often tasked with protecting biodiversity, and is therefore interested in delineating 

areas that contain the highest number of species. However, if 

an area is high in richness, but is dominated by one economically important species, protecting this area could contribute 

to resource use conflicts. The interplay between diversity and 

richness should be carefully evaluated.

22
Subsection 2.1.1: ASSEMBLAGE ANALYSES

ABOUT THESE ANALYSES

Managers have recently begun to understand the importance of studying 

entire ecosystems rather than looking at each species individually. This study 

took a first step in clarifying multi-species interactions by determining which 

species tended to be caught together, and where. Multivariate statistics were 

used to analyze fish species assemblages on the scale of the recreational 

fishery over marine habitats off central California. This data set, while fishery 

dependent, includes demersal, as well as midwater species captured on 

variable habitats, including rock, mud, and sand. Some species and habitats 

in this analysis are not covered with the other data sets in this study, and 

therefore provide complimentary information. Twenty-seven fish species were 

grouped into seven species assemblages (Figure 18), and 4,357 trip/location 

combinations were grouped into eight site groups (Table 1). Unfortunately, 

due to the nature of the data set (see methods), exact fishing locations could 

not be mapped. Therefore, the mean depth associated with each site group 

is provided in conjunction with a map showing the fishing locations in 2.5 

minute grids, which were color coded according to the average depth of the 

fishing trips within the grid cell. The two analyses mentioned above provide 

information on species which were caught together, and locations with similar 

catch. Combining the two results was the challenge. The average frequency of 

occurrence of species assemblages (percent occurrence calculated for each 

species and then averaged for each fish assemblage) within each site group 

was calculated to analyze the interaction between the species assemblages 

and site groups (Table 2). As with all data sets in this assessment, the most 

significant result was the effect of depth. This supports previous work done 

by Williams and Ralston (2002), Sullivan (1995), Field et al. (2002), Gabriel 

and Tyler (1980), and Matthews and Richards (1991), who found bathymetry 

to be an important factor in defining fish assemblages. All attempts to isolate 

and remove the effects of depth in order to determine secondary effects were 

unsuccessful. Certainly, secondary effects exist, but at the scale of this study 

they were not discernible. Through this analysis, a large amount of information has been condensed to assemblages of co-occurring species, as well as 

groups of similar locations. A map is provided to visually portray the spatial 

arrangement of the results. 

DATA SOURCES

Data from 2167 commercial passenger fishing vessels, fishing for rockfish or 

lingcod, using hook and line, were collected during all months between 1987 

and 1998 at depths between 2-360 meters. Each trip visited between 1 and 

8 locations, with each trip/location combination considered a unique site. For 

this data set, effort was not provided, and therefore only presence/absence 

was analyzed at each trip/location combination. The data set contained information on 103 fish species, but after removal of rare species, the data 

matrix used for classification contained information on 27 fish species at 4357 

trip/location combinations. A list of common and scientific names of the species included in the analysis is available on the accompanying CD-ROM. To 

protect individual fishing locations as requested by the CDF&G, results are 

presented in 2.5 minute grids. For more information on the data collection 

process see Wilson-Vandenberg et al. (1996). 

the results compared for persistence and precision. Additionally, the data 

from 1993 to 1998 was analyzed separately to determine if current conditions have changed enough to affect the resultant species assemblages. 

Conditions that could have changed through time include: abiotic shifts, such 

as decadal shifts in water temperature; biotic shifts, such as depletion of 

key species; and effort shifts, such as fishing farther offshore. To determine 

which species groups were influential in forming the site groups, the average frequency of occurrence for species assemblages in each site group 

was calculated. Species assemblages were considered influential if, on 

average, species were present in 25% of the trip/location combinations in 

a site group. The mean depth associated with each site group is provided 

in conjunction with a map showing the fishing locations in 2.5 minute grids, 

and color coded according to the average depth of the fishing trips within the 

grid cell. Two-way analyses of variance (ANOVA) were conducted with depth 

(pp. 37 Figure 32) and latitude, sediment (pp. 38 Figure 33), and bathymetric 

complexity (pp. 16 Figure 10) to determine if any of these factors have an 

influence on the site group results at the scale of this analysis. 

RESULTS AND DISCUSSION

Species Assemblages (Objective A)

Seven species assemblages were differentiated from the recreational data, 

and named according to the most influential species (Figure 18). When 

the data from 1993-1998 were analyzed separately, there were two minor 

changes: the yellowtail rockfish assemblage split into two assemblages, and 

squarespot rockfish moved from the Pacific mackerel assemblage to the 

bocaccio assemblage. Overall, the species assemblages delineated were 

surprisingly robust; almost all fish were consistently placed in the same assemblages for more than 80% of the random runs, providing confidence in 

the stability of the assemblages. Running the modified bootstrap technique 

can provide an estimate of the precision of results, but verifying the accuracy 

of the results is more difficult. Comparisons of the results with past studies 

can give feedback on the accuracy of the results. Assemblages are not 

static, and may modify in response to environmental conditions, such as 

warm or cold conditions (see CD-ROM for changes in species assemblages 

in response to water temperature or season).

Love et al. (2002) provides a summary of rockfish habitat requirements and 

species co-occurrences. The gopher rockfish and blue rockfish assemblages 

are supported by Love et al. (2002) as the species in each assemblage are 

described as having the same habitat or co-occurring. In addition, Mason 

(1995) looked at the recreational logbook and described a shallow rockfish 

assemblage composed of blue, black, brown, gopher, and olive rockfishes, 

all found within the gopher and blue assemblages described in this study. 

The greenspotted assemblage from this analysis is not necessarily intuitive. Greenspotted and greenstriped can both be found on mud near rocks 

(Love et al., 2002), but this is also a characteristic of some of bocaccio and 

yellowtail assemblage species (Love et al., 2002). Mason (1995) designated a deepwater red rockfish assemblage that included greenspotted, 

greenstriped, chilipepper, and bocaccio, which provides some support to 

the greenspotted assemblage of this study. Flag rockfish is an example of a 

species co-occurrence mentioned in Love et al. (2002) that is not supported 

here. Flag rockfish was placed in the bocaccio assemblage in this study, but 

METHODS

The aim of the entire assemblage analysis was to increase our understanding of the biogeography 

of fishes and macro-invertebrates in relationship to their environment, and identify important areas 

or habitats. Four of the five man objectives were addressed in this recreational analysis:

A. Determine which species tended to be caught together (species assemblages);

B. Analyze fishing locations to determine which locations contained similar catches (site 

 groups);

C. Resolve where the species assemblages were being caught by combining results from 

 objectives A and B and then utilizing GIS to map the results; and

D. Identify significant relationships between the site groups identified in objective B and

 broad scale habitat characteristics (bathymetry, bathymetric complexity, and large-scale 

 habitat classification).

Clustering is a technique used to summarize information into similar groups. The 1-Pearson correlation coefficients, with the average means clustering method (see "Introduction to Clustering" pp. 

14) was used to summarize fish species into assemblages and catch locations into site groups. In 

order to determine how variable the species assemblage results could be within the data, a modified 

bootstrapping procedure was employed on 50 random samples composed of 50% of the data and 

Figure 18. Species assemblage results for the recreational data. Assemblages are named for the most influential species in each group. Assemblages are arranged from shallow to deep, unless they are influential at 

all or none of the depths. The assemblages that were not influential at any depth were composed of relatively 

rare species, making depth associations indiscernible given the methodology for defining “influential” assemblages. Non-italicized species were consistently placed into the same species assemblage >80% of the time; 

italicized species tended to roam into other assemblages with random sampling.

Gopher Rockfish

Black Rockfish

Brown Rockfish

Cabezon

China Rockfish

Kelp Greenling 

Blue Rockfish

Olive Rockfish Yellowtail Rockfish

Canary Rockfish

Copper Rockfish

Lingcod

Rosy Rockfish

Starry Rockfish

Vermilion Rockfish

Pacific Sanddab Bocaccio

Flag Rockfish

Speckled Rockfish

Widow Rockfish

Yelloweye Rockfish Quillback Rockfish

Greenspotted Rockfish

Pacific Mackerel Greenstriped Rockfish 

Squarespot Rockfish Chilipepper

CDFG Recreational Hook and Line

Species Assemblages

Not in

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ue

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epth

Shallow to Deep

23

Pictures from FishBase and NMFS
according to Love et al. (2002), flag is often found with species from the yellowtail 

rockfish assemblage. Within the modified bootstrapping procedure, flag rockfish was 

placed with the Bocaccio assemblage 78% of the time, and with the yellowtail rockfish 

assemblage only 28% of the time, supporting its placement in this analysis. 

The results comply with the large scale assemblages designated by NMFS: nearshore, shelf, and slope species groups (NMFS). All of the rockfish in each species 

assemblage from this study come from the same NMFS group, except for the yellowtail assemblage, which contains four species designated as “shelf” and one species 

designated as “near-shore”. Williams and Ralston (2002) grouped rockfish from the 

NMFS shelf trawl data into eight groups. While their assemblages differ from this 

study's results, of the eleven species analyzed in both data sets, species from the 

bocaccio and greenspotted rockfish assemblages are placed together, and species 

from the gopher rockfish and yellowtail rockfish assemblages are placed together. 

Comparison of the results from this study with results based on trawl (NMFS; Williams 

and Ralston, 2002; Gabriel and Tyler, 1980; Jay, 1996), or results from submersibles 

(Yoklavich et al., 2000, 2002; Hixon et al., 1991; Hixon and Tissot, 1992; Field et al., 

2002), is difficult due to the species analyzed, the different habitats targeted, and the 

variable scale of the results. Matthews and Richards (1991) found different species 

assemblages over trawlable and untrawlable habitats, showing the effect targeting 

different environments can have on species assemblages. Scale is important since 

the recreational boat drifts over multiple habitats during a set, and fish from multiple 

habitats can be present in one trip/location combination. In addition, species assemblage results could also be confounded by ontogenetic habitat shifts because 

the sizes of the fish captured were not considered. 

Site Groups (Objective B)

Eight site groups were identified from the 4,357 trip/location combinations (Table 1). 

To make interpretation easier, the site groups are named according to mean depth. 

Maps with the location of the site groupings in the 2.5 minute grid are hard to interpret 

Subsection 2.1.1: ASSEMBLAGE ANALYSES

due to overlap of more than one group within the same cell. For 

example, within one grid cell on the southern side of Monterey Bay, 

the maximum depth fished ranged between 37 and 660 meters, 

and contained sites from all 8 cluster groups. Therefore, the mean 

depths fished ±SD are presented, which can be used in conjunction 

with Figure 19 to determine the approximate location of the site 

groups. Depth was the primary determinant of site groupings. All but 

two (groups 40 and 44) of the eight site clusters were significantly 

different in depth (see Table 1), suggesting that depth is highly influential in determining species distributions within the study area. 

The site groups we identified were similar to results of Sullivan 

(1995), who analyzed a subset of this same data to differentiate 

areas based on species composition. A direct comparison between 

Sullivan and this study is difficult because Sullivan describes his 

locations verbally using land identifiers, while this study describes 

locations by depth. The importance of depth in this ecosystem is 

not a new idea; many researchers have already commented on 

its influence (Williams and Ralston, 2002; Sullivan, 1995; Gabriel 

and Tyler, 1980; Field et al., 2002; Matthews and Richards, 1991). 

Latitude has also been described as having an influence on California fish species composition (Williams and Ralston, 2002; Horn 

and Allen, 1978; Sullivan, 1995), but for the area of this study, no 

latitudinal results were evident. 

Interaction of Species and Sites (Objective C)

The interaction between site groups and species assemblages (i.e. the location of In conclusion, this analysis provides results showing species assemblages, site as

species assemblages) reemphasized the relationship between species and depth. semblages, and the location of species assemblages for the important near-shore

Species assemblages which were influential in forming each site group are identified rocky environment. Understanding species assemblages and mapping their loca

(Table 2). Site group 44 did not seem to be associated with any fish assemblages tion provides important information for managers. For example, to include the mos

(none with a frequency of occurrence greater than 25). At this point, it is uncertain species assemblages, protecting an area that covers a large variation in depth ma

what factor caused the clustering of this group. For all of the trip/location combina- be more important than protecting an area that covers a large variation in latitude

tions, on average 68 fish were caught. The average number of fish caught for group The results of this analysis in conjunction with similar analyses on the three othe

44 was 12, suggesting that some outside factor, such as poor weather, was influenc- data sets provides a fairly comprehensive overview of fish and macro-invertebrat

ing catches at these sights. species within the study area.

Habitat Correlations (Objective D)

Other factors besides depth can have an impact on species assemblages. Examples 

include latitude (Horn and Allen, 1978; Sullivan, 1995), sediment type (Yoklavich et 

al., 2000, 2002; Field et al., 2002; Hixon et al., 1991; Hixon and Tissot, 1992), and 

substrate relief (see bathymetric complexity section pp. 16) (Yoklavich et al., 2000, 

2002; Field et al., 2002). Unfortunately, since there were significant interactions 

present between all of these variables and depth, it could not be determined if the 

significance detected for these factors was due to this interaction with depth. Even 

though bathymetric complexity increases as depth increases, groups 44, 59, and 

125 meters have a higher bathymetric complexity than the groups around them with 

similar depth. All attempts to remove depth and determine secondary influences on 

group designation were unsuccessful. The non-linear relationship between the fish 

species and depth made removal of depth impossible. While these other factors 

appear to have a decreased significance when compared to depth, more complex 

analyses exploring ways to remove the effects of depth and determine the relative 

significance of these factors may be completed in Phase II. 

Group 26 

meters

Group 40 

meters

Group 44 

meters

Group 59 

meters

Group 64 

meters

Group 77 

meters

Group 98 

meters

Group 125

meters

Gopher

Assemblage 0.36 0.23 0.14 0.09 0.09 0.01 0.01 0.00

Blue Assemblage 0.72 0.74 0.07 0.19 0.69 0.20 0.07 0.00

Yellowtail

Assemblage 0.22 0.42 0.08 0.31 0.74 0.31 0.57 0.08

Bocaccio

Assemblage 0.01 0.05 0.00 0.05 0.23 0.25 0.43 0.22

Greenspotted

Assemblage 0.00 0.00 0.02 0.02 0.07 0.10 0.50 0.59

Pacific Mackerel 

Assemblage 0.02 0.07 0.13 0.07 0.12 0.17 0.09 0.06

Quillback 0.01 0.06 0.05 0.04 0.09 0.01 0.02 0.00

Table 1. Site group results for recreational data. The numbers of trip/location combinations 

associated with each group as well as average depth, ± standard deviation, are provided. 

Different letters signify a significant difference using Tukey’s pairwise comparison on log 

Table 2. Average frequency of occurrence of fish species assemblages (percent occurrence calculated for eac

species and then averaged for each fish assemblage) for each recreational site group. Numbers in bold represe

influential species assemblages within that site group.

Site Group Depth±SD

(Names based on depth) N (meters)

Group 26 meters 581 26 ± 13a

Group 40 meters 688 40 ± 16b

Group 44 meters 183 44 ± 27b

Group 59 meters 235 59 ± 26c

Group 64 meters 1,501 64 ± 18d

Group 77 meters 207 77 ± 22e

Group 98 meters 683 98 ± 21f

Group 125 meters 279 125 ± 32g

-

, 

-

t 

y 

. 

r 

e 

adjusted depth with overall alpha set at 0.001.

h 

nt 

24
Figure 19. Location of CDF&G recreational fishing data in 2.5 minute grids which are color coded according to the average depth of the 

fishing trips within the grid cell. Lines showing the 50, 100, 200, and 2,000 depth contours are provided.

124°W

124°W

123°W

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122°W

122°W

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121°W

35°N35°N

36°N36°N

37°N37°N

38°N38°N

39°N39°N

CDF&G Recreational Data

0 20 40 60 80 10

Kilometers

Mean Depth

0 - 15 meters

15 - 25 meters

25 - 35 meters

35 - 45 meters

45 - 55 meters

55 - 65 meters

65 - 75 meters

75 - 85 meters

85 - 100 meters

>100 meters

100 m

50 m

200 m

2000 m

in 2.5' Grids

Subsection 2.1.1: ASSEMBLAGE ANALYSES

25
Subsection 2.1.1: ASSEMBLAGE ANALYSES

ABOUT THIS MAP

Recently managers and scientists have begun to understand the importance 

of studying communities of species rather than just managing by individual 

species. This study was an initial assessment aimed at determining which 

species tended to be caught together, and where. Multivariate statistics 

were used to analyze species assemblages over trawlable habitats of the 

continental shelf between 55 and 500 meters depth off California. For an 

introduction to the continental shelf ecosystem, see the Ecological Linkages 

Report. Sixty-one species were grouped into thirteen species assemblages 

(Figure 20), and 883 trawls grouped into eight site groups (Table 3, Figure 

21). The average frequency of occurrence of species assemblages (percent 

occurrence calculated for each species and then averaged for each fish assemblage) within each site group was calculated to analyze the interaction 

between the species assemblages and site groups (Table 4). As with all data 

sets, the most significant result was the effect of depth on species assemblages. All attempts to isolate and remove the effects of depth in order to 

determine secondary effects were unsuccessful. Certainly secondary effects 

exist, but at the scale of this study, they were not discernible. Our results 

support previous results by Williams and Ralston (2002), Sullivan (1995), 

Field et al. (2002), Gabriel and Tyler (1980), and Matthews and Richards 

(1991), who found bathymetry to be an important factor in defining west 

coast demersal fish assemblages. Through this analysis, a large amount of 

information has been condensed to assemblages of co-occurring species, 

as well as groups of similar locations. A map is provided to visually portray 

the spatial arrangement of the results. 

DATA SOURCES

Data from 883 fisheries independent research trawls (55-500 meters depth) 

were collected every third year, between 1977 and 2001, during the months 

of June-August. Gear included a nor’eastern trawl (127 mm stretched-mesh 

body; 89 mm stretched-mesh codend; and 32 mm stretched-mesh codend 

liner) with a rubber bobbin roller which was trawled for 15-30 minutes on 

the bottom. Data was adjusted for effort and to meet statistical assumptions 

by dividing number of fish caught by the area covered and then log transforming. The data set contained information on 167 fish species, but after 

removal of rare species, the data matrix used for clustering contained only 

58 fish and 3 invertebrate species. A list of common and scientific names 

of the species included in the analysis is available on the accompanying 

CD-ROM. Since each NMFS cruise hosted scientists with varying levels of 

expertise in invertebrate identification, NMFS scientists recommended that 

only well known/common invertebrate species be included in the analyses. 

Fish species assemblages were identical with and without the inclusion of 

invertebrates in the analysis. For more information on how the data were 

collected, including the site selection process and how it changed through 

time, see Shaw et al. (2000), Wilkins et al. (1998), and Zimmermann et al. 

(2001).

METHODS

The aim of the entire assemblage analysis was to increase our understanding of the biogeography of fishes and macro-invertebrates in relationship to 

their environment, and identify important areas or habitats. Four of the five 

main objectives were addressed in this analysis:

A. Determine which species tended to be caught together (species assemblages);

B. Analyze fishing locations to determine which locations contained similar catches (site 

 groups);

C. Resolve where the species assemblages were being caught by combining results from 

 objectives A and B and then utilizing GIS to map the results; and

D. Identify significant relationships between site groups identified in objective B and broad 

 scale habitat characteristics (bathymetry, bathymetric complexity, and large-scale habitat 

 classification).

Clustering is a technique used to summarize information into similar groups. The 1-Pearson correlation coefficients with the average means clustering method (see "Introduction to Clustering" pp. 14) 

was used to first summarize fish species into assemblages, and to then summarize catch locations 

into site groupings. In order to determine how variable the species cluster results could be within 

the data, a modified bootstrapping procedure was employed on 50 random samples composed of 

50% of the data and the results compared for persistence and precision. Additionally, the data from 

1989 to 2001 were analyzed separately to determine if current conditions have changed enough 

to affect the resultant species assemblages. Conditions that could have changed through time 

include: abiotic shifts, such as decadal shift in water temperature; biotic shifts, such as depletion 

of key species; or effort shifts, such as fishing farther offshore. The location of the eight site groups 

Pacific Herring Sharpchin Rockfish

American Shad Spot Shrimp

California Market Squid Threadfin Sculpin

Chinook Salmon

Curlfin Sole

Dungeness Crab

Longspine Combfish

Northern Anchovy

Pacific Pompano

White Croaker

Pacific Electric Ray

Big Skate

California Skate

Spiny Dogfish

Pacific Hake

Longnose Skate 

Spotted Ratfish Darkblotched Rockfish

Bank Rockfish

Redbanded Rockfish

Splitnose Rockfish

Pictures from FishBase and NMFS

Canary Rockfish 

Yellowtail Rockfish

Widow Rockfish

Rock Sole Sp

Halfbanded Rockfish

Pacific Mackerel Arrowtooth Flounder Jack Mackerel

Pacific Argentine Pacific Sanddab

English Sole

Petrale Sole

Pink Seaperch

Plainfin Midshipman 

Lingcod

Chilipepper

Bocaccio

Rex Sole Cowcod

Slender Sole Greenspotted Rockfish

Spotted Cusk-eel Greenstriped Rockfish

Shortbelly Rockfish

Stripetail Rockfish Shortspine

Thornyhead

Bering Skate

Bigfin Eelpout

Dover Sole Blackgill Rockfish 

Aurora Rockfish Sablefish Black Eelpout

Blacktail Snailfish

Brown Cat Shark

Filetail Cat Shark

Lanternfish

Shallow to Deep

All depths

NMFS Shelf Trawls

Species Assemblages

Not in

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epth

were mapped using GIS. To determine which species groups were influential 

in forming the site groups, the average frequency of occurrence for species 

assemblages in each site group was calculated. Species assemblages were 

considered influential if, on average, species were present in 25% of the trawls 

in a site group. Two-way analyses of variance (ANOVA) were conducted with 

depth (pp. 37) and latitude, sediment (pp. 38), and bathymetric complexity 

(pp. 16) to determine if any of these factors have an influence on the site 

group results at the scale of this analysis. 

RESULTS AND DISCUSSION

Species Assemblages (Objective A)

Thirteen species assemblages were determined in the NMFS trawl data 

set and named according to the most influential species (Figure 20). There 

were no differences in the results when data from 1989-2001 were analyzed 

separately. Overall, the species assemblages delineated were robust; eight 

of the thirteen groups were consistently placed together for more than 80% 

of the random samples. This provides confidence that the results do not represent just random groupings. Running the modified bootstrap technique can 

provide an estimate of the precision of results, but verifying the accuracy of 

the results is more difficult. Comparisons of the results with past studies can 

give feedback on the accuracy. Assemblages are not static and may modify 

in response to environmental parameters, such as warm or cold conditions 

(see CD-ROM for changes in species assemblages in response to water 

temperature).

The species cluster results from the shelf trawls make intuitive sense in many 

ways. For example, most of the pelagic species were clustered together 

(Pacific herring assemblage), and the soft bottom and hard bottom species 

are separated for most of the groups. Only a few assemblages contain both 

soft bottom and hard bottom species, for example the inclusion of the soft 

bottom- associated stripetail rockfish and rock sole with hard bottom assemblages (bocaccio and canary rockfish, respectively), and the placement of 

stripetail rockfish (hard bottom) in the darkblotched rockfish assemblage (soft 

bottom) (Love et al., 2002). The chilipepper group contains fish species that 

are benthic as well as midwater schoolers, suggesting that even though these 

species behave differently they are responding to similar habitat characterisFigure 20. Species assemblage results for the shelf trawls. Assemblages are named for the most influential 

species in each group. Assemblages are arranged from shallow to deep, unless they are influential at all or 

none of the depths. The assemblages that were not influential at any depth were composed of relatively rare 

species, making depth associations indiscernible given the methodology for defining “influential” assemblages. 

Non-italicized species were consistently placed into the same species assemblage >80% of the time; italicized 

species tended to roam into other assemblages with random sampling.

Site Group Depth±SD

(Names based on depth) N (meters)

Group 78 meters 125 78 ± 16a

Group 93 meters 103 93 ± 19b

Group 96 meters 136 96 ± 25b

Group 119 meters 72 119 ± 37c

Group 153 meters 171 153 ± 41d

Group 268 meters 116 268 ± 52e

Group 328 meters 37 328 ± 51f

Group 415 meters 123 415 ± 48g

Table 3. Site group results for shelf trawl data. The numbers of trawls associated 

with each group as well as average depth ± standard deviation are provided. Different letters signify a significant difference using Tukey’s pairwise comparison on log 

adjusted depth with overall alpha set at 0.001.

26
Subsection 2.1.1: ASSEMBLAGE ANALYSES

Figure 21. Location of site groups for NMFS shelf trawls. Lines showing the 50, 100, 200, and 2,000 depth 

contours are provided.

tics. Love et al. (2002) mention species co-occurrences, such as the association of 

cowcod (immature) with bocaccio and greenstripe rockfish, which are corroborated 

by the results of this analysis. However, this study, unlike Love, found that stripetail 

rockfish and a splitnose rockfish did not occur together. The placement of yellowtail 

rockfish, canary rockfish, and widow rockfish together in this analysis is supported 

by multiple studies (Tagart and Wallace, Leet, 2001, Star et al., 2002). 

All rockfish groups concurred with the broad characterization by NMFS (into nearshore, shelf, and slope species groups), which were based on an assemblage analysis 

completed by Gabriel and Tyler (1980). Williams and Ralston (2002) used the same 

data set as this study to examine rockfish species assemblages. Their “southern 

shelf group” contained species clustered together in this report's chilipepper and 

canary groups, while their “deep-water slope” group was split among three groups 

in this report. The results from submersibles (Yoklavich et al., 2000, 2002; Hixon et 

al., 1991; Hixon and Tissot, 1992; Field et al., 2002) provide relevant species/habitat 

interactions at a scale meaningful to fish, however, many of the results from these 

studies are not comparable with the current studies due to the large difference in 

scale. Hixon et al. (1991) documented that the species composition observed from 

the submersibles was different than species captured in trawls. 

Site Groups and Interaction of Species and Sites (Objectives B and C)

Eight site groups were identified from the 883 shelf trawls (Table 3). To make interpretation easier, the site groups are named according to mean depth. All but two 

groups are significantly different in depth using an ANOVA (Table 3). The importance 

of depth in this ecosystem is not a new idea; many researchers have already comGroup 78 

meters

Group 93 

meters

Group 96 

meters

Group 119 

meters

Group 153 

meters

Group 268 

meters

Group 328 

meters

Group 415 

meters

Rex Sole Assemblage 0.64 0.59 0.82 0.74 0.80 0.78 0.93 0.63

Pacific Hake

Assemblage 0.41 0.37 0.62 0.39 0.58 0.61 0.87 0.68

Shortspine Thornyhead

Assemblage 0.20 0.23 0.28 0.32 0.39 0.64 0.96 0.83

Pacific Herring 

Assemblage 0.63 0.31 0.34 0.21 0.06 0.01 0.01 0.01

Halfbanded Assemblage 0.22 0.27 0.11 0.24 0.07 0.02 0.01 0.01

Pacific Sanddab

Assemblage 0.90 0.91 0.88 0.82 0.55 0.13 0.10 0.03

Big Skate Assemblage 0.27 0.26 0.40 0.25 0.25 0.16 0.24 0.12

Chilipepper Assemblage 0.12 0.26 0.22 0.57 0.61 0.42 0.12 0.03

Darkblotched

Assemblage 0.01 0.00 0.03 0.03 0.10 0.41 0.41 0.17

Blackgill Rockfish

Assemblage 0.01 0.01 0.00 0.02 0.01 0.05 0.30 0.56

Canary Assemblage 0.02 0.10 0.06 0.21 0.15 0.04 0.01 0.00

Sharpchin Assemblage 0.01 0.01 0.02 0.05 0.13 0.23 0.10 0.01

Arrowtooth Flounder

Assemblage 0.00 0.05 0.01 0.01 0.11 0.14 0.14 0.02

Table 4. Average frequency of occurrence of fish species assemblages (percent occurrence 

calculated for each species and then averaged for each fish assemblage) for each shelf site 

group. Numbers in bold represent influential species assemblages within that site group.

mented on its influence (Williams and Ralston, 2002; Sullivan, 

1995; Gabriel and Tyler, 1980; Field et al., 2002; Matthews and 

Richards, 1991). Species assemblages which were influential in 

forming each site group are identified (Table 4). The interaction 

between site groups and species assemblages (i.e. the location 

of species assemblages) reemphasized the relationship between 

species and depth. Three species groups (rex sole, Pacific hake, 

and shortspine thornyhead assemblages) had a high frequency 

of occurrence in all trawl groups. The rest of the species groups 

were arranged from shallow to deep. In all cases, the assemblages with a low frequency of occurrence for all site groups were 

composed of relatively rare species. Depth associations were 

present, just not discernible given the methodology for defining 

“influential” assemblages. The location of the trawls designated 

to each site group were mapped using GIS (Figure 21). 

Habitat Correlations (Objective D)

Other factors besides depth can have an impact on species 

assemblages. Examples of these factors include latitude (Horn 

and Allen, 1978; Sullivan, 1995), sediment type (Yoklavich et 

al., 2000, 2002; Field et al., 2002; Hixon et al., 1991; Hixon and 

Tissot, 1992), and bathymetric relief (see bathymetric complexity 

pp. 16) (Yoklavich et al., 2000, 2002; Field et al., 2002). Unfortunately, since there were significant interactions present between 

all of these variables and depth, it could not be determined if the 

significance detected for these factors was due to this interaction 

with depth. Even though bathymetric complexity increases as 

depth increases, group 268 has a higher bathymetric complexity 

than the groups around them with similar depth. It is interesting 

to note that for this data set, 89% of the trawls occurred over 

areas delineated as mud, and 8% over areas delineated as sand 

(pp. 38) making it impossible to examine the effects of sediment. 

However, all 15 trawls that occurred over habitat designated as 

“mud-rock mix” were clustered together into the "415 meters 

group". All attempts to remove depth and determine secondary 

influences on group designation were unsuccessful. The nonlinear relationship between the fish species and depth made 

removal of depth impossible. While these other factors appear 

to have a decreased significance when compared to depth, more 

complex analyses exploring ways to remove the effects of depth 

and determine the relative significance of these factors may be 

completed in Phase II. 

In conclusion, this analysis provides results showing species 

assemblages, site assemblages, and the location of species 

assemblages for the important shelf environment. The species 

assemblages are relevant to the scale of a commercial trawl. The 

larger species assemblages that were reported in the literature 

were confirmed (NMFS near-shore, shelf and slope groups). For 

the most part, pelagic, soft bottom, and hard bottom species assemblages were distinguished, providing initial feedback to the 

accuracy of the species assemblages. 

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NMFS Shelf Trawls

Site Groups

0 10 20 40 60 80 100

Kilometers

Group 78 Meters

Group 93 Meters

Group 96 Meters

Group 119 Meters

Group 153 Meters

Group 268 Meters

Group 328 Meters

Group 415 Meters

200

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27
Subsection 2.1.1: ASSEMBLAGE ANALYSES

ABOUT THIS MAP

Little is known about the deep slope species, especially information on which 

species are found together on what habitats. Multivariate statistics were used 

to analyze species assemblages over trawlable habitats between 190 and 

1280 meters depth off California. This is the first attempt to exclusively define 

species assemblages on the deep slope community. For an introduction to 

the continental slope ecosystem, see the Ecological Linkages Report. Eight 

species assemblages (Figure 22) and seven site groups (Table 5, Figure 23) 

were identified. The average frequency of occurrence of species assemblages 

(percent occurrence calculated for each species and then averaged for each 

fish assemblage) within each site group was calculated to analyze the interaction between the species assemblages and site groups (Table 6). As with 

all data sets, the most significant result was the effect of depth on species 

assemblages. All attempts to isolate and remove the effects of depth in order 

to determine secondary effects were unsuccessful. Certainly secondary effects exist, but at the scale of this study, they were not discernible. Our results 

support previous results by Williams and Ralston (2002), Sullivan (1995), 

Field et al. (2002), Gabriel and Tyler (1980), and Matthews and Richards 

(1991), who found bathymetry to be an important factor in defining demersal 

fish assemblages on the West Coast. Through this analysis a large amount 

of information has been condensed down to assemblages of co-occurring 

species, as well as groups of similar locations. A map is provided to visually 

portray the spatial arrangement of the results.

DATA SOURCES

Data from 454 fisheries independent research trawls between depths of 190-

1280 meters were collected in 1991, 1997, 1999, 2000, and 2001, during the 

months of July-November. For 1999, 2000, and 2001 (NWFSC), gear included 

an aberdeen net with a small mesh liner (2 inches stretched) at the codend 

which was trawled along the bottom along east-west transects for 15 minutes. For 1991, 1997, 1999, and 2000 (AKFSC), gear included a nor’eastern 

(127 mm stretched-mesh body, 89 mm stretched-mesh codend, and 32 mm 

stretched-mesh codend liner) with a rubber bobbin roller which was trawled 

on the bottom for 15-30 minutes. Although different gears were utilized in this 

data set, preliminary analyses found no significant difference between years, 

allowing the data sets to be combined (pers com Tonya Builder, NMFS). Data 

was adjusted for effort and statistical assumptions as in the NMFS Shelf Trawls. 

The data set contained information on 161 fish species, but after removal 

of rare species, the matrix used for classification contained 52 fish and 10 

invertebrate species. A list of common and scientific names of species included in this analysis is available on the accompanying CD-ROM. Since each 

NMFS cruise hosted scientists with varying levels of expertise in invertebrate 

identification, NMFS scientists recommended that only well known/common 

invertebrate species be included in the analyses. Fish species assemblages 

were identical with and without the inclusion of invertebrates in the analysis. 

For more information on how the data were collected, including site selection 

procedures for each data set, see Turk et al. (2001) and Lauth (2001).

METHODS

The aim of the entire assemblage analysis was to increase our understanding 

of the biogeography of fishes and macro-invertebrates in relationship to their 

environment, and identify important areas or habitats. Four of the five main 

objectives were addressed in this analysis:

A. Determine which species tended to be caught together (species assemblages);

B. Analyze fishing locations to determine which locations contained similar catches 

 (site groups);

C. Resolve where the species assemblages were being caught by combining results 

 from objectives A and B and then utilizing GIS to map the results; and

D. Identify significant relationships between site groups identified in objective B and 

 broad scale habitat characteristics (bathymetry, bathymetric complexity, and large- 

 scale habitat classification).

Clustering is a technique used to summarize information into similar groups. The 1-Pearson 

correlation coefficients with the average means clustering method (see introduction to clustering pp. 14) was used to first summarize the fish species into assemblages, and to then summarize the catch locations into site groupings. In order to determine how variable the species 

cluster results could be within the data, a modified bootstrapping procedure was employed on 

random samples composed of 50% of the data and the results compared for persistence and 

precision. The location of the seven site groups were mapped using GIS. To determine which 

species groups were influential in forming the site groups, the average frequency of occurCalifornia Market Squid 

Blackbelly Eelpout 

Robust Clubhook Squid

Filetail Catshark

Black Eelpout

California Grenadier 

Flapjack Devilfish

Pacific Glass Shrimp Longspine Thornyhead

Black Skate 

Califonia Slickhead Pacific Viperfish

Crimson Pasiphaeid Black Hagfish

Aurora Rockfish Deepsea Sole Deepsea Skate

Blackgill Rockfish Giant Grenadier Fangtooth

Dover Sole Grooved Tanner Crab Longfin Dragonfish

Spiny Dogfish Pacific Flatnose Pacific Blackdragon

Bank Rockfish Pacific Grenadier Rhomboid Squid

Snakehead Eelpout Sawtooth Eel

Twoline Eelpout Smooth Grenadier

Threadfin Slickhead

Vampire Squid 

Magistrate Armhook Squid 

Stripetail Rockfish

Bocaccio

Chilipepper

Darkblotched Rockfish

English Sole

Greenstriped Rockfish Splitnose Rockfish Lingcod Bering Skate Petrale Sole Bigfin Eelpout Sharpchin Rockfish Longnose Skate Shortbelly Rockfish Pacific Hake Spot Shrimp Rex Sole Slender Sole Spotted Ratfish Redbanded Rockfish

Rosethorn Rockfish

Pacific Electric Ray

Sablefish

Blacktail Snailfish

Brown Catshark

Shortspine Thornyhead

All depths

Pictures from FishBase and NMFS

NMFS Slope Trawls

Species Assemblages

Not in

a

fl

t

ue

a

n

n

t

y

ia

d

l

epth

Shallow to Deep

rence for species assemblages in each site group was calculated. Species 

assemblages were considered influential if, on average, species were present 

in 25% of the trawls in a site group. Two-way analyses of variance (ANOVA) 

were conducted with depth and latitude, sediment, and bathymetric complexity, 

to determine if any of these factors have an influence on the site group results 

at the scale of this analysis. 

RESULTS AND DISCUSSION

Species Assemblages (Objective A)

Eight species assemblages were determined for the NMFS slope trawls, and 

named according to the most influential species (Figure 22). Overall, the species assemblages delineated were robust; seven of eight assemblages were 

consistently placed together for more than 80% of the random samples. This 

provides confidence that the results do not represent just random groupings. 

Running the modified bootstrap technique can provide an estimate of the precision of results, but verifying the accuracy of the results is more difficult. 

The species cluster results from these NMFS slope trawls seem much less 

intuitive than those from the NMFS shelf trawls. This is partly due to a lack of 

research and subsequent decreased understanding of the behavior of slope 

species. Many of the species from the NMFS slope trawls understandably 

overlap with species from the NMFS shelf trawls. Surprisingly, some of the 

species interactions noted with the shelf trawls are not upheld with the slope 

data. The stripetail rockfish slope assemblage is composed of all of the shallower species (soft and hard bottom) that were distributed among 6 shelf assemblages. This does not imply that species co-occurrences changed between 

the shelf and slope trawls, just that cluster results were sensitive to the depth 

range covered by the data set. 

Love et al. (2002) provides a summary of rockfish habitat requirements and 

species co-occurrences. However, since only 15 (24%) species are rockfish, 

this information cannot be used to assess all results. None of the assemblages 

in this study completely agree with species co-occurrences listed in Love et 

al. (2002). For example, Love et al. stated that stripetail rockfish and splitnose 

rockfish are found together. However, within both the shelf and slope data sets 

of this analysis the stripetail and splitnose rockfish were placed into different 

groups. The results are consistent with the large scale assemblages desigFigure 22. Species assemblage results for the slope trawls. Assemblages are named for the most influential 

species in each group. Assemblages are arranged from shallow to deep, unless they are influential at all 

or none of the depths. The assemblages that were not influential at any depth were composed of relatively 

rare species, making depth associations indiscernible given the methodology for defining “influential” assemblages. Non-italicized species were consistently placed into the same species assemblage >80% of 

the time; italicized species tended to roam into other assemblages with random sampling.

Site Group Depth±SD

(Names based on depth) N (meters)

Group 263 meters 84 263 ± a 49

Group 410 meters 86 410 ± b 46

Group 530 meters 43 530 ± c 42

Group 622 meters 29 622 ± d 27

Group 733 meters 48 733 ± e 71

Group 931 meters 90 931 ± f 132

Group 1112 meters 74 1112 ± g 95

Table 5. Site group results for slope trawl data. The numbers of trawls associated with 

each group as well as average depth ± standard deviation are provided. Different letters signify a significant difference using Tukey’s pairwise comparison on log adjusted 

28

depth with overall alpha set at 0.001.
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NMFS Slope Trawls

Site Groups

0 10 20 40 60 80

Kilometers

Group 263 Meters

Group 410 Meters

Group 530 Meters

Group 622 Meters

Group 733 Meters

Group 931 Meters

Group 1112 Meters

200

1

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m

m

m

Subsection 2.1.1: ASSEMBLAGE ANALYSES

Figure 23. Location of site groups for NMFS slope trawls. Lines showing the 50, 100, 200, and 2,000 depth contours are provided.

nated by NMFS: near-shore, shelf, and slope species groups 

(NMFS, 2002). All of the rockfish in each species assemblage 

from this study come from the same NMFS group. The rockfish groups identified by Williams and Ralston (2002) were not 

completely corroborated by this study. The species in their 

“southern shelf group” were placed into the stripetail rockfish 

group which included all shallow-water species. However, their 

“deep water slope” group was split among four of this report's 

groups. Comparisons of the results from this study with other 

assemblage studies are difficult due to the variability in species 

analyzed between studies, the different habitats targeted, and 

the discrepancy in scale. For example, results from submersibles (Yoklavich et al., 2000, 2002; Hixon et al., 1991; Hixon 

and Tissot, 1992; Field et al., 2002) record interactions at a 

much smaller scale compared to trawls, which can fish multiple 

habitats during a 1 km tow.

Site Groups and Interaction of Species and Sites (Objectives B and C)

Seven site clusters were identified from the 454 slope trawls 

(Table 5). To make interpretation easier, the site groups are 

named according to mean depth. Species assemblages which 

were influential in forming each site group are identified. The 

average frequency of occurrence of fish species assemblages 

for each site group (Table 6) was used to determine where 

species assemblages were found. An ANOVA determined that 

all groups were significantly different in depth (Table 5). The 

importance of depth in this ecosystem is not a new idea; many 

researchers have already commented on its influence (Williams 

and Ralston, 2002; Sullivan, 1995; Gabriel and Tyler, 1980; Field 

et al., 2002; Matthews and Richards, 1991). Latitude has also 

been described as having an influence on California fish species composition (Williams and Ralston, 2002; Horn and Allen, 

Group 263 Group 410 Group 530 Group 622 Group 733 Group 931 Group 1112

meters meters meters meters meters meters meters

Sablefish Assemblage 0.41 0.78 0.87 0.97 0.95 0.84 0.68

Aurora Rockfish

Assemblage 0.40 0.75 0.55 0.31 0.27 0.25 0.17

Stripetail Rockfish

Assemblage 0.51 0.08 0.00 0.00 0.00 0.00 0.00

Splitnose Rockfish

Assemblage 0.88 0.92 0.64 0.36 0.18 0.04 0.06

Filetail Catshark

Assemblage 0.03 0.33 0.51 0.43 0.23 0.08 0.05

Longspine Thornyhead

Assemblage 0.01 0.05 0.22 0.41 0.65 0.87 0.84

Pacific Viperfish

Assemblage 0.01 0.02 0.06 0.09 0.14 0.16 0.27

Market Squid

Assemblage 0.14 0.15 0.13 0.07 0.07 0.03 0.05

Table 6. Average frequency of occurrence of fish species assemblages (percent occurrence 

calculated for each species and then averaged for each fish assemblage) for each slope site 

1978; Sullivan, 1995), but for the area of this study, no latitudinal 

results were evident. 

The interaction between site groups and species assemblages (i.e. 

the location of species assemblages), reemphasized the relationship between species and depth (Table 6). The species groups 

were arranged such that they went from shallow to deep. In all 

cases, the assemblages with a low frequency of occurrence for all 

site groups were composed of relatively rare species. Depth associations were present, just not discernible, given the methodology 

for defining “influential” assemblages. The location of the trawls 

contained in each site group were mapped (Figure 23). 

Habitat Correlations (Objective D)

Other factors besides depth, such as latitude (Williams and 

Ralston, 2002; Horn and Allen, 1978; Sullivan, 1995), bottom 

composition (Yoklavich et al., 2000, 2002; Field et al., 2002; Hixon 

et al., 1991; Hixon and Tissot, 1992), or bathymetric complexity 

(pp. 16) (Yoklavich et al., 2000, 2002; Field et al., 2002) can have 

an impact on species assemblages. For this data set, 95% of the 

trawls occurred over areas delineated as mud (pp. 38), making 

it impossible to examine the effects of bottom composition. It is 

interesting to note that of all the 16 trawls completed over the 

bottom type designated as a combination of mud and rock, 33 

percent occurred in the "410 meters" site group, and 56 percent in 

the "deepest" group. For the slope trawls, there was no interaction 

present between depth and bathymetric complexity or latitude, so 

the effects of these parameters could be tested. Neither bathymetric complexity (pp 16), nor latitude, had a significant impact 

on site grouping when the effect for depth was accounted for 

(bathymetric complexity: df=1, F=0.94, P=0.33; latitude: df=1, 

F=0.11, P=0.74). 

In conclusion, this analysis provides results 

showing species assemblages, site assemblages, and the location of species assemblages for the deep slope environment that 

are relevant to the scale of a commercial 

trawl. The larger species assemblages 

that were reported in the literature were 

confirmed (NMFS, 2002) (near-shore, 

shelf and slope groups), but some of the 

smaller groups were not corroborated. Half 

of the sites designated as "1,112 meters" 

are located outside sanctuary boundaries. 

This is mainly due to the large number of 

deep sites located to the south and west of 

Sanctuary boundaries. The results of this 

analysis in conjunction with similar analyses 

on the three other data sets provides a fairly 

comprehensive overview of fish and macroinvertebrate species within the study area. 

group. Bold numbers represent influential species assemblages within that site group.

29
Subsection 2.1.1: ASSEMBLAGE ANALYSES

if, on average, species were present in 25% of the trawls in a site group. 

Interactions between environmental variables (salinity, temperature, density, 

bottom depth, and bathymetric complexity) were investigated by conducting 

step-wise discriminant analyses.

RESULTS AND DISCUSSION

Species Assemblages (Objective A)

The neritic environment is an important ecosystem in central California. Most 

benthic species have a larval stage dependent on the neritic environment. 

In addition, neritic species are an important base for the food web for fish, 

birds, and mammals. Due to the removed rare species, different species were 

included in the analyses depending on the year (1998, 1999, or all years). 

Ten species were present in 1999 that were absent in 1998, including six 

species of juvenile rockfish. For 1998 and 1999, there were five and six species assemblages identified, respectively, and seven species assemblages 

were differentiated in the entire data set. Species assemblages were named 

according to the most influential species (Figures 24, 25, 27). Overall, the 

species assemblages were much less robust than those from the other data 

sets. Average persistence (percentage of time species were grouped together) through random runs varied from 36% to 94% for all assemblages. 

This variability in results reflects two things: 1) the ephemeral nature of the 

neritic ecosystem and its expression through the species assemblages, and 

2) the higher variability in results from the random runs due to smaller sample 

size. Some of the persistent groups (persistent through random runs as well 

as persistent through the three analyses) were: 1) market squid, northern 

anchovy, Pacific electric ray, and Pacific sardine; 2) euphasid, Pacific hake, 

and deep sea smelt; and 3) myctophid and slender barracuda. Different 

juvenile rockfish were present in 1998 and 1999. In 1998, a warm year, only 

shortbelly and stripetail rockfish were in greater than 5% of the trawls, and 

were grouped together. In 1999, a cold year, 8 species of juvenile rockfish 

were identified, and all grouped together except for blue rockfish and stripetail 

rockfish. This supports the observation by Loeb et al. (1994), Yoklavich et al. 

(1996), and Moser et al. (2000), that warm (El Niño) years are not good for 

rockfish recruitment. For the entire data set there were thirteen species of 

rockfish, which were all grouped together except for copper rockfish complex 

and brown rockfish. The consistent grouping of juvenile rockfish together 

suggests that the rockfish species are responding to similar environmental 

conditions. The copper and brown rockfishes are not well known; however, 

Larson et al. (1994) looking at the midwater trawls in 1987 and 1988, determined that some species in the copper complex arrive later in the season 

than most other rockfish species, which could affect their association with 

assemblages. 

Running the modified bootstrap technique can provide an estimate of the 

precision of results, but verifying the accuracy of the results is more difficult. 

Only two studies were identified which have investigated species assemblages in the neritic environment (Larson et al., 1994; Calliet et al., 1979). 

Larson et al. (1994) analyzed this data set (1987-1988) for juvenile rockfish 

assemblages, looking at each sweep individually, and described the short 

term variation in assemblages and environmental conditions. Longer term 

trends were not analyzed. Since the species groups changed with each 

sweep, and most rockfish were grouped together for this study, comparing 

ABOUT THESE MAPS

The pelagic environment is home to many marine species at some stage in 

their life. Therefore, it is important to document what species interact in this 

environment, and determine environmental influences on species abundance. 

Multivariate statistics were used to analyze fish and invertebrate species 

assemblages caught in trawls conducted at 7 and 30 meters depth between 

Cordell Bank NMS and Monterey Bay. For more information on the neritic 

environment see the Ecological Linkages Report. When determining species 

assemblages, three separate analyses were completed: all data (1986-2001), 

only 1998 (warm year), and only 1999 (cold year). There were differences 

between years in the species present, as well as in the organization of 

species assemblages. The site groups identified were significantly related 

to environmental conditions, but the influential conditions varied between 

years. To investigate assemblages persistent over more than one year, all 

of the data collected was analyzed for species assemblages, but not for site 

assemblages, due to the difficulty in mapping assemblages through time as 

the same location may house any number of assemblages depending on 

environmental conditions. See Larson et al (1994) for a detailed analysis of 

rockfish assemblages in response to short-term environmental variability. 

Through this analysis a large amount of information has been condensed 

down to assemblages of co-occurring species, as well as groups of similar 

locations. Maps are provided to portray the spatial arrangement of the site 

groups for 1998 and 1999. 

DATA SOURCES

Data from 1543 fisheries independent research trawls were collected from 

1986-2001, during May and June. The purpose of the trawl was to determine 

the number and quantity of juvenile rockfish present during the upwelling 

season at night. The midwater trawl net was a “Cobb trawl” constructed of 

nylon webbing. A fine mesh (1.25 cm) liner was inserted in the codend to 

retain small midwater organisms. To open the net vertically, 42 8-inch floats 

were attached to the headrope and 145 pounds of chain was lashed to the 

footrope. To spread the net horizontally, 850 lb steel ‘V’ doors 5 x 7 feet in 

size were used. The net was deployed while the ship was underway at a 

speed of approximately 2.7 knots. Seventy-five meters of trawl cable were 

payed-out which nominally puts the headrope at a depth of 30 meters (100 

feet), the depth at which most species of juvenile rockfishes are most abundant (Lenarz et. al., 1991). The spatial effort was consistent between years 

with 1-4 hauls completed at 32 stations (see Figure 26 for spatial extent of 

data). Analyses were completed for the entire data set, as well as 1998 and 

1999 individually (representing warm and cold water years, respectively). Fish 

numbers were adjusted for effort by NMFS then log transformed for analyses. 

The data matrices used for classification contained data for 16, 24, and 41 

species in 1998, 1999, and all years, respectively. A complete list of common 

and scientific names of the species included in these analyses is available on 

the accompanying CD-ROM.

METHODS

The aim of the entire assemblage analysis was to increase our understanding 

of the biogeography of fishes and macro-invertebrates in relationship to their 

environment, and identify important areas or habitats. Four of the five main 

objectives were addressed in this analysis:

A. Determine which species tended to be caught together (species as assemblages);

B. Analyze fishing locations to determine which locations contained similar catches (site 

 groups);

C. Resolve where the species assemblages were being caught by combining results from 

 objectives A and B and then utilizing GIS to map the results; and

D. Identify significant relationships between site groups identified in objective B and broad 

 scale habitat characteristics (bathymetry, bathymetric complexity, and large-scale habitat 

 classification).

Clustering is a technique used to summarize information into similar groups. The 1-Pearson correlation coefficients with the average means clustering method (see "Introduction to Clustering" pp. 14) 

was used to first summarize the fish species into assemblages, and to then summarize the catch 

locations into site groupings. Species assemblages were determined for 1998, 1999, and all data, 

but site groups were only determined for 1998 and 1999. In order to determine how variable the 

species cluster results could be within the data, a modified bootstrapping procedure was employed 

on random samples composed of 75% of the data and the results compared for persistence and 

precision. The location of the site groups were mapped using GIS. To determine which species 

groups were influential in forming the site groups, the average frequency of occurrence for species 

assemblages in each site group was calculated. Species assemblages were considered influential 

Pacific Hake, juv.

Calif. Smoothtongue

Deep-sea Smelt Canary Rockfish, juv. Euphausiid Medusafish

Black Rockfish, juv. Myctophid King-of-the-salmon

Blue Rockfish, juv. Slender Barracudina Rex Sole, juv.

Bocaccio, juv. Slender Sole, juv. Chilipepper, juv. Pacific Tomcod, juv. Pygmy Rockfish,juv. Sand Sole, juv. Shortbelly Rockfish, juv. Slender Sole, adult Squarespot Rockfish, juv.

Stripetail Rockfish, juv.

Widow Rockfish, juv. Spiny Dogfish 

Pacific Hake, adult Yellowtail Rockfish, juv.

Pacific Sanddab, juv.

Brown Rockfish, juv. Market Squid

Copper Rockfish complex Lingcod, juv.

Dover Sole, juv. Northern Anchovy Northern Anchovy, larval Pacific Butterfish

Pacific Argentine, juv. Pacific Electric Ray Speckled Sanddab, juv. Pacific Sanddab, adult

Pacific Sardine

Plainfin Midshipman

Pictures from FishBase and NMFS 

NMFS Midwater Trawls

Species Assemblages 

(All Years)

Figure 24. Species assemblage results for the midwater trawls utilizing all data from 1986 to 2001. Assemblages 

are named for the most influential species in each group. Non-italicized species were consistently placed into 

the same species assemblage >80% of the time; italicized species tended to roam into other assemblages with 

random sampling.

30
Subsection 2.1.1: ASSEMBLAGE ANALYSES

Myctophid

Deep-sea Smelt

Slender Barracudina

Pacific Hake, juv.

Calif. Smoothtongue

Euphausiid

Stripetail Rockfish, juv.

Shortbelly Rockfish, juv.

Plainfin Midshipman

Market Squid

Northern Anchovy

Pacific Electric Ray

Pacific Sardine

Northern Anchovy, larval Pacific Sanddab, juv.

Pacific Sanddab, adult Speckled Sanddab, juv. Slender Sole, adult Not in

a

fl

t

ue

a

n

n

t

y

ia

d

l

epth

Pictures from FishBase and NMFS

NMFS Midwater Trawls

Species Assemblages 

(1998)

Site group A Site group B Site group C Site group D Site group E Site group F

N trawls 15 20 14 5 11 26

Myctophid

Assemblage 0.00 0.02 0.02 0.00 0.18 0.49

Pacific Hake, juv. 

Assemblage 0.40 0.17 0.31 0.40 0.76 0.62

Stripetail Rockfish, 

juv. Assemblage 0.13 0.08 0.55 0.00 0.18 0.15

Market Squid 

Assemblage 0.33 0.58 0.29 0.00 0.30 0.07

Pacific Sanddab 

Assemblage 0.27 0.10 0.07 0.07 0.12 0.01

results from the two studies is difficult. Calliet et al. 

(1979) analyzed midwater trawls, and purse seines, 

to determine species assemblages associated with 

market squid in shallow and deep environments. In 

the results from anchovy hauls, only three species 

showed high affinity with market squid in both shallow 

and deep hauls: northern anchovy, pacific electric ray, 

and Pacific herring. This study's results are similar 

since all species assemblages placed market squid, 

northern anchovy, and Pacific electric ray together. 

Pacific herring were not present in this analysis.

Site Groups and Interaction of Species and Sites 

(Objectives B and C)

For 1998 and 1999, six site groups were identified for 

each year. No analysis was run to group sites from the 

entire data set, since preliminary results suggested 

no spatial trends in results. Because groups are from 

midwater environments they are not named by depth, 

but distinguished as site group A, site group B, etc. 

Species assemblages which were influential in forming each site group are identified. The average frequency of occurrence of fish species assemblages for 

each site group (Tables 7 and 8) is used to determine 

where species assemblages were found. Maps with 

the location of the site groups are provided (Figures 

26 and 28). Multiple assemblages can be found at 

the same site as 3-4 sweeps were made per year 

and environmental conditions could change between 

sweeps (see Larson et al, 1995). 

Habitat Correlations (Objective D)

Depending on the data set, various environmental 

conditions had a significant influence on site groups. 

In 1998, a warm year, bottom depth (log transformed: 

N=91, F=18.94, P=<0.0001) was significant. In 1999, 

a colder year, bottom depth (log transformed: N=91, 

F=23.87, P=<0.0001), latitude (N=91, F=8.76, 

P=<0.0001), and water density (N=91, F=5.93, 

P<0.0001) were significant. The significance of bottom depth to each analysis highlights the importance 

of location on species assemblages even in the neritic 

environment. Groups were labeled according to their 

mean depth (i.e. the shallowest group was group A 

and the deepest was group F). The Pacific sanddab 

assemblage in 1998 and market squid assemblage in 

1999 were only influential in the shallowest site group. 

In 1999 there was a north/south split where group F 

was more southern and groups B and C more northern 

(except for one point each south of Point Año Nuevo). 

In 1998, there were only two rockfish species captured 

in greater than 5% of the trawls (stripetail rockfish asFigure 25. Species assemblage results for the midwater trawls conducted in 1998. 

Assemblages are named for the most influential species in each group. Non-italicized species were consistently placed into the same species assemblage >80% 

of the time; italicized species were more ephemeral and tended to roam into other 

assemblages with random sampling.

Table 7. Average frequency of occurrence of fish species assemblages (percent 

occurrence calculated for each species and then averaged for each fish assemblage) for each 1998 midwater site group. Number of trawls in each site group is 

provided in the first row. Bold numbers represent influential species assemblages 

within that site group.

Figure 26. Location of site groups for NMFS 1998 midwater trawls. Lines showing the 50, 100, 200, and 2,000 depth contours are 

provided.

123°W

123°W

122°W

122°W

N°73N°73

N°83N°83

NMFS Midwater Trawls

Site Groups

0 10 20

Kilometers

Site Group A

Site Group B

Site Group C

Site Group D

Site Group E

1998 Trawls

Site Group F

2

10

2

0

0

5

0

0

m

0

0

m

m

0 m

50

2

10

m

0

0

0

m

m

m0002

31
Subsection 2.1.1: ASSEMBLAGE ANALYSES

semblage) which were only influential in site group 

C. In 1999, there were six rockfish species grouped 

together (canary rockfish assemblage), which were 

influential for site groups C and E. The 1999 rockfish were caught in trawls further offshore than the 

trawls that contained rockfish in 1998. 

These analyses provide trends in species assemblages in the midwater environment during 

the upwelling season. The grouping of juvenile 

rockfish together suggests that when conditions 

are suitable for one species, they are also suitable for the other species. Within the entire data 

set, three species assemblages were consistently 

grouped together greater than 80% of the time: 

Pacific hake, juv. assemblage; canary rockfish, juv. 

assemblage; and spiny dogfish assemblage. Two 

groups were slightly less stable and were grouped 

together greater than 70% of the time: medusafish 

assemblage and market squid assemblage. Even 

though results were not as stable as with the other 

data sets, this analysis identifies assemblages that 

were consistent through time. The reduced number 

of species present in 1998 highlights the effects of 

water temperature on species assemblages in the 

neritic environment. For this data set, both bottom 

depth, latitude, and water density were found to 

have a significant influence on site groups. 

Site group A Site group B Site group C Site group D Site group E Site group F

N trawls 23 7 9 21 16 15

Pacific Hake, juv. 

Assemblage 0.21 0.37 0.40 0.33 0.69 0.77

Canary Rockfish, juv 

Assemblage 0.08 0.02 0.25 0.07 0.53 0.15

Medusafish 0.04 0.00 0.11 0.05 0.13 0.00

Pacific Hake, adult 0.04 0.00 0.00 0.38 0.06 0.00

Pacific Saddab, juv 

Assemblage 0.40 0.14 0.30 0.34 0.19 0.27

Market Squid 

Assemblage 0.55 0.11 0.06 0.12 0.05 0.03

Figure 28. Location of site groups for NMFS 1999 midwater trawls. Lines showing the 50, 100, 200, and 2,000 depth contours are 

provided.

Figure 27. Species assemblage results for the midwater trawls conducted in 1999. 

Assemblages are named for the most influential species in each group. Non-italicized 

species were consistently placed into the same species assemblage >80% of the time; 

italicized species were more ephemeral and tended to roam into other assemblages 

with random sampling.

Table 8. Average frequency of occurrence of fish species assemblages (percent occurrence calculated for each 

species and then averaged for each fish assemblage) for each 1999 midwater site group. Number of trawls in 

each site group is provided in the first row. Bold numbers represent influential species assemblages within that 

Pacific Hake, juv.

Calif. Smoothtongue

Deep-sea Smelt

Euphausiid Canary Rockfish, juv. Myctophid Black Rockfish, juv.

Bocaccio, juv. Medusafish

Chilipepper, juv.

Shortbelly Rockfish, juv. Pacific Hake, adult

Widow Rockfish, juv.

Slender Sole, juv. Pacific Sanddab, juv.

Blue Rockfish, juv.

Dover Sole, juv.

Lingcod, juv.

Pacific Argentine, juv.

Pacific Sanddab, adult

Speckled Sanddab, juv. Stripetail Rockfish, juv. Market Squid

Northern Anchovy

Pacific Electric Ray

Pacific Sardine

Not in

a

fl

t

ue

a

n

n

t

y

ia

d

l

epth

Pictures from FishBase and NMFS

NMFS Midwater Trawls

Species Assemblages 

(1999)

123°W

123°W

122°W

122°W

N°73N°73

N°83N°83

NMFS Midwater Trawls

Site Groups

0 10 20

Kilometers

Site Group A

Site Group B

Site Group C

Site Group D

Site Group E

1999 Trawls

Site Group F

2

10

2

0

0

5

0

0

m

0

0

m

m

0 m

50

2

10

m

0

0

0

m

m

m0002

site group.

32
Subsection 2.1.1: ASSEMBLAGE ANALYSES

SECTION SUMMARY 

Twenty-eight species assemblages were identified from the 

CDF&G recreational, NMFS 

shelf, and NMFS slope data sets. 

Figure 29 illustrates the overlap 

between the three data sets. The 

length of the vertical line depicts 

the depth interval where species 

assemblages were "influential" 

(see Tables 2, 4, 6-8). Shading 

was included to give the impression of where the continental shelf 

end and continental slope begins.

The edge between the shelf and 

slope, although variable within 

the study area, was presented at 

200 meters to be consistent with 

Williams and Ralston (2002). In 

all cases, the assemblages with a 

low frequency of occurrence at all 

depths were composed of species 

present in less than 20% of the 

trawls. For these assemblages, 

depth associations may have 

been present, just not discernible, 

given the methodology for defining 

“influential” assemblages. 

Data Sources

See associated sections for information and spatial extent 

of CDF&G recreational hook and line data (pp. 23), NMFS 

demersal trawls on the continental shelf (pp. 26), and NMFS 

demersal trawls on the continental slope (pp. 28).

Methods

Results from the overlap between species assemblages and 

site groups from each analysis (see Tables 2, 4, 6-8) were used 

to determine the depths at which species assemblages were 

present. For each assemblage, the shallowest site group (mean 

depth minus the standard deviation) from which their average 

frequency of occurrence was >25% was used to determine 

the minimum depth. Similarly, the mean plus the standard deviation for the deepest site group was used to determine the 

maximum depth. 

Results and Discussion

The shallow assemblages had more limited depth ranges, 

which is not obvious given the log scale of depth in Figure 29. 

Species included with the three data sets differed, especially 

since only species caught in at least 5% of the trawls were 

analyzed. Therefore, while the NMFS shelf and slope trawls 

may have overlapped for the 200-500 meters depth range, 

the species included in the analyses differed. It is interesting 

to note that the shallow water species included in the NMFS 

slope trawl analysis were all placed in one assemblage, the 

stripetail rockfish assemblage, and that this assemblage was 

only present in the shallowest slope trawl site group. The same 

species included in this stripetail rockfish assemblage were 

found in five different NMFS shelf assemblages. Conversely, 

the blackgill assemblage on the NMFS shelf trawls contains 

the deeper species caught in the shelf trawls and found within 

three different NMFS slope species assemblages. This does 

not imply that species co-occurrences changed between the 

shelf and slope trawls, just that cluster results were sensitive to 

the depth range covered by the data set. For example, bocaccio and English sole do not co-occur, as bocaccio is attracted 

to rocky ledges and English sole to soft bottom areas with low 

relief (Love et al., 2002). These species are grouped together 

92% of the time when included in an analysis with deep slope 

species, but never grouped together when included in an 

analysis with shelf species.

The overlap between the shelf and recreational trawls was 

more difficult to compare due to the different fishing methods 

employed. Only nine species overlap between the recreational 

data and the shelf trawls. For both data sets, chilipepper, greenstriped rockfish, and greenspotted rockfish were grouped together (chilipepper and greenspotted assemblages) and found 

at similar depths. For the most part, fish species were associated with a shallower depth with the recreational hook and line 

analysis than with the shelf trawl analysis. This difference could 

be due to the nature of the assemblage analysis or due to the 

variable size selectivity of the fishing methods and habitats. 

Many of the deepwater rockfish species settle as juveniles in 

shallow water, and slowly shift to deeper water as they mature 

(Love et al., 2002). Future analyses could include information 

on fish total length to determine if ontogenetic shifts occur and if 

they generate the differences in species’ depth range between 

data sets noted above. The effect water temperature has on the 

species present, and the composition of species assemblages, 

was investigated for the recreational and shelf data sets and 

provides preliminary results on which assemblages are persistent through environmental change (see CD-ROM).

For the midwater trawl data set, the importance of environmental conditions, especially seasonal water 

temperature (1998 warm year vs. 1999 cold 

year) was obvious in its influence on what 

species were present in the neritic environment during upwelling season. Using data 

from all years, species assemblages could 

be delineated, but these assemblages were 

more sensitive with regards to random 

samples. This emphasizes the ephemeral 

nature of the neritic environment, and the 

resulting transient nature of the species assemblages. There were three species assemblages that occurred together in all data 

sets: 1) Market squid, Northern anchovy, 

Pacific electric ray, and Pacific sardine; 

2) Euphausiids, Pacific hake, and deep 

sea smelt; and 3) Myctophid and slender 

barracuda. In addition, most larval rockfish 

species co-occur. More in-depth analyses, 

taking advantage of the available information on environmental conditions, could be 

conducted (see Larson et al., 1994). 

In conclusion, species assemblages and 

site groups were delineated and mapped 

for four separate data sets. Depth had a 

significant influence on all four data sets. 

The influence of depth is not a new concept (Williams and Ralston, 2002; Sullivan, 

1995; Gabriel and Tyler, 1980; Field et al., 

2002; Matthews and Richards, 1991); however, this is the 

first time a study has demonstrated its significance on three 

separate data sets. All attempts to remove depth and look for 

secondary influences on group designation were unsuccessful. 

For the neritic environment, depth, latitude, and water density 

had a significant impact on site groups in 1999. Starr (1998) 

addressed the implementation of rockfish no-take areas and 

made two important recommendations. First, in order to properly manage marine ecosystems, there is a need for a better 

understanding of fish assemblages. Once these assemblages 

are delineated, managers can take steps to ensure each assemblage receives proper management. The results from this 

study provide information on these assemblages for nearshore, shelf, slope, and midwater ecosystems. The second 

recommendation by Starr (1998) was to delineate rectangular 

no-take areas that cover 20-50 km of the coast and extend west 

to the edge of the continental shelf. From a biogeographic viewpoint, the spatial analyses coincide with that recommendation 

and also determined that deep slope communities contribute 

significantly to ground fish biogeographic patterns. Because 

assemblages follow bathymetry at the scale of this analysis, 

this approach could protect all demersal species assemblages 

Figure 29. Overlap between the three data sets that analyzed demersal fish: CDF&G recreational (yellow), NMFS shelf (green), and NMFS slope (orange). The length of the vertical line 

depicts the depth interval where species assemblages had an average frequency of occurrence in at least 25% of the trawls (see Tables 2,4,6-8). Non-italicized species were consistently 

placed into the same species assemblage; italicized species tended to roam into other assemblages with random sampling.

0

25

50

75

100

325

550

775

1000

Gopher Rockfish

Black Rockfish Depth Range of Species Assemblages Brown Rockfish

Cabezon Yellowtail Rockfish

China Rockfish Canary Rockfish

Copper Rockfish Kelp Greenling Lingcod Pacific Sanddab Rosy Rockfish English Sole Starry Rockfish Petrale Sole Vermilion Rockfish Chilipepper Pink Seaperch Pacific Sanddab Bocaccio Greenspotted Plainfin Midshipman Cowcod

Blue Rockfish Rockfish Lingcod Greenspotted Rockfish )

Olive Rockfish Greenstriped Halfbanded Rockfish s

Greenstriped Rockfish

r

Bocaccio Rockfish Pacific Mackerel Pacific Hake Shortbelly Rockfish

et

Flag Rockfish Chilipepper Jack Mackerel Longnose Skate Stripetail Rockfish e

Speckled Rockfish Pacific Argentine Spotted Ratfish

m(

Widow Rockfish Pacific Herring 

Yelloweye Rockfish American Shad

ht

Big Skate California Market Squid p

Shelf break California Skate Chinook Salmon Filetail Catshark e

Spiny Dogfish Darkblotched Rockfish Curlfin Sole Black Eelpout D

Bank Rockfish California Longspine Thornyhead Dungeness Crab Redbanded Rockfish Black Skate Longspine Combfish Grenadier Rex Sole Splitnose Rockfish Flapjack Devilfish Califonia Slickhead Northern Anchovy Slender Sole Crimson Pasiphaeid

Pacific Pompano Pacific Glass Spotted Cusk-eel Deepsea Sole

White Croaker Blackgill Rockfish Splitnose Shrimp Giant Grenadier

Pacific Electric Ray Aurora Rockfish Rockfish Grooved Tanner Crab

Black Eelpout Bering Skate Pacific Flatnose

Blacktail Snailfish Aurora Rockfish Pacific Grenadier Bigfin Eelpout Brown Cat Shark Blackgill Rockfish Snakehead Eelpout Longnose Skate Filetail Cat Shark Dover Sole Twoline Eelpout Pacific Hake Lanternfish Spiny Dogfish Pacific Viperfish Rex Sole Bank Rockfish Black Hagfish Spotted Ratfish Deepsea Skate

Fangtooth

Longfin Dragonfish

Assemblages with Low Frequency of Occurrence at All Depths Pacific Blackdragon

Rhomboid Squid

Sawtooth Eel

Canary Rockfish Smooth Grenadier Sharpchin Rockfish California Market Squid Pacific Mackerel Yellowtail Rockfish Threadfin Slickhead Quillback Rockfish Spot Shrimp Arrowtooth Flounder Blackbelly Eelpout Squarespot Rockfish Widow Rockfish Vampire Squid 

Threadfin Sculpin Robust Clubhook Squid Rock Sole Sp. Magistrate Armhook Squid

CDF&G Recreational 

Hook and Line

NMFS Shelf Trawls

NMFS Slope Trawls

Shortspine

Thornyhead

Bering Skate

Bigfin Eelpout

Dover Sole 

Sablefish

Stripetail Rockfish

Bocaccio

Chilipepper

Darkblotched Rockfish

English Sole

Greenstriped Rockfish

Lingcod

Petrale Sole 

Sharpchin Rockfish

Shortbelly Rockfish

Spot Shrimp

Slender Sole

Redbanded Rockfish

Rosethorn Rockfish

Pacific Electric Ray

Sablefish

Blacktail Snailfish

Brown Catshark

Shortspine

Thornyhead

identified in this study. 

33
Subsection 2.1.1: ASSEMBLAGE ANALYSES

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Shaw, F.R., Wilkins, M.E., Weinberg, K.L., Zimmermann, M., and 

R.R. Lauth. 2000. The 1998 Pacific west coast bottom trawl survey of 

groundfish resources: estimates of distribution, abundance, and length 

and age composition. U.S. Department of Commerce, NOAA Technical 

Memorandum NMFS-AFSC-114. Silver Spring, MD. 138 pp.

Starr, R.M. 1998. Marine harvest refugia for West Coast rockfish: A workshop. NOAA-TM-NMFS-SWFSC-255. Pacific Grove, 

California.14pp.

Starr, R.M, J.M. Cope, and L. A. Kerr. 2002. Trends in fisheries and 

fishery resources associated with the Monterey Bay National Marine 

Sanctuary from 1981-2000. California Sea Grant College Program 

Publication No. T-046. Monterey, CA. 156 pp.

Sullivan, C.M. 1995. Grouping of fishing locations using similarities 

in species composition for the Monterey Bay area Commercial Passenger Fishing Vessel Fishery, 1987-1992. California Department of 

Fish and Game, Marine Resources Technical Report No. 59. Monterey, 

CA. 37 pp.

Turk, T. A., T. Builder, C. W. West, D. J. Kamikawa, J. R. Wallace, 

R. D. Methot, A. R. Bailey, K. L. Bosley, A. J. Cook, E. L. Fruh, B. H. 

Hormess, K. Piner, H. R. Sanborn, and W. W. Wakefield. 2001. The 

1998 Northwest Fisheries Science Center Pacific west coast upper 

continental slope trawl survey of groundfish resources off Washington, 

Oregon, and California: Estimates of distribution, abundance, and 

length composition. U.S. Department of Commerce, NOAA Technical 

Memorandum NMFS-NWFSC-50. Seattle, WA. 122 pp.

Weinberg, K.L., M.E. Wilkins, F.R. Shaw, and M. Zimmermann. 

2002. The 2001 Pacific west coast bottom trawl survey of groundfish 

resources: Estimates of distribution, abundance, and length and age 

composition. U. S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC128. Seattle, WA. 140pp.

Williams, E.H. and S. Ralston. 2002. Distribution and co-occurrence 

of rockfishes over trawlable shelf and slope habitats of California and 

southern Oregon. Fish. Bull., Vol. 100, pp. 836-855.

Wilkins, M.E., M. Zimmerman, and K.L. Weinberg. 1998. The 1995 

Pacific west coast bottom trawl survey of groundfish resources: Estimates of distribution, abundance, and length and age composition. 

NOAA Tech. Memo NMFS-AFSC-89. Seattle, WA. 138 pp.

Wilson-Vandenberg, D., P.N. Reilly, and C.E. Wilson. 1996. Onboard 

sampling of the rockfish and lingcod commercial passenger fishing 

vessel industry in northern and central California, January through 

December 1994. Marine Resources Division Administrative Report 

No. 96-6. San Francisco, CA. 96 pp. 

Worm, B. and R. A. Myers. 2003. Meta-analysis of cod-shrimp

interactions reveal top-down control in oceanic food webs. Ecology,

84(1), pp. 162-173.

Yoklavich, M.M., H.G. Greene, G.M. Cailliet, D.E. Sullivan, R.N. Lea, 

and M.S. Love. 2000. Habitat associations of deep-water rockfishes 

in a submarine canyon: An example of a natural refuge. Fish. Bull., 

Vol. 98, pp. 625-641.

Yoklavich, M.M., V.J. Loeb, M. Nishimoto, and B. Daly. 1996. Nearshore assemblages of larval rockfishes and their physical environment 

off central California during an extended El Niño event, 1991-1993. 

Fish. Bull., Vol. 94, pp. 766-782.

Yoklavich, M.M, G.M. Cailliet, R.N. Lea, H.G. Greene, R.M. Starr, J. 

de Marignac, and J. Field. 2002. Deepwater habitat and fish resources 

associated with a marine reserve: implications for fisheries. Marine 

Ecological Reserves Research Program Research Results 1996-2001. 

California College Sea Grant Program CD-Rom. www.csgc.ucsd.edu. 

La Jolla, CA. 63 pp.

Zar, J.H. 1999. Biostatistical Analysis, fourth edition. Prentice-Hall, 

Inc. Upper Saddle River, New Jersey. 80 pp.

Zimmerman, M., M.E. Wilkins, K.L. Weinberg, R.R. Lauth, and F.R. 

Shaw. 2001. Retrospective analysis of suspiciously small catches in 

the National Marine Fisheries Service West Coast Triennial Bottom 

Trawl Survey. Alaska Fisheries Science Center Processed Report, 

2001-3. Anchorage, AK. 135 pp.

34
Subsection 2.1.2: HABITAT SUITABILITY MODELING

INTRODUCTIONHabitat suitability modeling (HSM) is a tool for predicting the suitability of habitat for a given species based on known affi nities with environmental parameters. This technique was chosen for this project to provide a synoptic view of habitat suitability for specific species as well as assess habitat suitability for species assemblages. One HSM technique is termed “habitat suitability index (HSI) modeling”. HSI models are simple mathematical expressions for calculating a unitless index of habitat quality as a function of one or more environmental variables. Using GIS, these index values can be mapped and analyzed to portray areas of potential distribution for a species (Brown et al., 2000) (Figure 30). High-quality habitat may provide high carrying capacity and support higher rates of growth, survival, or reproduction for a given species, whereas low-quality or unsuitable habitat may have little or no carrying capacity (Brown et al., 2000). The HSI methods were adapted from the U.S. Fish and Wildlife Service (USFWS) Habitat Evaluation Procedures program (USFWS, 1980a, 1980b, 1981) to provide spatially explicit estimates of suitability across the entire study area. It is important to note that the model results depict potentially suitable habitat for a given species and not actual distribution. This section provides the methodology, results, validation, and interpretation of HSI models developed for selected adult and subadult stages of commercially and recreationally important groundfish and invertebrate species. The models are based on 

species’ affinities to substrate types and bathymetric ranges 

(Monaco et al., 1998). DATA AND ANALYSESEnvironmental Data: Initially bathymetry, benthic substrate type, and bottom temperature were chosen as the environmental data to be included in the models. Although water temperature is an influential factor that affects species distributions and movement, several factors led to the exclusion of bottom temperature from final model development: 1) information regarding species associations with bottom temperature were too 

general or absent from scientific literature; 2) statistical analyses revealed collinearity between bottom temperatures collected with NMFS trawl samples and bathymetry; and 3) since most of the species modeled are benthic organisms where bottom temperature is not highly variable, numerous authors state that depth is the most significant factor regulating species distributions (Gabriel and Tyler, 1980; Matthews and Richards, 1991; Yoklavich et al., 2000; Williams and Ralston, 2002). As a result, water temperature was eliminated as a modeling variable. This does not preclude using water temperature as a variable for modeling pelagic species, however, more information will have to be collected to explore their affinities for this variable. Based 

on these considerations, bathymetry and substrate data were used to map HSI model results. Numerous data sources were combined to produce a digital, high resolution map of bathym

HSI Data/SI Development: Initially, suitafor bathymetry and substrate type werliterature review and modeled in GIS. Dthe methodological approach and resultby NMSP and NMFS staff who suggeficient data were available, bathymetry developed using NMFS trawl data. In requested separate models for adults result, a subset of NMFS trawl data on and slope (1984-1999) for the entire wedevelop SI values for adults and juvenilefor most species. SI values for bathymetry were developed from NMFS trawl data by fitting a polynomial regression to bathymetric classes and mean species abundance (log transformed) (Figure 31). Since trawl samples were not collected in waters less than 50 m, the bathymetric classes begin at 50 m with a range of 20 m between classes. The fitted curve was weighted by sampling effort to account for disproportionate sample sizes within bathymetric classes. Predicted mean abundance along the curve was then used to calculate SI’s for each bathymetric class by dividing each mean abundance value by the 

etry. Bathymetry was rasterized with 70 m cell size for most of the study area for depths to 4810 m. Benthic substrate was mapped from Point Arena in the north to Point Sal in the south to conform to the latitudinal limits of the study area. Substrates were characterized using 5 classifications: sand, mud, rock, pebble/cobble/gravel, and mud/rock mix.Species selected for HSM: The primary criteria to select species for which HSMs were developed was their commercial and ecological importance. In addition, several species were included based on recommendations by staff members from the NMSP. Overall, 20 species were modeled, 14 of which included models for adult and subadult distribution. Species with two life stage models include: bocaccio, canary rockfi sh, chilipepper rockfish, darkblotched rockfish, longspine thornyhead, shortspine thornyhead, lingcod, sablefish, Pacific whiting 

(hake), dover sole, english sole, petrale sole, rex sole, and Pacific sanddab. Potential adult distributions were modeled for Dungeness crab, California market squid, blue rockfish, widow 

rockfish, yelloweye rockfish, and yellowtail rockfish. Some of these species were chosen to represent species assemblages as determined in Section 2.1.1, and mapped to display the potential distribution of suitable habitats for the assemblage. For example, cluster analyses determined that Dover sole, sablefish, and shortspine thornyhead were commonly captured in NMFS trawl surveys, indicating a deep water shelf assemblage for these species. 

Map Layers Habitat Su

Bathymetry

+

Substrate

Species Habitat Affinities

depth category

1.00.5

0

substrate category 

1.00.5

0

S1

SI value

S2

=

1 n

=

∏

S

n

HSI

( i ) i =1

Figure 30. Species habitat suitability modeling approach.
most species outside of this range, but was omitted from modeling and mapping to 

match the depth range associated with the NMFS trawls. Trawls were conducted 

during June to November, thus models for different “seasons” could not be created. 

Therefore, modeled map surfaces represent species potential distributions for water 

depths from 50-1300 meters and for the summer and late fall time period. Also, 

many of the species modeled exhibit inshore/offshore migrations based on habitat 

shifts associated with life history requirements and/or spawning activity. Additional 

data will have to be collected to reflect these shifts in abundance and distribution; 

thusly, no attempt was made to model them here. 

HSI Results-Mapping: Once SI values were determined for bathymetry and substrate type, these values were inserted into the environmental grids. Once each 

species’ suitability indices were derived (either through regression or through the 

literature), the values were combined with the bathymetry and substrate map layers 

to calculate an index of habitat suitability. The habitat suitability was calculated as 

the geometric mean of suitability indices (S

I

) for the two (n) environmental factors 

(Rubec et al. (1999) (Figure 30): 

Subsection 2.1.2: HABITAT SUITABILITY MODELING

The resulting maps display the potential suitability of cells for each species 

based on the strength of their affinities to depth and substrate type in each 

cell. The map displays habitat suitability in a unitless index from 0 (unsuitable) 

to 10 (highly suitable). 

Validation of HSI Model: The remaining subsets (i.e. independent data) of NMFS 

trawl data from the shelf (1998-2001) and slope (2000-2001) were used to assess model performance. Mean abundance was calculated for each species 

from these data and superimposed over the predicted HSI values and compared 

by regressing observed catch data on the predicted HSI values. The statistical 

results are not intended to be definitive tests of the model, but provide supporting evidence for the existence and strength of the relationship between the 

model predictions and the catch data. It is important to note that these models 

are based on two independent parameters and are not the definitive predictors 

of habitat utilization for these species. Fishery-dependent data from CDF&G 

recreational surveys were also used to validate models for species that had 

limited trawl information, i.e. species that display affinities for rocky substrates 

(rockfishes) and had poor representation in trawl data. If the model performs 

correctly, this validation procedure should demonstrate increasing mean abundance with increasing habitat suitability.

Integrative Maps: Management plans are often developed for a group of species that exhibit similar life history strategies. Selected species assemblages, 

as defined in Section 2.1.1, were analyzed and mapped to identify the spatial 

distribution of their important habitats. In addition, two analyses were conducted 

(page 42) which examine the overlap of highly suitable habitat based on all species for which HSI maps were developed. Areas with the most overlap of high 

suitability could be considered important habitats for selected groundfish. 

ANALYTICAL MAP PRODUCTS

As part of the biogeographic assessment, digital data were developed as products from the study. Digital bathymetry and substrate maps were created as 

ArcView shape and raster files. Maps of these environmental data can be seen 

on pages 36-37, while digital files are located on the accompanying CD-ROM. 

Three representative HSI models are presented: bocaccio (adult and subadult), 

Dover sole (adult and subadult), and Dungeness crab (adult). The remaining 31 

species' HSI maps are on the CD-ROM. Representative maps displaying habitat 

importance based on all HSI models and select species assemblages are also 

included. Additional integrative maps for shelf assemblages, all rockfish, and 

all flatfish, are also included on the CD-ROM.

n

HSI=

∏

1

(S

n

i

)

i=1

DepthEffort Mean log Predicted mean log HSI

Class(m) (# of samples)abundanceabundance(x) (x/xmax)*10

50-69 219 .014 .0193

70-89 361 .029 .0355

90-109 447 .049 .0487

110-129 489 .060 .0588

130-149 398 .056 .0659

150-169 252 .100 .069 10

170-189 200 .094 .070 10

190-209 213 .065 .069 10

210-229 182 .037 .0649

230-249 98 .059 .0578

250-269 92 .019 .0477

270-289 89 .003 .0345

290-309 74 .008 .0183

310-329 98 .00300

330-349 52000

Table 9. Example data matrix for calculating bathymetry SI values for subadult bocaccio 

taken in NMFS trawl samples (Rubec et al., 1999). Depth Class (m) 100- 150- 200

-250-300-350-400-

Source 50-99 149199249299349399449

A11000000

B11100000

C11111000

D11111000

Sum44322000

SI=Sum/Total

References*10

1010

755000

Table 10. Example presence/absence information and SI calculation from scientific 

literature. 

36
Subsection 2.1.2: HABITAT SUITABILITY MODELING

ABOUT THIS MAP

Figure 32 displays a bathymetric model of the north/central California study area. Prominent bottom features, such as canyons, 

seamounts, banks, and other large scale geological formations, are evident at the scale presented.

DATA SOURCES

NOAA/NOS hydrographic survey data available from the National Geodetic Data Center (NGDC) and Monterey Bay Research 

Institute (MBARI) – multibeam data.

METHODS

Results were calculated from 3 arc second bathymetry (nominally 70 m) derived from NGDC and MBARI data sources. All available multibeam data were used. Hydrographic survey data (echo soundings) were eliminated from the calculation if it occurred 

coincidentally with multibeam information. Vertical and horizontal correction was performed on all data prior to modeling. All 

data were triangulated and rasterized using Vertical Mapper extension of MapInfo 6.5. Cell size varied throughout the study 

area, but significant portions were mapped at 70 m2 grid cell resolution. 

RESULTS AND DISCUSSION

The study area contains two distinct bathymetric regions. The northern portion of the study area, from Monterey Canyon northward, is characterized by having a broad continental shelf (15-50 km wide), while the southern region has a very narrow shelf 

with rapidly increasing depth close to shore. This pattern results in significantly shallower mean depth for Cordell Bank (394.9 

m) and Gulf of the Farallones (265.3 m) sanctuaries compared to the mean depth within Monterey’s sanctuary (876.9 m). For 

a more detailed description of bathymetric features see the explanation of the study area on page 1. 

This map is not intended for navigational purposes. Some areas on this map are created from old or sparse data, and are not 

necessarily representative of the actual seafloor characteristics.

Figure 32. Bathymetric map for the north/central California study area. Red lines indicate National Marine Sanctuary 

boundaries.

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High Resolution

Bathymetry

30

2

0

00

0

5

0

1

2

0

m

m

0

0

0

0

m

0

m

m

0 10 20 40 60 80 100

Kilometers

1

3

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0

0

0

0

0

0

0

0

0

m

m

m

20

5

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0

m

m

37
ABOUT THIS MAP

Figure 33 displays distribution of substrate types throughout 

the study area, from Point Arena to Point Sal California. The 

substrate is classified into 5 categories: mud, sand, pebbles/

cobbles/gravel (pcg), rock, and mud/rock mix. 

DATA SOURCES

California Continental Margin Geologic Map Series (Maps 4-

6) (Greene and Kennedy, 1989). These maps were originally 

created with a 1:250,000 resolution and were used as the 

basemaps for recent revisions and incorporation of new high 

resolution multibeam data in small portions of the study area.

METHODS

Initially, seven maps were developed that displayed substrate 

type and geologic formations throughout California’s coastal 

and marine environments. The original data were compiled by 

the California Division of Mines and Geology, USGS, and California Coastal Commission to produce paper maps. Geologists 

from California State University-Monterey Bay digitized these 

maps in 1999 and further interpreted these data to develop 

boundaries of substrate types (Greene et al., 1999). Three of 

the seven maps provide data for the study area and together 

provide the most comprehensive map of substrate type for the 

north/central California marine and near-shore region. For a 

detailed description of the development of the original maps 

and classification scheme, refer to Greene et al., 1999 and 

Greene et al., 2002. Eight substrate types were classified, however, some were grouped together when the digital substrate 

shapefile was rasterized into 1 km2 grid cells to facilitate their 

use in the HSI model analyses (See Section 2.1.2). “Boulders” 

and “Hard/Anthropogenic” polygons were grouped within the 

“Rock” substrate type, and “Gravel" was grouped with “Cobbles/

Pebbles” because boulder and gravel polygons were limited in 

number and affinities to these were considered to be similar to 

the group it was reclassified with.

RESULTS AND DISCUSSION

The substrate map covers an area of approximately 44,000 

km2, of which mud accounts for 86.4% (38,023 km2) of the 

total bottom area. Substrate containing pebble/cobble/gravel 

were the least abundant substrate types, only encompassing 100 km2

 of the study area. Rock substrates were mostly 

patchy throughout the region, encompassing 1,561 km2. Mud 

and rock mixed substrate (1,706 km2) was almost exclusively 

distributed in the southern portion of the study area, with small 

localized areas near Monterey canyon. Sand (2,611 km2

) is 

predominantly located near-shore with a large area located 

near and around Cordell Bank. Within sanctuary boundaries, 

soft sediments (mud, sand) account for almost 95% of the 

substrate. Rocky areas (including pebbles, cobbles, gravel) 

account for approximately 5%, while less than 1% consists of 

Subsection 2.1.2: HABITAT SUITABILITY MODELING

mud/rock mix. Within sanctuary boundaries, rocky substrates 

are distributed predominantly on the shelf, occurring in the areas near Cordell Bank, Farallone Islands, in many near-shore 

areas, and scattered within Monterey Bay. Outside sanctuary 

boundaries, several large areas of rock are found on the slope 

in depths greater than 1200 m. Mixed rock/mud substrate is 

scarce within the study area, with most occurring southwest of 

Monterey canyon. One large area of mixed rock/mud is present 

southwest of the southern Monterey Sanctuary boundary. Areas 

containing pebble, cobble, and gravel are found exclusively in 

Monterey’s sanctuary and are generally found within depths of 

100-200 m. The majority of sand substrate is found near-shore 

in the northernmost and southernmost portions of the study 

area, with significant coverage also occurring around Cordell 

Bank. Figure 33 displays the percent coverage of bottom types 

within each sanctuary. Other important substrate types exist 

within the study area, such as near-shore kelp beds, but were 

not included in the map based on their ephemeral distribution 

and the limitations associated with development of bathymetric 

SI’s in near-shore areas.

Although the substrate map is a probabilistic map of substrate 

types, it reflects the most complete and current knowledge of 

benthic substrates for the north/central California region. The 

map alone can be used to support investigations that require 

advanced knowledge of sea floor type. In addition, the maps 

are useful identifications of critical or important habitats for particular species or for determining essential fish habitat that can 

aid conservation and management plans for fisheries species. 

In this study, the map was primarily used as an environmental 

layer in GIS (in addition to bathymetry) to determine habitat 

suitability for groundfish species. This approach assumes that 

the underlying environmental GIS layers are an accurate representation of that particular variable, thus the model results 

are only as good as the underlying digital information. The 

substrate map is conservative, based on its original scale (1:

250,000), and may have fine scale inaccuracies throughout 

the study area. The majority of this map has not been field 

tested; therefore, inaccuracies in classification may exist. For 

example, several small polygons classified as rock near Point 

Reyes have been questioned. HSM results presented herein 

do not contain these polygons due to depth limitations with the 

fish and invertebrate catch data (50-1300 m). Small localized 

areas of high resolution information (on the scale of 10’s of 

meters) have been included in this map, however, these areas 

comprise a small percentage of the overall study area. More 

information is required to test the accuracy of the map; hence, 

thematic accuracy of substrate types is unknown.

Abbreviation: pcg= pebble/cobble/gravel

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Substrate Types

Legend

0 10 20 40 60 80 100

Kilometers

Mud

Sand

Pebbles/Cobble/Gravel

Rock

Rock/Mud

Cordell Bank

15% 4%

81%

Gulf of the Farallones

19% 7%

74%

Monterey Bay

6% 1% 4%

89%

rock pcg mud sand

Figure 33. Substrate types for the north/central California marine region.

38
Subsection 2.1.2: HABITAT SUITABILITY MODELING

ABOUT THESE MAPS

Figure 34 displays HSI model results for adult (left) and subadult (right) bocaccio during JuneNovember. The maps exhibit the potential distribution of the species based on affinities to bathymetry and substrate. Predicted HSI values range in scale from 10 (highest) to 0 (unsuitable) 

and were grouped into five classes: highest suitability (10-8), moderate (7-5), low (4-2), lowest 

(1), and unsuitable (0). SI values for bathymetry and substrate type are shown in the graphics 

below the mapped HSI results. Model performance graphics and statistical details are displayed 

in the map insets.

DATA SOURCES

Bathymetry SI: Alverson et al., 1964; Feder et al., 1974; Dark et al., 1983; Gunderson and 

Sample, 1980; Tagart and Kimura, 1982; Eschmeyer et al., 1983; Allen and Smith, 1988; Love 

et al., 1990; Wolotira et al., 1993; Wilkins et al., 1998; Yoklavich et al., 2000; Lauth, 2001; and 

Love et al., 2002.

Substrate SI: Feder et al., 1974; Eldridge, 1994; Yoklavich et al., 2000; and Love et al., 2002.

Validation: Wilson-Vandenberg et al., 1996; Wilkins et al., 1998; and Turk et al., 2001.

Life stage information: Love et al., 2002.

METHODS

Bathymetry SI values for adult bocaccio were developed using the literature review method, 

whereas subadult SI values were assigned based on the regression fitting technique using NMFS 

trawl data.

RESULTS AND DISCUSSION

Length at maturity information (Love et al., 2002) was used to determine life stage for bocaccio. 

Adults were defined as: females >360 mm and males >350 mm total length. Depth suitability for 

subadults was highest from 90-270 m, while highest suitability for adults was similar, ranging from 

50-299 m (Figure 34). Literature sources indicate that adult bocaccio are almost exclusively found 

around rocky substrates, while subadults exhibit broader affinity among substrate types (Figure 

34). Comparison of the two HSM maps show that the marked difference in substrate preference 

for adults yields a more limited spatial distribution than subadults. Less than 5% of the available 

habitat within each sanctuary was predicted highly suitable (HSI values >8) for adult bocaccio 

(Cordell Bank – 4.6%, Gulf of Farallones – 2.9%, Monterey – 1.7%) Within the study area, habitat 

of high suitability occurs exclusively inside sanctuary boundaries. High suitability covers more 

area for subadults than adults and extends well beyond sanctuary boundaries. Nearly 10% of 

Cordell Bank’s sanctuary was considered highly suitable for subadults. This percentage drops to 

1.6% for Gulf of Farallones, and 2.6% for Monterey. Approximately 556 km2

 of potential high suitable habitat was located within the three sanctuaries, while an additional 355 km2

 were predicted 

outside sanctuary boundaries. Although the proportion of highly suitable habitats were similar for 

adults and subadults, large areas of potentially moderate suitability for subadults were observed 

throughout the study area; whereas no areas were predicted moderate for adults. 

Generally, subadult bocaccio are more commonly found in shallower waters than adults (Love 

et al., 2002). Current scientific literature does not provide enough information to develop depth 

SI values for subadults; therefore, limited trawl information was used to develop SI values for 

bathymetry. Despite this, model performance for subadults yielded a strong positive correlation 

between observed abundance estimates from CDFG recreational catch data and predicted suitability (see map inset). Model performance for adult bocaccio also exhibited a strong positive 

correlation between predicted suitability and CDFG catch data. More information regarding bocaccio life history requirements are necessary to strengthen the HSI models; however, the mapped 

results and validation based on currently available information provide an adequate delineation 

Figure 34. Potential distribution of habitat suitability for adult and subadult bocaccio. Map inset contains validation statistics. SI values for bathymetry and substrate are of potential habitat suitability for adult and subadult bocaccio. graphically displayed below the map.

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Bocaccio

0 25 50 Km

Highest

Moderate

Low

Lowest

Unsuitable

0 25 50 Km

Highest

Moderate

Low

Lowest

Bocaccio

HSI Results

Unsuitable

HSI Results

seulaVIS

Validation - CDFG Rec. Data Validation - CDFG Rec. Data

Bathymetry Sediment Bathymetry Sediment 10 10

8 8

6 6 seu

4

la

4

VIS

2 2

0 0 9

9990

49

990

Sand Mud Pebble Rock 9

999

999999990

468024024680

0

Sand Mud Pebble Rock -

235

3

---

1112222233

0

00---------

---

1

Cobble 1

Cobble 0

57

000000000-

000

-

Gravel 9

135135790

Gravel

5

000

11122222

1

34

0

3

6

Adult Subadult

ee

cc

nn

aa

dd

nn

uu

bb

AA

nn

aa

ee

MM

HSI Value HSI Value

1.2

1

0.8

0.6

0.4

0.2

0

0 2 4 6 8 10

1

r

2

=0.70 r

2

=0.90

p=0.0046 p=0.0001 0.8

0.6

0.4

0.2

0

0 2 4 6 8 10

39
Subsection 2.1.2: HABITAT SUITABILITY MODELING

ABOUT THESE MAPS

Figure 35 displays the HSI model results for adult (left) and subadult (right) Dover sole during 

June-November. The maps exhibit the potential distribution based on affinities to bathymetry 

and substrate. Predicted HSI values range in scale from 10 (highest) to 0 (unsuitable) and 

were grouped into five classes: highest suitability (10-8), moderate (7-5), low (4-2), lowest 

(1), and unsuitable (0). SI values for bathymetry and substrate type are shown in the graphics below the mapped HSI results. Model performance graphics and statistical details are 

displayed in the map insets.

DATA SOURCES

Bathymetry SI: Wilkins et al., 1998 and Lauth, 2001.

Substrate SI: Demory, 1975; Demory et al., 1976; Barss et al., 1977; Pearcy, 1978; NOAA, 

1990; Stein et al., 1992; and CDFG, 2002.

Validation: Wilkins et al., 1998 and Turk et al., 2001.

Life stage information: PFMC, 1999.

METHODS

Bathymetry SI values for adults and subadults were developed from the regression fitting 

technique. Substrate SI values were developed through literature review. 

RESULTS AND DISCUSSION

Adult Dover sole are reported to be >300 mm total length for male and female individuals 

(PFMC, 1999). Both adult and subadult Dover sole inhabit deep water slope habitats; subadults exhibited a shallower range of depth preference (130-650 m) than adults (290-1070 

m) (Figure 35). Adults and subadults prefer soft sediments (sand and mud) throughout their 

range. Highest habitat suitability for subadults was predicted to occur along the shallower 

portions of the continental slope (200-550 m). A large area of moderate suitability was also 

predicted for an area that extends throughout the majority of the continental shelf. The most 

suitable habitats for adults consisted of deeper slope waters, with only moderate suitability 

extending onto the shelf region. Within Cordell Bank sanctuary, high subadult suitability (values 8-10) was calculated for 22% of the available habitat, 6.4% within Gulf of Farallones, and 

19% within Monterey sanctuaries. Cordell Bank and Gulf of the Farallone sanctuaries are 

comprised of shallower (50-300m) shelf waters, thus the percentage of highly suitable habitat 

for adults is lower (based on their calculated affinity for deeper waters) than that observed 

for subadults (21% and 12%, respectively). However, Monterey’s sanctuary is considerably 

deeper and a larger proportion of available habitats (30%) were predicted to be highly suitable 

for adults. Approximately 50% of areas that were predicted to be potentially suitable habitats 

for both adults and subadults occurred outside of sanctuary boundaries. These areas are 

most prominent south of Monterey’s sanctuary. 

Model performance was assessed by regressing predicted HSI values on mean log abundance 

values from NMFS trawl samples (1998-2001). Significant positive correlations were observed 

for both adult and subadult models, however, these are based on limited trawl samples (N = 

311). Discrepancies in model performance, such as small peaks of mean abundance within 

low suitability areas, are a result of limited observations within that category. Additional trawl 

information would strengthen model development and performance. 

Figure 35. Potential distribution of habitat suitability for adult and subadult Dover sole. Map inset contains validation statistics. SI values for bathymetry and 

substrate are displayed below the maps. 

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

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Dover sole

0 25 50 Km

Highest

Moderate

Low

Lowest

Unsuitable

0 25 50 Km

Highest

Moderate

Low

Lowest

Dover sole

HSI Results

Unsuitable

HSI Results

seulaVIS

Validation - NMFS Trawl Data Validation - NMFS Trawl Data

e

e

c

c

n

n

a

a

d

d

n

n

u

u

b

b

A

A

n

n

a

a

e

e

M

M

HSI Value HSI Value

Bathymetry Sediment Bathymetry Sediment 10 10

8 8

6 6 seu

4

la

4

VIS

2 2

0 0 9

9

9

999999999

9

999990

4

6

0

484842222

0

604040

-

-

Sand Mud Pebble Rock Sand Mud Pebble Rock 1

112234589

0

011223

0

0

-

---------

1

111111

Cobble Cobble 5

0

000000000

-

------

7

159595333

0

000000

Gravel Gravel

111223458

3

171515

9

001122

999

99999999999990

4826038404602680

0

--

112245666777783

0

0--------------

1

5

00000000000000-

9

37199515713790

1122456667777

18

2

1.5

1

0.5

0

0 2 4 6 8 10

Adult Subadult

1.5

r

2 2 =0.79 r =0.90 p=0.0005 p=0.0001 1.2

0.9

0.6

0.3

0

0 2 4 6 8 10

111111

40
Subsection 2.1.2: HABITAT SUITABILITY MODELING

ABOUT THIS MAP

This map displays HSI model results for adult Dungeness crab during June-November (Figure 36). The map displays the potential distribution based on affinities to bathymetry and substrate. Predicted HSI values range from 10 (highest) to 0 (unsuitable) and were grouped into five classes: highest suitability (10-8), moderate (7-5), low 

(4-2), lowest (1), and unsuitable (0). SI values for bathymetry and substrate type are shown in the graphics below the mapped HSI results. Model performance graphics 

and statistical details are displayed in the map insets.

DATA SOURCES

Bathymetry SI: Wilkins et al., 1998 and Lauth, 2001.

Substrate SI: Pauley et al., 1989; Emmett et al., 1991; Leet et al., 2001; and CDFG, 2002.

Validation: Wilkins et al., 1998 and Turk et al., 2001.

METHODS

Bathymetry SI values for adult Dungeness crab were developed using the regression fitting technique. Substrate SI values were developed through literature review. 

RESULTS AND DISCUSSION

Only adults were modeled within the study area because size information was lacking for crabs in the NMFS trawl data and scientific literature was not detailed enough 

to develop SI values for subadults. Dungeness crabs are an estuarine dependent species (Pauley et al., 1989), with adults exhibiting a shallow distribution (to 90 m) in 

coastal marine waters. Depth SI values derived from NMFS trawls confirmed this trend by exhibiting high SI values within 50-90 m. Suitability is probably high in the 

shallower near-shore environment (Emmett et al., 1991); however, trawl information was not available for this area. Literature sources described crab substrate preference to be soft sediments, with occasional utilization of rocky substrate. Habitat suitability based on these data resulted in a broad area of high suitability throughout the 

shallower waters of the Gulf of Farallones sanctuary (38% of available habitat), and much smaller proportions within Cordell (8.7%) and Monterey (10.4%) sanctuaries. 

Overall, this amounts to 2,809 km2

 of highly suitable habitat within the three sanctuaries. Moderate suitability, encompassing approximately 2,477.8 km2, extends further 

offshore to approximately 130 m. The potential suitability of habitats rapidly declines to unsuitable beyond 130 m in depth. The model performed well with NMFS validation data and exhibited a strong positive correlation with predicted suitability values. 

Figure 36. Potential distribution of habitat suitability for adult dungeness crab. Map inset contains validation statistics. SI values for bathymetry and substrate are graphically displayed below the map.

124°W

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Dungeness crab

0 25 50 Km

Highest

Moderate

Low

Lowest

Adult

HSI Results

Unsuitable

Validation - NMFS Trawl Data

ecnadnubAnaeM

HSI Value

Bathymetry Sediment 10

8

6

seula

4

VIS

2

0 9

99

9

99

0

4

68

0

24

0

-

--

Sand Mud Pebble Rock 1

11

3

0

00

-

--

1

Cobble 5

7

0

00

-

9

13

0

Gravel 1

1

51

0.5

0.4

0.3

0.2

0.1

0

0 2 4 6 8 10

r

2

=0.89

p=0.0014

41
ABOUT THESE MAPS

These maps display the results of two approaches that provide a synoptic view of 

overall habitat importance based on all the HSI models developed for the study area. 

Areas of potential habitat importance were first defined as an average view of habitat 

suitability across species and life stages. Secondly, individual maps of highly suitable 

habitats were overlain and areas or regions with the most overlap were considered 

important habitat or hot spots (Figure 37). 

Subsection 2.1.2: HABITAT SUITABILITY MODELING

Figure 37. Areas of groundfish potential hot spots based on mean fish species HSI models and overlap of predicted highly suitable habitats.

DATA SOURCES

See Individual HSI model results – CD-ROM.

124°W

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Mean HSI Model

0 25 50 Km

Highest

Moderate

Low

Lowest

HSI Results

Unsuitable

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HSI Model

Species Overlap

0 25 50 Km

15 - 20

12 - 14

8 - 11

1 - 7

# of species

0

METHODS

Mean HSI: HSI maps for all fish species and life stages were overlain and averaged 

by grid cell to evaluate overall suitability. Results were scaled in the same manner 

as individual HSI model results: Highest suitability (10-8), moderate (7-5), low (4-2), 

lowest (1) and unsuitable (0). 

Cumulative Suitability: Frequency of occurrence of predicted HSI values for each 

fish and invertebrate species life stage were calculated and values greater than one 

standard deviation above the mean were chosen to represent highest suitability. New 

individual maps were created and grid cells were reclassified as highest suitability (1) 

or other (0). All maps were overlain and summed to create a map of suitability overlap

within the study area. These areas represent potential groundfish hot spots. 

RESULTS AND DISCUSSION

The techniques described above are two possible approaches to estimate potential

hot spots or areas of habitat importance. Composite maps displaying these areas were

developed using all fish HSI model results to simulate the groundfish management

strategy employed by NMFS, where all groundfish (83 species) are managed under

one Fishery Management Plan. Mean HSI values across all 32 fish species and

life stages yield no areas ranked as highly suitable (HSI values 10-8). Moderate

suitability (7-5) occurs over the majority of the shelf region (to approximately 200

m) throughout the study area, most notably in the northern portion, where the shelf

extends significantly farther offshore than in the southern portion. The majority of the

area north of Monterey canyon consists of moderate suitability (to approximately 200

m), with low suitability extending through the deeper slope habitat. Smaller localized

areas of low suitability exist within the shelf and represent areas of hard substrate.

South of the Monterey canyon, low suitability comprises most of the study area, with

a narrow zone of moderate suitability along the shallower shelf waters. Suitability

drops from moderate to low just beyond the shelf edge throughout the study area. 

Throughout the study area, maximum overlap of cumulative high suitability occurs

on the shelf edge over soft sediments, which closely contour the 100 m isobath.

Approximately half of the models overlap in this zone. The top two quintals encompass

most of the shelf region and the zones of overlap are much broader in the northern

portion of the study area compared to the southern. 

These analyses reveal patterns of suitability related to depth and substrate. Highest

suitability occurs on the continental shelf, over soft sediments, based on the two

analytical approaches using the 33 HSI maps. These areas could be considered

as habitats of importance that support fish abundance and diversity. Both methods

portray highest suitability over the shelf that decline beyond the shelf edge. This

pattern conforms to literature sources which state that the shelf, and more importantly

the shelf break, are important areas for fish abundance and diversity (Yoklavich et

al., 2000; Williams and Ralston, 2002). In addition, soft sediments are potentially

more suitable than hard bottom throughout the study area. It is important to note that

the results of these analyses are based on 19 species and are only a subset of the

many groundfish species that occur within the study area. These results are clearly

biased based on the species modeled and may not provide adequate representation

of groundfish as a whole within the study area. Most of the species modeled have

substrate affinities for soft sediments, and most exhibit depth preferences that fall

within the shelf region. Ideally, many more models should be developed for additional

species and analyzed to provide a more representative depiction of groundfish

distribution within the study area. 

42
Subsection 2.1.2: HABITAT SUITABILITY MODELING

ABOUT THESE MAPS

The maps provide one approach to assess habitat suitability based on HSI results for multiple 

species (Figure 38). HSI model results were averaged to assess the potential distribution of 

suitable habitats for 8 species of adult rockfish (left) and 3 adult slope species (right). Predicted 

HSI values range in scale from 10 (highest) to 0 (unsuitable). HSI results were grouped into five 

classes: highest suitability (10-8), moderate (7-5), low (4-2), lowest (1), and unsuitable (0).

DATA SOURCES

Adult rockfish map – HSI maps for adult bocaccio, chilipepper, darkblotched, canary, yellowtail, 

yelloweye, and widow rockfishes (CD-ROM).

Slope assemblage adults – HSI maps for adult Dover sole, sablefish, and shortspine thornyhead (CD-ROM). 

METHODS

The slope assemblage was determined through cluster analysis of NMFS benthic slope trawl 

data (see Section 2.1.1 for methodology). All models for adult rockfish were combined to evaluate habitat suitability for these species as an assemblage. Both assemblages of fishes were 

analyzed by overlaying each individual HSI map and calculating the arithmetic mean across 

grid cells. 

RESULTS AND DISCUSSION

Typically, management plans are not based on single species, but rather groups of species that 

exhibit similar life histories (Williams and Ralston, 2002). Estimating potential distributions for 

species assemblages from HSI models could be a valuable tool for resource managers to aid 

in the development of fishery management plans and conservation strategies. This approach 

provides a spatial view of important habitats for a given assemblage and generates a baseline 

set of data which can be used for a variety of management needs.

Individual HSI results for the 8 species of rockfishes displayed similar patterns of habitat suitability within the study area and, not surprisingly, the map of mean habitat suitability for these 

species is nearly identical to the individual maps. Hard substrates (pebble, cobble, gravel, rocky) 

within the shelf region promote highest suitability areas for these species. Moderate suitability 

was predicted for areas with mixed mud/rock substrate and mud areas in waters with depths 

between 200-450 m. These areas are emphasized based on HSI results from darkblotched 

rockfish, which exhibited strong affinity for hard and soft substrates, rather than only rocky 

substrate preference exhibited by the other rockfish species. Also, darkblotched rockfish distribution occurs in deeper waters compared to the other species of rockfish and may necessitate 

their omission from this assemblage. Regardless, suitable habitat for this group of species is 

limited, based on the distribution of rocky substrate within the study area. Overall, highly suitable habitat comprises 364 km2

 within the three sanctuary boundaries or 2% of the available 

habitat. Moderate suitability comprises even less area, 247 km2, or 1.3% of available habitat. 

Cluster analysis of NMFS trawl data revealed many assemblages of species that tend to occur 

together (see Section 2.1.1). Dover sole, sablefish, and shortspine thornyhead were identified 

as members of a strong species assemblage that occurs over soft sediments in deep waters of 

the continental shelf and slope. Mean HSI calculations resulted in a broad range of highly suitable habitats throughout the study area. Overall, 23% (4,257 km2

) of the available habitat within 

the sanctuaries was predicted to be highly suitable habitat for this assemblage. An additional 

10% (1,907 km2) was predicted moderately suitable habitat. Because of its greater depths and 

larger area, Monterey Bay sanctuary contained significantly more highly suitable habitat (3,773 

km2) than Cordell Bank (170 km2) and Gulf of the Farallones (312 km2) sanctuaries. 

124°W

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All Rockfish

0 25 50 Km

Highest

Moderate

Low

Lowest

Adult

HSI Results

Unsuitable

Species:

Blue rockfish

Bocaccio

Chilipepper rockfish

Darkblotched rockfish

Canary rockfish

Yellowtail rockfish

Yelloweye rockfish

Widow rockfish

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Slope Assemblage

0 25 50 Km

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Moderate

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Lowest

Adult

HSI Results

Unsuitable

Species:

Dover sole

Sablefish

Shortspine thornyhead

Species: Species:

Blue rockfish Dover sole

Bocaccio Sablefish

Chilipepper rockfish Shortspine thornyhead

Darkblotched rockfish

Canary rockfish

Yellowtail rockfish

Yelloweye rockfish

Widow rockfish

N°53 N°63 N°73 N°83 N°93

Figure 38. Areas of potential habitat importance based on mean HSI models for selected species assemblages.

43
Subsection 2.1.2: HABITAT SUITABILITY MODELING

SECTION SUMMARY 

HSI modeling and mapping were considered to be a component of the biogeographic assessment because this approach 

provides spatial species- and lifestage-specific information for 

the north/central California marine region. This approach is intended to serve as an analytical tool for resource managers that 

can address a variety of needs: 1) developing maps in poorly 

sampled areas, 2) evaluating impact scenarios, 3) identifying 

habitats or areas for conservation or protection, and 4) assessing impacts of environmental change. The approach used here 

is similar to previous efforts that mapped near-shore rockfish 

distributions (Wright et al., 2000). The maps displayed nearshore rockfish distributions in relation to latitude, and maximum 

and common bathymetric ranges, based on information from 

peer-reviewed literature. The products generated from this 

study expand on this approach by including an additional parameter (substrate type). Also, models were developed which 

predicted the potential spatial distribution (based on affinities 

for bathymetric ranges and substrate type) for a select group 

of groundfish species. The maps provide a unique spatial view 

of potential groundfish habitats within and outside central California sanctuary boundaries. 

It is important to note that the model results previously described are not actual, but potential distributions based on 

species affinities to the environmental variables used in the 

models. Interpretation of these results should be conducted 

carefully due to the variety of limitations associated with the 

biological and environmental data. Both bathymetry and substrate-type maps were created from the most current information available; however, the scale of information may cause 

inaccuracies in the interpretation of the model results. The 

bathymetry map, created with 78 million data points, provides 

a high quality, high resolution image of depth throughout the 

study area. The digital substrate map is a probabilistic interpretation of imagery data that has yet to be field validated. 

Given its original resolution (1:250,000), the map may under 

or overestimate substrate distribution within the study area; 

however, localized areas have more accurate information. 

For example, predicted areas of potential high suitability were 

extremely limited for species that exhibit strong affinities for 

rock substrate (rockfish, lingcod). Generally, less than 1% of 

the study area was considered optimal habitat for these species and may underestimate actual habitat distribution. These 

results are reflective of the low percentage of rock substrate 

included in the substrate map, which could be a result of the 

scale in which the original data were collected. Nevertheless, 

the map provides the most comprehensive substrate inventory 

for this region and it is recommended that additional substrate 

information be collected to further refine the maps. Additional 

digital data are available (e.g. sea surface temperature, kelp 

distribution), and others can be developed and 

incorporated into the model as needed.

Decision making processes are typically not addressed at the species level but rather at a multispecies assemblage level. Thirty-four HSI models 

were created for 18 fish and 2 macro-invertebrate 

species to support multi-species analyses or assessments. Several techniques were conducted 

to assess habitat quality within the entire study 

area. One result indicated that the most potentially 

suitable habitat occurred on the shelf over mud 

substrates within depths of 100-120 m. As previously mentioned, these results were biased based 

on the selection of species modeled; however, 

the technique provides one method to identify 

areas of potential high habitat quality. Additional 

analyses identified important habitats for select 

species assemblages. Habitat suitability models 

for an assemblage of rockfish were developed and 

indicated that rocky habitats located on the shelf 

were identified as potential hot spots for adults; 

whereas, mud and sand substrates on the shelf 

were delineated as potentially important habitats 

for subadult rockfish.

In conclusion, the HSI maps can be used in a 

broad range of assessments which require information on habitat distribution and suitability. 

Individual species maps can be used to identify 

areas of varying habitat suitability and can be used 

to assess sensitivity to environmental or anthropogenic impacts. Lastly, it is recommended to 

continue developing HSI models for remaining 

groundfish species, as those presented here are 

only a small subset of the available resources 

within the study area. 

REVIEWS

Two reviews were completed for the fish assemblage and 

habitat suitability analyses. During May and June 2002 informal meetings were held in Monterey, San Francisco, and 

Seattle to receive feedback on the approach and verify from 

the scientists that collected the data that the analyses were 

valid. Formal review workshops were held in October, 2002 in 

San Francisco, Seattle, and Monterey Bay and hosted local 

scientists, fishermen, and National Marine Sanctuary Program 

staff. Review comments were either incorporated or addressed 

in this product. We appreciate all the reviewers’ time and effort 

when providing us this important feedback.

REVIEWERS

Tara Anderson, University of California, Santa Cruz

Carol Bernthal, Olympic Coast National Marine Sanctuary 

Program

Tonya Builder, Northwest Fisheries Science Center, NMFS

Gregor Cailliet, Moss Landing Marine Laboratory

Mark Carr, University of California, Santa Cruz

Josh Churchman, Fisherman

Elizabeth Clarke, Northwest Fisheries Science Center, 

NMFS

Steve Copps, Northwest Region, NMFS

Brad Damitz, Monterey Bay National Marine Sanctuary Program

Kathey Fosmark, Alliance of Communities for Sustainable 

Fisheries

Jim Glock, Sustainable Fisheries Division, NMFS

Gary Greene, Moss Landing Marine Laboratory

Chris Harvey, Northwest Fisheries Science Center, NMFS

Ruth Howell, Gulf of the Farallones National Marine Sanctuary 

Program

Roxanne Jordan, Alliance of Communities for Sustainable 

Fisheries

Chad King, Monterey Bay National Marine Sanctuary Program

Howatt King, California Department of Fish and Game

Bob Lauth, Alaska Fisheries Science Center, NMFS

Phil Levin, Northwest Fisheries Science Center, NMFS

Steve Lonhart, Monterey Bay National Marine Sanctuary 

Program

David Lott, Monterey Bay National Marine Sanctuary Program

Huff McGonigal, Monterey Bay National Marine Sanctuary 

Program

Nazila Merati, Pacific Marine Environmental Laboratory, 

NOAA

44
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Rubec, P.J., J.C. Bexley, H. Norris, M.S. Coyne, M.E. Monaco, S.G. Smith, and J.S. 

Ault. 1999. Suitability modeling to delineate habitat essential to sustainable fisheries. 

Am. Fish. Soc. Symp., Vol. 22: pp. 108-133.

Shaw, W.N., and T.J. Hassler. 1989. Species profiles: life histories and environmental 

requirements of coastal fishes and invertebrates (Pacific Northwest) – Lingcod. U.S. 

Fish Wildl. Serv. Biol. Rep. 82(11.119), U.S. Army Corps Eng. TR EL-82-4, 10 p.

Starr, R.M. 1998. Design principles for rockfish reserves on the U. S. West Coast. 

Marine harvest refugia for West Coast rockfish: A workshop., Pacific Grove, California. 

U.S. Department of Commerce. Magnuson-Stevens Act Provisions. Federal Register: January 11, 2002 (Vol. 67, No. 8). Washington, DC: U.S. Govt. Printing Office. 

p. 1582.

USFWS. 1980a. Habitat as a basis for environmental assessment. Report ESM 101. 

U.S. Fish Wildl.. Serv., Washington, DC.

USFWS. 1980b. Habitat evaluation procedures (HEP). Report ESM 102. U.S. Fish 

Wildl. Serv., Washington, DC.

USFWS. 1981. Standards for the development of habitat suitability index models 

for use with the habitat evaluation procedures. Report ESM 103. U.S. Fish Wildl. 

Serv., Washington, DC.

Wilkins, M.E., M. Zimmermann, and K.L. Weinberg. 1998. The 1995 Pacific West 

Coast Bottom Trawl Survey of Groundfish Resources: Estimates of Distribution, Abundance, and Length and Age Composition. NOAA Tech. Memo NMFS-AFSC-89.

Williams, E.H., and S. Ralston. In press. Distribution and co-occurrence of rockfishes (family Scorpaenidae) over trawlable shelf and slope habitats of California 

and Southern Oregon. Fishery Bulletin 000:000-000.

Wolotira, R.J., T.M. Sample, S.F. Noel, and C.R. Iten. 1993. Geographic and bathymetric distributions for many commercially important fishes and shellfishes off the 

West Coast of North America, based on research survey and commercial catch data, 

1912-84. NOAA Tech. Memo. NMFS-AFSC-6. 184 p.

Wright, N., J. Kum, C. King, E. Knaggs, B. Leos, and C. Perez. 2000. Marine fishery profiles. Volume 1: Nearshore-Version 1. California Department of Fish and 

Game, Marine Region. 150 pp.

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example of a natural refuge. Fish Bulletin, U.S. 98:625-641.

45
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

Table 11. Marine bird species used in this analysis.

Common Name Scientific Name Order/Family/SubFamily

Species that were mapped separately and used in the summary bird diversity and density analyses (n=31)

Pacific Loon Gavia pacifica Gaviiformes/Gaviiadae

Laysan Albatross Phoebastria immutabilis Procellariiformes/Diomedeidae

Black-footed Albatross Phoebastria nigripes Procellariiformes/Diomedeidae

Northern Fulmar Fulmarus glacialis Procellariiformes/Procellariidae

Pink-footed Shearwater Puffinus creatopus Procellariiformes/Procellariidae

Buller's Shearwater Puffinus bulleri Procellariiformes/Procellariidae

Sooty Shearwater Puffinus griseus Procellariiformes/Procellariidae

Black-vented Shearwater Puffinus opisthomelas Procellariiformes/Procellariidae

Fork-tailed Storm-petrel Oceanodroma furcata Procellariiformes/Hydrobatidae

Leach's Storm-petrel Oceanodroma leucorhoa Procellariiformes/Hydrobatidae

Ashy Storm-petrel Oceanodroma homochroa Procellariiformes/Hydrobatidae

Black Storm-petrel Oceanodroma melania Procellariiformes/Hydrobatidae

Brown Pelican Pelecanus occidentalis Pelecaniformes/Pelecanidae

Brandt's Cormorant Phalacrocorax penicillatus Pelecaniformes/Phalacrocoracidae

Double-crested Cormorant Phalacrocorax auritus Pelecaniformes/Phalacrocoracidae

Pelagic Cormorant Phalacrocorax pelagicus Pelecaniformes/Phalacrocoracidae

Red-necked Phalarope Phalaropus lobatus Charadriiformes/Scolopacidae

Red Phalarope Phalaropus fulicarius Charadriiformes/Scolopacidae

Heermann's Gull Larus heermanni Charadriiformes/Laridae/Larinae

Western Gull Larus occidentalis Charadriiformes/Laridae/Larinae

Glaucous-winged Gull Larus glaucescens Charadriiformes/Laridae/Larinae

Sabine's Gull Xema sabini Charadriiformes/Laridae/Larinae

California Gull Larus californicus Charadriiformes/Laridae/Larinae

Black-legged Kittiwake Rissa tridactyla Charadriiformes/Laridae/Larinae

Arctic Tern Sterna paradisaea Charadriiformes/Laridae/Sterninae

Common Murre Uria aalge Charadriiformes/Alcidae

Pigeon Guillemot Cepphus columba Charadriiformes/Alcidae

Marbled Murrelet Brachyramphus marmoratus Charadriiformes/Alcidae

Cassin's Auklet Ptychoramphus aleuticus Charadriiformes/Alcidae

Rhinoceros Auklet Cerorhinca monocerata Charadriiformes/Alcidae

Tufted Puffin Fratercula cirrhata Charadriiformes/Alcidae

Species mapped with related species & used in the summary diversity and density analyses (n=9, 4 maps)

Western Grebe Aechmophorus occidentalis Podicipediformes/Podicipedidae

Clark's Grebe Aechmophorus clarkii Podicipediformes/Podicipedidae

Black Scoter Melanitta nigra Anseriformes/Anatidae

Surf Scoter Melanitta perspicillata Anseriformes/Anatidae

White-winged Scoter Melanitta fusca Anseriformes/Anatidae

Caspian Tern Sterna caspia Charadriiformes/Laridae/Sterninae

Elegant Tern Sterna elegans Charadriiformes/Laridae/Sterninae

Xantus's Murrelet Synthliboramphus hypoleucus Charadriiformes/Alcidae

Craveri's Murrelet Synthliboramphus craveri Charadriiformes/Alcidae

Species in the data set used only in the summary bird diversity and density analyses (n=37)

Red-throated Loon Gavia stellata Gaviiformes/Gaviidae

Common Loon Gavia immer Gaviiformes/Gaviidae

Horned Grebe Podiceps auritus Podicipediformes/Podicipedidae

Red-necked Grebe Podiceps grisegena Podicipediformes/Podicipedidae

Eared Grebe Podiceps nigricollis Podicipediformes/Podicipedidae

Murphy's Petrel Pterodroma ultima Procellariiformes/Procellariidae

Cook's Petrel Pterodroma cookii Procellariiformes/Procellariidae

Parkinson's Petrel Procellaria parkinsoni Procellariiformes/Procellariidae

Flesh-footed Shearwater Puffinus carneipes Procellariiformes/Procellariidae

Short-tailed Shearwater Puffinus tenuirostris Procellariiformes/Procellariidae

Manx Shearwater Puffinus puffinus Procellariiformes/Procellariidae

Townsend's Shearwater Puffinus auricularis Procellariiformes/Procellariidae

Wilson's Storm-petrel Oceanites oceanicus Procellariiformes/Hydrobatidae

Wedge-rumped Storm-petrel Oceanodroma tethys Procellariiformes/Hydrobatidae

Markham's Storm-petrel Oceanodroma markhami Procellariiformes/Hydrobatidae

Least Storm-petrel Oceanodroma microsoma Procellariiformes/Hydrobatidae

Red-billed Tropicbird Phaethon aethereus Pelecaniformes/Phaethonidae

Brown Booby Sula leucogaster Pelecaniformes/Phaethonidae

White Pelican Pelecanus erythrorynchos Pelecaniformes/Pelecanidae

South Polar Skua Stercorarius maccormicki Charadriiformes/Laridae/Stercorariinae

Pomarine Jaeger Stercorarius pomarinus Charadriiformes/Laridae/Stercorariinae

INTRODUCTION

The California Current system runs south through the north/central California 

study area; it is one of the most productive ocean systems in the world (Glantz 

and Thompson, 1981). Hence, the study area contains a rich fauna of marine 

birds, as evidenced in species abundance and richness. In addition to a populous 

breeding community, the community of seasonal residents and migrants is even 

more robust, as central California is the destination for many marine bird species 

seeking productive feeding areas and acceptable habitat in which to spend their nonbreeding periods. Unlike many marine organisms, marine birds have a tremendous 

mobility and the fact that many seek this region to find food bespeaks the region’s 

trophic richness. Fortunately for the purpose of management of the central California 

National Marine Sanctuaries, the marine avifauna of the study area have been one 

of the most thoroughly surveyed.

DATA AND ANALYSES

Overview of Map Development and Analysis Process. The methods used in each 

survey were different, and because of this, careful consideration and correction are 

required to merge the data sets in a meaningful and scientifically acceptable way. The 

major steps of the data development for the bird analyses were as follows: species 

and study area selection; data set identification and collection; data corrections; 

data conversion into common comparable units; organizing the data into 5’ latitude 

by 5’ longitude cells; and calculating effort and density for each marine bird species. 

Seasonal density maps were then created for 40 species. Overall density, biomass 

density, and diversity maps were also created using distribution and abundance data 

for 76 bird species combined. These maps were reviewed at an expert workshop in 

October 2002. The draft bird report was also sent out for expert review in November 

(see list of reviewers at end of this section). Revisions were made to the maps and 

text based on that review.

Species Selected for Analysis. Selection criteria for bird species included in this 

assessment were: 1) the species must have a mostly marine distribution in the 

study area; and 2) adequate ocean survey data for the species is available and in 

a useable format. Species that are abundant, endangered, threatened, or a state 

species of concern were also a priority. The study area for the GIS assessment was 

seaward of the beach and did not include estuaries, so few shorebirds and waterfowl 

were included. Because marine distributions of birds are affected by where they 

breed and roost, we included information on the location and size of breeding and 

roosting sites, where available.

Table 11 contains the marine bird species that were selected for this analysis; data 

for 40 species were either mapped separately, or together for small species groups 

that generally co-occur (e.g., scoters). Ten of these species maps are included in this 

section; the remaining maps are on the accompanying CD-ROM. The remaining 37 

species that occurred in the study area and data set were used to develop summary 

marine bird maps on marine bird diversity and density.

About the Survey Data and Literature Used in this Assessment. The survey data 

used in this summary were not designed with sanctuary resource management in 

mind, but include the interests of individual researchers to study spatial and temporal 

patterns of marine birds, federal government efforts to assess potential biological 

impacts of oil development, and state government efforts to respond to oil spills, of 

which there have been several major ones in the study area. 

The Literature. Several reports, resulting from these surveys, provided background 

information on the occurrence patterns of marine birds in the region. The general 

composition and distribution of the marine avifauna was described by Ainley 

(1976) and Briggs et al. (1983, 1987a, b). Ainley and DeSante (1980) and Pyle 

and Henderson (1991) provide a fine-scale look at species’ seasonal presence and 

migratory periods, as viewed from the Farallon Islands; Ainley et al. (1995a, c), Veit 

et al. (1997) and Oedekoven et al. (2001) provide an interannual view of variability 

in spatial occurrence. The last four references, as well as Ainley et al. (1994), Spear 

and Ainley (1999) and Ainley and Divoky (2001), investigated long-term temporal 

trends in populations. Information on habitat preferences of marine birds and how 

these are affected by ocean climate variability are provided for selected species 

in Ainley and Boekelheide (1990), Oedekoven et al. (2001), and in a GIS analysis 

by Allen (1994). The food-web relationships of marine birds in this region are also 

remarkably well known (Balz and Morejohn 1977; Ainley and Sanger 1979; Briggs et 

al. 1984, Briggs and Chu 1987; Chu 1984; Ainley and Boekelheide 1990; Ainley et al. 

1996a, b; and Sydeman et al. 1997); and the breeding biology, including interannual 

variability in productivity and relationship to food-web variation, is very well known 

(Ainley and Boekelheide 1990, Ainley et al. 1995b). See the end of this section for 

complete list of references used.

The Data Sets. See Table 12, a summary of data sets used in the analyses, and 

Figures 39 and 40, which show the spatial extent of the individual data sets used 

CCromavemri's Mon Nurraemlete ScSyniethntlibifoicra Nmpahmus cr e averi Or

Cha

derard/Fariifomrmilyes/Al /SubFa cidaemily

Species in the data set used only in the summary bird diversity and density analyses (n=37)

Parasitic Jaeger Stercorarius parasiticus Charadriiformes/Laridae/Stercorariinae

Long-tailed Jaeger Stercorarius longicaudus Charadriiformes/Laridae/Stercorariinae

Bonaparte's Gull Larus philadelphia Charadriiformes/Laridae/Larinae

Mew Gull Larus canus Charadriiformes/Laridae/Larinae

Ring-billed Gull Larus delawarensis Charadriiformes/Laridae/Larinae

California Gull Larus californicus Charadriiformes/Laridae/Larinae

Thayer's Gull Larus thayeri Charadriiformes/Laridae/Larinae

Glaucous Gull Larus hyperboreus Charadriiformes/Laridae/Larinae

Red-legged Kittiwake Rissa brevirostris Charadriiformes/Laridae/Larinae

Royal Tern Sterna maxima Charadriiformes/Laridae/Sterninae

Common Tern Sterna hirundo Charadriiformes/Laridae/Sterninae

Forster's Tern Sterna forsteri Charadriiformes/Laridae/Sterninae

Thick-billed Murre Uria lomvia Charadriiformes/Alcidae

Ancient Murrelet Synthliboramphus antiquus Charadriiformes/Alcidae

Parakeet Auklet Aethia psittacula Charadriiformes/Alcidae

Horned Puffin Fratercula corniculata Charadriiformes/Alcidae

Table 11 cont. Marine bird species used in this analysis.

46

Parasitic Jaeger Stercorarius parasiticus Charadriiformes/Laridae/Stercorariinae

Long-tailed Jaeger Stercorarius longicaudus Charadriiformes/Laridae/Stercorariinae

Bonaparte's Gull Larus philadelphia Charadriiformes/Laridae/Larinae

Mew Gull Larus canus Charadriiformes/Laridae/Larinae

Ring-billed Gull Larus delawarensis Charadriiformes/Laridae/Larinae

California Gull Larus californicus Charadriiformes/Laridae/Larinae

Pacific Loon Gavia pacifica Gaviiformes/Gaviiadae

Laysan Albatross Phoebastria immutabilis Procellariiformes/Diomedeidae

Black-footed Albatross Phoebastria nigripes Procellariiformes/Diomedeidae

Northern Fulmar Fulmarus glacialis Procellariiformes/Procellariidae

Pink-footed Shearwater Puffinus creatopus Procellariiformes/Procellariidae

Buller's Shearwater Puffinus bulleri Procellariiformes/Procellariidae

Sooty Shearwater Puffinus griseus Procellariiformes/Procellariidae

Black-vented Shearwater Puffinus opisthomelas Procellariiformes/Procellariidae

Fork-tailed Storm-petrel Oceanodroma furcata Procellariiformes/Hydrobatidae

Leach's Storm-petrel Oceanodroma leucorhoa Procellariiformes/Hydrobatidae

Ashy Storm-petrel Oceanodroma homochroa Procellariiformes/Hydrobatidae

Black Storm-petrel Oceanodroma melania Procellariiformes/Hydrobatidae

Brown Pelican Pelecanus occidentalis Pelecaniformes/Pelecanidae

Brandt's Cormorant Phalacrocorax penicillatus Pelecaniformes/Phalacrocoracidae

Double-crested Cormorant Phalacrocorax auritus Pelecaniformes/Phalacrocoracidae

Pelagic Cormorant Phalacrocorax pelagicus Pelecaniformes/Phalacrocoracidae

Red-necked Phalarope Phalaropus lobatus Charadriiformes/Scolopacidae

Red Phalarope Phalaropus fulicarius Charadriiformes/Scolopacidae

Heermann's Gull Larus heermanni Charadriiformes/Laridae/Larinae

Western Gull Larus occidentalis Charadriiformes/Laridae/Larinae

Glaucous-winged Gull Larus glaucescens Charadriiformes/Laridae/Larinae

Sabine's Gull Xema sabini Charadriiformes/Laridae/Larinae

California Gull Larus californicus Charadriiformes/Laridae/Larinae

Black-legged Kittiwake Rissa tridactyla Charadriiformes/Laridae/Larinae

Arctic Tern Sterna paradisaea Charadriiformes/Laridae/Sterninae

Common Murre Uria aalge Charadriiformes/Alcidae

Pigeon Guillemot Cepphus columba Charadriiformes/Alcidae

Marbled Murrelet Brachyramphus marmoratus Charadriiformes/Alcidae

Cassin's Auklet Ptychoramphus aleuticus Charadriiformes/Alcidae

Rhinoceros Auklet Cerorhinca monocerata Charadriiformes/Alcidae

Tufted Puffin Fratercula cirrhata Charadriiformes/Alcidae

Western Grebe Aechmophorus occidentalis Podicipediformes/Podicipedidae

Clark's Grebe Aechmophorus clarkii Podicipediformes/Podicipedidae

Black Scoter Melanitta nigra Anseriformes/Anatidae

Surf Scoter Melanitta perspicillata Anseriformes/Anatidae

White-winged Scoter Melanitta fusca Anseriformes/Anatidae

Caspian Tern Sterna caspia Charadriiformes/Laridae/Sterninae

Elegant Tern Sterna elegans Charadriiformes/Laridae/Sterninae

Xantus's Murrelet Synthliboramphus hypoleucus Charadriiformes/Alcidae

Craveri's Murrelet Synthliboramphus craveri Charadriiformes/Alcidae

Red-throated Loon Gavia stellata Gaviiformes/Gaviidae

Common Loon Gavia immer Gaviiformes/Gaviidae

Horned Grebe Podiceps auritus Podicipediformes/Podicipedidae

Red-necked Grebe Podiceps grisegena Podicipediformes/Podicipedidae

Eared Grebe Podiceps nigricollis Podicipediformes/Podicipedidae

Murphy's Petrel Pterodroma ultima Procellariiformes/Procellariidae

Cook's Petrel Pterodroma cookii Procellariiformes/Procellariidae

Parkinson's Petrel Procellaria parkinsoni Procellariiformes/Procellariidae

Flesh-footed Shearwater Puffinus carneipes Procellariiformes/Procellariidae

Short-tailed Shearwater Puffinus tenuirostris Procellariiformes/Procellariidae

Manx Shearwater Puffinus puffinus Procellariiformes/Procellariidae

Townsend's Shearwater Puffinus auricularis Procellariiformes/Procellariidae

Wilson's Storm-petrel Oceanites oceanicus Procellariiformes/Hydrobatidae

Wedge-rumped Storm-petrel Oceanodroma tethys Procellariiformes/Hydrobatidae

Markham's Storm-petrel Oceanodroma markhami Procellariiformes/Hydrobatidae

Least Storm-petrel Oceanodroma microsoma Procellariiformes/Hydrobatidae

Red-billed Tropicbird Phaethon aethereus Pelecaniformes/Phaethonidae

Brown Booby Sula leucogaster Pelecaniformes/Phaethonidae

White Pelican Pelecanus erythrorynchos Pelecaniformes/Pelecanidae

South Polar Skua Stercorarius maccormicki Charadriiformes/Laridae/Stercorariinae

Pomarine Jaeger Stercorarius pomarinus Charadriiformes/Laridae/Stercorariinae

Parasitic Jaeger Stercorarius parasiticus Charadriiformes/Laridae/Stercorariinae

Long-tailed Jaeger Stercorarius longicaudus Charadriiformes/Laridae/Stercorariinae

Bonaparte's Gull Larus philadelphia Charadriiformes/Laridae/Larinae

Mew Gull Larus canus Charadriiformes/Laridae/Larinae

Ring-billed Gull Larus delawarensis Charadriiformes/Laridae/Larinae

California Gull Larus californicus Charadriiformes/Laridae/Larinae

Species in the data set used only in the summary bird diversity and density analyses (n=37)

Species that were mapped separately and used in the summary bird diversity and density analyses (n=31)

Species mapped with related species & used in the summary diversity and density analyses (n=9, 4 maps)

Parkinson's Petrel Procellaria parkinsoni Procellariiformes/Procellariidae

Flesh-footed Shearwater Puffinus carneipes Procellariiformes/Procellariidae

Short-tailed Shearwater Puffinus tenuirostris Procellariiformes/Procellariidae

Manx Shearwater Puffinus puffinus Procellariiformes/Procellariidae

Townsend's Shearwater Puffinus auricularis Procellariiformes/Procellariidae

Wilson's Storm-petrel Oceanites oceanicus Procellariiformes/Hydrobatidae

Wedge-rumped Storm-petrel Oceanodroma tethys Procellariiformes/Hydrobatidae

Markham's Storm-petrel Oceanodroma markhami Procellariiformes/Hydrobatidae

Least Storm-petrel Oceanodroma microsoma Procellariiformes/Hydrobatidae

Red-billed Tropicbird Phaethon aethereus Pelecaniformes/Phaethonidae

Brown Booby Sula leucogaster Pelecaniformes/Phaethonidae

White Pelican Pelecanus erythrorynchos Pelecaniformes/Pelecanidae

South Polar Skua Stercorarius maccormicki Charadriiformes/Laridae/Stercorariinae

Pomarine Jaeger Stercorarius pomarinus Charadriiformes/Laridae/Stercorariinae

yp

Cassin's Auklet Ptychoramphus aleuticus Charadriiformes/Alcidae

Rhinoceros Auklet Cerorhinca monocerata Charadriiformes/Alcidae

Tufted Puffin Fratercula cirrhata Charadriiformes/Alcidae

Western Grebe Aechmophorus occidentalis Podicipediformes/Podicipedidae

Clark's Grebe Aechmophorus clarkii Podicipediformes/Podicipedidae

Black Scoter Melanitta nigra Anseriformes/Anatidae

Surf Scoter Melanitta perspicillata Anseriformes/Anatidae

White-winged Scoter Melanitta fusca Anseriformes/Anatidae

Caspian Tern Sterna caspia Charadriiformes/Laridae/Sterninae

Elegant Tern Sterna elegans Charadriiformes/Laridae/Sterninae

Xantus's Murrelet Synthliboramphus hypoleucus Charadriiformes/Alcidae

Red-throated Loon Gavia stellata Gaviiformes/Gaviidae

Common Loon Gavia immer Gaviiformes/Gaviidae

Horned Grebe Podiceps auritus Podicipediformes/Podicipedidae

Red-necked Grebe Podiceps grisegena Podicipediformes/Podicipedidae

Eared Grebe Podiceps nigricollis Podicipediformes/Podicipedidae

Murphy's Petrel Pterodroma ultima Procellariiformes/Procellariidae

Cook's Petrel Pterodroma cookii Procellariiformes/Procellariidae

Parkinson's Petrel Procellaria parkinsoni Procellariiformes/Procellariidae

Flesh-footed Shearwater Puffinus carneipes Procellariiformes/Procellariidae

Short-tailed Shearwater Puffinus tenuirostris Procellariiformes/Procellariidae

Manx Shearwater Puffinus puffinus Procellariiformes/Procellariidae

Townsend's Shearwater Puffinus auricularis Procellariiformes/Procellariidae

Wilson's Storm-petrel Oceanites oceanicus Procellariiformes/Hydrobatidae

Wedge-rumped Storm-petrel Oceanodroma tethys Procellariiformes/Hydrobatidae

Markham's Storm-petrel Oceanodroma markhami Procellariiformes/Hydrobatidae

Least Storm-petrel Oceanodroma microsoma Procellariiformes/Hydrobatidae

Red-billed Tropicbird Phaethon aethereus Pelecaniformes/Phaethonidae

Brown Booby Sula leucogaster Pelecaniformes/Phaethonidae

White Pelican Pelecanus erythrorynchos Pelecaniformes/Pelecanidae

South Polar Skua Stercorarius maccormicki Charadriiformes/Laridae/Stercorariinae

Pomarine Jaeger Stercorarius pomarinus Charadriiformes/Laridae/Stercorariinae

Parasitic Jaeger Stercorarius parasiticus Charadriiformes/Laridae/Stercorariinae

Long-tailed Jaeger Stercorarius longicaudus Charadriiformes/Laridae/Stercorariinae

Bonaparte's Gull Larus philadelphia Charadriiformes/Laridae/Larinae

Mew Gull Larus canus Charadriiformes/Laridae/Larinae

Ring-billed Gull Larus delawarensis Charadriiformes/Laridae/Larinae

California Gull Larus californicus Charadriiformes/Laridae/Larinae

Thayer's Gull Larus thayeri Charadriiformes/Laridae/Larinae

Glaucous Gull Larus hyperboreus Charadriiformes/Laridae/Larinae

Red-legged Kittiwake Rissa brevirostris Charadriiformes/Laridae/Larinae

Royal Tern Sterna maxima Charadriiformes/Laridae/Sterninae

Common Tern Sterna hirundo Charadriiformes/Laridae/Sterninae

Forster's Tern Sterna forsteri Charadriiformes/Laridae/Sterninae

Thick-billed Murre Uria lomvia Charadriiformes/Alcidae

Ancient Murrelet Synthliboramphus antiquus Charadriiformes/Alcidae

Parakeet Auklet Aethia psittacula Charadriiformes/Alcidae

Horned Puffin Fratercula corniculata Charadriiformes/Alcidae

Species mapped with related species & used in the summary diversity and density analyses (n=9, 4 maps)
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS 

Spatial Extent of Data Sets: Ship-based Surveys 

129"W 128"W 127"W 126"W 125"W 124"W 123"W 122"W 121"W 124"W 123"W 122"W 121"W 

+ % Midwater Trawls for Juvenile Rockfish 

5 - ~3 3 1985-2001 

Mainly upwelling period 

R 2 Z. - kp( 

0 25 50Km 

$ - 

f 

4- a 

Mainly oceanic perio 

129"W 128"W 127"W 126"W 125"W 124"W 123"W 122"W 121"W 124"W 123"W 122"W 121"W 

Source Data: See text. 

Figure 39. Spatial extent of data sets used in the marine bird analysis: ship-based surveys. 

in the bird analyses. The ship and aerial strip transect data used in the GIs assessment were 

collected from 1980-2001 and occurred from Point Arena south to Point Sal, and offshore to the 

extent of data availability. However, the species maps do not generally include the full extent of 

available data, primarily because the assessment was focused on the national marine sanctuaries 

off central California. Also, estuaries were not part of the study area, but coastal colonies in 

estuaries were mapped to provide a more complete view of important areas for breeding species. 

See a more detailed description of data sets on the accompaning CD-ROM. 

Data Synthesis. 

Summarizina Transect Data into Grid Cells. The above data sets required a significant amount 

of processing and correction in order to synthesize them. Because wind speed affects detection 

of marine birds, data collected when wind speed exceeded 25 knots were excluded. Data were 

allocated into 5' latitude by 5' longitude cells. All aerial data were continuous; each ship-based 

data set was converted separately into a continuous transect format to the extent possible. The 

Table 12. Summary of at-sea survey data sets used in the analyses 

I Ocean Total 

Princi~al Platform Habitat Seasons Transect 

Data Set investigator Height Covered2 Years Sampled Width 

Surface survey 

MMS Low of the shelf, 

Altitude Aerial slope & deep All three 

Surveys Briggs Pembroke, 62m ocean beyond 1980-1 983 seasons 50m 

Surveyor, l2m, 

EPOCS Discoverer, Surface survey 

Shilsboard 

lsu&eys l~inle~ 

ICA Seabird I 

Ecology LOWAltitude Aerial 

Surveys Briggs 

Midwater Trawl 

Juv. Rockfish 

Assessment: 

Ship Surveys l~inle~ 

Oceano- of the deels 

Igrapher, 15m locean 

I I 

Surface survey 

Partenavia, of shelf and F slope 

Surface survey 

I David Starr of shelf and I dordan, 1 Om 1 slope to 3000 m 

1 

I 

1 

1984-1994 

1985-2001 

1 

I 

1 

All three 

seasons 

Mainly 

Upwelling 

Mainlv 

upwellkg 

I 

I 

I 

300-600m 

300m 

I 

I 

OSPR Low I I Surface survev I 

Altitude Aerial Partenavia, of shelf and 

Surveys Bonnell, Tyler 62m slope Allthree 

seasons I 5Om 

MMS Santa 

Barbara 

Channel Low Surface survey 

Altitude Aerial Partenavia, of shelf and All seasons three 

Surveys Bonnell 62m slope 

Surface survey 

SF-DODS Ship of shelf and All three 

Surveys Ainley Point Sur, 8m slope to 3000 m seasons 300m 

Surface survey 200-300m, 

NMFSISWFSC of the shelf, 

ORCAWALE deep Shi~ Survev Ballance MacArthur, I I m ocean bevond 2001 

Mainly 

k depending on 1 1 1 1 conditions 

Note 

See description of data sets on the CD for more information 

continuous aerial data were binned into the appropriate cell. For the SF-DODS and EPOCS 

studies, and the Rockfish Assessment cruises prior to 1997, the beginning position, ship heading, 

and speed were used to compute the end position of each 2-4 km continuous transect. From 

this, a midpoint ofthe transect was determined. As times of observations were not available, the 

position of the midpoint was used to select the cell to which the survey effort was assigned. If 

this midpoint fell on a cell boundary, it was assigned to the cell to the north or west. To maintain 
129°W 128°W 127°W 126°W 125°W 124°W 123°W 122°W 121°W

N°35 N°36 N°37 N°38 N°39

124°W 123°W 122°W 121°W

N°35 N°36 N°37 N°38 N°39

129°W 128°W 127°W 126°W 125°W 124°W 123°W 122°W 121°W

N°35 N°36 N°37 N°38 N°39

124°W 123°W 122°W 121°W

N°35 N°36 N°37 N°38 N°39

Midwater Trawls for Juvenile Rockfish

1985-2001

Mainly upwelling period

Spatial Extent of Data Sets: Ship-based Surveys

2000 m 200 m 2000 m 200 m SF-DODS Cruises 1996-2000

Year round

0 5 25 0Km

a b

2000 m 200 m NMFS ORCAWALE Cruises 2000 m 200 m EPOCS Cruises 2001 1984-1994

Mainly oceanic period Year round

c d

Source Data: See text.

Figure 39. Spatial extent of data sets used in the marine bird analysis: ship-based surveys.

in the bicollected extent of available off centrestuaries See a mData SySummar

Section 2.2: BIO GE OG RA PHY OF MA RINE BIRDS

of procesof marinallocated data set continuo

Table 12

Data 

MMS Low Altitude ASurveys EPOCS ShipboarSurveys 

CA SeabEcology Altitude ASurveys NMFSMidwater Juv. RocAssessmShip SurOSPR LoAltitude A

Surveys MMS SaBarbaraChannel Altitude ASurveys 

SF-DODSurveys NMFS/SW

ORCAW

Ship Sur

NoteSee desc

studies, and spethis, a mposition this midp
Table 13. Summary of combined data set effort by ocean season.

the correspondence between effort and bird observations, observations were also assigned 

to the transect midpoints. For the Rockfish Assessment Cruises from 1997 onward, effort was 

assigned to the cells through which the vessel passed based on the proportion of trackline that 

fell within each cell, and observations were interpolated along the cruise track according to 

the time of each observation. The marine bird survey data from the ORCAWALE cruise were 

recorded continuously using automatic recording software and were processed like the aerial 

survey data. 

Data Analysis.

Effort. The combined at-sea survey effort for birds included 133,705 kilometers of trackline, as 

well as 128,886 observations of 973,318 birds in the analyzed data set. Survey effort by ocean 

season is summarized in Figure 41 and Table 13. 

Calculating Density. From the digitized survey data, we mapped the distribution of effort and of 

species observations into a grid of 5-minute latitude by 5-minute longitude cells, using MMSCDAS (Marine Mammal and Seabird Computer Database Analysis System, MMS 2001). The 

species data were first transformed into densities on the basis of strip widths (which varied by 

platform, depending on speed and height above water; see Table 12). The number of birds of 

each species seen was then divided by area surveyed to estimate density in each cell for that 

data set. For construction of density plots, if a cell was censused in other years or the same 

year by another survey, densities in cells were averaged and weighted according to effort. 

Organizing Data into Ocean Seasons. Effort and species data were organized and mapped into 

three distinct ocean seasons (Bolin and Abott 1963): Upwelling, Oceanic, and Davidson Current, 

because ocean conditions differ distinctly among them and are known to affect the biota of the 

California Current (e.g. Ainley 1976, Briggs et al. 1987). As there is significant interannual variation 

in the actual initiation and termination of these seasons, the following dates were defined for each 

season for purposes of analysis: Upwelling Season is 15 March-14 August; Oceanic Season is 

15 August-14 November; and Davidson Current Season is 15 November-14 March. 

Seasonal Density Maps for Individual Species. Seasonal density maps were generated for 40 bird 

species. These maps were then reviewed to characterize the spatial and seasonal occurrence 

pattern of each species in the study area. 

Seasonal High Use Areas for Individual Species. In order to provide a summary map of space 

use, seasonal density data were binned into 10-minute latitude by 10-minute longitude cells 

for each species or species group. The purpose of the seasonal high use maps is to provide 

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

Dates Used for Number Kilometers of Number of

Ocean Each Ocean of Years Trackline Number 5' Cells

Season Season Months Included Surveyed of Visits Sampled

1980-1982,

Upwelling 15 Mar-14 Aug 5 1985-2001 64177 11050 1335

1980-1982,

1991, 1994-

Oceanic 15 Aug-14 Nov 3 2001 29263 4171 1130

Davidson 1980-1986,

Current 15 Nov-14 Mar 4 1991-2001 40265 5878 1593

TOTAL 1 Jan – 31 Dec 12 1980-2001 133705 21099 2294

Note. The total number of cells sampled is not a straight sum; it refers to the number of unique

cells surveyed.

Figure 40. Spatial extent of data sets used in the analysis: aerial surveys.

129°W 128°W 127°W 126°W 125°W 124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

129°W 128°W 127°W 126°W 125°W 124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

MMS Aerial Surveys

1980-1983

Year round

Spatial Extent of Data Sets: Aerial Surveys

2

2

2

0

0

20

0

0

0 

0

0

0 

0

OSPR Aerial Surveys

m

m

 m

m

1994-1998, 2001

Year round

0 25 50Km

e f

2

2

0

0

00

0

Seabird Ecology Aerial Surveys 2

2

0

0

00

0

m

 m

MMS Santa Barbara Channel

m

1985 m

Aerial Surveys

Mainly upwelling period 1995-1997

Year round

g h

Source Data: See text.

48
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

one overall map for each species (or group of species) that 

describes the spatial and temporal use patterns, as clearly as 

possible. The seasonal high use index is based on the top 20% 

of sampled cells within a given season. The index is therefore 

sensitive to cells which were not sampled in any one of the 

three seasons, causing a downward bias in the index. 

Use of a 10-minute block size greatly reduces the magnitude 

of this bias. Non-zero cells were then ranked and those in the 

top 20 percent were selected and defined as seasonal high use 

areas. Cells were then mapped with colors corresponding to 

the number of seasons of high use. Cells in which there was 

effort but birds were not observed, and cells where sightings 

occurred but were never high use areas, were also mapped 

with two additional colors.

Major Breeding Colonies. Best available breeding colony data 

(number of breeding birds, mostly from Carter, et al. 1992, 

with some updates) were mapped for each species for which 

colony information was available, on the same map as the 

"seasonal high use" information. A map (pp. 81) and table (p. 

53) of the top 40 breeding colonies is included in Section 2.2; 

the complete colony table, based on best available data, will 

be included on the CD-ROM. 

Spatial and Temporal Patterns Summary Table. Density 

maps for 44 species were inspected to identify which cells 

exhibited the highest density each season. Using the two 

highest density categories for each species, relatively high 

density areas associated with large bathymetric areas (inner 

shelf, outer shelf, upper slope) were identified, as well as with 

several smaller discrete habitat features (e.g., Monterey Bay 

Canyon) (p. 51).

Summary of Overall Density, Biomass and Diversity Maps 

for 76 Marine Bird Species. Overall marine bird densities 

were mapped for each season and for all seasons combined. 

Densities of all species in a cell were converted to biomass by 

multiplying density for each species by its average body mass 

(from Dunning 1993), then summing for all species detected 

in that cell. Biomass was then mapped in a fashion similar to 

the individual species’ density maps.

The Shannon Index (Shannon and Weaver 1949) 

was used to quantify species diversity. This index measures 

the degree to which the species assemblage is dominated by 

a single species. If species A dominates all the species seen 

within a cell, then diversity is low, and vice versa. Diversity 

was calculated for each season and all seasons combined. To 

standardize for variable effort among cells and variable strip 

width for species, density was used for each species in each 

cell as the basis for calculating the diversity index value.

The Shannon Index was selected as the diversity metric 

because it is widely used and accepted in community ecology. 

It has three desirable properties for a diversity index, noted 

below. Most diversity indices do not take these three qualities 

into account. For more information on diversity indices, see 

Ecological Diversity, E.C. Pielou, pp 7-18.

1. The diversity index is greatest when all species in the 

community are equally represented in numbers (e.g., evenness. 

in a community). Or, for a given number of species (e.g., 

richness value), the diversity index should have it’s greatest 

value when the proportion of each species is the same.

2. Given two completely diverse or even communities, the 

one with the higher number of species has a greater diversity 

value.

3. The last property is difficult to summarize: This property takes 

into account the hierarchical nature, or "representativeness" in 

the biological classification of each species when estimating 

diversity. 

Evaluating Variation in Species Abundance. In order to 

evaluate factors that affect the abundance of marine birds 

in the study area, a regression model was developed (Seber 

1977, Kleinbaum et al. 1988), with marine bird density as 

the dependent variable. Independent variables that could be 

addressed in the limited time frame included: ocean season, 

year, ocean depth, distance to nearest breeding colony, 

distance to shelf break (estimated to the 200 meter isobath), 

distance to deep ocean (estimated to the 2000 meter isobath), 

latitude, periods of short-term ocean climate anomalies (e.g., 

El Niño or La Niña events), and latitude. The data used for 

the multiple regression analyses was a subset of the mapping 

data set; the regression data set included cell-based density 

data from 1985 - 2002 (6,641 cell samples, all with effort ≥ 

0.24km2 per cell).

Response to Variation in Marine Climate. Short-term ocean 

climate anomaly in this report is often referred to as ENSO 

(El Niño/Southern Oscillation), and generally refers to the 

climatic events that cause significant interannual changes in 

thermocline depth and water temperature in the study area, 

resulting in warm-water periods (often known as El Niño 

events), cold-water periods (often known as La Niña events), 

or neutral periods, when the water is neither unusually warm 

nor cold (Ainley et al. 1995b and references therein). 

Figure 41. Total survey effort for marine bird analyses.

S  n  H ∑    n  ′ = −  i  ln  i  i =1  n   n 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Combined At-Sea Effort for Marine Bird Analysis

Upwelling Season

(Mar. 15 - Aug. 14)

>1000.00

500.01 - 1000.00

250.01 - 500.00

100.01 - 250.00

50.01 - 100.00

25.01 - 50.00

5.01 - 25.00

0.01 - 5.00

2

2

2

2

0

0

0

0

00

0

0

0

m

m

0 m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Effort

(Km of trackline)

0 25 50 Km

a b

20

2

0

0

0

0

Davidson Current Season 2

2

0

0

00

0

m

m

m

m

All Seasons

(Nov. 15 - Mar. 14)

c d

Source Data: See text.

49
The official ENSO events and time periods tracked by NOAA 

are relevant for regions to the far south and well outside of the 

study area; the official NOAA ENSO periods do not accurately 

reflect the timing of the ENSO-related periods that occur off 

central California. In part, this is because the marine climate of 

the central and northern California Current region is affected 

as well by variation in atmospheric pressure centers in the 

Gulf of Alaska. 

To determine the time periods and effects of interannual climate 

anomalies of marine birds as evidenced in the study area (i.e., 

warm-water, cold-water and neutral periods), two sea-surface 

temperature data sets for central California were analyzed: 

daily temperatures taken as part of a Scripps Institution of 

Oceanography program at Southeast Farallon Island and 

the NOAA CoastWatch data off central California. Both data 

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

sets ranged from 1975-2001. Table 14 indicates the periods 

of unusual weather (warm water, cold water, and neutral) as 

determined from these data.

Also affecting marine climate are decadal-scale factors involved 

in the Pacific Decadal Oscillation (Mantua and Hare 2002). A 

regime shift occurred in 1976, from cold to warm, and may 

have occurred again in the winter of 1998/1999, from warm to 

cold. This means that the overall average state of the system 

could be characterized as warm or cold, with other shorterterm variation embedded (e.g., ENSO). The effect of regime 

shifts on marine bird occurrence is addressed near the end 

of this report.

ANALYTICAL MAP PRODUCTS

The analytical map products (Figures 42-60) include seasonal 

density maps for 13 species and nine summary analyses maps 

for marine birds. These maps are a subset of the total mapped 

results for this analysis. Additional maps and text products 

are included on the CD-ROM. Of the 35 species maps, these 

ten were chosen for inclusion in the document because they 

represent a variety of spatial and temporal patterns in and 

around the sanctuaries.

Table 14. Assignment of warm, cold and neutral periods, 

based on surface water temperatures off Cental California. Davidson Current Upwelling Oceanic

Year Season Season Season

1975ColdColdCold

1976ColdCold Warm

1977 WarmColdNeutral

1978 Warm WarmCold

1979ColdNeutralNeutral

1980 WarmNeutralCold

1981 WarmColdCold

1982NeutralNeutralNeutral

1983 Warm Warm Warm

1984 WarmNeutralNeutral

1985Cold WarmCold

1986NeutralNeutralNeutral

1987 Warm Warm Warm

1988NeutralNeutralCold

1989ColdNeutralNeutral

1990ColdColdNeutral

1991ColdColdNeutral

1992 Warm Warm Warm

1993 Warm Warm Warm

1994 WarmNeutralCold

1995Neutral WarmNeutral

1996 WarmNeutralCold

1997NeutralNeutral Warm

1998 Warm WarmCold

1999ColdColdCold

2000ColdColdCold

2001ColdCold

-

50
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 42a, b, and c show the density (birds/km2) of western 

and Clark’s grebes (combined) in the Upwelling, Oceanic, and 

Davidson Current seasons, displayed in five minute latitude by 

five minute longitude cells. Densities are based on the combined 

data sets of several studies (see “Methods” and “Data Sources” 

below). The color and mapping intervals were customized to 

show the most structure and to highlight significant areas, while 

allowing comparisons among marine bird species. Cells that 

were surveyed but in which no grebes were observed have a 

density of zero. Areas not surveyed appear white; no information is available for these areas. Blue lines indicate the boundaries of the National Marine Sanctuaries in the study area: Cordell 

Bank, Gulf of the Farallones, and Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, displayed in 10 minute latitude by 10 minute longitude cells. The 

seasonal high use map provides a further synthesis of densities 

presented in maps a, b and c, and portrays the relative importance of various areas to the species. Areas with consistently 

high use are highlighted on this map. To provide a relative reference for the “high use” areas, cells are also shown where the 

species were absent (i.e., the cell was sampled but the species 

was not recorded there), or present but at lesser concentrations 

in any particular season. See the "Methods" section below for 

further explanation of seasonal high-use areas.

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management 

Service. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS 

2001), and California Department of Fish and Game, Office of 

Spill Prevention and Response (CDF&G-OSPR, unpublished 

data). Early data were collected using methods described by 

Briggs et al. (1983, 1987b); more recent data were collected 

using updated technology but using the same general method. 

Data sources for ship-based survey data include: David Ainley 

of H. T. Harvey and Associates and Carol Keiper of Oikonos 

(unpublished data; see Oedekoven et al., 2001 for details on 

survey methods); and Lisa T. Ballance, from the Ecology Program of the Southwest Fisheries Science Center, NMFS, NOAA 

(unpublished data). 

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above water) were used to estimate the area sampled. The number of 

birds of each species seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was surveyed 

more than once, densities were averaged, with an adjustment 

made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’ x 10’ cells. For each season, the cells with densities in the top 20% of non-zero values were designated “high 

use” for that season. Cells were scored for “high use” in one, 

two, or three seasons and are depicted by color. To provide a 

relative reference for the “high use” areas, cells are also shown 

where the species were absent (i.e., the cell was sampled but 

the species was not recorded there) or present (but densities 

were never in the top 20% for any season).

RESULTS AND DISCUSSION

Individuals of this closely-related species pair (separable by 

plumage, but sharing the same ecological niche) are abundant 

in the near-shore waters of the study area. Surveys tallied 

2,511 sightings of 13,525 individuals. During most oil spills in 

this region, these species have been near the top of the list, by 

number, of oiled birds. These birds breed inland at freshwater 

lakes and marshes.

A multiple regression model of nine independent variables exFigure 42. Western and Clark’s grebes, seasonal density and high use areas. plained 15.5% of variation in cell density; most important vari124°W 123°W 122°W 121°W °N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

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°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Western and Clark's Grebes Aechmophorus occidentalis, A. clarkii

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

0

0

0

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50 Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

These species do not

c d breed within the study area.

Source Data: See text.

51
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ables were season, and an inverse relationship with distance 

to land and to depth; see Table 19. These results reflect the 

large number of grebes found in shallow waters (mean depth 

was 131 ± 37 m) within a few kilometers of shore (mean distance to land was 7.4 ± 1 km), and primarily during the Oceanic 

Season. Moderate numbers are present during the Upwelling 

and Davidson Current seasons. During the latter, these grebes 

expanded farther offshore to the middle continental shelf (mean 

depth of occurrence 260 ± 80 m). 

Inshore waters of the Gulf of the Farallones (San Francisco Bay 

tidal plume), Monterey Bay, and Estero/San Luis Obispo bays 

had particularly high concentrations of these birds. North and 

south of marine sanctuary boundaries in the study area, these 

species were found only at isolated river mouths. Therefore, the 

sanctuary boundaries encompass the majority of the species 

habitat in the study area, except for the ‘sanctuary exclusion 

area’ off San Francisco and Pacifica, which contained many 

grebes. The broad continental shelf off central California is ideal 

for these grebes, which capture prey by diving; it is likely they 

are capable of exploiting most of the water column lying over 

the shelf, in spite of their inshore occurrence. Abundance of this 

species-pair remained stable between 1985 and 2002.

These grebes feed mainly on long-bodied, fusiform fish, such 

as herring and anchovy. See Tables 15 and 16 for related summary information.

52
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 43 a, b, and c show the density (birds/km2) of northern 

fulmar in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in five minute latitude by five minute 

longitude cells. Densities are based on the combined data sets 

of several studies (see “Methods” and “Data Sources” below). 

The color and mapping intervals were customized to show the 

most structure and to highlight significant areas, while allowing 

comparisons among marine bird species. Cells that were 

surveyed but in which no fulmars were observed have a density 

of zero. Areas not surveyed appear white; no information is 

available for these areas. Blue lines indicate the boundaries 

of the National Marine Sanctuaries in the study area: Cordell 

Bank, Gulf of the Farallones, and Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, 

displayed in 10 minute latitude by 10 minute longitude cells. 

The seasonal high use map provides a further synthesis of 

densities presented in Maps a, b and c, and portrays the 

relative importance of various areas to the species. Areas 

with consistently high use are highlighted on this map. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there), or present 

but at lesser concentrations in any particular season. See the 

"Methods" section below for further explanation of seasonal 

high-use areas. 

Because the sighting data for this species extends beyond 

the western extent of the standard map frame shown here, 

additional maps were made that include a greater western 

extent. These maps (with the word "pelagic" in the filename) 

are included on the CDROM.

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management 

Service. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS 

(2001), and California Department of Fish and Game, Office 

of Spill Prevention and Response (CDF&G-OSPR, unpublished 

data). Early data were collected using methods described by 

Briggs et al. (1983, 1987b); more recent data were collected 

using updated technology but using the same general method. 

Data sources for ship-based survey data include: David Ainley 

of H. T. Harvey and Associates and Carol Keiper of Oikonos 

(unpublished data; see Oedekoven et al., 2001 for details 

on survey methods); and Lisa T. Ballance, from the Ecology 

Program of the Southwest Fisheries Science Center, NMFS, 

NOAA (unpublished data). 

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of birds of each species seen in a cell was then divided by 

the area sampled in the cell to estimate density. If a cell was 

surveyed more than once, densities were averaged, with an 

adjustment made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’ x 10’ cells. For each season, the cells with 

densities in the top 20% of non-zero values were designated 

“high use” for that season. Cells were scored for “high use” 

in one, two, or three seasons and are depicted by color. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there) or present 

(but densities were never in the top 20% for any season).

RESULTS AND DISCUSSION

Northern fulmar, which nests on islands in the Aleutian Island 

chain and Bering Sea, is common in waters of the continental 

Figure 43. Northern fulmar, seasonal density and high use areas. slope as well as the outer waters of the continental shelf off 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Northern Fulmar Fulmarus glacialis

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

00

0 

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

This species does not

c d breed within the study area.

Source Data: See text.

53
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

north/central California. Surveys recorded 4,486 sightings of 

6,345 individuals. In some winters, fulmars were particularly 

abundant off this coast, such as in 1986, 1991, 1996, and 

1999.

A multiple regression analysis of nine independent variables 

explained 21.3% of the variability of this species’ cell density; 

important explanatory variables were season, ENSO period 

(periods of unusually warm or cold sea temperatures), and year; 

see Table 19. The species’ occurrence is confined principally to 

the Davidson Current Season, especially prevalent during La 

Niña. For a subarctic species, surprisingly high densities are 

present during the Upwelling Season; many of these individuals 

exhibit heavy molt indicating that they might be juveniles. 

Based on the data available, the species’ population trajectory 

during the study period exhibited a curvilinear pattern: a slight 

decline between 1985 and 1989, followed by an increase from 

1990 to 2002. Numbers rose particularly in the last few years, 

perhaps indicating a response to the shift in 1999 from a warm 

to a cold ocean regime (see subsection on response to climate 

change). 

Like the albatrosses, this species is attracted to trawlers, where 

the species scavenges offal. Therefore, areas of concentration 

for northern fulmars during the study period were (and may still 

be) important areas of traditionally higher fishing activity such as 

Cordell Bank, Fanny Shoal, and nearby canyons. This pattern 

is better illustrated during the Upwelling Season, when the 

species is much less abundant. In the latter season, the species 

spreads far more widely, occurring farther offshore and over 

deeper depths. Although fulmars are widespread off central 

California, the boundaries of the National Marine Sanctuaries 

encompass an important area for this species. 

Northern fulmars are generalists that feed on live and dead prey 

found at the surface. They are one of the few marine species 

that feed extensively on gelatinous zooplankton, e.g. jellyfish. 

See Tables 15 and 16 for related summary information.

54
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 44a, b, and c show the density (birds/km2) of sooty 

shearwater in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in five minute latitude by five minute 

longitude cells. Densities are based on the combined data 

sets of several studies (see “Methods” and “Data Sources” 

below). The color and mapping intervals were customized to 

show the most structure and to highlight significant areas, 

while allowing comparisons among marine bird species. Cells 

that were surveyed but in which no sooty shearwaters were 

observed have a density of zero. Areas not surveyed appear 

white; no information is available for these areas. Blue lines 

indicate the boundaries of the National Marine Sanctuaries 

in the study area: Cordell Bank, Gulf of the Farallones, and 

Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, 

displayed in 10 minute latitude by 10 minute longitude cells. 

The seasonal high use map provides a further synthesis of 

densities presented in Maps a, b and c, and portrays the 

relative importance of various areas to the species. Areas 

with consistently high use are highlighted on this map. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there), or present 

but at lesser concentrations in any particular season. See the 

"Methods" section below for further explanation of seasonal 

high-use areas. 

Because the sighting data for this species extends beyond 

the western extent of the standard map frame shown here, 

additional maps were made that include a greater western 

extent. These maps (with the word "pelagic" in the file name) 

are included on the CDROM.

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management 

Service. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS, 

2001), and California Department of Fish and Game, Office of 

Spill Prevention and Response (CDF&G-OSPR, unpublished 

data). Early data were collected using methods described by 

Briggs et al. (1983, 1987b); more recent data were collected 

using updated technology but using the same general method. 

Data sources for ship-based survey data include: David Ainley 

of H. T. Harvey and Associates and Carol Keiper of Oikonos 

(unpublished data; see Oedekoven et al., 2001 for details 

on survey methods); and Lisa T. Ballance, from the Ecology 

Program of the Southwest Fisheries Science Center, NMFS, 

NOAA (unpublished data). 

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of birds of each species seen in a cell was then divided by 

the area sampled in the cell to estimate density. If a cell was 

surveyed more than once, densities were averaged, with an 

adjustment made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’ x 10’ cells. For each season, the cells with 

densities in the top 20% of non-zero values were designated 

“high use” for that season. Cells were scored for “high use” 

in one, two, or three seasons and are depicted by color. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there) or present 

(but densities were never in the top 20% for any season).

Figure 44. Sooty shearwater, seasonal density and high use areas.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Sooty Shearwater Puffinus griseus

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

00

0 

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

This species does not

c d breed within the study area.

Source Data: See text.

55
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

RESULTS AND DISCUSSION

Sooty shearwaters nest in the sub-Antarctic, particularly on 

island of Tierra del Fuego and New Zealand, and winters in 

the Peru and California current regions. During the Upwelling 

Season, the sooty shearwater is the most abundant marine 

bird off California, and this is the case, by far, for waters within 

the boundaries of the north/central California national marine 

sanctuaries. Surveys tallied 20,750 sightings of 323,176 

individuals, indicating that the species usually occurs in large 

concentrations. 

A multiple regression analysis of nine independent variables 

explained 43.3% of the variation in cell density, with season, 

an inverse relationship to year, and ENSO period (periods of 

unusually warm or cold sea temperatures) being the most 

important variables; see Table 19. These results further reflect 

the restriction of this species’ occurrence off California largely to 

the Upwelling Season, and to greater abundance when ocean 

climate is unaffected by short-term climate anomaly. In other 

words, sooty shearwaters were less abundant in the study area 

during El Niño and La Niña. From a decadal perspective they 

declined over the years, although this effect was curvilinear: 

a slight increase between 1985 and 1991, a steep decline to 

1998, and a moderate increase subsequently. Whether or not 

the latter increase is a response to the shift to a cold ocean 

regime in 1999 remains to be seen. The continental shelf and 

upper slope are the main habitats frequented by this species 

(mean ocean depth where sooty shearwaters occurred was 

380 ± 10m). 

The sooty shearwater was present in greatest densities in 

Monterey Bay. Throughout the California current (Veit et al, 

1997), this species has declined severely in abundance during 

the recent warm regime (1976-1999), as noted above. Even 

now, though, it is still very abundant in Monterey Bay, probably 

because of the large anchovy source there. Other important 

areas (but not comparable to Monterey Bay), include Pioneer 

and Ascension canyons, Farallon Escarpment and Fanny 

Shoal, as well as the ocean area off Pacifica and Estero/San 

Luis Obispo bays. National marine sanctuary waters become 

even more important to this species during the Oceanic Season, 

as remnants of the population, just before their long southward 

migration, fatten on the oil-rich anchovies. 

Sooty shearwaters feed on fish, squid, and invertebrates that 

they acquire by pursuit, plunging to a depth of 10-15 m. During 

the early Upwelling Season the main prey are euphausiids and 

squid, a diet that shifts more to oily fish, such as anchovy, in 

the late Upwelling Season. See Tables 15 and 16 for related 

summary information.

56
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

32

ABOUT THESE MAPS 

Figures 45a, b, and c show the density (birds/km2) of ashy 

storm-petrel in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in five minute latitude by five minute 

longitude cells. Densities are based on the combined data 

sets of several studies (see “Methods” and “Data Sources” 

below). The color and mapping intervals were customized 

to show the most structure and to highlight significant areas, 

while allowing comparisons among marine bird species. Cells 

that were surveyed but in which no ashy storm-petrels were 

observed have a density of zero. Areas not surveyed appear 

white; no information is available for these areas. Blue lines 

indicate the boundaries of the National Marine Sanctuaries 

in the study area: Cordell Bank, Gulf of the Farallones, and 

Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, 

displayed in 10 minute latitude by 10 minute longitude cells, 

and breeding colonies. The seasonal high use map provides 

a further synthesis of densities presented in Maps a, b and c, 

and portrays the relative importance of various areas to the 

species. Areas with consistently high use are highlighted on this 

map. To provide a relative reference for the “high use” areas, 

cells are also shown where the species were absent (i.e., the 

cell was sampled but the species was not recorded there), or 

present but at lesser concentrations in any particular season. 

See the "Methods" section below for further explanation of 

seasonal high-use areas. Breeding colonies are also shown; 

the relative size of the symbols indicates the colony size.

Because the sighting data for this species extends beyond 

the western extent of the standard map frame shown here, 

additional maps were made that include a greater western 

extent. These maps (with the word "pelagic" in the filename) 

are included on the CDROM.

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management 

Service. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS, 

2001), California Department of Fish and Game, Office of Spill 

Prevention and Response (CDF&G-OSPR, unpublished data). 

Early data were collected using methods described by Briggs 

et al. (1983, 1987b); more recent data were collected using 

updated technology but using the same general method. Data 

sources for ship-based survey data include: David Ainley of 

H. T. Harvey and Associates and Carol Keiper of Oikonos 

(unpublished data; see Oedekoven et al., 2001 for details 

on survey methods); and Lisa T. Ballance, from the Ecology 

Program of the Southwest Fisheries Science Center, NMFS, 

NOAA (unpublished data). Data on ashy storm-petrel colonies 

were obtained from Carter et al. (1992) supplemented by 

Sydeman et al. (1998), Whitworth et al. (2002). 

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991 and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of birds of each species seen in a cell was then divided by 

the area sampled in the cell to estimate density. If a cell was 

surveyed more than once, densities were averaged, with an 

adjustment made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’x10’ cells. For each season, the cells with 

densities in the top 20% of non-zero values were designated 

“high use” for that season. Cells were scored for “high use” 

in one, two, or three seasons and are depicted by color. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there) or present 

Figure 45. Ashy storm-petrel, seasonal density, high use areas, and breeding colonies. (but densities were never in the top 20% for any season).

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Ashy Storm-Petrel Oceanodroma homochroa

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

00

0 

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

Colony Size

10,000 - 50,000

5001 - 10,000

1001 - 5000

501 - 1000

101 - 500

51 - 100

2 - 50

(Breeding birds)

Historical

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

c d

Source Data: See text.

57
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

RESULTS AND DISCUSSION

Ashy storm-petrel is endemic to the California Current and is 

considered by the State to be a “Species of Special Concern”; 

a major colony is at the Farallon Islands. It is common in the 

study area and the most abundant storm-petrel in waters of 

the central California national marine sanctuaries. Surveys 

recorded 1,472 sightings of 4,339 individuals.

A multiple regression model of nine variables explained 17.3% 

of variation in cell density, with important explanatory variables 

being ENSO period (i.e., periods of unusually warm or cold ocean 

temperature), season, and year; see Table 19. The species was 

more abundant during the Oceanic Season and during years of 

La Niña, indicating that when ocean temperatures were cold, 

Ashy storm-petrels were concentrated closer to the Farallon 

breeding colony, which they visit only at night. During nesting 

(Upwelling Season), this species occupies waters mainly over 

the outer slope (mean depth of occurrence 1,615 ± 52 m), 

mostly outside of National Marine Sanctuary boundaries. During 

the period of molt (Oceanic Season), ashy storm-petrels move 

inshore to frequent shallower slope waters (mean depth of 

occurrence 1,144 ± 61 m) and a large concentration occurred 

over the Monterey Bay canyon as shown in maps on upwelling 

and seasonal high use areas. 

In recent years, however, this post-breeding concentration 

has shifted to the area around Cordell Bank (not shown on 

the maps). As the species begins its seasonal return to the 

Farallon nesting colony (Davidson Current Season), they again 

shift north to deeper waters of the outer slope (mean depth 

of occurrence then was 2,579 ± 121 m). The species seems 

to be most dispersed during the Davidson Current Season, 

but in all seasons the Farallon Escarpment is by far its most 

important area. 

Overall, ashy storm-petrel numbers increased from 1985 to 

2002 in a curvilinear fashion: steeper increase in numbers 

between 1985 and 1992, followed by a less steep increase 

to 2002.

This species feeds on invertebrates and larval fish found 

at the surface. See Tables 15 and 16 for related summary 

information. 

58
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 46a, b, and c show the density (birds/km2) of Leach’s 

storm-petrel in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in five minute latitude by five minute 

longitude cells. Densities are based on the combined data 

sets of several studies (see “Methods” and “Data Sources” 

below). The color and mapping intervals were customized to 

show the most structure and to highlight significant areas, while 

allowing comparisons among marine bird species. Cells that 

were surveyed but in which no Leach’s storm-petrels were 

observed have a density of zero. Areas not surveyed appear 

white; no information is available for these areas. Blue lines 

indicate the boundaries of the National Marine Sanctuaries 

in the study area: Cordell Bank, Gulf of the Farallones, and 

Monterey Bay. An additional set of maps was done for this 

species to show the offshore extent of its distribution; these 

maps are included on the CD-ROM.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, 

displayed in 10 minute latitude by 10 minute longitude cells, 

and breeding colonies. The seasonal high use map provides a 

further synthesis of densities presented in Maps a, b and c, and 

portrays the relative importance of various areas to the species. 

Areas with consistently high use are highlighted on this map. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there), or present 

but at lesser concentrations in any particular season. See the 

"Methods" section below for further explanation of seasonal 

high-use areas. Breeding colonies are also shown; the relative 

size of the symbols indicates the colony size. An additional set 

of maps was developed for this species to include the offshore 

extent of its distribution. These maps are on the CD-ROM.

Because the sighting data for this species extends beyond 

the western extent of the standard map frame shown here, 

additional maps were made that include a greater western 

extent. These maps (with the word "pelagic" in the filename) 

are included on the CDROM.

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management 

Service. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS, 

2001), California Department of Fish and Game, Office of Spill 

Prevention and Response (CDF&G-OSPR, unpublished data). 

Early data were collected using methods described by Briggs 

et al. (1983, 1987b); more recent data were collected using 

updated technology but using the same general method. 

Data sources for ship-based survey data include: David 

Ainley of H. T. Harvey and Associates and Carol Keiper of 

Oikonos (unpublished data; see Oedekoven et al., 2001 for 

details on survey methods); and Lisa T. Ballance, from the 

Ecology Program of the Southwest Fisheries Science Center, 

NMFS, NOAA (unpublished data). Data on Leach’s stormpetrel colonies were obtained from Carter et al. (1992, and 

supplements).

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of birds of each species seen in a cell was then divided by 

the area sampled in the cell to estimate density. If a cell was 

surveyed more than once, densities were averaged, with an 

adjustment made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’x10’ cells. For each season, the cells with 

densities in the top 20% of non-zero values were designated 

“high use” for that season. Cells were scored for “high use” 

in one, two, or three seasons and are depicted by color. To 

provide a relative reference for the “high use” areas, cells are Figure 46. Leach’s storm-petrel, seasonal density, high use areas, and breeding colonies.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Leach's Storm-Petrel Oceanodroma leucorhoa

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

00

0 

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

Colony Size

10,000 - 50,000

5001 - 10,000

1001 - 5000

501 - 1000

101 - 500

51 - 100

2 - 50

(Breeding birds)

Historical

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

c d

Source Data: See text.

59
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there) or present 

(but densities were never in the top 20% for any season).

RESULTS AND DISCUSSION 

The Leach’s storm-petrel, which has a breeding population 

numbering in the millions in Alaska, is represented south to 

Baja California by smaller colonies as latitude decreases. In 

comparison, the estimated 12,551 birds breeding along the 

California coast is miniscule (Carter et al, 1992). This, and 

the fact that this species is highly migratory, suggests that 

many of the birds seen in the study areas are migrants from 

the north. This was also indicated by the lack of importance in 

a multiple regression model of distance to colony as a factor 

explaining this species’ variation in cell density; see Table 19. 

Surveys recorded 1,118 sightings of 1,576 individuals, although 

survey effort was sparse in the offshore waters this species 

frequents.

This common species frequents waters much farther offshore 

than the other storm-petrels, i.e. well beyond the continental 

slope. Thus, the National Marine Sanctuary boundaries (and 

most of the data sets in this study) do not encompass much of 

this species’ preferred habitat. The species was most abundant 

during the Upwelling Season (breeding) and occurred in greater 

numbers closer to the coast. They visit the Farallon colony only 

at night, but are at-sea during the day. During the Oceanic 

and Davidson Current seasons few occurred near the shelf. 

The birds present during the latter two seasons likely were 

migrants from more northern populations. Given the huge North 

Pacific population, the number recorded during surveys in the 

study area was relatively small, because they were mostly far 

offshore and not observed as often in the surveys available 

for this assessment.

Yet, a multiple regression model of nine independent variables 

explained 28.4% of variation in cell density, indicating that this 

species responded consistently to the variables examined. 

Most important of the nine variables were season, distance to 

the 2000 m isobath, and ENSO period (periods of unusually 

warm or cold ocean temperature); see Table 19. Abundance 

of this species in the study area has increased between 1985 

and 2002, and it was more abundant during periods of warmwater conditions.

This species feeds on invertebrates captured at the surface. 

See Tables 15 and 16 for related summary information.

60
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 47a, b, and c show the combined density (birds/km2) 

of three scoter species (white-winged, surf, and black) in the 

Upwelling, Oceanic, and Davidson Current seasons, displayed 

in five minute latitude by five minute longitude cells. Densities 

are based on the combined data sets of several studies (see 

“Methods” and “Data Sources” below). The color and mapping 

intervals were customized to show the most structure and to 

highlight significant areas, while allowing comparisons among 

marine bird species. Cells that were surveyed but in which 

no scoters were observed have a density of zero. Areas not 

surveyed appear white; no information is available for these 

areas. Blue lines indicate the boundaries of the National Marine 

Sanctuaries in the study area: Cordell Bank, Gulf of the Farallones, and Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, displayed in 10 minute latitude by 10 minute longitude cells. The 

seasonal high use map provides a further synthesis of densities 

presented in Maps a, b and c, and portrays the relative importance of various areas to the species. Areas with consistently 

high use are highlighted on this map. To provide a relative reference for the “high use” areas, cells are also shown where the 

species were absent (i.e., the cell was sampled but the species 

was not recorded there), or present but at lesser concentrations 

in any particular season. See the "Methods" section below for 

further explanation of seasonal high-use areas. 

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management Service. Of the data sets on the original MMS-CDAS CDROM, four aerial survey data sets contained data in the study 

area from Point Arena to Point Sal.. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS, 

2001), California Department of Fish and Game, Office of Spill 

Prevention and (CDF&G-OSPR, unpublished data). Early data 

were collected using methods described by Briggs et al. (1983, 

1987b); more recent data were collected using updated technology but using the same general method. Data sources for 

ship-based survey data include: David Ainley of H. T. Harvey 

and Associates and Carol Keiper of Oikonos (unpublished data; 

see Oedekoven et al., 2001 for details on survey methods); and 

Lisa T. Ballance, from the Ecology Program of the Southwest 

Fisheries Science Center, NMFS, NOAA (unpublished data). 

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above water) were used to estimate the area sampled. The number of 

birds of each species seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was surveyed 

more than once, densities were averaged, with an adjustment 

made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’x10’ cells. For each season, the cells with densities in the top 20% of non-zero values were designated “high 

use” for that season. Cells were scored for “high use” in one, 

two, or three seasons and are depicted by color. To provide a 

relative reference for the “high use” areas, cells are also shown 

where the species were absent (i.e., the cell was sampled but 

the species was not recorded there) or present (but densities 

were never in the top 20% for any season).

RESULTS AND DISCUSSION 

The distribution of white-winged, surf, and black scoters in 

the north/central California study area is very similar to that 

of the grebes (see above), although they are somewhat less 

abundant and found closer to shore. There they forage mostly 

just outside the surf break. On the outer coast, the abundant 

surf scoter dominates over the other two scoters, and black 

scoters, which occur in more protected waters, are rare. Surveys recorded 1,787 sightings of scoters that included 42,691 

individuals; more than half were identified as surf scoter. The 

most important areas for surf scoters within the study area is Figure 47. Black, surf and white-winged scoters, seasonal density and high use areas.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Black, Surf and White-winged Scoters Melanitta nigra, M. perspicillata, M. fusca

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

00

0 

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

These species do not

c d breed within the study area.

Source Data: See text.

61
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

the San Francisco Bay tidal plume, especially southward along 

the Pacifica shore to Half Moon Bay, and the shallow parts of 

Bodega, Monterey, Estero, and San Luis Obispo bays. These 

birds nest in the arctic tundra along the north slope of North 

America; specific nesting areas of birds found wintering in the 

marine sanctuary boundaries have not been identified.

The apparent movement of these sea ducks’ offshore, i.e. to 

the outer parts of the Gulf of the Farallones, in the Upwelling 

Season is an artifact of their migration north or south, to or from 

Alaskan breeding areas. That portion of the population wintering 

south of central California takes the shortest distance across 

the Gulf of the Farallones; the offshore density cells highlighted 

in the maps is a record of flying scoters. 

These scoters do not forage far from the mainland beach, where 

they eat invertebrates; several dozen usually winter around the 

Farallon Islands. The inshore distribution of these ducks, like 

the grebes, makes them vulnerable to coastal oil spills. See 

Tables 15 and 16 for related summary information.

62
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 48a, b, and c show the density (birds/km2) of brown 

pelicans in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in five minute latitude by five minute 

longitude cells. Densities are based on the combined data 

sets of several studies (see “Methods” and “Data Sources” 

below). The color and mapping intervals were customized to 

show the most structure and to highlight significant areas, while 

allowing comparisons among marine bird species. Cells that 

were surveyed but in which no brown pelicans were observed 

have a density of zero; areas not surveyed are white. Blue lines 

indicate the boundaries of the National Marine Sanctuaries 

in the study area: Cordell Bank, Gulf of the Farallones, and 

Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, 

displayed in 10 minute latitude by 10 minute longitude cells, 

and breeding colonies (in this species’ case, a site where it 

bred in the past). The seasonal high use map provides a 

further synthesis of densities presented in Maps a, b and c, 

and portrays the relative importance of various areas to the 

species. Areas with consistently high use are highlighted on this 

map. To provide a relative reference for the “high use” areas, 

cells are also shown where the species were absent (i.e., the 

cell was sampled but the species was not recorded there), or 

present but at lesser concentrations in any particular season. 

See the "Methods" section below for further explanation of 

seasonal high-use areas. Breeding colonies are also shown; 

the relative size of the symbols indicates the colony size.

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management 

Service. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS, 

2001), and California Department of Fish and Game, Office of 

Spill Prevention and Response (CDF&G-OSPR, unpublished 

data). Early data were collected using methods described by 

Briggs et al. (1983, 1987b); more recent data were collected 

using updated technology but using the same general method. 

Data sources for ship-based survey data include: David Ainley 

of H. T. Harvey and Associates and Carol Keiper of Oikonos 

(unpublished data; see Oedekoven et al., 2001 for details 

on survey methods); and Lisa T. Ballance, from the Ecology 

Program of the Southwest Fisheries Science Center, NMFS, 

NOAA (unpublished data). Data on brown pelican colonies were 

obtained from Carter et al. (1992, and supplements).

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991 and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of birds of each species seen in a cell was then divided by 

the area sampled in the cell to estimate density. If a cell was 

surveyed more than once, densities were averaged, with an 

adjustment made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’x10’ cells. For each season, the cells with 

densities in the top 20% of non-zero values were designated 

“high use” for that season. Cells were scored for “high use” 

in one, two, or three seasons and are depicted by color. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there) or present 

(but densities were never in the top 20% for any season).

RESULTS AND DISCUSSION 

Brown pelicans are included in the State and Federal 

endangered species lists, and are common year-round in 

Monterey Bay and to the south. Surveys recorded 1,447 

sightings of 3,003 individuals. 

Figure 48. Brown pelican, seasonal density and high use areas.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W 124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

Brown Pelican Pelecanus occidentalis

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

0

0

0

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50 Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

Seasonal High Use Areas and

m

m

(Nov. 15 - Mar. 14) m

Breeding Colonies

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

This species does not

c d breed within the study area.

°N53 °N63 °N73 °N83 °N93 °N53 °N63 °N73 °N83 °N93

Source Data: See text.

63
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

This population breeds on selected islands off Baja Mexico 

and southern California, with small colonies extending north 

to the Channel Islands. Brown pelicans once bred on rocks off 

Monterey, but are now concentrated in the central California 

study area at roosts such as Morro Rock, Monterey Breakwater, 

Año Nuevo Island, Southeast Farallon Island, Bird Rock in 

Monterey county, and Bodega Rock. Nesting occurs in southern 

California and Baja Mexico and begins in November and can 

extend through June, when the species is most sparse in 

the central California study area. The brown pelican is most 

abundant in the study area during the Oceanic Season; the 

species’ presence then constitutes a post-breeding increase 

from southern breeding grounds. 

North of Monterey and Estero/San Luis Obispo bays, this 

species’ presence is much more seasonal and dependent on 

ocean climate. Most sightings in the Gulf of the Farallones 

during the Davidson Current and Upwelling seasons occurred 

during warm-water years, often associated with the species 

choosing to forego breeding at southern colonies. Thus, 

wintering birds may remain in central California waters, while 

others may move farther north than usual at that time. In most 

cool-or coldwater years, adults are not abundant north of 

Monterey Bay during these two seasons. This could change, 

however, as sardines, an important prey item, continue to 

increase in California waters. 

The species frequents waters within several miles of shore 

(mean distance to land was 10.3 ± 0.4 km) and rarely occurs 

in waters deeper than the shelf break (mean depth was 

266 ± 21 m). Consistent with these patterns are results of 

a multiple regression model of nine independent variables, 

which explained 15.2% of the variation; important variables 

were season, and inverse relationships to distance to land and 

latitude; see Table 19. Therefore, the broad shelf of central 

California is well suited to this species; its occurrence becomes 

sporadic north of Point Reyes. Inshore Monterey, Estero, and 

San Luis Obispo bays are especially important, where this 

species is common year round; the San Francisco Bay tidal 

plume is also important. Abundance of this species in the study 

area has increased between 1985 and 2002. 

This species preys exclusively on fish, especially anchovies, 

mackerel, and sardines, that it catches by plunging to just 

below the surface. See Tables 15 and 16 for related summary 

information.

64
Section 2.3: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 49a, b, and c show the density (birds/km2) of blacklegged kittiwakes in the Upwelling, Oceanic, and Davidson 

Current seasons, displayed in five minute latitude by five minute 

longitude cells. Densities are based on the combined data sets 

of several studies (see “Methods” and “Data Sources” below). 

The color and mapping intervals were customized to show 

the most structure and to highlight significant areas, while 

allowing comparisons among marine bird species. Cells that 

were surveyed but in which no black-legged kittiwakes were 

observed have a density of zero. Areas not surveyed appear 

white; no information is available for these areas. Blue lines 

indicate the boundaries of the National Marine Sanctuaries 

in the study area: Cordell Bank, Gulf of the Farallones, and 

Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, displayed in 10 minute latitude by 10 minute longitude cells. The 

seasonal high use map provides a further synthesis of densities 

presented in Maps a, b and c, and portrays the relative importance of various areas to the species. Areas with consistently 

high use are highlighted on this map. To provide a relative reference for the “high use” areas, cells are also shown where the 

species were absent (i.e., the cell was sampled but the species 

was not recorded there), or present but at lesser concentrations 

in any particular season. See the "Methods" section below for 

further explanation of seasonal high-use areas. 

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management Service. Of the data sets on the original MMS-CDAS CDROM, four aerial survey data sets contained data in the study 

area from Point Arena to Point Sal. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS, 

2001), and California Department of Fish and Game, Office of 

Spill Prevention and Response (CDF&G-OSPR, unpublished 

data). Early data were collected using methods described by 

Briggs et al. (1983, 1987b); more recent data were collected 

using updated technology but using the same general method. 

Data sources for ship-based survey data include: David Ainley 

of H. T. Harvey and Associates and Carol Keiper of Oikonos 

(unpublished data; see Oedekoven et al., 2001 for details 

on survey methods); and Lisa T. Ballance, from the Ecology 

Program of the Southwest Fisheries Science Center, NMFS, 

NOAA (unpublished data). 

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above water) were used to estimate the area sampled. The number of 

birds of each species seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was surveyed 

more than once, densities were averaged, with an adjustment 

made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’x10’ cells. For each season, the cells with densities in the top 20% of non-zero values were designated “high 

use” for that season. Cells were scored for “high use” in one, 

two, or three seasons and are depicted by color. To provide a 

relative reference for the “high use” areas, cells are also shown 

where the species were absent (i.e., the cell was sampled but 

the species was not recorded there) or present (but densities 

were never in the top 20% for any season).

RESULTS AND DISCUSSION 

The black-legged kittiwake, like the northern fulmar, breeds on 

islands along the northern coast of North America and Asia, but 

large numbers ‘winter’ in the study area off central California. It 

is a common species in the study area; surveys recorded 2,079 

sightings of 5,003 individuals. A multiple-regression model of 

eight independent variables explained 28.9% of variation in 

cell density; important variables were season, ENSO period 

(i.e., periods of climatic variation), and year (increasing abundance). The black-legged kittiwake was most abundant in the Figure 49. Black-legged kittiwake, seasonal density and high use areas.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Black-legged Kittiwake Rissa tridactyla

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

0

0

0

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50 Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

This species does not

c d breed within the study area.

Source Data: See text.

65
Section 2.3: BIOGEOGRAPHY OF MARINE BIRDS

study area during the Davidson Current Season and less so 

during the early Upwelling Season; it was largely absent during 

the late-Upwelling Season and Oceanic Season (which corresponds to the breeding season at northern-latitude nesting 

sites). Abundance was highest during periods of La Niña. Most 

kittiwakes occurred in waters overlying the continental slope, 

and deeper waters seaward of National Marine Sanctuary 

boundaries (mean depth of occurrence was 1,408 m; mean 

distance from shore was 29.0 km). A minority of kittiwakes occurred over the shelf, mainly where the shelf is narrow. There 

was an “invasion” of kittiwakes in 1999, coincident with the 

beginning of the cold-water regime shift (see below). 

This species feeds on fish and pelagic invertebrates that they 

catch by dipping and plunging to the surface. No studies of 

kittiwake diet at sea were available. See Tables 15 and 16 for 

related summary information.

66
Section 2.3: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 50a, b, and c show the density (birds/km2) of common 

murre in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in five minute latitude by five minute 

longitude cells. Densities are based on the combined data 

sets of several studies (see “Methods” and “Data Sources” 

below). The color and mapping intervals were customized to 

show the most structure and to highlight significant areas, 

while allowing comparisons among marine bird species. Cells 

that were surveyed but in which no common murres were 

observed have a density of zero. Areas not surveyed appear 

white; no information is available for these areas. Blue lines 

indicate the boundaries of the National Marine Sanctuaries 

in the study area: Cordell Bank, Gulf of the Farallones, and 

Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, 

displayed in 10 minute latitude by 10 minute longitude cells, 

and breeding colonies. The seasonal high use map provides a 

further synthesis of densities presented in Maps a, b and c, and 

portrays the relative importance of various areas to the species. 

Areas with consistently high use are highlighted on this map. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there), or present 

but at lesser concentrations in any particular season. See the 

"Methods" section below for further explanation of seasonal 

high-use areas. Breeding colonies are also shown; the relative 

size of the symbols indicates the colony size.

DATA SOURCES

Densities for marine birds at sea are based on data from 

eight survey programs conducted between 1980 and 2001, 

which were combined into a new MMS-CDAS data set (MMS, 

2001) using software (CDAS) developed for the Minerals 

Management Service. Of the data sets on the original MMSCDAS CD-ROM, four aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program is ongoing and data from recent years 

were added to this data set. In addition, data from four shipbased survey programs were converted to a compatible format 

for analysis (see section overview for details on individual 

data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS, 

2001), and California Department of Fish and Game, Office of 

Spill Prevention and Response (CDF&G-OSPR, unpublished 

data). Early data were collected using methods described by 

Briggs et al. (1983, 1987b); more recent data were collected 

using updated technology but using the same general method. 

Data sources for ship-based survey data include: David Ainley 

of H. T. Harvey and Associates and Carol Keiper of Oikonos 

(unpublished data; see Oedekoven et al., 2001 for details 

on survey methods); and Lisa T. Ballance, from the Ecology 

Program of the Southwest Fisheries Science Center, NMFS, 

NOAA (unpublished data). Data on common murre colonies 

were obtained from Carter et al. (1992), with updates for Devil’s 

Slide (Gerry McChesney, USFWS, pers. comm) and South 

Farallon Island (Warzybok et al. 2002).

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of birds of each species seen in a cell was then divided by 

the area sampled in the cell to estimate density. If a cell was 

surveyed more than once, densities were averaged, with an 

adjustment made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’x10’ cells. For each season, the cells with 

densities in the top 20% of non-zero values were designated 

“high use” for that season. Cells were scored for “high use” 

in one, two, or three seasons and are depicted by color. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there) or present 

(but densities were never in the top 20% for any season).

RESULTS AND DISCUSSION

The common murre is very abundant in the study area, being 

the second most numerous marine bird in Central California. 

There have been 21,893 sightings of 141,964 individuals, Figure 50. Common murre, seasonal density and high use areas and breeding colonies.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Common Murre Uria aalge

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

00

0 

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

Colony Size

50,001 - 104,000

10,001 - 50,000

5001 - 10,000

1001 - 5000

501 - 1000

101 - 500

50 - 100

(Breeding birds)

Historical

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

c d

Source Data: See text.

67
Section 2.3: BIOGEOGRAPHY OF MARINE BIRDS

with the ratio between these numbers indicating that murres 

usually occur in flocks. The species nests at a complex of 

related and densely occupied colonies including the Farallon 

Islands, Point Reyes, Double Point (including Point Resistance 

and Millers Point Rocks), and a small colony at Devils Slide. 

This complex constitutes one of the largest, if not the largest, 

breeding population of this species south of Alaska. Two small, 

disjunct breeding colonies, the southernmost for this species, 

occur off the Big Sur coast.

Based on analysis of the data, common murres reside in the 

study area year-round, being particularly abundant in waters 

overlying the shelf and upper slope (mean depth of 110 ± 5 

m), with little seasonal change in distribution. Murre densities, 

however, were, in general, significantly higher during the 

Upwelling Season, probably because the entire population is 

present at that time. During the other seasons, some breeding 

individuals disperse outside of the study area. A multiple 

regression model of nine independent variables explained 

52.3% of variation in density; especially through inverse 

relationships with distance to colony, ocean depth, and distance 

to land; see Table 19. No significant trend in common murre 

abundance existed between 1985 and 2002, and abundance 

was not affected by short-term climate fluctuations (e.g., periods 

of unusually warm or cold sea temperatures). 

Near the large Farallon Islands colony during nesting, many 

murres range seaward beyond the continental slope (and 

outside sanctuary boundaries), perhaps as a response to 

increased intraspecific competition for prey at that time. As 

a result, the Farallon Escarpment became an area of high 

concentration as well as the Farallon Ridge and shelf waters 

inshore of it. Murres occur in Monterey Bay after nesting and 

mainly during the Oceanic Season. During years of unusually 

warm waters (and depleted prey), murres occur more frequently 

inshore, especially along the coast from Point Reyes south to 

Año Nuevo Island, the usual area of concentration during the 

relatively warm Oceanic Season.

This species is a deep diver (to 180m depth, Ainley et al, 

2002) that feeds on fish and invertebrates. During winter and 

early spring, major prey include herring, market squid and 

euphausiids; this diet then shifts mostly to juvenile rockfish 

and anchovies in mid-summer. See Tables 15 and 16 for related 

summary information. 

68
Section 2.3: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 51a, b, and c show the density (birds/km2) of 

Rhinoceros Auklet in the Upwelling, Oceanic, and Davidson 

Current seasons, displayed in five minute latitude by five minute 

longitude cells. Densities are based on the combined data 

sets of several studies (see “Methods” and “Data Sources” 

below). The color and mapping intervals were customized 

to show the most structure and to highlight significant areas, 

while allowing comparisons among marine bird species. Cells 

that were surveyed but in which no Rhinoceros Auklets were 

observed have a density of zero. Areas not surveyed appear 

white; no information is available for these areas. Blue lines 

indicate the boundaries of the National Marine Sanctuaries 

in the study area: Cordell Bank, Gulf of the Farallones, and 

Monterey Bay.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence and abundance 

in the study area, map d shows seasonal high-use areas, 

displayed in 10 minute latitude by 10 minute longitude cells, 

and breeding colonies. The seasonal high use map provides 

a further synthesis of densities presented in Maps a, b and c, 

and portrays the relative importance of various areas to the 

species. Areas with consistently high use are highlighted on this 

map. To provide a relative reference for the “high use” areas, 

cells are also shown where the species were absent (i.e., the 

cell was sampled but the species was not recorded there), or 

present but at lesser concentrations in any particular season. 

See the "Methods" section below for further explanation of 

seasonal high-use areas. Breeding colonies are also shown; 

the relative size of the symbols indicates the colony size.

DATA SOURCES

Densities for marine birds at sea are based on data from eight 

survey programs conducted between 1980 and 2001, which 

were combined into a new MMS-CDAS data set (MMS, 2001) 

using software (CDAS) developed for the Minerals Management 

Service. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, the OSPR survey 

program is ongoing and data from recent years were added 

to this data set. In addition, data from four ship-based survey 

programs were converted to a compatible format for analysis 

(see section overview for details on individual data sets). 

Data sources for aerial, at-sea data include MMS-CDAS (MMS, 

2001), and California Department of Fish and Game, Office of 

Spill Prevention and Response (CDF&G-OSPR, unpublished 

data). Early data were collected using methods described by 

Briggs et al. (1983, 1987b); more recent data were collected 

using updated technology but using the same general method. 

Data sources for ship-based survey data include: David Ainley 

of H. T. Harvey and Associates and Carol Keiper of Oikonos 

(unpublished data; see Oedekoven et al., 2001 for details 

on survey methods); and Lisa T. Ballance, from the Ecology 

Program of the Southwest Fisheries Science Center, NMFS, 

NOAA (unpublished data). Data on breeding colonies in the 

study area were obtained from Carter et al. (1992), with most 

recent estimates for Año Nuevo from Thayer and Sydeman 

(2002).

Although the at-sea data span the years from 1980 to 2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” below). Bird 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of birds of each species seen in a cell was then divided by 

the area sampled in the cell to estimate density. If a cell was 

surveyed more than once, densities were averaged, with an 

adjustment made for effort.

The seasonal high-use areas on map d were developed using 

a similar approach as for Maps a, b and c, but the data were 

binned into 10’x10’ cells. For each season, the cells with 

densities in the top 20% of non-zero values were designated 

“high use” for that season. Cells were scored for “high use” 

in one, two, or three seasons and are depicted by color. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there) or present 

(but densities were never in the top 20% for any season).

RESULTS AND DISCUSSION 

In the study area, this common species nests principally at 

the Farallon Islands; a smaller nesting population occurs at 

Año Nuevo. The Farallones constitute the southernmost large 

nesting colony. At-sea surveys recorded 5,415 sightings of Figure 51. Rhinoceros auklet, seasonal density and high use areas and breeding colonies.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Rhinoceros Auklet Cerorhinca monocerata

Upwelling Season

(Mar. 15 - Aug. 14)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

20

0

2

0

0

00

0 

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas and

(Nov. 15 - Mar. 14) m

Breeding Colonies

Colony Size

10,000 - 50,000

5001 - 10,000

1001 - 5000

501 - 1000

101 - 500

51 - 100

2 - 50

(Breeding birds)

Historical

3 Seasons

2 Seasons

1 Season

Birds present

a b

Persistence of

High Use

Birds absent

c d

Source Data: See text.

69
Section 2.3: BIOGEOGRAPHY OF MARINE BIRDS

15,454 individuals. Based on the analysis of the combined data 

sets described in this section, the abundance of Rhinoceros 

Auklets has increased significantly since the 1970s (Ainley et 

al. 1994). Based on patterns apparent in the maps, the current 

at-sea population probably far exceeds the estimates of nesting 

populations in central California (Michelle Hester, pers.comm.). 

Therefore, if there was more nesting habitat (e.g., burrows, 

holes, crevices on offshore islands), the nesting population 

would probably be much larger.

Rhinoceros auklets, which mainly visit colonies at night, 

occurred principally in waters overlying the slope (mean depth 

of occurrence was 762 ± 22 m), particularly the shelf break, 

and, including the Farallon Escarpment. A sizeable portion of 

the population occurs outside of the National Marine Sanctuary 

boundaries. This is especially true in the vicinity of the Gulf 

of the Farallones during the Upwelling (nesting) and Oceanic 

seasons, when these auklets occur farther offshore (mean 

depths were 791 m and 1,370 m, respectively). This expansion 

of habitat, causing a ‘halo’ of increased density around the 

islands, may be a response to the large numbers nesting at the 

Farallones, a pattern typical of the Western Gull and Common 

Murre (see those accounts). The species’ concentration, 

especially along the shelf break and upper continental slope, 

is particularly evident during the Oceanic Season, when the 

nesting populations are no longer associated with colonies. 

A multiple-regression model of nine independent variables 

explained 19.8% of variation in cell density; important variables 

were a negative relationship to distance to land, and positive 

ones to season and ocean depth; see Table 19. The relationship 

with season reflected a dramatic increase in abundance during 

the Davidson Current Season (mean density of 161 birds per 

100km

2

) compared to the Upwelling and Oceanic seasons 

(mean densities of 48 and 62 birds per 100 km

2

, respectively). 

This increase during the Davidson Current Season was likely 

due to an influx of birds from the north where much larger 

populations breed, compared to those of the study area.

This species feeds by diving, probably to relatively deep depths 

(100 m, Ainley and Boekelheide, 1990), capturing mostly fish 

but also euphuasiids. Important prey are juvenile rockfish, 

anchovy and saury. See Tables 15 and 16 for related summary 

information.

70
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THESE MAPS 

Figures 52a, b, and c show the combined density (birds/km2) 

of 76 species of marine birds in the Upwelling, Oceanic, and 

Davidson Current seasons, displayed in five minute latitude by 

five minute longitude cells. Map d shows density for all seasons 

and years combined. Densities are based on combined data 

of several studies (see “Methods” and “Data Sources” above). 

The color and mapping intervals were customized to show the 

most structure and highlight significant areas. Cells that were 

surveyed but in which no birds were observed have a density 

of zero; unsurveyed areas are white. Blue lines indicate the 

National Marine Sanctuary boundaries of Cordell Bank, Gulf of 

the Farallones, and Monterey Bay; bathymetric contours for the 

200 meter and 2,000 meter isobaths are also shown in blue.

DATA SOURCES 

At-sea densities are based on data from eight survey programs 

conducted in 1980-2001, which were combined using software 

developed for MMS-CDAS (2001) and expanded for this 

project. Of the data sets on the original CD-ROM, four aerial 

survey data sets provided data in the study area from Point 

Arena to Point Sal. Of these, one program was still ongoing and 

data from recent years were added to this data set. In addition, 

data from four ship-based survey programs were converted to 

a compatible format for analysis. See section introduction for 

details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001), and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR, unpublished 

data). Early data were collected using methods described by 

Briggs et al. (1987b); more recent data were collected using 

updated technology but the same general method. Data 

sources for ship-based survey data include: David Ainley and 

Carol Keiper (unpublished data; see Oedekoven et al., 2001 

for details on survey methods). 

Although the at-sea data span the years 1980 to 2001, data 

are not available for all seasons in all years. For the Upwelling 

Season, data are from 1980-1982 and 1985-2001. For the 

Oceanic Season, data are from 1980-1982, 1991, and 1994-

2001. For the Davidson Current Season, data are from 1980-

1986 and 1991-2001. 

METHODS 

At-sea densities are the result of a synthesis of data from 

eight shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources” 

above). Observation and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells. The length and 

width of the survey trackline in a given cell (estimated trackline 

width varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of marine birds seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

RESULTS AND DISCUSSION

Overall density is dominated by two abundant marine bird 

species: common murre and sooty shearwater. 

Based on visual inspection of the maps, density was highest, 

during the Upwelling Season with cells of highest density 

most widespread as well. Except for a few highest-density 

‘hot spots,’(see Table 17) marine birds were distributed evenly 

at high density (>10 individuals per km2

) over the shelf and 

slope from north to south in the study area. Particular hot spots 

were inshore Monterey Bay, Farallon Ridge and Cordell Bank. 

The pattern during this season generally matched the pattern 

apparent when all seasons were combined. 

During the Oceanic Season, highest density areas increased 

in prevalence inshore. At that time, hot spots were the San 

Francisco Bay tidal plume, inshore near Año Nuevo, innermost 

Monterey Bay and San Luis Obispo Bay. 

During the Davidson Current Season, birds shifted more to 

the mid-shelf. 

Figure 52. Marine bird density, by season and for all seasons.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Marine Bird Density

Upwelling Season

(Mar. 15 - Aug. 14)

2

20

2

0

2

0

00

0

0

0

0

0

m

m

m

m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

a b

20

2

0

0

0

0

Davidson Current Season 2

2

0

0

00

0

m

m

m

m

All Seasons

(Nov. 15 - Mar. 14)

c d

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

Source Data: See text.

71
ABOUT THESE MAPS

Figure 53a, b, and c shows total marine bird biomass (kg/ 

km2) in each five minute latitude by five minute longitude cell 

for each oceanographic season and for all seasons combined 

53d. Density for each of 76 species was multiplied by average 

body mass for that species. These products were summed 

for all species in a cell. The color and mapping intervals were 

customized to show the most structure and highlight significant 

areas. Cells that were surveyed but in which no birds were 

observed have a biomass density of zero; unsurveyed areas 

are white. Blue lines indicate the National Marine Sanctuary 

boundaries of Cordell Bank, Gulf of the Farallones, and 

Monterey Bay; bathymetric contours for the 200 meter and 

2,000 meter isobaths are also shown in blue.

DATA SOURCES 

At-sea biomass densities are based on data from eight survey 

programs conducted in 1980-2001, which were combined using 

software developed for MMS-CDAS (2001) and expanded for 

this project. Of the data sets on the original CD-ROM, four aerial 

survey data sets provided data in the study area from Point 

Arena to Point Sal. Of these, one program was still ongoing and 

data from recent years were added to this data set. In addition, 

data from four ship-based survey programs were converted to 

a compatible format for analysis. See section introduction for 

details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Briggs et al. (1987b); more recent data were collected using 

updated technology but the same general method. Data 

sources for ship-based survey data include David Ainley and 

Carol Keiper (unpublished data; see Oedekoven et al., 2001 

for details on survey methods). Although the at-sea data span 

the years 1980-2001, data are not available for all seasons in 

all years. For the Upwelling Season, data are from 1980-1982 

and 1985-2001. For the Oceanic Season, data are from 1980-

1982, 1991 and 1994-2001. For the Davidson Current Season, 

data are from 1980-1986 and 1991-2001. 

Data on average biomass for each species were derived 

from Body Weights of 686 Species of North American Birds

(Dunning 1993). In a few instances, a species was not listed in 

this reference; in these cases, the biomass of a closely related 

bird of a similar size was used.

METHODS 

At-sea densities are the result of a synthesis of data from 

eight shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources” 

above). Observation and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells. The length and 

width of the survey trackline in a given cell (estimated trackline 

width varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of marine birds seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

Once the weighted densities had been determined for each 

species in each cell, densities of each species were multiplied 

by the average body mass of that species. These ‘biomass 

densities’ were then summed for each cell and the results 

plotted.

RESULTS AND DISCUSSION

In general, the biomass maps are dominated by two, relatively heavy-bodied, numerically dominant species: common murre and sooty shearwater. These maps are also 

influenced, to a lesser degree, by the species identified as 

abundant in the study area (see Table 15). 

Looking first at a summary of all seasons, high biomass densities occurred in the Gulf of the Farallones, especially around 

the Farallon Islands, the San Francisco Bay tidal plume, off 

Half-moon Bay, just south of Point Año Nuevo and in inner 

Monterey Bay.

During the Upwelling season, high biomass densities occurred 

over the shelf and upper slope with highest density areas occurring at Monterey Bay, Farallon Ridge, and Cordell Bank. 

The distribution of high biomass during the Upwelling Season 

mimicked that described in the all seasons map (map d).

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

During the Oceanic Season high biomass was concentrated 

more over the inner shelf than in the Upwelling Season, particularly evident from Point Reyes to Monterey, as well as San 

Luis Obispo Bay.

During the Davidson Current Season (DCS), virtually the entire 

continental shelf from Point Reyes to Point Sur exhibited high 

marine bird biomass. 

Figure 53. Marine bird biomass, by season and for all seasons.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Marine Bird Biomass

Upwelling Season

(Mar. 15 - Aug. 14)

> 100

51 - 100

21 - 50

11 - 20

6 - 10

4 - 5

3

2

1

0

2

2

0

2

2

0

0

0

00

0

0

0

0

m

m

m

m

Oceanic Season

(Aug. 15 - Nov. 14)

Biomass

(kg/km2)

0 25 50Km

a b

20

2

0

0

0

0

Davidson Current Season 2

2

0

0

00

0

 m

m

m

All Seasons

(Nov. 15 - Mar. 14) m

c d

Source Data: See text.

72
124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Marine Bird Species Diversity

Upwelling Season

(Mar. 15 - Aug. 14)

2.001 - 3.000

1.801 - 2.000

1.501 - 1.800

0.801 - 1.500

0.000 - 0.800

2

2

0

0

2

0

2

00

0

0

0

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Diversity

(H')

0 25 50Km

a b

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

All Seasons

(Nov. 15 - Mar. 14) m

c d

Source Data: See text.

ABOUT THESE MAPS

Species diversity was calculated for each five minute latitude 

by five minute longitude cell using density as the variable in the 

Shannon [Diversity] Index (Shannon and Weaver 1949). This 

index measures the degree to which a species assemblage is 

dominated by a few species. If a cell contains high densities 

of a few species and low densities of all others, the value of 

diversity (H’) will be low, indicating low diversity. Alternatively, 

if many species are present at similar densities, the value will 

be high, indicating high diversity. Figures 54a, b, and c show 

the diversity index H’ in three oceanographic seasons; map d 

shows diversity for all seasons and years combined. Although 

a density-based calculation of the Shannon Index is less 

influenced by differences in effort as compared with the index 

calculated using species counts, a significant correlation (p< 

0.001) remained between diversity and effort.

To standardize for variable effort among cells and variable 

strip width among species, density was used for each species 

in each cell as the basis for calculating the diversity index 

value. All 76 marine bird species that had been recorded in 

the data set were included. Cells are colored based on the 

value of H’ computed for a particular season. Red indicates 

high diversity, blue indicates low diversity. Unsurveyed areas 

are colored white. Blue lines indicate the National Marine 

Sanctuary boundaries of Cordell Bank, Gulf of the Farallones, 

and Monterey Bay; bathymetric contours for the 200 meter and 

2,000 meter isobaths are also shown in blue. 

DATA SOURCES 

At-sea densities are based on data from eight survey programs 

conducted in 1980-2001, which were combined using CDAS 

software into an MMS-CDAS data set (MMS, 2001) developed 

for Minerals Management Service and expanded for this project. 

Of the data sets on the original CD-ROM, four aerial survey 

data sets provided data in the study area from Point Arena to 

Point Sal. Of these, one program was still ongoing and data 

from recent years were added to this data set. In addition, 

data from four ship-based survey programs were converted to 

a compatible format for analysis. See section introduction for 

details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (2001) 

and California Department of Fish and Game Office of Spill 

Prevention and Response (CDF&G-OSPR), unpublished data. 

Early data were collected using methods described by Briggs 

et al. (1987b); more recent data were collected using updated 

technology but the same general method. Data sources for 

ship-based survey data include David Ainley and Caol Keiper 

(unpublished data; see Oedekoven et al., 2001 for details on 

methods). Although the at-sea data span the years 1980-2001, 

data are not available for all seasons in all years. For the 

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991 and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS 

At-sea densities are the result of a synthesis of data from 

eight shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources” 

above). Observation and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells. The length and 

width of the survey trackline in a given cell (estimated trackline 

width varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of marine birds seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

The Shannon Index (Shannon and Weaver 1949) was used to 

quantify species diversity. For each cell, diversity was calculated 

using the formula 

where ni is the density of species in that cell. Density was 

used for calculating the index value in order to compensate for 

variable effort among cells and species. We looked at three 

oceanographic seasons and at all seasons combined. 

The Shannon Index was selected as the diversity metric 

because it is widely used and accepted in community ecology. 

It has three desirable properties for a diversity index, noted 

below. Most diversity indices do not take these three qualities 

into account. For more information on diversity indices, see 

Ecological Diversity, E.C. Pielou, pp 7-18.

1. The diversity index is greatest when all species in the 

community are equally represented in numbers (e.g., evenness 

in a community). Or, for a given number of species (e.g., 

richness value), the diversity index should have it’s greatest 

value when the proportion of each species is the same.

2. Given two completely diverse or similiar communities, the 

one with the higher number of species has a greater diversity 

value.

Figure 54. Marine bird diversity, by season and for all seasons.

S  n  H ∑    n  ′ = −  i  ln  i  i =1  n   n 

73
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

3. The last property is difficult to summarize but is something 

like this: This property takes into account the hierarchical 

nature, or representativeness in the biological classification of 

each species, when estimating diversity. 

RESULTS AND DISCUSSION

Looking first at a summary of all seasons, the marine avifauna 

was most diverse in areas largely outside of National Marine 

Sanctuary boundaries, especially in areas of the continental 

slope and particularly the Farallon Escarpment. Localized areas 

of high diversity occurring within sanctuary boundaries include: 

Pioneer, Ascension/Cabrillo, and Carmel canyons, as well as 

the continental slope off Point Sur. 

During the Upwelling Season, the avifauna was the least 

diverse; areas of highest diversity in this season included the 

Farallon Escarpment, and Pioneer, Ascension, and Carmel 

canyons.

During the Oceanic Season, diversity was comparable to that 

of the Upwelling Season in general. Areas of high diversity 

continued to include the Farallon Escarpment area, Pioneer 

Canyon, and inner Monterey Bay Canyon.

During the Davidson Current Season, marine bird diversity, in 

general, was the highest of the year. Areas of high diversity 

were all localized, and most occurred over the continental slope 

(e.g., Farallon Escarpment, and Pioneer, Ascension, Monterey 

Bay and Carmel canyons) but some also occurred over the 

shelf (e.g., the inner San Francisco Bay tidal plume and inner 

portions of Monterey Bay).

However, because of the significant correlation between diversity and effort, some of the diversity patterns may be influenced 

by differences in effort across the study area. See the additional 

analysis and discussion of diversity in the Integration section.

74
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

ABOUT THIS MAP

The 40 largest marine bird breeding colonies in the study 

area were chosen for this map (Figure 55). The total number 

of breeding marine bird species is indicated by the size of 

the circle, and the number of species using a particular 

colony is indicated by the circle color. The large symbol at 

the San Francisco Bay entrance represents a summary of 

all the colonies in San Francisco Bay. See Table 18 for more 

information on these colonies.

DATA SOURCES

Data on marine bird colonies were derived primarily from 

Breeding Populations of Seabirds in California, 1989-1991 

(Carter et al., 1992, unpublished data). Colony data were 

updated where more current information was available. 

Updated information is presented for some species on South 

Farallon Island (Sydeman et al., 1998, Warzybok et al., 2002), 

Año Nuevo Island (Thayer and Sydeman 2002 a, b), Bird Rock, 

Point Reyes, and Double Point Rocks (Whitworth et al., 2002), 

Big Basin State Park and vicinity (Laird Henkel, pers. comm) 

and Devil’s Slide Rock (Gerry McChesney, USFWS, pers. 

comm).

METHODS

Colony locations were plotted using latitude and longitude 

coordinates from Breeding Populations of Seabirds in California, 

1989-1991 (Carter et al., 1992, unpublished data).

RESULTS AND DISCUSSION

The study area is in a geologic subduction zone of the eastern 

Pacific and adjacent continental margin. Therefore, as with 

analogous regions elsewhere on the globe (e.g., west coasts 

of South America and Africa), islands are not common. In 

somewhat of a departure from this pattern, the Gulf of the 

Farallones contains far more coastal rocks and offshore islands 

than anywhere else in the study area and, in fact, this is the 

case for 400 miles to the north and south. Obvious in this 

map is the importance to breeding marine birds of the Gulf of 

the Farallones, defined as the broad shelf from Point Reyes/

Tomales Point to Año Nuevo and out to the Farallon Islands. A 

disproportionate number of breeding colonies and, certainly, 

most of various species’ regional breeding populations, occur 

here. These colonies are large and diverse owing to the high 

productivity of surrounding waters and the complexity of 

habitats in the region. See Table 18 for a numerical summary 

of each colony’s contribution to the breeding marine avifauna 

of the study area, composed of 16 species, 12 of which breed 

within the Gulf of the Farallones. 

Figure 55. Major marine bird breeding colonies. 

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

°N53°N53

°N63°N63

°N73°N73

°N83°N83

°N93°N93

2

2

0

0

00

0

m

m

0 25 50Km

50,001 - 153,000

10,001 - 50,000

5001 - 10,000

1001 - 5000

501 - 1000

Major Marine Bird Breeding Colonies

Colony Populations

Number of Species

Number of Birds

250 - 500

Fish Rocks

Gualala Point Island

Russian River Rocks

Arched Rock

Bodega Rock

9 - 12

7 - 8 Point Reyes Point Resistance 6 Millers Point Rocks 5 San Francisco Bay

and Alcatraz Island*

4 North Farallon Islands 3

South Farallon Island 1 - 2

Devil's Slide Rock

Big Basin State Park and vicinity Vicinity of Año Nuevo Island and Point El Jarro Point to Davenport

Davenport to Sand Hill Bluff

Bird Rock

Bird Island

Castle Rocks and Mainland

Anderson Canyon Rocks

Plaskett Rock

Cape San Martin

La Cruz Rock

Piedras Blancas Island

Fairbank Point

Pup Rock and Pecho Rock Adjacent Mainland

* Summary of all San Francisco Bay colonies.

Source Data: See text.

75
ABOUT THESE MAPS 

A comparison of the abundance and distribution of 76 marine 

birds during warm-water periods (including El Niño), cold-water 

periods (La Niña) and normal (neutral) periods is provided here 

as an example of how marine birds may respond to short-term 

variation in marine climate. In this synthesis, what is shown is 

density, which treats all species equally regardless of body size. 

Therefore, the patterns demonstrated by tiny, more abundant 

species, such as storm-petrels and phalaropes, are more 

greatly expressed. For a description of how these periods were 

chosen, see the following topic in the bird section: "Response 

to Variation in Marine Climate" (pages 49-50).

Figures 56a, b and c show the combined density (birds/km2) 

of 76 species of marine birds in cold-water, neutral, and 

warm-water periods, displayed in five minute latitude by 

five minute longitude cells. Map d shows overall patterns of 

density. Densities are based on combined data of several 

studies (see “Methods” and “Data Sources” below). The 

color and mapping intervals were customized to show the 

most structure and highlight significant areas. Cells that were 

surveyed but in which no birds were observed have a density 

of zero; unsurveyed areas are white. Blue lines indicate the 

National Marine Sanctuary boundaries of Cordell Bank, Gulf of 

the Farallones, and Monterey Bay; bathymetric contours for the 

200 meter and 2,000 meter isobaths are also shown in blue.

DATA SOURCES

At-sea densities are based on data from eight survey programs 

conducted in 1980-2001; these data sets were combined using 

CDAS software into an MMS-CDAS data set (MMS, 2001) and 

expanded for this project. Of the data sets on the original CDROM, four aerial survey data sets provided data in the study 

area from Point Arena to Point Sal. Of these, one program was 

still ongoing and data from recent years were added to this data 

set. In addition, data from four ship-based survey programs 

were converted to a compatible format for analysis. See section 

introduction for details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Briggs et al. (1983); more recent data were collected using 

updated technology but the same general method. Data 

sources for ship-based survey data include David Ainley and 

Carol Keiper (unpublished data; see Oedekoven et al., 2001 

for details on methods). Although the at-sea data span the 

years 1980-2001, data are not available for all seasons in all 

years. 

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

METHODS 

At-sea densities are the result of a synthesis of data from 

eight shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources” 

above). Observation and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells. The length and 

width of the survey trackline in a given cell (estimated trackline 

width varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of marine birds seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort. 

Marine bird density data was then organized into periods where 

surface ocean conditions were warm (including El Niños), 

cold (including La Niñas) or neither (neutral). The density of 

all species seen within respective cells was summed for that 

cell. 

To illustrate these temperature conditions, a comparison of 

marine bird densities was made by making maps that use 

selected season/year periods that represented these cold, 

warm and neutral periods. The data for each "condition" map 

was grouped as shown below; these groupings were based 

on the assignments made in Table 14. Once the selection of 

data were made for each analysis period (i.e., warm, neutral or 

cold), the density of all birds seen within each cell was summed 

for that cell.

For the warm-water conditions (including El Niños) map, the 

following seasons and years were used: Davidson Current 

Season: 1981, 1983, 1984, 1992, 1993, 1994, 1996, 1998. 

Upwelling Season: 1985, 1987, 1992, 1993, 1995, 1998. 

Oceanic Season: 1983, 1997.

For the neutral conditions map, the following seasons and years 

were used: Davidson Current Season: 1982, 1986, 1995, 1997. 

Upwelling Season: 1980, 1982, 1986, 1988, 1989, 1994, 1996, 

1997. Oceanic Season: 1982, 1991, 1995.

For the cold-water conditions (including La Niñas) map, the 

following seasons and years were used: Davidson Current 

Season: 1985, 1991, 1999, 2000, 2001, 2002. Upwelling 

Season: 1981, 1990, 1991, 1999, 2000, 2001. Oceanic Season: 

1980, 1981, 1994, 1996, 1998, 1999, 2000, 2001.

Figure 56. Density in warm, cold, and neutral periods: 1980-2001. 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Density in Warm, Cold and Neutral Periods: 1980-2001

Warm-water Conditions

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

2

2

0

2

2

0

0

0

0

0

0

00

0

m

m

m

m

Neutral Conditions

Density

(Animals/km2)

0 25 50Km

a b

20

2

0

0

0

0 m

Cold-water Conditions 2

2

0

0

00

0

m

m

m

Overall Patterns

c d

Source Data: See text.

76
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

RESULTS AND DISCUSSION 

There was not a great deal of difference in density apparent in 

the exhibited patterns for the different periods. Nevertheless, 

during warm-water conditions (e.g., El Niño events) marine 

bird populations appear to contract more into the area defined 

by the boundaries of the central California National Marine 

Sanctuaries, from Tomales Point south to Monterey. Generally, 

this area contains most of the shelf habitat of the study area, 

which tends to have a greater complexity of microhabitats than 

deeper waters. The reason there was not much of an apparent 

pattern or major difference seen in these maps, is that individual 

species respond differently to the three different temperature 

conditions shown. For instance, some may move out of an 

area but others may move in, and therefore, when species are 

combined, these individual responses are homogenized. 

During both warm and cold excursion from ‘normal’/neutral 

marine climate, populations seemed to be slightly more 

widespread, with major concentrations in Monterey Bay. 

During cold-water conditions (e.g., La Niña events), densities 

appeared to be the highest, especially in waters close to the 

coast (e.g., see contiguous high-density, red and orange cells 

along the coast). During warm-water events, the concentrations 

are further offshore in the mid to outer shelf and there are fewer 

highest density (red) cells.

As noted earlier, overall marine bird density in this analysis 

is generally dominated by two numerically dominant species, common murre and sooty shearwater, and to a lesser 

degree, by the species identified as abundant in the study 

area (see Table 15). 

77
ABOUT THESE MAPS 

A comparison of the abundance and distribution of 76 marine 

birds during warm-water (El Niño) compared to cold-water (La 

Niña) and normal (neutral) periods provides an example of how 

marine birds respond to short-term excursions from the usual 

marine climate. In this comparison, densities were converted to 

biomass by multiplying density by body mass of each species. 

This comparison, thus, emphasizes more the larger-bodied 

species, such as Sooty Shearwater and Common Murre.

Figures 57a, b, and c show the combined biomass density 

(kg/km2) of 76 species of marine birds in cold-water, neutral, 

and warm-water periods, displayed in five minute latitude by 

five minute longitude cells. Map d shows overall patterns of 

biomass density. Densities are based on combined data of 

several studies (see “Methods” and “Data Sources” below). 

The color and mapping intervals were customized to show the 

most structure and highlight significant areas. Cells that were 

surveyed but in which no birds were observed have a density 

of zero; unsurveyed areas are white. Blue lines indicate the 

National Marine Sanctuary boundaries of Cordell Bank, Gulf of 

the Farallones, and Monterey Bay; bathymetric contours for the 

200 meter and 2,000 meter isobaths are also shown in blue.

DATA SOURCES 

At-sea densities are based on data from eight survey programs 

conducted in 1980-2001. These data were combined using 

CDAS software into an MMS-CDAS data system (MMS, 2001) 

for the Minerals Management Service and expanded for this 

project. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, one program was still 

ongoing and data from recent years were added to this data 

set. In addition, data from four ship-based survey programs 

were converted to a compatible format for analysis. See section 

introduction for details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Briggs et al. (1987b); more recent data were collected using 

updated technology but the same general method. Data 

sources for ship-based survey data include David Ainley and 

Carol Kieper (unpublished data; see Oedekoven et al., 2001 

for details on methods). Although the at-sea data span the 

years 1980-2001, data are not available for all seasons in all 

years. 

Data on average mass for each species were derived from 

Body Weights of 686 Species of North American Birds (Dunning 

1993). In a few instances, a species was not listed in this 

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

reference; in these cases, the mass of a closely related bird 

of a similar size was used.

METHODS 

At-sea densities are the result of a synthesis of data from 

eight shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources” 

above). Observation and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells. The length and 

width of the survey trackline in a given cell (estimated trackline 

width varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of marine birds seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

For each species that occurred in a cell, the average density 

was then multiplied by a species’ body mass (from Dunning, 

1993). This resulted in an estimate of biomass for that species. 

The biomass of all species in each cell was summed to give 

the cell biomass.

Marine bird density data was then organized into periods where 

surface ocean conditions were warm (including El Niños), 

cold (including La Niñas) or neither (neutral). The density of 

all species seen within respective cells was summed for that 

cell.

To illustrate these temperature conditions, a comparison of 

marine bird densities was made by making maps that use 

selected season/year periods that represented these cold, 

warm and neutral periods. The data for each condition map 

was grouped as shown below; these groupings were based 

on the assignments made in Table 14. Once the selection of 

data were made for each analysis period (i.e., warm, neutral or 

cold), the density of all birds seen within each cell was summed 

for that cell.

For the warm-water conditions (including El Niños) map, the 

following seasons and years were used: Davidson Current 

Season: 1981, 1983, 1984, 1992, 1993, 1994, 1996, 1998. 

Upwelling Season: 1985, 1987, 1992, 1993, 1995, 1998. 

Oceanic Season: 1983, 1997.

For the neutral conditions map, the following seasons and years 

were used: Davidson Current Season: 1982, 1986, 1995, 1997. 

Figure 57. Biomass in warm, cold and neutral periods: 1980-2001.

124°W 123°W 122°W 121°W

N°53 N°63 N°73 N°83 N°93

124°W 123°W 122°W 121°W

N°53 N°63 N°73 N°83 N°93

124°W 123°W 122°W 121°W

N°53 N°63 N°73 N°83 N°93

124°W 123°W 122°W 121°W

N°53 N°63 N°73 N°83 N°93

Biomass in Warm, Cold and Neutral Periods: 1980-2001

Warm-water Periods

> 100

51 - 100

21 - 50

11 - 20

6 - 10

4 - 5

3

2

1

0

20

2

2

2

0

0

0

0

0

0

0

0 

0

m

m

m

m

Neutral Periods

Biomass

(kg/km2)

0 25 50Km

a b

2

2

C 2

00

0

0 

old-water Periods 20

0

0 

00

0

m

m

m

 m

Overal Patterns l 

c d

Source Data: See text.

78
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

Upwelling Season: 1980, 1982, 1986, 1988, 1989, 1994, 1996, 

1997. Oceanic Season: 1982, 1991, 1995.

For the cold-water conditions (including La Niñas) map, the 

following seasons and years were used: Davidson Current 

Season: 1985, 1991, 1999, 2000, 2001, 2002. Upwelling 

Season: 1981, 1990, 1991, 1999, 2000, 2001. Oceanic Season: 

1980, 1981, 1994, 1996, 1998, 1999, 2000, 2001.

RESULTS AND DISCUSSION 

There was slightly more difference in biomass than was observed 

for the analogous comparison of density. Biomass was generally 

more concentrated during warm and cold conditions than during 

neutral conditions, especially cold-water periods, which were 

mimicked by the overall all-conditions summary. Many inner 

shelf habitat areas exhibited high marine bird biomass during 

cold-water periods. The Farallon Ridge and Monterey Bay had 

relatively high biomass under all conditions.

As noted earlier, marine bird biomass in this analysis is generally dominated by two, relatively heavy-bodied, numerically 

dominant species: common murre and sooty shearwater, and 

to a lesser degree, by the species identified as abundant in 

the study area (see Table 15). 

79
ABOUT THESE MAPS 

A comparison of the abundance and distribution of marine birds 

during warm-water periods (e.g., El Niño events), cold-water 

periods (e.g., La Niña events) and normal (neutral) periods 

provides an example of how marine birds may respond to 

short-term excursions from the usual marine climate. These 

maps (Figure 58) show species diversity, calculated for each 

five minute latitude by five minute longitude cell using density 

as the variable in the Shannon [Diversity] Index (Shannon 

and Weaver 1949); all 76 marine bird species that had been 

recorded in the data set were included. 

The Shannon Index measures the degree to which a species 

assemblage is dominated by a few species. If a cell contains 

high densities of a few species and low densities of all others, 

the value of H’ will be low, indicating low diversity. Alternatively, 

if many species are present at similar densities, the value will 

be high, indicating high diversity. Maps a, b and c show the 

diversity index H’ in cold-water, neutral, and warm-water 

periods; map d shows overall patterns. Cells are colored 

based on the value of H’ computed for a particular season. Red 

indicates high diversity, blue indicates low diversity. Although 

there was a significant correlation between diversity and effort, 

the observed patterns of bird diversity are robust and were 

largely unchanged by methods designed to correct for effort.

Unsurveyed areas are white. Blue lines indicate the National 

Marine Sanctuary boundaries of Cordell Bank, Gulf of the 

Farallones, and Monterey Bay; bathymetric contours for the 

200 meter and 2,000 meter isobaths are also shown in blue. 

DATA SOURCES 

At-sea densities are based on data from eight survey programs 

conducted in 1980-2001, which were combined using software 

developed for MMS-CDAS (MMS, 2001) and expanded for this 

project. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets provided data in the study area 

from Point Arena to Point Sal. Of these, one program was still 

ongoing and data from recent years were added to this data 

set. In addition, data from four ship-based survey programs 

were converted to a compatible format for analysis. See section 

introduction for details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Briggs et al. (1983); more recent data were collected using 

updated technology but the same general method. Data 

sources for ship-based survey data include David Ainley and 

Carol Keiper (unpublished data; see Oedekoven et al., 2001 for 

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

details on methods). Although the at-sea data span the years 

1980-2001, data are not available for all seasons in all years. 

METHODS 

At-sea densities are the result of a synthesis of data from 

eight shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources” 

above). Observation and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells. The length and 

width of the survey trackline in a given cell (estimated trackline 

width varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of marine birds seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

The Shannon Index (Shannon and Weaver 1949) was used to 

quantify species diversity.

This index measures the degree to which the species 

assemblage is dominated by a single species. If species A 

dominates all the species seen within a cell, then diversity is 

low; and vice versa. To standardize for variable effort among 

cells and variable strip width among species, we used the 

density for each species in each cell as the basis for calculating 

the index value.

Marine bird density data was then organized into periods where 

surface ocean conditions were warm (including El Niños), cold 

(Including La Niñas) or neither (neutral). The diversity of all 

species seen within respective cells was determined for that 

cell.

To illustrate these temperature conditions, a comparison of 

marine bird densities was made by making maps that use 

selected season/year periods that represented these cold, 

warm and neutral periods. The data for each condition map 

was grouped as shown below; these groupings were based 

on the assignments made in Table 14. Once the selection of 

data were made for each analysis period (i.e., warm, neutral or 

cold), the density of all birds seen within each cell was summed 

for that cell.

Figure 58. Diversity in warm, cold and neutral periods: 1980-2001.

S  n  H ∑    n  ′ = −  i  ln  i  i =1  n   n 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Diversity in Warm, Cold and Neutral Periods: 1980-2001

Warm-water Conditions

2.001 - 3.000

1.801 - 2.000

1.501 - 1.800

0.801 - 1.500

0.000 - 0.800

20

2

20

2

0

0

0

0

0

0

0

0

m

m

m

 m

Neutral Conditions

Diversity

(H')

0 25 50 Km

a b

20

2

0

0

0

0

Cold-water Conditions 2

2

0

0

00

0

m

m

m

m

Overall Patterns

c d

Source Data: See text.

80
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

For the warm-water conditions (Including El Niños) map, the 

following seasons and years were used: Davidson Current 

Season: 1981, 1983, 1984, 1992, 1993, 1994, 1996, 1998. 

Upwelling Season: 1985, 1987, 1992, 1993, 1995, 1998. 

Oceanic Season: 1983, 1997.

For the neutral conditions map, the following seasons and years 

were used: Davidson Current Season: 1982, 1986, 1995, 1997. 

Upwelling Season: 1980, 1982, 1986, 1988, 1989, 1994, 1996, 

1997. Oceanic Season: 1982, 1991, 1995.

For the cold-water conditions (Including La Niñas) map, the 

following seasons and years were used: Davidson Current 

Season: 1985, 1991, 1999, 2000, 2001, 2002. Upwelling 

Season: 1981, 1990, 1991, 1999, 2000, 2001. Oceanic Season: 

1980, 1981, 1994, 1996, 1998, 1999, 2000, 2001.

RESULTS AND DISCUSSION 

Under all variations of climate, marine bird diversity was highest 

over the continental slope, with the Farallon Escarpment 

and Pioneer Canyon, in particular, standing out. Of lesser 

importance was outer Monterey Bay Canyon and Point Sur 

slope. Areas of high diversity were more spread out along 

the slope when ocean temperatures were warm. Adding to 

the latter hot spots was the area around Ascension Canyon. 

During neutral conditions, diversity everywhere was relatively 

low, when compared with higher diversities during the warmwater and cold-water periods.

Although there was a significant correlation between diversity 

and effort, the observed patterns of bird diversity are robust 

and were largely unchanged by methods designed to correct 

for effort.

81
ABOUT THESE MAPS 

A comparison of the density and distribution for two species 

during an intense El Niño (1997-98) and an adjacent and intense La Niña (1999-00) provides an example of how marine 

birds respond to short-term anomalies of marine climate (Figure 

59). In this comparison, the responses of individual species 

do not cancel out the effects of another, as was the case in 

comparisons when measures of overall abundance were used 

(Figures 52, 53, 56 and 57).

Densities are based on combined data of several studies (see 

“Methods” and “Data Sources” below). The color and mapping 

intervals were customized to show the most structure and highlight significant areas. Cells that were surveyed but in which no 

birds were observed have a density of zero; unsurveyed areas 

are white. Blue lines indicate the National Marine Sanctuary 

boundaries of Cordell Bank, Gulf of the Farallones, and Monterey Bay; bathymetric contours for the 200 meter and 2,000 

meter isobaths are also shown in blue.

DATA SOURCES 

At-sea densities are based on data from eight survey programs 

conducted in 1980-2001. These data were combined using 

CDAS software into an MMS-CDAS data system (MMS, 2001) 

for the Minerals Management Service and expanded for this 

project. Of the data sets on the original MMS-CDAS CD-ROM, 

four aerial survey data sets contained data in the study area 

from Point Arena to Point Sal. Of these, one program was still 

ongoing and data from recent years were added to this data 

set. In addition, data from four ship-based survey programs 

were converted to a compatible format for analysis. See section 

introduction for details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (2001) 

and California Department of Fish and Game Office of Spill 

Prevention and Response (CDF&G-OSPR), unpublished data. 

Early data were collected using methods described by Briggs 

et al. (1983); more recent data were collected using updated 

technology but the same general method. Data sources for 

ship-based survey data include David Ainley and Carol Keiper 

(unpublished data; see Oedekoven et al., 2001 for details on 

methods). Although the at-sea data span the years 1980-2001, 

data are not available for all seasons in all years. For the Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991 and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS 

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” above). 

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

Observation and trackline data from these studies were converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into five 

minute latitude by five minute longitude cells using CDAS, a 

custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above 

water) were used to estimate the area sampled. The number 

of marine birds seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

The most intense events were selected for this comparison, 

as well as events that occurred very close in time. In that way, 

long-term changes in populations were not involved in the species’ occurrence patterns. For El Niño, data were used from 

the Oceanic Season 1997 through Upwelling Season 1998; for 

La Niña the data were from the Oceanic Season 1998 through 

Oceanic Season 1999; see Table 14.

RESULTS AND DISCUSSION 

During intense warm periods, species such as brown pelican, 

black storm-petrel and black-vented shearwater, which zoogeographically are centered to the south of central California 

(where waters are normally warmer and food availability relatively lower), move into central California waters when warmer 

ocean temperatures expand northward. Many of these individuals have foregone breeding owing to depleted food availability, 

which is often more extreme in areas to the south where these 

species breed. Shown here are comparisons for brown pelican and black-vented shearwater. In both cases, densities are 

much higher in central California during warm-water periods. 

In fact, during these conditions brown pelicans expand as far 

north as the Columbia River and even farther; black-vented 

shearwaters, however, don’t go much farther than central 

California waters.

The response of species to short-term cold-water conditions (La 

Niña) is far less dramatic and, in fact, no examples could be found 

to clearly illustrate this. This is due to many factors, perhaps the 

most important being that the geographic affinity of central California 

marine birds is largely ‘subarctic’ and therefore, the central California 

avifauna is at the southern extreme of its range. As a result, there is 

little reason for northern species to shift into the area when the latter 

becomes slightly colder. The other main reason for lack of examples 

illustrating response to cold conditions is that a major regime shift 

coincided with the best example, i.e. intense La Niña conditions 

in 1999-00 (see Figure 60). Therefore, it is difficult to separate the Figure 59. Density during El Niño and La Niña events, 1997-2000. 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Density During El Niño and La Niña Events, 1997-2000

El Niño ('97 - '98)

20

2

0

0

0

0 m

Brown Pelican 20

2

0

0

0

0

m

m

 m

Brown Pelican

La Niña ('99 - '00)

Density

(Animals/km2)

0 25 50 Km

a b

20

2

0

0

0

0 m

Black-vented Shearwater 2

2

0

0

00

0 m

Black-vented Shearwater

m

El Niño ('97 - '98) mLa Niña ('99 - '00)

c d

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

Source Data: See text.

factors responsible in the avifaunal shifts observed.

82
ABOUT THESE MAPS 

A comparison of the abundance and distribution of two species 

during intense El Niño events compared to La Niña events 

provides an example of how marine birds may respond to 

short-term anomalous marine climate. In the case of regime 

shifts, which involve climate change on a decadal time scale, a 

shift may have occurred during the study period corresponding 

also to the switch from intense El Niño (Oceanic Season 1997 

- Upwelling Season 1998) to intense La Niña (Oceanic Season 

98 - Oceanic Season 2000). Therefore, at this time, it is difficult 

to perceive whether the changed bird distributional patterns 

were short-term or long-term. Subsequently the cold conditions 

continued, thus indicating a longer-term regime shift (Bogard et 

al., 2000, Schwing and Moore 2000, Schwing et al. 2002).

Densities are based on combined data of several studies (see 

Methods and Data Sources below). The color and mapping 

intervals were customized to show the most structure and 

highlight significant areas. Cells that were surveyed but in which 

no birds were observed have a density of zero; unsurveyed 

areas are white. Blue lines indicate the National Marine 

Sanctuary boundaries of Cordell Bank, Gulf of the Farallones, 

and Monterey Bay; bathymetric contours for the 200 meter and 

2,000 meter isobaths are also shown in blue. 

DATA SOURCES 

At-sea densities for this analysis are based on a subset of data 

from the eight survey programs. These data were combined 

using CDAS software into an MMS-CDAS data system (MMS, 

2001) for the Minerals Management Service and expanded for 

this project. Of the data sets on the original MMS-CDAS CDROM, four aerial survey data sets contained data in the study 

area from Point Arena to Point Sal. Of these, one program was 

still ongoing and data from recent years were added to this data 

set. In addition, data from four ship-based survey programs 

were converted to a compatible format for analysis. See section 

introduction for details on individual data sets. Data collected 

since 1996 was used for this comparison.

METHODS 

At-sea densities for this analysis are the result of a synthesis of 

subsetted data from eight shipboard and aerial survey programs 

conducted in the study area in the years 1980-2001 (see Data 

Sources above). Observation and trackline data from these 

studies were converted to a common format. All aerial data 

were continuous; ship-based data were converted separately 

into a continuous transect to the extent possible. From the 

digitized survey data, the distributions of effort and of species 

were mapped into five minute latitude by five minute longitude 

cells using CDAS, a custom geographic information system 

for analyzing marine bird and mammal surveys (MMS, 2001). 

The length and width of the survey trackline in a given cell 

Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

(estimated trackline width varied by platform, depending on 

speed and height above water) were used to estimate the area 

sampled. The number of marine birds seen in a cell was then 

divided by the area sampled in the cell to estimate density. If a 

cell was censused more than once, densities were averaged, 

with adjustment made for effort.

Species densities were mapped by grid cells on either side of 

the regime shift node, Oceanic Season 1997 through Upwelling 

Season 1998 versus Oceanic Season 1998 through Oceanic 

Season 2000.

RESULTS AND DISCUSSION

In 1999-2000, the mean state of the California Current System 

may have moved from a “warm regime”, present since 1976, 

to a “cold” regime (Schwing et al. 2002). On the other hand, 

subsequent years of observation may indicate that we only 

witnessed the transition from one of the strongest El Niños to 

one of the strongest La Niñas seen in the past 100 years. 

Regardless, in response, more northern species such as 

fork-tailed storm-petrel and black-legged kittiwake, which are 

present mostly during the Davidson current season, found 

the cooler, central California waters more to their liking and, 

rather than avoiding the area as in the 20 previous years of the 

warm regime, arrived or remained longer to winter in very large 

numbers. Unfortunately, data during the Oceanic and Davidson 

current seasons of years since 2000 were not collected.

Figure 60. El Niño/La Niña Event changes, as an example of regime shift effects.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Density During El Niño and La Niña Events: 1997-2000

El Niño ('97 - '98)

> 100.00

50.01 - 100.00

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

20

20

Fork-tailed Storm-Petrel 20

2

0

0

0

0

0

0

0

m

 m

 m

m

Fork-tailed Storm-Petrel

La Niña ('99 - '00)

Density

(Animals/km2)

0 25 50 Km

a b

20

2

0

0

0

0 m

Black-legged Kittiwake 2

2

0

0

00

0

m

m

 m

Black-legged Kittiwake

El Niño ('97 - '98) La Niña ('99 - '00)

c d

Source Data: See text.

83
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

SECTION SUMMARY Table 15. Life history and management information for selected marine birds off north/central California.

The following section provides a summary discussion of 

the marine bird analyses, relative to the study area and 

the three national marine sanctuaries off north/central 

California. 

Life History and Management Characteristics 

The marine avifauna off north/central California, as 

represented in the summary data set, are composed of 

76 marine bird species, with 39 occurring regularly enough 

to assess and map patterns of their occurrence. Table 15 

is a summary of selected life history and management 

information for 39 of the marine bird species.

Species Relative Abundance in the Study Area. Based on 

the analysis of the at-sea data and as indicated in Table 

15, among the more regularly occurring species, two are 

very abundant, eight are abundant, 16 are common, 12 

are uncommon, and two are rare. Relative abundance was 

estimated on a logarithmic scale of number of individuals 

seen within the study area on surveys during the study 

period. The majority of the species (26) are present only 

seasonally, but of the 14 species that breed in the study 

area, 10 are present year round. 

Food Types. With regard to trophic relationships, the 

majority of marine bird species are either zooplanktivores 

(generally smaller-bodied) and/or piscivores. Major prey 

items are: euphausiids (Thysanoessa spinifera and 

Euphausia pacifica), market squid (Loligo opalescens), 

juvenile rockfish (Sebastes spp, especially Sebastes 

jordani), anchovy (Engraulis mordax), herring (Clupea 

harengus), smelt (Atherinops californiensis and Spirinchus 

starksi), Pacific saury (Cololabis saira), sardine (Sardinops 

sagax), midshipman (Porichthys notatus), surfperch 

(several species) and myctophids (several species), with 

importance varying by the habitat and time of year in which 

a particular bird species was foraging (Briggs and Chu 

1987, Ainley and Boekelheide 1990).

Summary of Spatial and Temporal Patterns in Large 

and Relatively Smaller Areas

Table 16 is a summary of the temporal and spatial patterns 

observed for the regularly occurring marine birds of the 

study area. This summary was developed by visual 

inspection of the species seasonal density maps and is 

provided as a simple summary of species distributions 

and abundance by season and for selected habitat and 

management features.

It is obvious that large numbers of marine birds occur in the 

study area year round. The species composition, however, 

Population Status in Study Area Temporal Occurrence in Study Area 3 Major Food Items

Protection Population

Relative

Abundance Seasonal

Primary

Months of

Months

When n t k no

h

p ah ol op sd

i u , d o o ct us) p

p ah su ii sd

li )l

n ht ci

r e et r b t a se

e m ar il t s

ed r e

Common Name Scientific Name 1 Status Trend6 2 at Sea 5 Occurrence 5 Presence Breeding5

P alF si

e C

( qs

uE

( r k

e B

I vn

e G

eF

Loons/Grebes

Pacific loon Gavia pacifica Unknown Common Seasonal Nov-Apr x

Common loon Gavia immer Unknown Uncommon Seasonal Nov-Apr x

Western & Clark's grebes Aechmorphorus occidentalis, A. clarksii Unknown Abundant Year-round Nov-Sept Apr-Sept x

Albatrosses/Petrels

Black-footed albatross Phoebastria nigripes Decreasing Common Year-round Mar-Aug x x

Laysan's albatross Phoebastria immutabilis Unknown Rare Seasonal Nov-Mar x x

Northern fulmar Fulmarus glacialis Increasing Common Seasonal Nov-Mar x

Sooty shearwater Puffinus griseus Declining V.Abundant Seasonal Apr-Aug x x x x

Pink-footed shearwater Puffinus creatopus Stable? Common Seasonal Apr-Aug x x

Buller's shearwater Puffinus bulleri Unknown Common Seasonal Aug-Nov x

Black-vented shearwater Puffinus opisthomelas Stable? Uncommon Seasonal Aug-Nov x?

Leach's storm-petrel Oceanodroma leucorhoa Unknown Common Seasonal March-Sept April-Sept x x x

Ashy storm-petrel Oceanodroma homochroa SSC Increasing Common Year-round All Feb-Oct x x x

Fork-tailed storm-petrel Oceanodroma furcata Decreasing? Uncommon Seasonal Nov-Mar x x x

Black storm-petrel Oceanodroma melania SSC Unknown Uncommon Seasonal Nov-Mar x x

Sea Ducks (Scoters)

Surf scoter Mellanita perspicillata Stable Abundant Seasonal Nov-Apr x

Pelican/Cormorants

California brown pelican Pelecanus occidentalis californicus FE, SE Increasing Common Seasonal Aug-Nov x

Pelagic cormorant Phalacrocorax pelagicus Stable? Uncommon Year-round All Apr-Sept x x x x

Brant's cormorant Phalacrocorax pennicilatus Stable? Abundant Year-round All Apr-Sept x

Double-crested cormorant Phalacrocorax auritus Increasing? Uncommon Year-round All Mar-Aug x

Phalaropes

Red phalarope Phalaropus fulicaria Stable? Common Seasonal Mar-Aug x x x

Red-necked phalorope Phalaropus lobatus Stable? Common Seasonal Mar-Aug x x x

Gulls/Terns

Western gull Larus occidentalis Declining Abundant Year-round All Apr-Aug x x

California gull Larus californicus Increasing Abundant Seasonal Nov-Mar x

Glaucous-winged gull Larus glaucescens Stable Uncommon Seasonal Nov-Mar x

Heermann's gull Larus heermanni Stable? Common Year-round Aug-Nov x

Sabine's gull Xerna sabini Stable Common Seasonal Mar-Aug x x

Black-legged kittiwake Rissa tridactyla Increasing Common Seasonal Nov-Mar x

Caspian tern Sterna caspia SSC Stable Uncommon Seasonal Mar-Nov Apr-Aug x

Elegant tern Sterna elegans Stable Uncommon Seasonal July?-Nov x

Arctic tern Sterna paradisaea Stable? Common Seasonal Mar-Nov x

Alcids

Common murre Uria aalge Increasing V.Abundant Year-round All Apr-Aug x x x x

Pigeon guillemot Cepphus columba Stable? Uncommon Seasonal Mar-Aug Mar-Aug x x x

Cassin's auklet Ptychoramphus aleuticus Decreasing? Abundant Year-round All Mar-July x x

Marbled murrelet Synthliboramphus marmoratus FT, ST Stable Uncommon Year-round All Apr-Aug x x

Xantus’ murrelet Synthliboramphus hypoleucus ST Unknown Uncommon Seasonal May-July x

Craveri’s murrelet Synthliboramphus craveri Unknown Rare Seasonal May-July x

Tufted puffin Fratercula cirrhata Decreasing Uncommon Seasonal Mar-Aug Apr-Aug x x

Rhinoceros auklet Cerorhinca monocerata Stable Abundant Year-round Nov-Aug Apr-Aug x x x x

Notes

1. Management status categories are as follows: FE–federally endangered; FT–federally threatened; SE–state endangered; ST–state threatened; SSC–state species of special concern.

2. Relative abundance estimates are based on the number of individuals tallied in the at-sea survey data, and the categories are defined as follows:

 Rare – up to 100 birds; Uncommon – up to 1,000; Common – up to 10,000; Abundant – up to 100,000; and Very Abundant – up to 1,000,000. 

3. Information on food items are from Ainley & Sanger 1979, Briggs & Chu 1987, and Ainley & Boekelheide 1990.

4. Entries with question marks are the principal investigators best estimate.

5. Timing information is from Cogswell, 1977 and Ainley and Boekelheide, 1990, except for Caspian tern breeding time, which came from Joelle Buffa, FWS, pers. comm.

6. Information on population status was based on analysis of the shipboard data sets, from 1985-2001. 

7. Months of presence and breeding in the study area are approximations, because timing is strongly influenced by the interannual variability of environmental conditions in the study area.

8. Information on population status and temporal occurrence refers only to birds and their activities in the study area.

changes greatly due to the presence of southern 

hemisphere-breeding species that are ‘wintering’ in 

large numbers in the study area during the Upwelling 

Season and subarctic-breeding species ‘wintering’ in 

large numbers during the Davidson Current Season. 

Additionally, many migrants pass through the region, 

but foraging as they go, during the Oceanic and early 

Upwelling seasons. 

In general, the highest concentrations and the greatest 

variety of marine birds are found over the continental 

shelf and slope, where there are more microhabitats 

defined by ocean complexity (depth, currents, tide rips, 

etc.). A number of smaller, more discrete areas attract 

marine birds because more food is available; the most 

important of these are Farallon Escarpment, Farallon 

Ridge, San Francisco Bay tidal plume, inner Monterey 

Bay, and Estero/San Luis Obispo bays.

Patterns Observed in Density, Biomass Density and 

Diversity Across Species

Another way to summarize occurrence patterns of 

marine birds in the study area is to combine species 

distribution and abundance data and analyze for the 

biological metrics of species diversity, biomass and 

density. Analyses for overall density, biomass and 

diversity were done with respect to ocean season 

and to periods of unusual ocean climate (i.e., warmwater, cold-water and neutral periods). For these 

summary analyses across species, we used the data 

for 76 marine bird species that were contained in the 

combined data set. 

Overall Density and Biomass. The seasonal and 

‘combined-season” densities of 76 marine birds were 

calculated for each five-minute by five-minute cell as 

the number of individuals per km2. Biomass (kg/km2) 

was then calculated as the product of density and the 

mean body mass for each species, taken from Dunning 

(1993). If a species was not listed in this reference, 

the body weight of a related species of a similar size 

was used.

The distribution of marine birds across all taxa is similar 

for density (Figure 52) and biomass density (Figure 53). 

This is because the avifauna is dominated (in terms of 

both number of individuals and their body mass) by the 

Common Murre and Sooty Shearwater. Therefore, the 

patterns in sum are close to what is evident individually 

for these particular dominant species. Accordingly, the 

major biomass and density areas i.e., the inner and 

outer shelf, are biased toward these two species. 

84
Section 2.2: BIO GE OG RA PHY OF MA RINE BIRDS

Table 16. A summary of temporal and spatial patterns in the at-sea survey data (1980-2001) of selected marine birds off north/central California.

Family Name/Species Common Name

Seasonal Occurrence

Associations with Large

Bathymetrically-Defined Areas

Species

Occurs in 

Study

Area, But 

Mostly

Outside

Sanctuary

Bounds

Associations with Discrete Physiographic/Oceanic Features

Upwelling

Season

(3/15-8/14)

Ocean

Season

(8/15-

11/14)

Davidson

Current

Season

(11/15-

3/14)

Coast & 

Inner

Shelf (~0

100m)

Outer

Shelf

(~100-

200m)

Upper

Slope

(~200-

1000m)

Lower

Slope

(~1000-

2000m)

Deep

Ocean

(beyond

2000m)

Cordell

Bank

BodegaCanyon

Fanny

Shoal

Farallon

Escarpment Farallon Ridge

San Francisco

Bay

Plume

Pioneer

Sea

mount

PioneerCanyon

Ascencion,

Cabrillo,

& Año 

Canyons

Pt.

Ano

Nuevo

Monterey

Canyon

Monterey

Bay

Inshore

Carmel

Canyon

Pt. Su

Slope

PodicipedidaeWestern and Clark's grebes

GaviidaePacific loonDiomedeidaeBlack-footed albatross

x

X

***X

x **X

***X

x

X

x

X

X

X

x

xx

XX 

Laysan albatross

ProcellariidaeNorthern fulmarSooty shearwater

x

x

***X

x

o

x

x

***X

***X

o X

X

X

X

X

X

X

X

X

X

X

X

x

x

x

x

x

X

X

x

X

x

x

X

x

x

X

x

x

x X

x

x

X

x

x

X

X

x

X X

x

x

x

x

Short-tailed shearwater o o ***X X X x x X x

x

Pink-footed shearwater ***X x o X X X x x x x X x x X xBuller's shearwater o ***X o X X X x X x X x x x x x Black-vented shearwater o **X x X X x X x x xHydrobatidaeLeach's storm-petrel **X **X o X X X x x x 

Fork-tailed storm-petrel o o X x X X x X X x x 

Ashy storm-petrel

Black storm-petrel

AnatidaeWhite-winged scoter

Surf scoterPelecanidae

**X

o

o

o

***X

**X

x

x

**X

**X

**X

**X

X

X

X

x

x

X

X

X

X

x X x X

x

X

X

XX

X

x

x

x

x

X

X x

Brown pelican

PhalacrocoracidaeBrandt's cormorantPelagic cormorant

**X

***X

**X

**X

***X

**X

x

***X

**X

X

X

x x

x

x

x

x

X

X

X

x

X

X

x

X 

Double-crested cormorant *X o o

X

X

x

x X X

X

x

ScolopacidaeRed phalarope ***X x o X X X x X x X x x x x 

Red-necked phalarope

Laridae

***X x o X X x x x x x x x x x x 

Glaucous-winged gull

Western gull

o

***X

x

***X

***X

***X

X

X

X

X

x

X x

x

x

x

x

x

X X

x

X

X

X

x x

X

X

X 

California gull o x ***X X X x x X x X 

Ring-billed gull o x **X X x X

Mew gull o x **X X x X

Heermann's gull o x **X X x XBonaparte's gull ***X x o x X X x X x X

Sabines gull ***X x o X X X x X x x X

Black-legged kittiwake x o ***X X X X x X x x X x x x x x x 

Caspian/Elegant terns **X x o X X

Arctic tern ***X ***X o x x X X x X x x x xForster's ternAlcidae

**X x o X X

Common murrePigeon guillemot

***X

**X

***X

x

***X

o

X

X

X

X

x x x x x X

X

X x

x

x 

Tufted puffin *X x o x X X X X X x

Rhinoceros auklet ***X ***X x x X X x x x x x x X x x xCassin's auklet ***X ***X x X X x X x X X X x xMarbled murrelet *X *X *X X x X XXantus'/Craveri's murrelets ***X x x X X X X XAll Xs 29 35 27 21 28 24 22 16 11 13 14 14 22 17 20 6 18 19 11 15 18 6 8 Large X's 25 14 21 20 19 19 13 5 11 3 1 4 16 9 17 0 2 1 5 7 16 0 8 

X X 

X 

XXX 

X

Notes1. A summary of temporal and spatial patterns in the occurrence of 44 marine birds off north/central California, based on visual inspection of the species' seasonal density maps by the principal investigators.

2. The spatial and temporal patterns summarized here may be affected by variation in the sampling effort of the combined data sets; that said, this table is included because it provides a summary of the relative use of the various habitat features, as viewed in the species 

3. In the "seasonal occurrence" columns, the number of asterisks indicate the number of sanctuaries in the study area that are used by the species during the season. A large "X" means a relatively major occurrence in the data sets, a small "x" means a minor occurrence and a "o" means the species was mostly absent. 4. Under the heading for "large, bathymetrically-defined areas", a large "X" indicates where the species was most abundant, a small "x" means a minor occurrence, and a "o" means the species was mostly absent. 5. Under the heading for "discrete physiographic/oceanic features", large X’s refer to ‘hot spots’; small x's indicate areas of secondary importance for that species.6. A blank in the table means a species was not present at the location indicated in the maps/data reviewed. 
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

Table 17. Important at-sea areas and ocean seasons for marine birds off north/central California, based on maps 

of biomass, density and diversity.

Biomass/Density Diversity

Davidson Davidson

Current Upwelling Oceanic Current Upwelling Oceanic

Area Season Season Season Season Season Season

Cordell Bank x X

Farallon Escarpment X x x X X X

(slope)

Farallon Ridge (includes X X x

Farallon Island area)

San Francisco Bay Tidal x X X

Plume

Pioneer Canyon X x x

Año Nuevo Shelf X X

Ascension, Año and X x x X x

Cabrillo Canyons

Monterey Bay Inshore X x X X

Monterey Bay Canyon X x

Carmel Canyon X

Point Sur Shelf x

Point Sur Slope X x

Estero Bay & San Luis X x

Obispo Bay

Note: Large, bold Xs refer to most important areas, and smaller xs refer to other important areas.

Important Marine Areas for Birds: Considering Overall 

Biomass, Density and Diversity of Marine Birds. All 

marine habitat off central California, especially that of the 

continental shelf and slope, is fully used by marine birds. 

Based on the analyses of maps for overall density, biomass 

density, and diversity, the following at-sea areas were identified 

as important (Table 17). Areas with more and bigger Xs may 

be more important, as they show more expression of density, 

biomass and diversity. 

Important Breeding Colonies for Marine Birds. Although 

breeding colonies and roosts are on land and technically not 

part of the study area, a table and map of the major colonies 

are included in this section because they provide a context for 

understanding the distributions of species that breed or roost 

in the study area based on size and species composition (most 

data was from Carter et al., 1992, with updates, as available). 

Table 18 shows the top 40 marine bird breeding colonies in the 

study area; see Figure 55 for a map of these locations; see the 

CD-ROM X for a full listing of breeding sites. 

Marine birds in this area breed mainly during the Upwelling 

Season, anticipating that food availability will be greatest 

from July-October, toward the end of this season and into the 

Oceanic Season. During this period ample supplies of prey will 

be needed to feed growing chicks and recently fledged young. 

Egg laying occurs in March-May, depending on species, and 

different species require different amounts of time to complete 

the breeding task (petrels longest, gulls shortest).

The greatest concentration of colonies occurs in the Gulf of 

the Farallones, in the broad shelf area from Point Reyes south 

to Año Nuevo and out to the Farallon Islands. The breeding 

avifauna is dominated by alcids, with six species. Fifteen 

species of marine birds breed at sites within or immediately 

adjacent to the National Marine Sanctuaries in the study area; 

several others breed inland or in San Francisco Bay and to a 

lesser degree use marine sanctuary waters.

Importance of Ocean Seasons to Marine Birds. As seen in 

the maps for individual species, temporal differences in species occurrence patterns are strong for many species in the 

study area (see Tables 15 and 16). Below is a brief summary 

of marine bird activity in the three ocean seasons. 

Upwelling Season (~Spring/Summer). With the onset of upwelling, when cold, nutrient-rich water is brought to the surface by 

persistent northwest wind and the Coriolis effect, most of the 

seasonal winter residents depart and several other species 

migrate through the region (e.g. Sabine’s Gull, Arctic Tern). Arriving are several species that nest in the Southern Hemisphere, 

thus spending their ‘wintering’ period in the region. The Sooty 

Shearwater is one of these and becomes the most abundant 

species in the study area. 

Owing to the addition of Sooty Shearwaters to the avifauna and 

the continued abundance of Common Murres, overall density 

and biomass of marine birds is highest during the Upwelling 

and Oceanic Seasons and is widely spread from the coast 

to beyond the shelfbreak. Diversity over the shelf, where the 

shearwaters and murres mostly reside, is relatively low.

Oceanic Season (~Autumn). In this season, when upwelling 

winds have noticeably relaxed, allowing offshore, warmer 

oceanic water to flow shoreward, the avifauna begins to 

diversify. However, as more sooty shearwaters and other 

southern hemisphere seasonal residents depart the avifauna 

becomes more sparse. At this time, resident breeding species 

are also dispersing more widely as they finish breeding 

duties. 

Additionally, several species (e.g., phalaropes, jaegers, Arctic 

terns, Sabine’s gulls) are migrating through the region, the local 

nesting species are all present, and several species that nest 

elsewhere are abundant as well (e.g. several shearwaters, 

brown pelican, and Heermann’s gull). 

Biomass remains high but shifts closer to shore than during 

the Upwelling Period, in large part due to an inshore shift of 

murres and shearwaters.

Davidson Current Season (~Winter). During this season, 

when ocean temperatures are relatively warm and there is 

no upwelling (but frequent downwelling owing to southerly 

storms) the area is inundated by such species as black-legged 

kittiwake, northern fulmar and several larger gulls. All these 

species nest outside of the region. Also present are nesting 

species that reside year-round in the region, such as Brandt’s 

cormorant, western gull, common murre, rhinoceros auklet 

and Cassin’s auklet. In fact, many of the latter species begin 

to occupy nesting colonies during this season, well before the 

nesting period. 

During this season, 

the species diversity 

of shelf waters 

increases. In fact, 

areas of high 

diversity are more 

widespread in this 

season than in the 

others.

Analysis of 

V a r i a t i o n 

in Species 

A b u n d a n c e 

Patterns. Many 

factors influence 

the distribution 

and abundance 

of marine birds; 

in this study, the 

effects of nine 

i n d e p e n d e n t 

variables on 

species density 

were investigated 

for 26 species. 

The data used for 

the regression analyses were a subset of the mapped 

data, and included data from the Davidson Current Period 

from 1985 through the same for 2002; also, cells with area 

surveyed less than 0.25km2

 were excluded. 

Among the nine variables investigated, the three most 

important variables that explained variation in species density 

were “Distance to Land” (16 of 25 species), “Ocean Season” 

(13 species), and “Ocean Depth” (11 species, see Table 19). 

The next three variables of importance were “ENSO” (eight 

species), “Year” (seven species), and “Distance to Colony”. In 

some respects, for species having many small colonies (e.g. 

pelagic cormorant), Distance to Land and Distance to Colony 

may have co-varied. The variable “Year” indicated whether 

there was an increasing or decreasing trend in the species’ 

abundance. An effect of ENSO would indicate an especially 

complex relationship, possibly meaning either an effect of prey 

availability or ocean climate. 

Please note that while the three most important variables of 

those evaluated are indicated in Table 19, for most species 

there are likely other variables of greater importance (e.g., 

prey availability, depth of thermocline). On average, only 

about 20% of the variance was explained with the top three 

variables presented. Additional data and time would be required 

to evaluate other variables that might be of greater importance 

in explaining the variation in a species’ distributions.

Species Use of the Water Column. Several marine bird 

species are capable of exploiting the entire water column of the 

shelf, e.g. Pacific loon, western/Clark’s grebes, and common 

murre, but for unknown reasons (possibly prey selection, 

perhaps interference competition from murres and shearwaters) 

the grebes mainly frequent the inner most portion of the shelf. 

The very abundant common murre is found everywhere on the 

shelf especially during the breeding/Upwelling season. Other 

diving species, such as scoters or marbled murrelet, frequent 

only shallow waters of the inner shelf, while other species, 

such as tufted puffin, rhinoceros auklet and Cassin’s auklet 

frequent waters much deeper (continental slope) than their 

diving capabilities allow. Species such as the very abundant 

sooty shearwater (a shallow diver to 20 meters) are found 

everywhere from outer slope to inner shelf. 

These differences in patterns of habitat use are likely related 

to factors such as the occurrence patterns of different 

prey (species/sizes), interspecific competition, or temporal 

occurrence of certain prey (species/sizes). The latter would 

account for why some year-round resident species feed over 

waters of different depths during one season compared to 

another. Species such as the sooty shearwater, which use a 

wide range of ocean depths and habitats, are likely to be more 

generalized in prey selection, possibly due to their fast, efficient 

flight allowing them to forage over much larger areas than many 

other marine birds, particularly the alcids and cormorants. 

Response to “Short-Term” Changes in Ocean Climate. The 

study area is subjected frequently to shifts in marine climate of 

different scales and periodicity and this makes management 

a challenge, because populations are affected by natural 

environmental factors that cannot be addressed proactively 

86
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

Table 18. Major marine bird colonies along the central California coast 

Double- Other Site Total 

USFWS Leach's Ashy Brandt's crested Pelagic Pigeon Rhino- Species (No. of

CA Colony Colony Storm- Storm- Cor- Cormor Cor- Western Caspian Common Guille- Marbled Cassin's ceros Tufted (see Breeding

Colony/Composite Name Number Number Latitude Longitude Petrel Petrel morant ant morant Gull Tern Murre mot Murrelet Auklet Auklet Puffin notes) Birds)

Fish Rocks ME-384-10 404-003 38°47'59" N 123°35'31" W 100 211 123 170 119 P 4 15 6 748

Gualala Point Island SO-384-01 404-004 38°45'3" N 123°31'42" W 521 4 26 29 1 581

Russian Gulch SO-382-08 404-033 38°28'0" N 123°9'35" W 227 42 20 7 296

Russian River Rocks SO-382-09 404-005 38°27'14" N 123°8'34" W 51 422 125 44 5 2 649

Arched Rock SO-382-11 404-006 38°25'53" N 123°7'31" W 717 9 34 2 762

Bodega Rock SO-380-02 404-008 38°17'48" N 123°2'49" W 1,228 24 30 2 1,284

Bird Rock MA-380-04 404-010 38°13'49" N 122°59'35" W 15 55 37 168 115 3 H 6 399

Point Resistance MA-374-03 429-024 37°59'54" N 122°49'40" W P 46 H H 8 3,518 50 3,622

Point Reyes MA-374-01 429-001 37°59'30" N 122°58'59" W 15 1,522 266 178 15,155 616 4 6 17,762

Millers Point Rocks MA-374-04 429-002 37°58'52" N 122°48'34" W 114 59 30 358 55 1 617

Double Point Rocks MA-374-05 429-003 37°56'50" N 122°47'8" W 30 180 9 8 4,464 22 4,713

San Francisco Bay & Alcatraz Island Composite Composite 37°49'33" N 122°25'19" W 9 2,789 4 4,174 2,818 10 8498 18,302

North Farallon Islands SF-FAI-01 429-051 37°46'4" N 123°5'56" W 161 62 32 27,308 42 27,605

South Farallon Island SF-FAI-02 429-052 37°42'0" N 123°0'0" W 1,400 1,990 9,466 486 442 15,095 103,588 499 18,807 516 128 30 152,447

Devil's Slide Rock SF-372-03 429-014 37°34'28" N 122°31'39" W 7 46 16 246 30 345

Big Basin State Park and vicinity None None 37°8'48" N 122°17'58" W 600 600

Vicinity of Año Nuevo Island and Point Composite Composite 37°6'30" N 122°20'8" W 4 117 1,382 219 24 224 27 1,997

Greyhound Rock to El Jarro Point SC-370-01 429-049 37°3'31" N 122°15'0" W 66 2 321 9 398

El Jarro Point to Davenport SC-370-02 429-050 37°1'5" N 122°12'23" W 308 22 313 1 644

Davenport to Sand Hill Bluff SC-364-01 454-038 36°59'44" N 122°10'32" W 13 495 1 509

Cannery Row MO-362-02 454-044 36°36'46" N 121°53'47" W 198 86 88 372

Bird Rock MO-362-03 454-006 36°35'30" N 121°57'59" W 2,651 16 2 2,669

Guillemot Island Area MO-362-06 454-023 36°31'45" N 121°56'47" W 554 20 30 18 10 632

Bird Island MO-362-09 454-009 36°30'24" N 121°56'32" W 6,151 4 90 5 2 6,252

Castle Rocks and Mainland MO-362-19 454-010 36°22'35" N 121°54'25" W P 750 46 12 1,050 19 1,877

Hurricane Point Rocks MO-362-20 454-011 36°21'40" N 121°54'25" W P 29 H 14 613 20 H 676

Anderson Canyon Rocks MO-360-13 454-016 36°9'7" N 121°39'53" W 321 5 26 2 32 386

Burns Creek Rocks MO-360-14 454-017 36°8'29" N 121°39'28" W 323 2 12 337

Plaskett Rock MO-354-07 477-002 35°55'13" N 121°28'41" W 849 H 5 H 1 855

Cape San Martin MO-354-08 477-003 35°53'16" N 121°27'54" W 750 2 18 349 H 1,119

Redwood Gulch Rock MO-354-12 477-005 35°50'19" N 121°24'3" W 372 2 H 374

La Cruz Rock SL-354-04 477-006 35°42'22" N 121°18'45" W 678 18 696

Piedras Blancas Island SL-352-01 477-007 35°39'51" N 121°17'17" W 2,627 34 29 3 H 1 2,694

Morro Rock and Pillar Rock SL-352-07 477-026 35°22'13" N 120°52'8" W 117 24 53 114 24 332

Fairbank Point SL-352-08 477-044 35°21'5" N 120°50'37" W 331 331

Unnamed Rocks SL-350-03 477-010 35°14'40" N 120°53'38" W 174 49 242 6 471

Lion Rock SL-350-05 477-011 35°13'3" N 120°52'16" W 277 H 24 18 1 320

Pup Rock and Adjacent Mainland SL-350-04 477-028 35°13'17" N 120°52'13" W 1,309 44 2 1,355

Pecho Rock SL-350-09 477-032 35°10'45" N 120°48'59" W 321 14 335

Table Notes

1. This table contains numbers of breeding birds at specific colonies or composite sites, for the species indicated. The table shows the best available data for approximately 40 of the largest colonies and colony composites for selected marine birds that occur in the study area. 

 All colonies shown have 296 or more breeding birds, and sites are listed from north to south.

2. The primary source for these data is Carter et al. 1992 (unpublished data); most estimates from this source were made from 1989-1991. Older data older data are indicated by italics (e.g., data for Leach's storm-petrel), and more recent or updated data (from various sources,

 identified below) are indicated in bold type.

3. Key to symbols in table: H=historically nesting species; P = present and probably breeding. A blank in the table for a species/colony cell means the species was not present in the available data.

4. The column titled "Other Species" contains available estimates for all other breeding bird species. For most sites, this includes Black Oystercatcher. For the San Francisco Bay/Alcatraz composite site, the "Others" estimate includes California Gull, Forster's Tern, and Least Tern, 

 which breed at sites in the Bay.

5. For Ashy Storm-petrel, the updates at Bird Rock, Point Reyes and Double Point are from 2001 (Whitworth et al. 2002). The update at South Farallon Island is from 1992 (Sydeman et al. 1998).

6. The estimate of 600 breeding Marbled Murrelets at Big Basin State Park and Vicinity was provided by Laird Henkel, pers. comm.

7. For Cassin's Auklet and Rhinoceros Auklet, the updates in the vicinity of Año Nuevo are from 2002 and do not include the small breeding area within the Brandt's Cormorant colony. Sources: Thayer and Sydeman 2002a,b. 

8. The estimates of breeding birds for Leach's Storm-petrels are in italics and from Ainley and Lewis (1974); these older estimates are likely much higher than the current colonies' status. The number of breeding birds at Fish Rock has likely signficantly decreased; in August 1989, no Leach's

 Storm-petrels were captured at Fish Rocks, but this may be due to low sample effort (Harry Carter, pers. comm). And based on annual mark-recapture efforts since 1992, the number of breeding birds at S. Farallon Island has also likely significantly decreased (Bill Sydeman, pers. comm.).

9. Updates from 2002 (in bold) are included for the following eight species at South Farallon Island: Cassin's Auklet, Common Murre, Tufted Puffin, Pigeon Guillemot, Double-crested Cormorant; Pelagic and Brandt's cormorants, and Western Gull. Source: Warzybok et al. 2002.

10. The 2002 update for 246 breeding Common Murres at Devil's Slide Rock was provided by Gerry McChesney, U.S. Fish and Wildlife Service.

11. Fork-tail Storm-petrels have been noted as present and probably breeding at South Farallon Island, but no estimate is available.

87
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

Number of Percent

Birds Variance

Recorded Explained by

During Top Three Three Most Important Variables of Those Investigated,

Species Surveys Variables in Order of Importance

Pacific loon 3,802 10.6 Ocean season, distance to land (-), latitude (-)

Western grebe 7,080 15.5 Ocean season, distance to land (-), ocean depth (-)

Black-footed albatross 3,149 22.2 ocean depth (+), distance to land (-), year (-)

Laysan albatross 96 6.9 Ocean season, ocean depth (+), distance to land (+)

Northern fulmar 5,882 21.3 Ocean season, ENSO period, year (+)

Sooty shearwater 296,065 43.4 Ocean season, year (-), ENSO period

Pink-footed shearwater 4,145 13.1 Ocean depth (-), distance to land (-), ESNO period

Leach’s storm-petrel 1,414 28.4 Ocean season, distance to 2000m isobath (+), ENSO period

Ashy storm-petrel 4,201 17.3 ENSO period, season, year (+)

Fork-tailed storm-petrel 393 9.2 ENSO period, season, ocean depth (+)

Brown pelican 2,333 15.2 Distance to land (-), latitude (-), Ocean season

Brandt’s cormorant 9,482 28.7 Distance from colony (-), dist. to 200 m isobath, dist. to land (-)

Pelagic cormorant 396 6.1 Distance to land (-), ocean depth (-), dist. to 200 m isobath (-)

Double-crested cormorant 300 9.7 Dist. from colony (-), dist. To 200m isobath (-), dist. to land (-)

Red & Red-necked phalaropes 49,195 9.6 ENSO period, distance to land (-), ocean depth (-)

Western gull 29,545 44.2 Distance from colony (-), distance to land (-), ENSO period

Glaucous-winged gull 767 17.1 Ocean season, ocean depth (-), latitude (+)

Heermann’s gull 1,121 6.5 Distance to land (-), ENSO period, latitude (-)

California gull 13,721 24 Ocean season, year (+), latitude (+)

Black-legged kittiwake 4,565 28.9 Ocean season, ENSO period, year (+)

Common murre 131,675 52.3 Distance to colony (-), ocean depth (-), distance to land (-)

Rhinoceros auklet 14,679 19.8 Distance to land (-), season, ocean depth (+)

Tufted puffin 235 10.1 Distance from colony (-), year (-), distance to 200 m iso (+)

Cassin’s auklet 63,465 25.8 Distance to land (-), year (-), ocean depth (-)

Marbled murrelet 273 4.7 Distance to land (-), latitude (+), ENSO period

Table 19. Three most important variables (of nine investigated) having independent effects in explaining the variance in density of 25 selected 

marine bird species.

Table 20. Effects of ocean season and ENSO events on the abundance of 26 marine bird 

species off central California between 1985 and 2002, as determined through multiple regression analyses.

Notes

1. For “continuous” variables, a positive (+) included with a variable indicates that density increased with an increase in 

 the magnitude of that variable; (-) denotes the opposite.

2. The nine independent variables used in the regression analysis were: distance to nearest land; ocean season; ocean depth; 

 ENSO period; year; latitude; distance to colony; distance to 200m isobath; and distance to 2,000m isobath. 

3. Species that breed in the study area are shown in bold.

by management. The individual species text (accompanying 

each map) details where selected species become more or less 

abundant in north/central California during periods of warmer 

or colder than average ocean temperatures. Actually, the shift 

in temperature is a proxy for many other changes, all of which 

ultimately affect the food web.

To illustrate the short-term ocean climate effects using species 

maps, a comparison was done using selected species density 

maps for a specific El Niño and La Niña period. For the El 

Niño period, the most recent, and very intense El Niño event, 

Oceanic Season 1997 through Upwelling Season 1998, was 

used; for the La Niña event, the period covering the Oceanic 

Season 1998 through Oceanic Season 1999 was used. These 

two periods were chosen because climate differences were 

extreme, i.e. among the strongest ENSO events of the past 100 

years, and they occurred adjacent to one another. Therefore, 

a comparison of population response was not confounded by 

long-term trajectories in base population size. Tables 20 and 21, 

as well as Figure 58, provide some examples of these changes 

due to interannual climate events (see Table 14).

Warm-water Periods (e.g., El Niño events). During warm-water 

events (including El Niño), many marine bird species tended 

to occur closer to shore than during other years (Ainley and 

Boekelheide 1990, Oedekoven et al. 2001). During warmwater periods, five of the predominant species became more 

abundant in central California waters in general, and inside 

the marine sanctuaries; these species include pinkfooted shearwater, Leach’s storm-petrel, and western, 

glaucous-winged and Heermann’s gulls; see Table 20 

below. Also increasing in the study area during warmwater periods were less abundant species including 

black and least storm-petrels and black-vented 

shearwater.

Cold-water Periods (e.g., La Niña events). During 

coldwater periods, areas 

of relatively high avifaunal 

biomass and density 

expanded to cover broader 

portions of the study area; 

11 of the predominant 

species became more 

abundant. Species whose 

abundance showed the 

greatest increases were the 

western grebe, northern 

fulmar, ashy storm-petrel, red 

and red-necked phalaropes 

(grouped), and black-legged 

kittiwake (Table 20). Others, 

whose abundance were also 

significantly greater during La 

Niña periods were Pacific loon, 

Laysan albatross, California 

gull, rhinoceros auklet, and 

marbled murrelet. 

Neutral Periods (i.e., neither 

unusually warm nor cold 

water). Four species, blackfooted albatross, sooty 

shearwater, tufted puffin 

and Cassin’s auklet were 

significantly more abundant 

during the neutral period than 

during the warm or cold periods.

Other Responses to Short-Term 

Climatic Change

both were greater during these periods than during the Neutral 

period. On the other hand, the brown pelican responded strongly 

to the disparity of conditions between the very strong 1997-98 

El Niño and the very strong 1999-00 La Niña (Figure 59). The 

black-vented shearwater, for which there were insufficient data 

for long-term trend analysis, responded much more dramatically, 

with large numbers invading central California waters during the 

1997-98 El Niño. Finally, there were no significant differences 

Ocean Season(s)

of Highest ENSO Event of

Species Abundance* Highest Abundance*

Pacific Loon DC LA

Western Grebe DC LA

Black-footed Albatross UP NE

Laysan Albatross DC LA

Northern Fulmar DC LA

Sooty Shearwater UP NE

Pink-footed Shearwater OC EL

Leach’s Storm-Petrel DC/UP EL

Ashy Storm-Petrel OC LA

Fork-tailed Storm-Petrel DC LA/EL

Brown Pelican OC LA/EL

Brandt’s Cormorant UP ns

Pelagic Cormorant UP ns

Double-crested Cormorant UP ns

Red & Red-necked Phalaropes OC LA

Western Gull UP EL

Glaucous-winged Gull DC EL

Heermann’s Gull ns EL

California Gull DC LA

Black-legged Kittiwake DC LA

Common Murre UP ns

Rhinoceros Auklet DC LA

Tufted Puffin UP/DC NE

Cassin’s Auklet UP NE

Marbled Murrelet DC/UP LA . In regression 

analyses, the densities of the brown * Notes. Ocean seasons are: Davidson Current (DC), Upwelling (UP), and Oceanic (OC); pelican and fork-tailed storm-petrel 

were not significantly different during ENSO periods are El Niño (EL), La Niña (LA), and neutral (NE). For species having

warm-water and cold-water periods. significant differences in abundance during respective seasons/periods (Sidak tests,

Basically, this was because such P < 0.01), the season/period in which they were most abundant is given. If

periods varied greatly in intensity, densities did not differ between the two seasons/periods in which they were most

thus reducing effects especially if abundant, then the two are listed (eg. DC/UP, where densities were slightly higher

other factors (not studied) were more in DC season that the UP season). Species for which there was no significant effect

important. However, the densities of of season or period are denoted with “ns”.

88
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

in the abundance of common murre and the three cormorant 

species among the three climate-related periods. 

Breeding species (e.g. common murre, Cassin’s auklet) whose 

populations are not increased by an influx of visitors from 

colonies outside the study area during warm-water periods, 

and the cormorant species, are more dispersed during the 

national marine sanctuaries off north/central California 

generally encompass the areas of high concentrations and 

diversity for marine birds, except for the western edge of the 

Gulf of Farallones area and the "sanctuary exclusion area" off 

San Francisco and Pacifica.

Owing perhaps to a response to competition for food by the 

large numbers of marine birds nesting on the Farallon Islands 

and Point Reyes Headlands, during the breeding (Upwelling) 

season high concentrations of several breeding species extend 

seaward of the western boundary of the Gulf of the Farallones

National Marine Sanctuary, over the Farallon Escarpment and 

beyond. This is especially true of Ashy Storm-petrel, Western 

Gull, Common Murre, and Rhinoceros Auklet. For the gull and 

murre these deeper waters are not their preferred foraging 

habitat, but they choose to forage there during breeding 

because more suitable continental shelf habitat to the north 

and south is too far out of range. 

To a lesser degree, a smaller high density area existed seaward 

of Año Nuevo Island, where there is a smaller, but important 

colony. These three colonies (Farallon Islands, Point Reyes 

Headlands and Año Nuevo Island), and the waters between 

them which comprise the Gulf of the Farallones, possess 

populations that interact regularly in the shallow waters that 

lie between them; many individuals marked at one have been 

seen at the other two sites. Therefore, in terms of marine birds 

the waters of the Gulf of the Farallones, as defined above, 

constitute a natural management unit.

In addition, it was apparent from visual inspection of the maps, 

that the "sanctuary exclusion area" (i.e., the ocean area off San 

Francisco and Pacifica that is excluded from the Monterey Bay 

National Marine Sanctuary) represents a very important area 

for marine birds, especially those that breed at localities within 

the Gulf of the Farallones National Marine Sanctuary (e.g. Point 

Reyes, Farallon Islands) (David Ainley, pers. comm.). This area 

is influenced strongly by the San Francisco Bay tidal plume, 

which provides habitat for many forage fish. This "sanctuary 

exclusion area" is also one of the main foraging areas of the 

Devil’s Slide murre colony, which is in the process of being 

restored (David Ainley, pers. comm.).

With regard to the offshore bounds of the sanctuaries, among 

the species of marine birds mapped, only 11 had significant 

concentrations seaward of sanctuary boundaries (see Table 

16). In terms of management, it is important to consider Ashy 

storm-petrel and its habitat, because it is listed as a "State 

Species of Concern". The Xantus’ murrelet, a recently listed 

species, also deserves consideration, although the proportion 

of this species’ population that visits the central California 

National Marine Sanctuaries is relatively low.

Table 21. A summary of changes in marine bird occurrence patterns, as a response to 

warm and cold ocean anomalies, as determined by visual comparison of species’ maps 

during the 1997-1998 El Niño event and the 1999-2000 La Niña event.

breeding season during warm-water periods 

(Table 21). This spreading is often affected 

most strongly by Farallon breeding species, 

Species

Effect on Distribution 

No Change El Niño La Niña

Western grebe X

Pacific loon X

Black-footed albatross X

Laysan albatross X

Northern fulmar More spread

To Monterey 

Sooty shearwater Bay

Pink-footed shearwater X

Buller’s shearwater X

To Gulf of 

Black-vented shearwater Farallones

Leach’s storm-petrel X

Ashy storm-petrel More spread

Fork-tailed storm-petrel X

Black storm-petrel

To Gulf of 

Farallones

Brown pelican More spread

Brandt’s cormorant More spread

Pelagic cormorant More spread

Red phalarope X

Red-necked phalarope X

Glaucous-winged gull More confined

Western gull X

California gull More confined

Heermann’s gull

To Monterey 

Bonaparte’s gull Bay

Sabine’s gull X

Confined to

Black-legged kittiwake slope More spread

Caspian tern X

Elegant tern X

Arctic tern X

Common murre More spread

Pigeon guillemot More spread

Tufted puffin More spread

Rhinoceros auklet X

Cassin’s auklet More spread

Marbled murrelet More offshore

Xantus/Craveri murrelets X

which usually concentrate near the Gulf of the 

Farallones (outer shelf), and which move more 

to coastal waters. 

Population Trends. Owing mainly to longerterm, decadal shifts in marine climate (Hare 

and Mantua, 2000, Mantua and Hare 2002), a 

number of species exhibited gradual changes 

in population size within the study area, from 

1985 to 2002. These patterns were revealed 

using regression analyses, especially in cases 

where Year was an important explanatory 

variable to species occurrence (Table 19). 

Ashy storm-petrel and California gull 

exhibited a gradual increase in population 

(from 1985-2002); Tufted puffin showed a 

gradual decrease. The Black-legged kittiwake 

increased gradually, too, but was especially 

abundant after 1998 (Figure 60). 

For other species the pattern was more 

complex. Black-footed albatross, sooty 

shearwater, fork-tailed storm-petrel and 

Cassin’s auklet showed a gradual decrease 

from 1985 until about 1999, when they began 

to increase. 

The year 1999 is when the system likely 

shifted from a ‘warm’ to a ‘cold’ ocean regime 

(Bogard, 2000; Schwing and Moore, 2000). 

The northern fulmar exhibited a variable but 

‘steady’ population size during the 1980s and 

early 1990s but then began to increase with 

arrival of the ‘cold’ regime. The population of 

the common murre remained stable through 

most of the study period following a dramatic 

decline in 1982 (Ainley and Divoky 2001, 

Manuwal and Carter 2001), but recently it has 

begun to increase (H. Carter, pers. comm.). 

These responses to decadal regime shifts 

present challenges to the researchers and 

managers even greater than those offered by 

short-term climate shifts (e.g., ENSO events). It takes several 

years of monitoring to detect long-term shifts in population 

size.

Relevance of Marine Sanctuary Boundaries to Marine 

Birds. Based on the available data, the boundaries of the 

MAJOR SECTION CONTRIBUTORS

David Ainley, H.T. Harvey and Associates 

R. Glenn Ford, R.G. Ford Consulting Co. 

Janet Casey R.G. Ford Consulting Co. 

Larry Spear, H.T. Harvey and Associates 

Carol Keiper, Oikonos 

Lisa Ballance, Southwest Fisheries Science Center, NOAA 

Tracy Gill, NCCOS, NOAA

Wendy Willams, R.G. Ford Consulting Co. 

Ken Buja, NCCOS, NOAA

REVIEWERS

Two reviews were done for the marine bird analyses. The first 

was a workshop to review draft maps in October 2002, and the 

second review focused on the overall draft bird report (which 

contains the maps) and was conducted via email November 

and December, 2002. Most of the review comments were addressed or incorporated for this product, which is a summary 

of a full bird report to be released later this year. 

Workshop Participants/Reviewers:

David Ainley, H.T. Harvey and Associates

Sarah Allen, Point Reyes National Seashore, National Park 

Service

Lisa Ballance, Southwest Fisheries Science Center, NOAA

Janet Casey, R.G. Ford Consulting Co.

Glenn Ford, R.G. Ford Consulting Co.

Carol Keiper, Oikonos

Nora Rojek, formerly of California Department of Fish and 

Game

Jan Roletto, Gulf of the Farallones National Marine Sanctuary 

Program, NOAA 

Ed Ueber, NOAA, Gulf of the Farallones National Marine 

Sanctuary Program

And several other members of the NOAA project team and 

sanctuary programs.

Reviewers of the Draft Bird Report:

Sarah Allen, Point Reyes National Seashore, National Park 

Service

Scott Benson, Southwest Fisheries Science Center, NOAA

Karin Forney, Southwest Fisheries Science Center, NOAA

Doug Forsell, Chesapeake Bay Program, U.S. Fish and Wildlife 

Service

Laird Henkle, H.T. Harvey and Associates

David Hyrenbach, Duke University Marine Lab 

Hannah Nevins, Moss Landing Marine Laboratories

Jan Roletto, Gulf of the Farallones National Marine Sanctuary 

Program, NOAA

Franklin Schwing, Southwest Fisheries Science Center, 

NOAA

And several other members of the NOAA project team and 

sanctuary programs.

89
Section 2.2: BIOGEOGRAPHY OF MARINE BIRDS

PERSONAL COMMUNICATIONS

Laurence Breaker, Moss Landing Marine Laboratory

Harry R. Carter, U.S. Geological Survey, Dixon CA

Laird Henkel, H.T. Harvey and Associates, San Jose CA

Michelle Hester, Oikonos, Bolinas, CA

Gerry McChesney, U.S. Fish and Wildlife Service

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91
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

INTRODUCTION

The California Current passes south through the study area 

off north/central California, which, along with areas of strong 

coastal upwelling, makes this area one of the most productive 

ocean systems in the world (Glantz and Thompson, 1981). 

Because of this productive environment, the study area 

contains a rich fauna of marine mammals, as evidenced in 

marine mammal abundance and richness.

In addition to many marine mammal species that live here yearround and use the region’s coasts and islands for breeding and 

hauling out, the community of seasonal residents and migrants 

is even more robust. Central California is the destination for 

many marine mammal species seeking productive feeding 

areas and acceptable habitat in which to spend their 

nonbreeding periods, providing evidence of the region’s 

trophic richness. Over 29 species of marine mammals occur 

in the study area off north/central California; over 22 cetaceans 

(whales, dolphins, and porpoises), six pinnipeds (seals and 

sea lions), and one fissiped species (the sea otter).

The objectives of this assessment were to: 1) identify spatial 

and temporal distributions and patterns for marine mammals 

that occur in ocean waters off north/central California between 

Point Arena (38.91oN) and Point Sal (34.90oN); 2) identify 

important areas and time periods associated with higher 

concentrations of these species; and 3) identify important data 

and information gaps observed as a result of this analysis. 

In this analysis, ‘important’ season or area refers to those 

having relatively higher concentrations of a particular species; 

in Phase II diversity may also be considered.

Preliminary Results. Summarized below are the spatial 

and temporal occurrence patterns of data for 13 species that 

regularly occur in marine waters off north/central California. The 

results of this marine mammal assessment are preliminary

(Phase I) and feature highlights of work in progress. Due to 

the difficulty in obtaining adequate distributional data sets and 

the complexity of combining available marine mammal data 

sets, maps for only 13 species were completed in Phase 1, 

and are included in this document. These maps are referred 

to as CDAS maps, and represent a compilation of data sets 

from 1980 through 2001, as described below. Also included in 

this document and on the CDROM are sighting and effort maps 

for 16 marine mammals from a single data set (the marine 

mammal stock assessment surveys from NOAA's Southwest 

Fisheries Science Center (SWFSC)). These data will likely be 

incorporated into Phase II of the analysis. 

Additional data compilation, data analysis and expert review 

are needed to complete the final analyses of marine mammals 

occurrences in the study area. More complete results will be 

presented in a final report in Phase II of this project. Additional 

products planned for Phase II are listed at the end of this 

section.

DATA AND ANALYSES

Overview of Map Development and 

Analysis Process To Date. The methods 

used in each survey were different, and 

because of this, careful consideration and 

correction are required to merge the data 

sets in a meaningful and scientifically 

acceptable way. Data preparation for the 

mammal analyses included the following 

steps: species and study area selection, 

data set identification and collection, data 

corrections, data conversion into common 

units, organizing the data into 10’x10’ cells 

or leaving them as sightings and effort, and 

map development. For species present in 

sufficient numbers, seasonal density maps 

were developed, and for infrequently sighted 

species, sighting and effort maps were 

developed. CDAS maps were created for 

13 species. The original draft maps were 

reviewed at an expert workshop in October 

2002; there it was determined that additional 

data, corrections and analyses were required 

to improve the mammal maps; this work will 

be done in Phase II of this project. Some 

revisions have been made to the maps and 

text of this document since its draft release 

in April 2003.

Species Selected for Analysis. Selection 

criteria for marine mammal species included 

in this assessment were: 1) the species 

distribution includes the study area, and 2) 

survey data for the species was available 

in a useable format. Some species of marine mammals are 

infrequently sighted and their distributions are therefore difficult 

to map. In addition, some data sets were unavailable at the 

time of the analysis. Over the past few months, additional data 

sets have been made available, and these will be added in 

Phase II. Improvements and updates are planned for the at-sea 

maps, as well as for the haulout and rookery maps, if funding 

is made available.

Table 22 is a list of marine mammal species that were 

considered for this analysis; density maps were developed 

for eight species in MMS-CDAS (MMS, 2001) a data display 

system developed by R.G. Ford Consulting Co. for the Minerals 

Management Service. Sightings maps were developed in CDAS 

for an additional four species. Maps of sea otter counts and 

pinniped haulouts and rookeries were also developed. Also 

included in this document are maps for three species from 

NOAA’s Southwest Fisheries Science Center (SWFSC). These 

maps are included to illustrate one of the data sets that will 

likely be incorporated into the mammal map analysis in Phase 

II. SWFSC maps for an additional 13 species are included 

on the CD-ROM. Plans for Phase II include the following: 1) 

acquire the additional available data sets; 2) correct the data 

sets for species’ sightability, detectability and other factors; 

and 3) develop composite maps for about 23 species, singly 

or in combination.

About the Literature and Survey Data Used in this 

Assessment. This assessment is based on the efforts of 

individual researchers to study marine mammal spatial and 

temporal patterns, federal and state government efforts to 

assess stock size and the potential biological impacts of oil 

development, and state government efforts to respond to oil 

spills. 

No. of Draft No. of No. of Maps

CDAS Maps, SWFSC Planned for

Common Name Scientific Name Order/Suborder Family Phase l Maps, Phase l Phase II 

Fissiped

Southern sea otter Enhydra lutris nereis Carnivora/(none) Mustelidae 1 1

Pinnipeds

California sea lion Zalophus californianus Carnivora/PinnipediaOtariidae 2 1

Steller sea lion Eumetopias jubatus Carnivora/PinnipediaOtariidae 1 1

Northern fur seal Callorhinus ursinus Carnivora/PinnipediaOtariidae 1 1

Harbor seal Phoca vitulina richardsi Carnivora/PinnipediaPhocidae 1 1

Northern elephant seal Mirounga angustirostris Carnivora/PinnipediaPhocidae 1 1

Cetaceans

Dall's porpoise Phocoenoides dalli Cetacea/Odontoceti Phocoenidae 1 1 1

Harbor porpoise (stocks: Northern CA, San

Francisco/Russian River, Monterey Bay) Phocoena phocoena Cetacea/Odontoceti Phocoenidae 1 1?

Pacific white-sided dolphin Lagenorhynchus obliquidens Cetacea/Odontoceti Delphinidae 1 1 1

Risso's dolphin Grampus griseus Cetacea/Odontoceti Delphinidae 1 1 1

Bottlenose dolphin (California coastal stock) Tursiops truncatus Cetacea/Odontoceti Delphinidae 1 1?

Short-beaked common dolphin Delphinus delphis Cetacea/Odontoceti Delphinidae 1 1

Northern right whale dolphin Lissodelphis borealis Cetacea/Odontoceti Delphinidae 1 1 1

Killer whale Orcinus orca Cetacea/Odontoceti Delphinidae 1 1?

Baird's beaked whale Berardius bairdii Cetacea/Odontoceti Ziphiidae 1 1?

Cuvier's beaked whale Ziphius cavirostris Cetacea/Odontoceti Ziphiidae 1 1?

Beaked whales (Mesoplodonts) Mesoplodon spp. Cetacea/Odontoceti Ziphiidae 1 1?

Sperm whale Physeter macrocephalus Cetacea/Odontoceti Physeteridae 1 1?

Blue whale Balaenoptera musculus Cetacea/Mysticeti Balaenopteridae 1 1 1

Humpback whale Megaptera novaeangliae Cetacea/Mysticeti Balaenopteridae 1 1 1

Fin whale Balaenoptera physalus Cetacea/Mysticeti Balaenopteridae 1 1?

Minke whale Balaenoptera acutorostrata Cetacea/Mysticeti Balaenopteridae 1 1?

Gray whale Eschrichtius robustus Cetacea/Mysticeti Eschrichtiidae 1 1

MAP TOTALS 14 16 14-23

Table 22. Marine mammal species included in this assessment and map types developed for them (Phase I and Phase II)

92
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Related Literature. The at-sea distribution and abundance of 

marine mammals within the study area has been described 

in many publications, some of which include the following: 

Bonnell et al. (1983), Dohl et al. (1983), Calambokidis et 

al (1988, 1990, 1996), and Allen (1994). Numerous marine 

mammal stock assessment studies have been conducted by 

the Southwest Fisheries Science Center, LaJolla, CA (NMFS/

SWFSC ship surveys): Barlow (1988, 1995), Barlow and Forney 

(1994), Barlow and Gerrodette (1996), and Forney and Barlow 

(1998). A few ecosystem studies of marine mammals in this 

region have also been conducted by Schoenherr (1991), Black 

(1994), Kieckhefer (1992), Croll et al. (1998), Forney and 

Barlow 1998, Forney 2000, Benson et al. (2002) and Keiper 

et al. (In Review). 

The Data Sets. The ship and aerial strip transect data used in 

this assessment were collected from 1980-2001 and ranged 

from Point Arena south to Point Sal, and offshore to the extent 

of data availability. Estuaries were not part of the GIS study 

area, but coastal haulouts and rookeries, when available, were 

mapped to provide a more complete view of important areas 

for pinniped species. See Table 23 for additional information 

on the data.

Data Synthesis.

Summarizing Transect Data into Grid Cells for CDAS Maps

Table 24. Summary of combined data set effort at sea for mammals, by ocean season.

Number

Dates Used for Number Kilometers of 10' 

Ocean Each Ocean of Years of Trackline Number Cells

Season Season Months Included Taxa Surveyed of Visits Sampled

Upwelling 15 Mar-14 Aug 5

1980-1982,

1985-2001

Pinnipeds: 63,262 10,902 283

Cetaceans: 96,978 15,280 317

Oceanic 15 Aug-14 Nov 3

1980-1982,

1991, 1994-

2001

Pinnipeds: 30,443 4270 263

Cetaceans: 49,981 6821 322

Davidson

Current 15 Nov-14 Mar 4

1980-1986,

1991-2001

Pinnipeds: 38,816 5594 360

Cetaceans: 64,048 8897 383

TOTAL 1 Jan-31 Dec 12 1980-2001

Pinnipeds: 132,521 20,766 395

Cetaceans: 211,007 30,998 416

. The 

above data sets were processed to compensate and correct 

for differences in survey methodology, including platform type 

(ship or aerial) and transect width, among the various studies. 

Because wind speed affects detection of marine mammals, data 

collected when wind speed exceeded 25 kt were excluded. Data 

were allocated into 10’ x 10’ cells (i.e., 10-minute latitude by 

10-minute longitude cells). All aerial data were continuous; each 

ship-based data set was converted separately into a continuous 

transect format to the extent possible. The continuous aerial 

data were binned into the appropriate cell. For the SF-DODS 

and EPOCS studies, and the Rockfish Assessment cruises prior 

to 1997, the beginning position, ship heading, and speed were 

used to compute the end position of each 2-4 km continuous 

transect. From this, a midpoint of the transect was determined. 

As times of observations were not available, the position of 

the midpoint was used to select the cell to which the survey 

effort was assigned. If this midpoint fell on a cell boundary, it 

was assigned to the cell to the north or west. To maintain the 

correspondence between effort and mammal observations, 

observations were also assigned to the transect midpoints. 

For the Rockfish Assessment Cruises from 1997 onward, effort 

was assigned to the cells through which the vessel passed 

based on the proportion of trackline that fell within each cell, and 

observations were interpolated along the cruise track according 

to the time of each observation. 

Data Analysis.

Effort Summary. For all surveys, 132,521 kilometers of trackline 

(pinnipeds and cetaceans) and 78,486 kilometers of additional 

trackline (cetaceans only) were analyzed (Table 24). A total of 

3,459 observations of 7,039 pinnipeds and 2,313 observations 

of 69,286 cetaceans were included in analyzed data. Survey 

effort used in this assessment for pinnipeds and cetaceans are 

summarized as maps in Figure 61.

Organizing Data into Ocean Seasons. Effort and species 

data were organized and mapped into three distinct ocean 

seasons (Bolin and Abott 1963): Upwelling, Oceanic, and 

Table 23. Summary of at-sea data sets used in the preliminary marine mammal analyses.

Davidson Current, because ocean conditions differ distinctly 

among them and are known to affect the biota of the California 

Current (e.g. Ainley 1976, Briggs et al. 1987). As there is 

significant interannual variation in the actual duration of these 

seasons, the following dates were ‘defined’ for each season for 

purposes of analysis: Upwelling Season is 15 March-14 August, 

Oceanic Season is 15 August-14 November, and Davidson 

Current Season is 15 November-14 March. 

As evident in Table 24, the Upwelling Season had the greatest 

amount of survey effort, followed by the Davidson Current 

Season. The Oceanic Season had the lowest effort. Unlike 

the other seasons, the Oceanic Season had no data from 

the 1980s. Because of the variation in effort coverage across 

space and time (and methods, as well as many other factors), 

interpretation of the data requires careful consideration.

Data Set

Principal

Investigator

Vessel Name

& Platform

Height

Habitat

Covered2 Years

Ocean

Seasons

Covered

Total Transect

Width:

Pinnipeds

Total Transect

Width:

Cetaceans

MMS HighAltitude Aerial

Surveys Dohl

Pembroke,

270m

Surface survey 

of the shelf, 

slope & deep

ocean beyond 1980-1983

All three

seasons N/A

harbor porpoise, 

254m; great 

whales, 1130m; 

all others, 885m

MMS LowAltitude Aerial

Surveys Bonnell Pembroke, 62m

Surface survey 

of the shelf, 

slope & deep

ocean beyond 1980-1983

All three

seasons 109m 109m

EPOCS

Shipboard

Surveys Ainley

Surveyor, 12m, 

Discoverer,

Oceanographer, 15m

Surface survey 

of the deep

ocean 1984-1994

All three

seasons 300-600m 800m

CA Seabird

Ecology LowAltitude Aerial

Surveys Briggs

Partenavia,

62m

Surface survey 

of shelf and

slope 1985

Mainly

Upwelling 50m 50m

NMFS

Midwater

Trawls for Juv. 

Rockfish:

Ship Surveys Ainley

David Starr

Jordan,10m

Surface survey 

of shelf and

slope to 3000 m 1985-2001

Mainly

Upwelling 300m 800m

OSPR Low

Altitude Aerial Partenavia,

Surface survey 

of shelf and 1994-1998, All three

Surveys Bonnell 62m slope 2001 seasons 50m 50m

MMS Santa

Barbara

Channel Low

Altitude Aerial Partenavia,

Surface survey 

of shelf and All three

Surveys Bonnell 62m slope 1995-1997 seasons 50m 50m

SF-DODS

Shipboard

Surveys Ainley Point Sur, 8m

Surface survey 

of shelf and

slope to 3000 m 1996-2000

All three

seasons 300m 800m

Notes

See additional description of these data sets on the CD for more information on the CDAS data sets. 

Data from the marine mammal stock assessment of NOAA's SWFSC were not included in the preliminary CDAS asssessment.

93

Table 23. A Summary of At-Sea Data Sets Used in the Preliminary Marine Mammal Assessment
Calculating Density and Developing Seasonal Density CDAS 

Maps. From the digitized survey data, we mapped the distribution 

of effort and of species observations into a grid of 10’ by 10’ 

cells, using the MMS-CDAS mapping system (MMS, 2001). 

The larger cell size was determined to be more meaningful by 

experts at a preliminary map/data review session.

The species data were first transformed into densities on the 

basis of strip widths (which varied by ship or aerial platform, 

depending on speed and height above water; see Table 23). 

The number of individuals of each species seen was then 

divided by area surveyed to estimate density in each cell for 

that data set. For construction of density plots, if a cell was 

censused in other years or the same year by another survey, 

densities in cells were averaged and weighted according to 

effort. These maps display observed densities; in Phase II these 

densities will be corrected to account for additional factors such 

as sightability.

Seasonal High Use Areas for Individual Species. The purpose 

of the seasonal high use maps is to provide a summary map 

for a species' spatial patterns. These maps were developed for 

mammal species with density data, with the seasonal density 

data binned into 10’ x 10’ cells for each species or species 

group. Non-zero cells were then ranked and those in the top 

20 percent were selected and defined as seasonal high use 

areas. Cells were then mapped with color corresponding to the 

number of ocean seasons of high use. The index is therefore 

sensitive to cells that were not sampled in any one of the three 

seasons, causing a downward bias in the index. Use of a 10'x10' 

cell size greatly reduces the magnitude of this bias.

Cells in which there was effort but animals were not observed, 

and cells where sightings occurred but were never high use 

areas, were also provided.

Developing Sighting and Effort CDAS Maps for Infrequently 

Sighted Species. Where sightings were too few to warrant 

seasonal density maps, observations were mapped as point 

locations. For context, overall survey effort is also presented. 

This display method was chosen in response to comments by 

expert reviewers at the October 2002 workshop and in view of 

the low numbers of sightings of certain species. 

Preliminary Rookeries and Haulouts by Species

Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

. Pinniped 

rookeries and haulouts are monitored and surveyed by a variety 

of institutions and individuals. Recent data (varying by species, 

but generally from 1998-2002) were used to represent locations 

of rookeries and haulout sites for five pinniped species. In 

Phase II, additional information on harbor seal pupping sites 

Figure 61. Total at-sea survey effort for marine mammal analyses.

129°W 128°W 127°W 126°W 125°W 124°W 123°W 122°W 121°W

°N53

°N53

°N63

°N63

°N73

°N73

°N83

°N83

°N93

°N93

129°W 128°W 127°W 126°W 125°W 124°W 123°W 122°W 121°W

°N53

°N53

°N63

°N63

°N73

°N73

°N83

°N83

°N93

°N93

Combined At-Sea Effort for Marine Mammal Analysis

2

2

0

0

0

0

0 m

m

Pinniped Effort

a

2

2

0

0

0

0

0 m

m

Cetacean Effort

b

Effort

(Km of trackline)

0 25 50 Km

> 1500

1000.01 - 1500.00

500.01 - 1000.00

250.01 - 500.00

100.01 - 250.00

50.01 - 100.00

25.01 - 50.00

5.01 - 25.00

0.01 - 5.00

Effort

(Km of trackline)

0 25 50 Km

> 1500

1000.01 - 1500.00

500.01 - 1000.00

250.01 - 500.00

100.01 - 250.00

50.01 - 100.00

25.01 - 50.00

5.01 - 25.00

0.01 - 5.00

Source Data: See text.

will be added and an overall rookery and haulout map for the 

pinnipeds will be developed.

ANALYTICAL MAP PRODUCTS

A series of over 50 preliminary maps (41 CDAS maps and 12 

SWFSC maps) and related results are presented in this section; 

additional SWFSC maps for 13 mammal species/species 

groups are included on the CD-ROM. These preliminary maps 

will be finalized and included in a Phase II report.

94
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 62. Maps for southern sea otter: rangewide count and linear density, fall 2001 and spring 2002. 

ABOUT THESE MAPS

Maps 62a and b display the locations of groups of southern sea 

otters during the Fall 2001 and Spring 2002 rangewide counts. 

Maps 62c and d summarize these rangewide count data into 

coastal strips approximately 10km in length, in order to display 

linear densities along the shore. The northern extent of the data 

is south of Half Moon Bay; sea otters are also present to the 

south of the mapped area. 

DATA SOURCES

Data were collected by wildlife biologists from the U.S. Department of the Interior (currently the USGS Biological Resources 

Division), California Department of Fish and Game, the Monterey Bay Aquarium, and trained volunteers during semi-annual rangewide counts in Fall 2001 and Spring 2002. The Fall 

2001 count was conducted during the period 4-20 November 

2001, the Spring 2002 count was conducted during the period 

5-22 May 2002. The data set was provided by Mike Kenner, 

UCSC but is sourced to USGS; contact Brian Hatfield for more 

information. 

METHODS

The original data were entered from hand marked maps into a 

custom designed digitizing program which assigned coordinates 

to each observed sea otter group. Positions of animals toward 

the ends of the range and in Elkhorn Slough were not assigned 

coordinates by this program. Each group was also assigned to 

an ATOS (As The Otter Swims) number, which are numbers 

approximately 0.5 km apart along a smoothed 5 fathom contour 

line along the coast from Golden Gate to approximately Santa 

Barbara. These numbers were used to get approximate positions for otters without assigned coordinates.

A series of coastal segments approximately 2 km in width was 

created for display purposes. Each segment was approximately 

10 km in length; divisions were based on the ATOS numbers 

described above. Twenty ATOS numbers approximately 500m 

apart were included in each segment. The coordinates of each 

otter group were used to place it within a particular segment, 

and the otters in each segment were summed. This provides 

an estimate of linear density (otters per segment or otters 

per 10km) since the segments were approximately 10km in 

length.

RESULTS AND DISCUSSION 

The southern sea otter (Enhydra lutris nereis) is one of three 

subspecies: southern (E.l.nereis), northern (E.l.kenyoni), and 

Russian (E.l.lutris). The southern sea otter is listed as threatened under the Federal Endangered Species Act, and depleted 

under the Marine Mammal Protection Act (MMPA). Under California Fish and Game Code, the southern sea otter is listed as 

a “fully protected” species. The southern sea otter generally 

inhabits the near-shore waters of the central California coast, 

from Half Moon Bay to Goleta, just south of Point Conception 

with uncommon sightings of animals beyond these areas (pers. 

comm. B. Hatfield); the distribution of otters along the south 

end has been highly variable since the expansion of the sea 

otter range south of Point Conception (pers.comm. M.Harris). 

In the study area, sightings have occurred as far north as Point 

Reyes (Point Reyes Headlands, Double Point, Duxbury Reef; 

not shown on map; pers.comm. S. Allen). Sea otters occur 

along rocky shorelines with kelp beds (but also in open water 

habitats, sandy/soft bottom areas, and tidal estuaries) and in 

depths of water about 20-40 m (some to 60 m, and rarely to 

100 m; M. Kenner pers. comm). 

Overall, numbers of otters per segment were greater in the 

southern portion of the Monterey Bay National Marine Sanctuary. In the census of Fall 2001 (map a), greater numbers of 

otters per segment occurred along the Carmel coast and from 

Piedras Blancas south to Point San Luis. Seasonal changes 

in abundance and distribution of sea otters are believed to 

be affected by male movements during the period when most 

breeding occurs (June/July through October/November) when 

they move from the periphery of the range toward the center of 

the range in search of estrous females (Bonnell et al., 1983). 

From December to April, many males migrate to the range peripheries, perhaps in search of more abundant prey (M.Harris 

pers. comm.). However, this is not evident in the maps. Seasonal changes also are affected by factors such as weather, 

sea conditions and abundance of kelp canopy (see Reidman 

and Estes, 1990). 

From 1983 until the mid 1990’s, trends in spring southern sea 

otter counts indicated sea otters increased steadily; in the midto late 1990’s, sea otter numbers declined (USFWS, 2000) 

and have since remained relatively constant (pers.comm. B. 

Hatfield). Sea otter count data is used as an index to assess 

trends in the population dynamics, not as a population estimate 

(pers.comm. M.Harris). The 2002 spring count was 1% below 

the 2001 count, from 2161 otters in 2001 to 2139 in 2002. The 

2001 count was 6.7% below counts from the previous year 

(USGS 2002). Due to its small population size, the southern sea 

otter population is especially vulnerable to human disturbance, 

competition with fisheries, and pollution, including the threat 

of a major oil spill. The lack of population growth and recent 

decline coincides with an increase in mortality (e.g., infectious 

diseases, white shark attacks) as indicated by the number of 

beach-cast sea otter carcasses (Estes et al., 2003). Otters near 

heavy freshwater flows are three times more likely to have been 

infected by Toxoplasma gondii, a protozoan parasite caused by 

parasite eggs in cat droppings (see Miller et al., 2002). 

Southern sea otters are key predators of benthic species (e.g. 

sea urchins, sea stars, mussels, clams, abalone, crabs) and 

123°W 122°W 121°W

123°W 122°W 121°W

°N53 °N63 °N73

123°W 122°W 121°W

123°W 122°W 121°W

°N53 °N63 °N73 °N83

Southern sea otter Enhydra lutris nereis

20

2

0 

0

m

0 

Rangewide Count 20

2

m

0

0

0

0

m

0 m

Spring 2002

Number of

Sea Otters

0 25 50Km

a b

20

Li ear Density 2

0

n 00

2

Linear Density 0

m

Rangewide Count 2

m

0

0

0 

0

m

0 m

Rangewide Count

Fall 2001 Spring 2002

c d

Rangewide Count

Fall 2001

151 - 200

101 - 150

51 - 100

26 - 50

11 - 25

1 - 10

Otters per

Segment

0

16 - 28

11 - 15

6 - 10

2 - 5

DRAFT

1

°N53 °N63 °N73 °N53 °N63 °N73

Source Data: See text.

octopus (see Riedman and Estes, 1990).

95
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 63. Map for California sea lion: haulouts and rookeries.

ABOUT THIS MAP

Figure 63 summarizes information on California sea lion 

haulouts and rookeries in the study area based on number of 

animals, frequency of use, and rookery status. 

DATA 

Haulout data and rookery information are from aerial counts 

(July, 1998-2002) provided by Mark Lowry of the NMFS’ 

Southwest Fisheries Science Center.

METHODS 

Haulout locations were mapped using coordinates included 

in the files from Mark Lowry, SWFSC. Data from July counts 

in four years, 1998-2002, were used to calculate frequency of 

use for each haulout location and mean number of animals 

using each location when that location was occupied. Rookery 

status was determined by the inclusion of pups in the counts. 

Pups were observed in all years at two sites, while three sites 

had pups only in 1998, an El Niño year.

RESULTS AND DISCUSSION 

Haulout sites for the California sea lion are located along the 

coast from Fish Rocks (just south of Point Arena) to the south, 

at Point Sal Rock, and inside San Francisco Bay (Pier 39). 

Minor rookeries are located on the Southeast Farallon Island 

and Año Nuevo Island. 

Periods of unusually warm ocean waters associated with El 

Nino oceanographic conditions affect pup production (i.e., fewer 

pups are born) and result in higher mortality rates for pups and 

juveniles. During the El Niño periods of 1983, 1992, and 1998, 

pup production decreased by 35, 27, and 64%, respectively at 

rookeries in southern California (SWFSC 2001). 

Similar to at-sea occurrence patterns, haulout patterns and 

rookery locations also change during warmer water periods. For 

example, rookery locations during the strong El Niño of 1998 

(shown on the map) included the rookeries at the Farallones 

and Año Nuevo as well as additional rookeries located near 

Partington Point, and Lion, Pecho, and Pup Rocks located to 

the south of the Monterey Bay National Marine Sanctuary. Haulout patterns at the Farallon Islands and Point Reyes National 

Seashore also changed, indicated by an influx of immatures 

(Sydeman and Allen, 1999; S. Allen pers.comm.). 

Greater numbers of California sea lions in the study area during 

El Niño events likely reflected a greater than usual northward 

migration in response to a reduction of food resources near 

southern breeding grounds.

California sea lions feed on a diversity of fish (e.g., Pacific hake, 

northern anchovy, Pacific sardine, herring, rockfish, salmon, 

steelhead) and invertebrates (e.g., squid and octopus) (Weise, 

2000; see also Riedman 1990).

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

N°53N°53

N°63N°63

N°73N°73

N°83N°83

N°93N°93

Source Data: See text.

2

2

0

0

00

0

m

m

California sea lion Zalophus californianus

Haulout Sites

0 25 50 Km

2501 - 6706

501 - 2500

101 - 500

51 - 100

26 - 50

1 - 25

Fish Rocks

Haulout Occupancy

1998 - 2001

Bodega Rock Frequent (4 years)

Occasional (3 years)

Infrequent (1-2 years)

Point Reyes

Sea Lion Cove

Pier 39 North Farallon Islands

Southeast Farallon Island Number of Sea Lions

Año Nuevo Island

Monterey Breakwater

Sea Lion Rocks

Lobos Rocks

Unnamed; N of Partington Pt

San Martin Rocks

Point Piedras Blancas

White Rock

Lion Rock

Pecho Rock

Point Sal Rock

Minor Rookery,

1998-2001

Occasional Minor

Rookery

(e.g. El Niño years)

Mean of July Counts*: 

1998-2001

DRAFT

* When occupied.

96
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 64. Maps for California sea lion: seasonal at-sea densities, high use areas, and rookeries.

ABOUT THESE MAPS

Figures 64a, b, and c show the at-sea density (animals/km2) of 

California sea lions in the Upwelling, Oceanic, and Davidson 

Current seasons, displayed in 10’x10’ cells. Densities are 

based on combined data of several studies; see “Methods” 

and “Data Sources” sections. The color and mapping intervals 

were customized to show the most structure and to highlight 

significant areas, while allowing comparisons among marine 

mammal species. Cells that were surveyed but which had 

no California sea lions have a density of zero; unsurveyed 

areas appear white. Blue lines indicate the National Marine 

Sanctuary boundaries of Cordell Bank, Gulf of the Farallones, 

and Monterey Bay; bathymetric contours for the 200 m and 

2,000 m isobaths are also shown in blue.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence in the study 

area, map d shows seasonal high use areas, displayed in 

10’x10’ cells. This map provides a further synthesis of densities 

presented in maps a, b and c (see “Methods” section for details), 

and portrays the relative importance of various areas to the 

species. Areas with consistent high use are highlighted on this 

map. To provide a relative reference for the “high use” areas, 

cells are also shown where the species were absent (i.e., the 

cell was sampled but the species was not recorded there), or 

present but at lesser concentrations in any particular season. 

DATA SOURCES

At-sea densities for the California sea lion are based on data 

from seven survey programs conducted in 1980-2001. These 

data were combined using CDAS software into the MMS-CDAS 

data system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, four aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See section text for details on individual 

data sets. 

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983); more recent data were collected using 

updated technology but with the same general method. Data 

sources for ship-based survey data include David Ainley, 

unpublished data (see Oedekoven et al., 2001 for details 

on methods). Although the at-sea data span the years 1980-

2001, data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. The rookery and haulout counts 

are shown as a general range, based on counts of all animals 

(pups and adults) in three years, 1999-2001. 

METHODS

At-sea densities are the result of a synthesis of data from 

seven shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources” 

section). Pinniped observation data and trackline data from 

these studies were converted to a common format. All aerial 

data were continuous; ship-based data were converted 

separately into a continuous transect to the extent possible. 

From the digitized survey data, the distributions of effort and of 

species were mapped into 10’x10’ cells using CDAS, a custom 

geographic information system for analyzing marine bird and 

mammal surveys (MMS, 2001). The length and width of the 

survey trackline in a given cell (estimated trackline width varied 

by platform, depending on speed and height above water) were 

used to estimate the area sampled. The number of cetaceans 

of each species seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and to 

exclude observations with winds greater than 25 knots (smaller 

or less obvious species are often less detectable even at wind 

speeds of less than 25 knots). Additional corrections are 

planned for Phase 2 of this project and are briefly discussed 

below. 

For example, no adjustments or corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies. 

Map d was developed using the same approach as for maps a, 

b and c. For each season, the cells with densities in the top 20% 

of non-zero values were designated “high use” for that season. 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

California sea lion Zalophus californianus

Upwelling Season

(Mar. 15 - Aug. 14)

2

2

2

0

20

00

0

00

0 

0

0

m

m

m

 m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

0

0 m

Davidson Current Season 2

2

0

0

00

0

m

 m

Seasonal High Use Areas

(Nov. 15 - Mar. 14) m

and Rookeries

3 Seasons

2 Seasons

1 Season

Sea lions present

a b

Persistence of

High Use

Sea lions absent

c d

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

See additional California sea lion map

for haulout and rookery locations.

Source Data: See text.

DRAFT

97
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Cells were scored for “high use” in one, two, or three seasons 

and are depicted by color. To provide a relative reference for 

the “high use” areas, cells are also shown where the species 

were absent (i.e., the cell was sampled but the species was not 

recorded there) or present (but densities were never in the top 

20% for any season). Further detail on methods is provided in 

the Data and Analysis section.

RESULTS AND DISCUSSION 

The California sea lion (Z.c.californianus) is subdivided into 

three stocks (U.S., Western Baja California, and Gulf of 

California); the United States stock begins at the U.S. Mexico 

border and extends northward into Canada (Carretta et al. 

2001). The breeding areas are on islands located in southern 

California, western Baja California, and the Gulf of California. 

In the study area, a small number of pups are born on Año 

Nuevo Island and Southeast Farallon Island; otherwise the 

central California population is composed of non-breeders. 

Adult females and immatures remain near the rookeries yearround, whereas adult males (along with most immatures) 

migrate northward to feeding areas from central California to 

British Columbia. 

In the study area, this species was the most abundant of the 

pinnipeds (at-sea sightings: n=1,497 individuals: n=4,411) and 

was widely distributed throughout the shelf and upper slope 

regions of the three national marine sanctuaries. The seasonal 

abundance of California sea lions off central California is linked 

to spring and fall pre- and post-breeding migrations. Densities 

were greatest during the Oceanic Season (just after breeding) 

and Davidson Current Season (before the next breeding period) 

and somewhat lower during the Upwelling Season (breeding 

period). 

Periods of unusually warm ocean waters associated with El 

Niño oceanographic conditions affect pup production (i.e., fewer 

pups are born) and result in higher mortality rates for pups and 

juveniles. During the 1983, 1992, and 1998 El Niño events, 

pup production decreased by 35, 27, and 64%, respectively, 

at rookeries in southern California (SWFCS 2001). At-sea 

distribution patterns were also altered; greater numbers of sea 

lions were sighted off central California during these warmer 

periods (see also Bonnell & Ford 1987, Trillmich & Ono 1991, 

Allen 1994, Keiper 2001, and Keiper et al. In Review.).

98
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 65. Map for Steller sea lion: at-sea sightings and survey effort, rookeries and haulouts.

ABOUT THIS MAP

Figure 65 shows individual sightings of Steller sea lions at sea 

along with the locations of haulouts, rookeries, and at-sea effort 

in the study area. At-sea observations are based on combined 

data of several studies (see “Methods” and “Data Sources” 

sections). For context, the amount of combined survey effort 

(km of trackline) is also shown, summarized in 10’x10’ cells. 

Haulout locations are based on counts conducted in July 2000. 

Blue lines indicate the National Marine Sanctuary boundaries 

of Cordell Bank, Gulf of the Farallones, and Monterey Bay; 

bathymetric contours for the 200 m and 2,000 m isobaths are 

also shown in blue.

DATA SOURCES

At-sea sightings for the Steller sea lion are based on data from 

seven survey programs conducted in 1980-2001. These data 

were combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, four aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See section overview for details on individual data sets. 

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDFG-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983); more recent data were collected using 

updated technology but with the same general method. Data 

sources for ship-based survey data include David Ainley, unpublished data (see Oedekoven et al., 2001 for details on methods). 

Although the at-sea data span the years 1980-2001, data are 

not available for all seasons in all years. For the Upwelling Season, data are from 1980-1982 and 1985-2001. For the Oceanic 

Season, data are from 1980-1982, 1991 and 1994-2001. For 

the Davidson Current Season, data are from 1980-1986 and 

1991-2001. Rookery and haulout data are from Mark Lowry 

of NMFS’ Southwest Fisheries Science Center. Rookery and 

haulout data are from Mark Lowry of NMFS’ Southwest Fisheries Science Center. The rookery numbers represent a general 

range based on counts of all animals (pups and adults) in three 

years, 1999-2001. The haulout data are from July 2000.

METHODS

The latitude and longitude coordinates of Steller sea lions at 

sea were used to plot the individual sightings; the coordinates 

from Mark Lowry were used to plot the haulouts and rookeries. 

At-sea sightings and effort are the result of a synthesis of data 

from eight shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources”). 

Cetacean observation data and trackline data from these studies were converted to a common format. All aerial data were 

continuous; ship-based data were converted separately into a 

continuous transect to the extent possible. From the digitized 

survey data, effort was mapped into 10’x10’ cells using CDAS, 

a custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above water) were used to estimate the area sampled.

Note that the these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and 

to exclude observations with winds greater than 25 knots; 

additional corrections are planned for Phase 2 of this project 

and are briefly discussed below. 

For example, no adjustments/corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors,and the associated adjustments for 

observations, vary among the studies. 

The data in these maps include wind conditions of up to 25 

knots; smaller or less obvious species are often less detectable 

even at wind speeds of less than 25 knots. The seasonal maps 

contain different combinations of shipboard and aerial data; 

therefore the seasonal densities from these platforms may not 

be directly comparable. A full consideration of these factors, and 

revised maps, are planned for Phase 2 of this project. 

RESULTS AND DISCUSSION 

Steller sea lions range from northern Japan, the Aleutian Islands 

and Gulf of Alaska, south to Año Nuevo Island, California (the 

southernmost rookery). Steller sea lion females and pups are 

found at the rookeries year-round, but adult bulls are only at 

the rookery during the breeding season (mid-May to mid-July). 

In the study area, the Steller sea lion occurred over the shelf 

and slope, and, although there were few at-sea sightings in 

the data set, most occurred in the area between Cordell Bank 

and Año Nuevo Island. 

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

°N53°N53

°N63°N63

°N73°N73

°N83°N83

°N93°N93

2

2

0

0

00

0

m

m

0 25 50Km

3

2

Steller sea lion Eumetopias jubatus

Number of Sea Lions

1

Survey Effort

(km of trackline)

At Sea

Sightings

Rookeries

> 3000.00

1500.01 - 3000.00

1000.01 - 1500.00

500.01 - 1000.00

100.01 - 500.00

Haulouts

0.01 - 100.00

16 - 36

3 - 15

Fish Rocks

Northwest Cape Rocks

Bodega Rock

1 - 2 Point Reyes

North Farallon Islands 450 - 502

50-215

South Farallon Island

Año Nuevo Island

Sea Lion Rocks (Pt. Lobos)

Lobos Rocks

Cape San Martin

Pecho Rock

DRAFT

Source Data: See text.

99
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

The Steller sea lion population has declined approximately 

64% throughout its range (NMFS Biological Opinion, 2000; 

see also NMFS 1992). Based on distributional data, Steller 

sea lions are classified into two separate stocks within U.S. 

waters: 1) the western stock, that includes animals at, and 

west of, Cape Suckling, Alaska, (classified as endangered); 

and 2) the eastern stock (including the California population) 

that includes animals east of Cape Suckling (classified as 

federally threatened). Greatest concentrations of Steller sea 

lions occur north of central California, hence, relatively few 

sightings (n=45 sightings; n=50 individuals) occurred in the 

study area. Insufficient data precluded mapping the Steller 

sea lion by seasons. 

The breeding season is from mid-May to mid-July. In the study 

area, rookeries are located at the Farallon Islands (where they 

breed in small numbers and haul-out in slightly larger numbers 

throughout the year, USFWS 2000) and at Point Año Nuevo 

Island (see LeBoeuf et al. 1991). From 1977 to 1996 on the 

Farallon Islands, adult females present during the breeding 

season declined by 5.9% and maximum number of pups 

counted declined significantly (see Hastings and Sydeman 

2002). Until the early 1970’s, Steller sea lions used to breed 

at the Point Reyes Headlands but in recent years numbers 

have been low (fewer than 50; S. Allen pers. comm., 2003). 

Haulout sites north of San Francisco are located at Fish Rocks, 

Northwest Cape Rocks, Bodega Rocks, Point Reyes and the 

Farallon Islands. Another haulout site not on the map is located 

north of Fort Ross at “Sea Lion Rocks”; maximum counts at this 

site occur in June (approx. 50) and consist mostly of females 

with pups of the year (J. Mortenson pers.comm., 2003). Adult 

males disperse widely during the non-breeding season. 

Numbers of Steller sea lions off southern and central California 

have declined significantly, from 5,000-7,000 non-pups in 

1927-1947, to 1,500-2,000 non-pups between 1980-1998 

(NMFS Biological Opinion, 2000). Threats to Steller sea 

lions include incidental take by commercial fisheries, getting 

shot, entanglement in marine debris, declining trends in prey 

availability, disease, and contaminants (e.g. premature births 

accounted for 20-60% of pup mortality in the South Farallon 

Islands between 1973-83). Organochlorine and trace metal 

contaminant levels are still elevated in central California Steller 

sea lions (NMFS Biological Opinion 2000).

Steller sea lions feed on walleye pollock, capelin, mackerel, 

rockfish, herring, salmon, octopus and squid (see Riedman, 

1990). 

100
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 66. Maps for northern fur seal: seasonal at-sea densities, high use areas, and rookery.

ABOUT THESE MAPS

Figures 66a, b and c show the density (animals/km2) of northern 

fur seals in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in 10’x10’ cells. Densities are based on 

combined data of several studies (see “Methods” and "Data 

Sources" sections). The color and mapping intervals were 

customized to show the most structure and highlight significant 

areas, while allowing comparisons among marine mammal 

species. Cells that were surveyed but which had no northern fur 

seal’s have a density of zero; unsurveyed areas appear white. 

Blue lines indicate the National Marine Sanctuary boundaries 

of Cordell Bank, Gulf of the Farallones, and Monterey Bay; 

bathymetric contours for the 200 m and 2,000 m isobaths are 

also shown in blue.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence in the study 

area, map d shows seasonal high use areas, displayed in 

10’x10’ cells. This map provides a further synthesis of densities 

presented in maps a, b and c (see “Methods” section for details), 

and portrays the relative importance of various areas to the 

species. Areas with consistent high use are highlighted on this 

map. To provide a relative reference for the “high use” areas, 

cells are also shown where the species were absent (i.e., the 

cell was sampled but the species was not recorded there), or 

present but at lesser concentrations in any particular season. 

The single rookery location is also shown.

DATA SOURCES

At-sea densities for the northern fur seal are based on data 

from seven survey programs conducted in 1980-2001. These 

data were combined using CDAS software into the MMS-CDAS 

data system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, four aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See "Data and Analyses" subsection in 2.3 

for details on individual data sets. 

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983); more recent data were collected using 

updated technology but with the same general method. Data 

sources for ship-based survey data include David Ainley, 

unpublished data (see Oedekoven et al. 2001 for details on 

methods). Although the at-sea data span the years 1980-2001, 

data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

Oceanic Season, data are from 1980-1982, 1991, and 1994-

2001. Davidson Current Season, data are from 1980-1986 and 

1991-2001. 

Information on the northern fur seal rookery was provided in 

2003, courtesy of William Sydeman of PRBO Conservation 

Science, and Joelle Buffa of the Farallon Islands National 

Wildlife Refuge.

METHODS 

At-sea densities are the result of a synthesis of data from seven 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources”). Pinniped 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into 

10’x10’ cells using CDAS, a custom geographic information 

system for analyzing marine bird and mammal surveys (MMS, 

2001). The length and width of the survey trackline in a given 

cell (estimated trackline width varied by platform, depending on 

speed and height above water) were used to estimate the area 

sampled. The number of each species seen in a cell was then 

divided by the area sampled in the cell to estimate density. If a 

cell was censused more than once, densities were averaged, 

with adjustment made for effort.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and to 

exclude observations with winds greater than 25 knots (smaller 

or less obvious species are often less detectable even at wind 

speeds of less than 25 knots). Additional corrections are 

planned for Phase 2 of this project and are briefly discussed 

below. 

For example, no adjustments or corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of 

time spent submerged, are all factors known to affect detection 

and hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

124°W 123°W 122°W 121°W observations, vary among the studies.

N°53 N°63 N°73 N°83 N°93

124°W 123°W 122°W 121°W

N°53 N°63 N°73 N°83 N°93

124°W 123°W 122°W 121°W

N°53 N°63 N°73 N°83 N°93

124°W 123°W 122°W 121°W

N°53 N°63 N°73 N°83 N°93

Northern fur seal Callorhinus ursinus

Upwelling Season

(Mar. 15 - Aug. 14)

2

2

2

2

0

0

0

0

0

0

0

0

0

0

m

 m

m

m

Oceanic Season

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

2

2

00

0

0

0

Davidson Current Season 2

2

0

0

00

0

m

m

 m

Seasonal High Use Areas

(Nov. 15 - Mar. 14) m

and Rookery

3 Seasons

2 Seasons

1 Season

Seals present

Seals absent

a b

Persistence of

High Use

Rookery

c d

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

DRAFT

0.00

Source Data: See text.

101
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Map d was developed using the same approach as for maps 

a, b and c. For each season, the cells with densities in the top 

20% of non-zero values were designated “high use” for that 

season. Cells were scored for “high use” in one, two, or three 

seasons and are depicted by color. To provide a relative reference for the “high use” areas, cells are also shown where the 

species were absent (i.e., the cell was sampled but the species 

was not recorded there) or present (but densities were never 

in the top 20% for any season). Further detail on methods is 

provided in the "Data and Analysis" section.

RESULTS AND DISCUSSION 

The northern fur seal, one of the most pelagic of the pinnipeds, 

is most abundant in continental shelf-slope waters of midlatitudes off western North America during winter and early 

spring. Except for a small, recently re-established rookery 

(south Farallon Island, see below), rookeries occur primarily 

outside of the study area. The breeding and pupping season 

is June-July, and suckling can continue for three additional 

months. During autumn, adult females and juveniles migrate 

from rookeries on San Miguel Island in the southern California 

Bight (the San Miguel Island stock) and from the Eastern Pacific 

stock of the Pribilof Islands in the Bering Sea (Kajimura, 1980; 

Kenyon and Wilke, 1953; Pyle et al., 2001). Adult females and 

pups from the Pribilof Islands migrate into the North Pacific 

Ocean and to waters off Oregon and California. 

In data used for this assessment (1980-2001), the northern fur 

seal was the second most abundant pinniped observed, with 

a total of 1,459 sightings and 2,070 individuals. In the study 

area, greatest densities occurred seaward of National Marine 

Sanctuary boundaries in the shelf-break, slope, and deep ocean 

habitats. The distinctly seasonal presence of this species is 

clearly evident in the study area, with greater numbers from 

February to May (Kajimura 1984). Greatest densities occur 

during the Upwelling and Davidson Current seasons (nonbreeding period) and lesser densities during the Oceanic 

Season (breeding period). 

Severe declines associated with periods of unusually warm 

ocean conditions affect pup production, mortality rates on San 

Miguel Island and the Pribilof Islands, and at-sea presence of 

this species (see DeLong and Antonelis, 1991; Allen, 1994; 

DeLong and Melin, 1999; Melin and DeLong, 2000; Keiper, 

2001; and Keiper et al., In Review) In the early 19th century, 

American, British, and Russian sealers removed the breeding 

population from the South Farallon Islands (Pyle et al., 2001). 

Beginning in 1996, however, the species has re-established a 

breeding population on the South Farallon Islands, with fewer 

than 10 pups produced each year, 1997-2001 (Pyle et al., 

2001). Seasonal high use areas occurred mostly to the west 

of National Marine Sanctuary boundaries. 

Northern fur seals feed on a great diversity of seasonally 

abundant prey, and, off California, primary prey species include 

Pacific hake, northern anchovy, mesopelagic fishes, and market 

squid (Kajimura, 1984; see also Riedman, 1990). 

102
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 67. Map for harbor seal: at-sea sightings, survey effort and haulouts.

ABOUT THESE MAPS

Figure 67 shows individual sightings of harbor seals at sea 

along with the locations of haulouts and at-sea survey effort in 

the study area. At-sea observations are based on combined 

data of several studies (see “Methods” and “Data Sources” 

sections). For context, the amount of combined survey effort 

(km of trackline) is also shown, summarized in 10’x10’ cells. 

Haulout locations are based on aerial counts from 2002. Blue 

lines indicate the National Marine Sanctuary boundaries of 

Cordell Bank, Gulf of the Farallones, and Monterey Bay; bathymetric contours for the 200 m and 2,000 m isobaths are also 

shown in blue.

DATA SOURCES

At-sea sightings for the harbor seal are based on data from 

seven survey programs conducted in 1980-2001. These data 

were combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, four aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See "Data and Analyses" subsection of this 

mammal section (2.3).

Data sources for aerial at-sea data include MMS-CDAS (2001) 

and California Department of Fish and Game Office of Spill 

Prevention and Response (CDFG-OSPR), unpublished data. 

Early data were collected using methods described by Bonnell 

et al. (1983); more recent data were collected using updated 

technology but with the same general method. Data sources for 

ship-based survey data include David Ainley, unpublished data 

(see Oedekoven et al., 2001 for details on methods). Although 

the overall at-sea data span the years 1980-2001, data are not 

available for all seasons in all years. For the Upwelling Season, 

data are from 1980-1982 and 1985-2001. For the Oceanic 

Season, data are from 1980-1982, 1991 and 1994-2001. For 

the Davidson Current Season, data are from 1980-1986 and 

1991-2001. Haulout information is from 2002 aerial survey data 

(6/12/2002-7/1/2002), from Mark Lowry of NMFS’ Southwest 

Fisheries Science Center.

METHODS

The latitude/longitude coordinates of harbor seals at sea were 

used to plot the individual sightings. Haulouts were mapped 

coordinates provided by Mark Lowry. At-sea sightings and effort are the result of a synthesis of data from eight shipboard 

and aerial survey programs conducted in the study area in the 

years 1980-2001 (see “Data Sources”). Cetacean observation 

data and trackline data from these studies were converted to 

a common format. All aerial data were continuous; ship-based 

data were converted separately into a continuous transect to 

the extent possible. From the digitized survey data, effort was 

mapped into 10’x10’ cells using CDAS, a custom geographic 

information system for analyzing marine bird and mammal surveys (MMS-CDAS, 2001). The length and width of the survey 

trackline in a given cell (estimated trackline width varied by 

platform, depending on speed and height above water) were 

used to estimate the area sampled.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and 

to exclude observations with winds greater than 25 knots; 

additional corrections are planned for Phase 2 of this project 

and are briefly discussed below. 

For example, no adjustments/corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of 

time spent submerged, are all factors known to affect detection 

and hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies.

The data in these maps include wind conditions of up to 25 

knots; smaller or less obvious species are often less detectable 

even at wind speeds of less than 25 knots. The seasonal maps 

contain different combinations of shipboard and aerial data; 

therefore the seasonal densities from these platforms may not 

be directly comparable. A full consideration of these factors, and 

revised maps, are planned for Phase 2 of this project. 

RESULTS AND DISCUSSION 

The harbor seal is distributed from the eastern Aleutian Islands 

to Baja California and inhabits near-shore estuarine, coastal 

and shelf areas. When at sea, harbor seals were distributed 

in shelf habitats in relatively low densities in all three national 

marine sanctuaries; therefore, insufficient data precluded 

generating seasonal maps. Harbor seals forage throughout 

the coastal waters. Because the at-sea locations in this map 

are influenced by survey effort (where survey effort was unequal 

and coverage was less along the coast), the map may not 

accurately represent the foraging distribution of harbor seals. 

Although not evident in the maps, densities are higher in the 

Gulf of the Farallones because there are more and larger 

haul-out sites in this area (Allen et al., 2002). Harbor seals do 

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

°N53°N53

°N63°N63

°N73°N73

°N83°N83

°N93°N93

2

2

0

0

00

0

m

m

Harbor seal Phoca vitulina

Number of Seals

Survey Effort

(km of trackline)

0 25 50 Km

7 - 15

4 - 6

2 - 3

At Sea

Sightings Haulout Sites

1

> 3000.00

1500.01 - 3000.00

1000.01 - 1500.00

500.01 - 1000.00

100.01 - 500.00

0.01 - 100.00

401 - 835

201 - 400

51 - 200

1 - 50

DRAFT

Source Data: See text.

103
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

not make extensive migrations, and tend to remain relatively 

close to their haul-out sites throughout the year. Harbor seals 

are inconspicuous at sea and may explain the relatively 

low numbers of animals surveyed at sea (sightings: n=192; 

individuals: n=235). A long-term monitoring project at Bolinas 

Lagoon (Gulf of the Farallones Sanctuary Education Awareness 

and Long-term Stewardship Program) protects the seals from 

human disturbance. During breeding and molting, relative 

abundance increases at Drakes Estero, whereas during winter 

(and during herring spawns) relative abundance increases in 

Tomales Bay. The Point Reyes region represents ~20% (6000 

seals) of the breeding population of the state of California (S. 

Allen pers. comm.). Results of recent (2002) tagging studies 

have indicated individuals from San Francisco Bay travel to 

Duxbury Reef and out to the Farallon Islands to forage (S. Allen 

pers.comm.). Harbor seals feed on seasonally abundant prey 

that includes topsmelt, night smelt, white croaker, English sole 

(Harvey et al., 1995), salmonids (Weise, 2001), and squid and 

octopus (see also Riedman, 1990). 

In the study area, the species is present year-round, and on 

land it is found on sandy beach, mudflat and rocky habitats. 

Haulout sites (identified by Lowry 2002) are located along the 

coast from Point Arena south to Point Conception, within San 

Francisco Bay, and at the Southeast Farallon Islands; habitat 

use at these sites, however, varies seasonally throughout the 

year (S. Allen, pers. comm.). 

Breeding and pupping occurs March-July, and many pupping 

sites occur in the study area. Along the Point Reyes National 

Seashore, major pupping sites occur at the following locations 

(S. Allen pers.comm.): Bodega Rock, Bodega Point, Tomales 

Bay (four sites), Tomales Point (five sites), Drakes Estero 

(five sites), Limantour Spit, Double Point (two sites), Abalone 

Point, Bolinas Point, Duxbury Reef, Bolinas Lagoon (3 sites), 

Slide Ranch, and Point Bonita. Sites along the coast south of 

San Francisco may exist at Pescadero and Bean Hollow, but 

these sites are poorly documented (D.Greig, pers.comm.). 

Pupping sites within San Francisco Bay are located at Mowry 

Slough and Castro Rocks. Farther south, pupping sites also 

occur at Año Nuevo Island, Elkhorn Slough, Hopkins Marine 

Station, Cypress Point, Fanshell Beach and Cypress Point, 

San Lorenzo River and Point Lobos (D.Greig pers.comm.). A 

few pups (less than five) were also produced on South Farallon 

Island (USFWS, 2000). 

104
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 68. Map for northern elephant seal: at-sea sightings and survey effort, rookeries and haulouts.

ABOUT THIS MAP

Figure 68 shows individual at-sea sightings of northern elephant 

seals at sea, along with the locations of rookeries and at-sea 

survey effort in the study area. At-sea observations are based 

on combined data of several studies (see “Methods” and “Data 

Sources” sections). For context, the amount of combined survey 

effort (km of trackline) is also shown, summarized in 10’x10’ 

cells. Blue lines indicate the National Marine Sanctuary boundaries of Cordell Bank, Gulf of the Farallones, and Monterey Bay; 

bathymetric contours for the 200 m and 2,000 m isobaths are 

also shown in blue.

DATA SOURCES

At-sea sightings for the northern elephant seal are based on 

data from seven survey programs conducted in 1980-2001. 

These data were combined using CDAS software into the 

MMS-CDAS data system (MMS, 2001), developed for Minerals Management Service and expanded for this project. Of the 

data sets on the original CD-ROM, four aerial survey data sets 

contained data in the study area from Point Arena to Point Sal. 

Of these, the OSPR survey program was still ongoing and data 

from recent years were added to this data set. In addition, data 

from three ship-based survey programs were converted to a 

compatible format for analysis; see Data and Analysis subsection for more information on individual data sets. 

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDFG-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983); more recent data were collected using 

updated technology but with the same general method. Data 

sources for ship-based survey data include David Ainley, 

unpublished data (see Oedekoven et al., 2001 for details 

on methods). Although the at-sea data span the years 1980-

2001, data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991, and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. Information on rookery locations 

was obtained from Pat Morris, USCS; Brian Hatfield, USGS; 

and Joelle Buffa, FWS.

METHODS

The latitude/longitude coordinates of northern elephant seals at 

sea were used to plot the individual sightings; the coordinates 

for rookeries and haulouts were used to plot their locations. 

At-sea sightings and effort are the result of a synthesis of data 

from eight shipboard and aerial survey programs conducted in 

the study area in the years 1980-2001 (see “Data Sources”). 

Cetacean observation data and trackline data from these studies were converted to a common format. All aerial data were 

continuous; ship-based data were converted separately into a 

continuous transect to the extent possible. From the digitized 

survey data, effort was mapped into 10’x10’ cells using CDAS, 

a custom geographic information system for analyzing marine 

bird and mammal surveys (MMS, 2001). The length and width 

of the survey trackline in a given cell (estimated trackline width 

varied by platform, depending on speed and height above water) were used to estimate the area sampled.

Note that the these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and 

to exclude observations with winds greater than 25 knots; 

additional corrections are planned for Phase 2 of this project 

and are briefly discussed below. 

For example, no adjustments/corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies.

The data in these maps include wind conditions of up to 25 

knots; smaller or less obvious species are often less detectable 

even at wind speeds of less than 25 knots. The seasonal maps 

contain different combinations of shipboard and aerial data; 

therefore the seasonal densities from these platforms may not 

be directly comparable. A full consideration of these factors, and 

revised maps, are planned for Phase 2 of this project. 

RESULTS AND DISCUSSION 

The northern elephant seal is present year-round in the 

study area; however, because they spend very little time 

at the surface, at-sea sightings are rare, as evidenced by 

the relatively few sightings during surveys in the study area 

(n=266 sightings; n=273 individuals). Therfore, insufficient data 

precluded mapping the northern elephant seal by seasons. 

Northern elephant seals were widely distributed in shelf, shelfbreak, and slope habitats within the three national marine 

sanctuaries, and also occurred in deep ocean habitats seaward 

of the 2000 m isobath. They also occurred well to the north, 

west, and south of sanctuary boundaries. In these data sets, 

age classes of at-sea sightings of seals are unknown. 

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

°N53°N53

°N63°N63

°N73°N73

°N83°N83

°N93°N93

2

2

0

0

00

0

m

m

Northern elephant seal Mirounga angustirostris

Number of Seals

Survey Effort

(km of trackline)

0 25 50 Km

At Sea Rookery and

Sightings Haulout Sites

> 3000.00

1500.01 - 3000.00

1000.01 - 1500.00

500.01 - 1000.00

100.01 - 500.00

0.01 - 100.00

5

2 Point Reyes

1

South Farallon Island

Año Nuevo Mainland/Island

Cape San Martin

Pt. Piedras Blancas

DRAFT

Source Data: See text.

105
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

The northern elephant seal breeds, gives birth, and molts on 

islands and coastal regions in California, as well as offshore 

islands of Baja California. The breeding period in the study 

area is generally December through March (Stewart and 

Huber,1993). Northern elephant seals migrate between 

rookeries located within sanctuary boundaries, Farallon Islands, 

Point Reyes, Año Nuevo Island and the mainland, Piedras 

Blancas, Cape San Martin, and San Simeon, and waters to 

the north, where they spend eight to ten months of the year 

feeding. Adult males feed in the eastern Aleutian Islands and 

the Gulf of Alaska; adult females feed to the west and south of 

45o N in deep, oceanic water (Le Boeuf et al., 1993; Stewart 

and Huber, 1993; Stewart et al., 1994).

On land, there are three peaks in abundance: 1) during the 

breeding/pupping season December to March, with peaks 

the last week of January; 2) during the molting season when 

female and immatures are on shore April to July with peaks in 

May, and adult males are on shore June to early August; and 

3) during September to October when immatures haul-out (S. 

Allen, pers. comm). Pups depart the pupping sites during the 

Upwelling Season. Recent tagging studies indicate that pups 

from this region travel as far as Alaska (S.Allen, unpublished 

data, National Park Service). 

Each year at Año Nuevo Island and mainland, there are 

approximately 2,400 females and 300-400 males present, 

and approximately 2,200 pups are produced (P. Morris, pers. 

comm, 2003). Based on pup counts, the population there 

steadily increased through the mid 1990s, but now appears to 

be stable (P. Morris, pers. comm., credited to B.J. Le Boeuf). 

In contrast, the colony at Piedras Blancas has continued to 

rise (in general) over the past five years (B. Hatfield, pers. 

comm.) Productivity has declined at two major breeding sites 

on Southeast Farallon Island (Sydeman and Allen, 1999; 

Nusbaum, 2002), with erosion playing a major role in limiting 

the species’ population (USFWS 2000). In California, the net 

productivity rate for northern elephant seals also appears to 

have declined in recent years (Carretta et al., 2002). However, 

the colony at Point Reyes Headlands has continued to increase 

by 5-10% per year (Sydeman and Allen, 1999; S. Allen, pers. 

comm. 2003). Due to the high surf during the strong El Niño 

of 1998, extensive pup mortality occurred at the Point Reyes 

colony (Pettee, 1999), but also forced the relocation of the 

breeding area; some moved from the main colony at Point 

Reyes Headlands to South Beach and North Drakes Bay Beach 

(Pettee, 1999). 

Northern elephant seals are prolonged deep divers that feed on 

deepwater fishes and invertebrates, including Pacific hagfish (Eptatretus stouti), ratfish (Hydrolagus colliei), Pacific hake, 

rockfish, sharks, rays, squid and octopus (Antonelis et al., 1987; 

Condit and LeBoeuf, 1984).

106
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

ABOUT THESE MAPS

Figures 69a, b and c show the density (animals/km2) of Dall’s 

porpoise in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in 10’x10’ cells. Densities are based on 

combined data of several studies (see “Methods” and “Data 

Sources” sections). The color and mapping intervals were 

customized to highlight significant areas and the structure of 

species spatial occurrence, while allowing comparisons among 

marine mammal species. Cells that were surveyed but which 

had no Dall’s porpoise have a density of zero; unsurveyed 

areas appear white. Blue lines indicate the National Marine 

Sanctuary boundaries of Cordell Bank, Gulf of the Farallones, 

and Monterey Bay; bathymetric contours for the 200 m and 

2,000 m isobaths are also shown in blue.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence year-round in the 

study area, map d shows seasonal high use areas, displayed in 

10’x10’ cells. This map provides a further synthesis of densities 

presented in maps a, b and c (see the “Methods” section for 

details), and portrays the relative importance of various areas 

to the species. Areas of consistent high use (colored according 

to the number of high seasonal use) are highlighted on this 

map. To provide a relative reference for the “high use” areas, 

cells are also shown where the species were absent (i.e., the 

cell was sampled but the species was not recorded there) or 

present but at lower concentrations (densities in a cell were 

never in the top 20%) in any particular season.

DATA SOURCES

At-sea densities for cetaceans are based on data from eight 

survey programs conducted in 1980-2001. These data were 

combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, five aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See "Data and Analyses" subsection in 2.3 

for details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983) and Dohl et al. (1983); more recent data 

were collected using updated technology but with the same 

general method. Data sources for ship-based survey data 

include David Ainley, unpublished data (see Oedekoven et al. 

2001 for details on methods). Although the at-sea data span 

the years 1980-2001, data are not available for all seasons in 

all years. For the Upwelling Season, data are from 1980-1982 

and 1985-2001. For the Oceanic Season, data are from 1980-

1982, 1991, and 1994-2001. For the Davidson Current Season, 

data are from 1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard or aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources”). Cetacean 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into 

10’x10’ cells using CDAS, a custom geographic information 

system for analyzing marine bird and mammal surveys (MMS, 

2001). The length and width of the survey trackline in a given 

cell (estimated trackline width varied by platform, depending on 

speed and height above water) were used to estimate the area 

sampled. The number of cetaceans of each species seen in a 

cell was then divided by the area sampled in the cell to estimate 

density. If a cell was censused more than once, densities were 

averaged, with adjustment made for effort.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and to 

exclude observations with winds greater than 25 knots (smaller 

or less obvious species are often less detectable even at 

wind speeds of less than 25 knots). Additional corrections are 

planned for Phase 2 of this project and are briefly discussed 

below. 

For example, no adjustments or corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies.

Map d was developed using the same approach as for maps a, 

b and c. For each season, the cells with densities in the top 20% 

of non-zero values were designated “high use” for that season. 

Cells were scored for “high use” in one, two, or three seasons 

Figure 69. Maps for Dall’s porpoise: seasonal at-sea densities and high use areas. and are depicted by color. To provide a relative reference for 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Dall's porpoise Phocoenoides dalli

Upwelling Season

(Mar. 15 - Aug. 14)

20

2

2

2

0

00

0

00

0

0

0

m

m

 m

m

Ocea ic Season n

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

Davidson Current Season 2

2

0

0

0

0

0 

0

0

m

 m

 m

Seasonal High Use Areas

(Nov. 15 - Mar. 14) m

3 Seasons

2 Seasons

1 Season

Porpoises present

a b

Persistence of

High Use

Porpoises absent

c d

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

DRAFT

0.00

Source Data: See text.

107
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

the “high use” areas, cells are also shown where the species 

were absent (i.e., the cell was sampled but the species was not 

recorded there) or present (but densities were never in the top 

20% for any season). Further detail on methods is provided in 

the "Data and Analysis" section.

RESULTS AND DISCUSSION 

Dall’s porpoise is widely distributed in temperate North Pacific 

waters. In the study area, this species was the fourth most 

numerous small cetacean. Dall’s porpoise was present during 

all seasons in shelf, upper/lower slope, canyon, and deep ocean 

habitats seaward of the 2000 m isobath. 

During the Upwelling Season densities were somewhat greater 

in the Cordell Bank National Marine Sanctuary (NMS) and 

northern regions of the Gulf of the Farallones NMS. During 

the Oceanic Season, densities were somewhat greater within 

and to the north of Cordell Bank and the northern portion of 

the Monterey Bay National Marine Sanctuary (MBNMS). The 

widespread and deep ocean distribution of the Dall’s porpoise 

(well to the west of the National Marine Sanctuary boundaries) 

was most evident during the Davidson Current Season (when 

effort was greater offshore). No clear seasonal pattern was 

evident. 

The distribution of Dall’s porpoise is highly variable between 

years and appears to be affected by oceanographic conditions 

(Forney and Barlow 1998). North-south movements of this 

species occur as oceanographic conditions change on seasonal 

and interannual time scales (see Green et al., 1992; Barlow, 

1995; Forney et al., 1995). 

High use areas (based on the CDAS maps) occurred along the 

200 m isobath in the Cordell Bank and Gulf of the Farallones 

NMS. Given the highly variable distribution of Dall’s porpoise, 

the apparent higher relative density in these regions may not 

be a seasonal pattern.

See map of SWFSC survey data for Dall’s porpoise (Figure 76) 

in this section for the greater geographic extent of the range 

and interannual variations for this species.

Dall’s porpoise feeds mostly on Pacific hake (Merluccius 

productus), northern anchovy (Engraulis mordax), Pacific 

saury (Cololabis saira), juvenile rockfish (Sebastes spp), and 

cephalopods (Koskii et al., 1998; Morejohn, 1979). 

108
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

ABOUT THESE MAPS 

Figures 70a, b and c show the density (animals/km2) of Pacific 

white-sided dolphin in the Upwelling, Oceanic, and Davidson 

Current seasons, displayed in 10’x10’ cells. Densities are 

based on combined data of several studies (see “Methods” 

and “Data Sources” sections). The color and mapping intervals 

were customized to show the most structure and highlight 

significant areas, while allowing comparisons among marine 

mammal species. Cells that were surveyed but which had no 

Pacific white-sided dolphins have a density of zero; unsurveyed 

areas appear white. Blue lines indicate the National Marine 

Sanctuary boundaries of Cordell Bank, Gulf of the Farallones, 

and Monterey Bay; bathymetric contours for the 200m and 

2,000m isobaths are also shown in blue.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence in the study area, 

map d shows seasonal high use areas, displayed in 10’x10’ cells. 

This map provides a further synthesis of densities presented 

in maps a, b and c (see the “Methods” section for details), and 

portrays the relative importance of various areas to the species. 

Areas with consistent high use are highlighted on this map. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there), or present 

but at lesser concentrations in any particular season.

DATA SOURCES

At-sea densities for cetaceans are based on data from eight 

survey programs conducted in 1980-2001. These data were 

combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, five aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See "Data and Analyses" subsection in 2.3 

for details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983) and Dohl et al. (1983); more recent data 

were collected using updated technology but with the same 

general method. Data sources for ship-based survey data 

include David Ainley, unpublished data (see Oedekoven et al., 

2001 for details on methods). Although the at-sea data span 

the years 1980-2001, data are not available for all seasons in 

all years. For the Upwelling Season, data are from 1980-1982 

and 1985-2001. For the Oceanic Season, data are from 1980-

1982, 1991 and 1994-2001. For the Davidson Current Season, 

data are from 1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” section). 

Cetacean observation data and trackline data from these 

studies were converted to a common format. All aerial data were 

continuous; ship-based data were converted separately into a 

continuous transect to the extent possible. From the digitized 

survey data, the distributions of effort and of species were 

mapped into 10’x10’ cells using CDAS, a custom geographic 

information system for analyzing marine bird and mammal 

surveys (MMS, 2001). The length and width of the survey 

trackline in a given cell (estimated trackline width varied by 

platform, depending on speed and height above water) were 

used to estimate the area sampled. The number of cetaceans 

of each species seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and to 

exclude observations with winds greater than 25 knots (smaller 

or less obvious species are often less detectable even at wind 

speeds of less than 25 knots). Additional corrections are 

planned for Phase 2 of this project and are briefly discussed 

below. 

For example, no adjustments or corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies.

Map d was developed using the same approach as for Maps a, 

b and c. For each season, the cells with densities in the top 20% 

of non-zero values were designated “high use” for that season. 

Cells were scored for “high use” in one, two, or three seasons 

and are depicted by color. To provide a relative reference for 

Figure 70. Maps for Pacific white-sided dolphin: seasonal at-sea densities and high use areas. the “high use” areas, cells are also shown where the species 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Pacific white-sided dolphin Lagenorhynchus obliquidens

Upwelling Season

(Mar. 15 - Aug. 14)

20

2

2

2

0

00

0

00

0

0

0

m

m

 m

m

Ocea ic Season n

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

Davidson Current Season 2

2

0

0

0

0

0 

0

0

m

 m

 m

Seasonal High Use Areas

(Nov. 15 - Mar. 14) m

3 Seasons

2 Seasons

1 Season

Dolphins present

a b

Persistence of

High Use

Dolphins absent

c d

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

DRAFT

0.00

Source Data: See text.

109
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

were absent (i.e., the cell was sampled but the species was not 

recorded there) or present (but densities were never in the top 

20% for any season). Further detail on methods is provided in 

the "Data and Analysis" section.

RESULTS AND DISCUSSION 

The Pacific white-sided dolphin is one of the most abundant 

dolphin species of the temperate eastern North Pacific. In the 

present study, it was the most abundant of the small cetaceans 

(sightings: n=456; numbers of individuals: n=28,809). Pacific 

white-sided dolphins occurred throughout the study area during 

all oceanographic seasons in outer shelf, upper/lower slope 

and canyon habitats. 

Some seasonal shifts in the occurrence of Pacific white-sided 

dolphins were observed in the data; densities were relatively 

greater during the Oceanic Season, with concentrations near 

Pioneer Canyon and Pioneer Seamount and regions over 

Monterey Canyon. Because the occurrence of Pacific whitesided dolphins is highly variable and this species responds to 

oceanographic conditions on both seasonal and interannual 

time scales (see Forney and Barlow, 1998), the apparent 

seasonal shifts observed in these data may not be a seasonal 

pattern. 

However, in a study in Monterey Bay (Black, 1994), group size 

and relative abundance of the Pacific white-sided dolphin varied 

seasonally and was greater during the Oceanic and Davidson 

Current Seasons than during the Upwelling Season, when 

relative individual and group abundance was low and group 

sizes were small (not shown in maps; Black, 1994). 

Furthermore, in habitats over and near shelf-breaks and greater 

bottom relief, feeding behavior was observed more than other 

behaviors (Black, 1994). Based on available information, high 

use areas mostly occurred over the slope. 

Prey of the Pacific white-sided dolphin includes: Pacific whiting, 

northern anchovy, rockfish, Pacific saury, and market squid 

(Loligo opalescens) (Stroud et al., 1981; Black, 1994).

110
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

ABOUT THESE MAPS 

Figures 71a, b and c show the density (animals/km2) of Risso’s 

dolphin in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in 10’x10’ cells. Densities are based on 

combined data of several studies (see “Methods” and "Data 

Sources" sections). The color and mapping intervals were 

customized to show the most structure and highlight significant 

areas, while allowing comparisons among marine mammal 

species. Cells that were surveyed but which had no Risso’s 

dolphins have a density of zero; unsurveyed areas appear white. 

Blue lines indicate the National Marine Sanctuary boundaries 

of Cordell Bank, Gulf of the Farallones, and Monterey Bay; 

bathymetric contours for the 200m and 2,000m isobaths are 

also shown in blue.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence in the study area, 

map d shows seasonal high use areas, displayed in 10’x10 cells. 

This map provides a further synthesis of densities presented 

in maps a, b and c (see “Methods” section for details), and 

portrays the relative importance of various areas to the species. 

Areas with consistent high use are highlighted on this map. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there) or present but 

at lesser concentrations in any particular season.

DATA SOURCES

At-sea densities for cetaceans are based on data from eight 

survey programs conducted in 1980-2001. These data were 

combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, five aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See "Data and Analyses" subsection in 2.3 

for details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS,, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983) and Dohl et al. (1983); more recent data 

were collected using updated technology but with the same 

general method. Data sources for ship-based survey data 

include David Ainley, unpublished data (see Oedekoven et al. 

2001 for details on methods). Although the at-sea data span 

the years 1980-2001, data are not available for all seasons in 

all years. For the Upwelling Season, data are from 1980-1982 

and 1985-2001. For the Oceanic Season, data are from 1980-

1982, 1991 and 1994-2001. For the Davidson Current Season, 

data are from 1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” section). 

Cetacean observation data and trackline data from these 

studies were converted to a common format. All aerial data were 

continuous; ship-based data were converted separately into a 

continuous transect to the extent possible. From the digitized 

survey data, the distributions of effort and of species were 

mapped into 10’x10’ cells using CDAS, a custom geographic 

information system for analyzing marine bird and mammal 

surveys (MMS, 2001). The length and width of the survey 

trackline in a given cell (estimated trackline width varied by 

platform, depending on speed and height above water) were 

used to estimate the area sampled. The number of cetaceans 

of each species seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and to 

exclude observations with winds greater than 25 knots (smaller 

or less obvious species are often less detectable even at wind 

speeds of less than 25 knots). Additional corrections are 

planned for Phase 2 of this project and are briefly discussed 

below. 

For example, no adjustments or corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of 

time spent submerged, are all factors known to affect detection 

and hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies.

Map d was developed using the same approach as for maps a, 

b and c. For each season, the cells with densities in the top 20% 

of non-zero values were designated “high use” for that season. 

Cells were scored for “high use” in one, two, or three seasons 

and are depicted by color. To provide a relative reference for 

the “high use” areas, cells are also shown where the species Figure 71. Maps for Risso’s dolphin: seasonal at-sea densities and high use areas.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Risso's dolphin Grampus griseus

Upwelling Season

(Mar. 15 - Aug. 14)

20

2

2

2

0

00

0

00

0

0

0

m

m

 m

m

Ocea ic Season n

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

Davidson Current Season 2

2

0

0

0

0

0 

0

0

m

 m

 m

Seasonal High Use Areas

(Nov. 15 - Mar. 14) m

3 Seasons

2 Seasons

1 Season

Dolphins present

a b

Persistence of

High Use

Dolphins absent

c d

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

Source Data: See text.

DRAFT

111
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

were absent (i.e., the cell was sampled but the species was not 

recorded there) or present (but densities were never in the top 

20% for any season). Further detail on methods is provided in 

the "Data and Analysis" section.

RESULTS AND DISCUSSION 

The Risso’s dolphin is widely distributed in warm-temperate 

waters from southern California north to Washington, and in 

the study area, occurred over outer shelf, upper and lower 

slope, and canyon habitats, and in offshore waters seaward 

of the 2000 m isobath. Risso’s dolphin was the third most 

abundant dolphin in the study area, with 250 sightings of 

2,248 individuals. 

During the Upwelling Season, Risso’s dolphins were distributed 

throughout the study area over the outer shelf, slope and deep 

ocean, with greatest densities in (and to the south and west 

of) the Monterey Bay National Marine Sanctuary (MBNMS). 

During the Oceanic Season, greatest densities occurred within 

and south and west of the southern portion of MBNMS. During 

the Davidson Current Season, overall densities were mostly 

in the southern portion of the MBNMS and areas to the south 

and west of the MBNMS boundary. 

Distribution of Risso’s dolphin off California, Oregon, and 

Washington is highly variable, apparently in response to 

seasonal and interannual oceanographic changes (Forney 

and Barlow, 1998). Dolphins found off California during colder 

water months are thought to shift northward into Oregon and 

Washington as water temperatures increase in late spring and 

summer (Carretta et al., 2001; Green et al., 1992). Given the 

highly variable distribution of Risso’s dolphin, the apparent 

relative decrease in relative density observed in this study 

during the Davidson Current Season may not be a seasonal 

pattern. Based on this data set, most high use areas occurred 

in the Monterey Bay national marine sanctuary and adjacent 

areas to the south (see map). 

Risso’s dolphin feed almost exclusively on squid (Koski et al., 

1998; Orr, 1966).

112
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

ABOUT THESE MAPS

Figures 72a, b and c show the density (animals/km2) of northern 

right whale dolphins in the Upwelling, Oceanic, and Davidson 

Current seasons, displayed in 10’x10’ cells. Densities are based 

on combined data of several studies (see “Methods” and “Data 

Sources”). The color and mapping intervals were customized to 

show the most structure and highlight significant areas, while 

allowing comparisons among marine mammal species. Cells 

that were surveyed but which had no northern right whale 

dolphins have a density of zero; unsurveyed areas appear white. 

Blue lines indicate the National Marine Sanctuary boundaries 

of Cordell Bank, Gulf of the Farallones, and Monterey Bay; 

bathymetric contours for the 200m and 2,000m isobaths are 

also shown in blue.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence in the study 

area, map d shows seasonal high use areas, displayed in 

10’x10’ cells. This map provides a further synthesis of densities 

presented in maps a, b and c (see “Methods” section for details), 

and portrays the relative importance of various areas to the 

species. Areas with consistent high use are highlighted on this 

map. To provide a relative reference for the “high use” areas, 

cells are also shown where the species were absent (i.e., the 

cell was sampled but the species was not recorded there), or 

present but at lesser concentrations in any particular season.

DATA SOURCES

At-sea densities for cetaceans are based on data from eight 

survey programs conducted in 1980-2001. These data were 

combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, five aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See section introduction for details on 

individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983) and Dohl et al. (1983); more recent data 

were collected using updated technology but with the same 

general method. Data sources for ship-based survey data 

include David Ainley, unpublished data (see Oedekoven et al., 

2001 for details on methods). Although the at-sea data span 

the years 1980-2001, data are not available for all seasons 

in all years. Upwelling Season, data are from 1980-1982 and 

1985-2001. Oceanic Season, data are from 1980-1982, 1991 

and 1994-2001. Davidson Current Season, data are from 1980-

1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources” section). 

Cetacean observation data and trackline data from these 

studies were converted to a common format. All aerial data were 

continuous; ship-based data were converted separately into a 

continuous transect to the extent possible. From the digitized 

survey data, the distributions of effort and of species were 

mapped into 10’x10’ cells using CDAS, a custom geographic 

information system for analyzing marine bird and mammal 

surveys (MMS, 2001). The length and width of the survey 

trackline in a given cell (estimated trackline width varied by 

platform, depending on speed and height above water) were 

used to estimate the area sampled. The number of cetaceans 

of each species seen in a cell was then divided by the area 

sampled in the cell to estimate density. If a cell was censused 

more than once, densities were averaged, with adjustment 

made for effort.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and to 

exclude observations with winds greater than 25 knots (smaller 

or less obvious species are often less detectable even at wind 

speeds of less than 25 knots). Additional corrections are 

planned for Phase 2 of this project and are briefly discussed 

below. 

For example, no adjustments or corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies.

Map d was developed using the same approach as for maps a, 

b and c. For each season, the cells with densities in the top 20% 

of non-zero values were designated “high use” for that season. 

Cells were scored for “high use” in one, two, or three seasons 

and are depicted by color. To provide a relative reference for 

Figure 72. Maps for northern right-whale dolphin: seasonal at-sea densities and high use areas. the “high use” areas, cells are also shown where the species 

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Upwelling Season

(Mar. 15 - Aug. 14)

20

2

2

2

0

00

0

00

0

0

0

m

m

 m

m

Ocea ic Season n

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

Davidson Current Season 2

2

0

0

0

0

0 

0

0

m

 m

 m

Seasonal High Use Areas

(Nov. 15 - Mar. 14) m

3 Seasons

2 Seasons

1 Season

Dolphins present

a b

Persistence of

High Use

Dolphins absent

c d

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

Northern right-whale dolphin Lissodelphis borealis

Source Data: See text.

DRAFT

113
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

were absent (i.e., the cell was sampled but the species was not 

recorded there) or present (but densities were never in the top 

20% for any season). Further detail on methods is provided in 

the "Data and Analysis" section.

RESULTS AND DISCUSSION 

The northern right whale dolphin occurs in the temperate 

North Pacific, primarily in shelf, slope, and to some degree, 

deep ocean waters. In the study area, this species occurred 

in outer shelf, slope and canyon habitats. The northern right 

whale dolphin was the second most abundant small cetacean 

in the study area, with 135 sightings of 22,578 individuals. 

Distribution of northern right whale dolphins is highly 

variable, apparently in response to seasonal and interannual 

oceanographic changes (Forney and Barlow, 1998). Northern 

right whale dolphins are found primarily off California during 

colder-water months and shift northward into Oregon and 

Washington as water temperatures increase in late spring 

and summer (Carretta et al., 2001; Forney and Barlow, 

1998). Patterns of seasonal abundance have been observed 

throughout their range, but there is no information to indicate 

that large numbers move between California, Oregon, and 

Washington waters (Green et al., 1992). In this study, the 

apparent increase in relative densities in the southern portion 

of MBNMS during the Davidson Current Season may not 

be a seasonal pattern, given the highly variable distribution 

of northern right whale dolphins, apparently in response to 

seasonal and interannual oceanographic changes (Forney 

and Barlow, 1998). 

Northern right whale dolphins feed on mesopelagic fishes (e.g. 

lanternfish) and squid (Leatherwood and Reeves, 1983). 

114
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 73. Map for blue whale: at-sea sightings and survey effort.

ABOUT THIS MAP

Figure 73 shows the individual sightings of blue whales at sea, 

along with at-sea survey effort. Due to insufficient sightings in 

the data set (49 sightings of 77 individuals) for the study area, 

seasonal maps of blue whale density were not generated. 

At-sea sightings for cetaceans are from several studies (see 

“Methods” and “Data Sources” sections). For context, the combined survey effort is also shown, summarized in 10’x10’ cells. 

Blue lines indicate the National Marine Sanctuary boundaries 

of Cordell Bank, Gulf of the Farallones, and Monterey Bay; 

bathymetric contours for the 200m and 2,000m isobaths are 

also shown in blue. Additional data to be added in Phase II may 

make it possible to develop seasonal maps.

DATA SOURCES

At-sea sightings for cetaceans are based on data from eight 

survey programs conducted in 1980-2001. These data were 

combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, five aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See section introduction for details on 

individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDFG-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983) and Dohl et al. (1983); more recent data 

were collected using updated technology but with the same 

general method. Data sources for ship-based survey data include David Ainley, unpublished data (see Oedekoven et al., 

2001 for details on methods). Although the at-sea data span 

the years 1980-2001, data are not available for all seasons in 

all years. For the Upwelling Season, data are from 1980-1982 

and 1985-2001. For the Oceanic Season, data are from 1980-

1982, 1991 and 1994-2001. For the Davidson Current Season, 

data are from 1980-1986 and 1991-2001. 

METHODS

The latitiude and longitude coordinates for blue whales at sea 

were used to plot the individual sightings. At-sea sightings and 

effort are the result of a synthesis of data from eight shipboard 

and aerial survey programs conducted in the study area in the 

years 1980-2001 (see “Data Sources”). Cetacean observation 

data and trackline data from these studies were converted to 

a common format. All aerial data were continuous; ship-based 

data were converted separately into a continuous transect to 

the extent possible. From the digitized survey data, effort was 

mapped into 10’x10’ cells using CDAS, a custom geographic 

information system for analyzing marine bird and mammal 

surveys (MMS, 2001). The length and width of the survey 

trackline in a given cell (estimated trackline width varied by 

platform, depending on speed and height above water) were 

used to estimate the area sampled.

Note that the these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and 

to exclude observations with winds greater than 25 knots; 

additional corrections are planned for Phase 2 of this project 

and are briefly discussed below. 

For example, no adjustments/corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies.

The data in these maps include wind conditions of up to 25 

knots; smaller or less obvious species are often less detectable 

even at wind speeds of less than 25 knots. The seasonal maps 

contain different combinations of shipboard and aerial data; 

therefore the seasonal densities from these platforms may not 

be directly comparable. A full consideration of these factors, and 

revised maps, are planned for Phase 2 of this project. 

RESULTS AND DISCUSSION

The blue whale is federally listed as endangered under the 

Endangered Species Act. One population of blue whale (there 

may be as many as five (Carretta et al., 2001; Reeves et al., 

1998)) is present in California waters, generally from June 

through November. Arrival and departure times in the study 

area are highly variable both seasonally and inter-annually (see 

Benson et al., 2002; Calambokidis et al., 1998). 

Movement patterns, distribution, and occurrence of blue whales 

off California are related to their annual migration between 

foraging areas predominately off central California (but some 

north to British Columbia and south to Baja Mexico and the 

Costa Rican Dome), and the following breeding areas: 1) off 

the west coast of Baja California (September-December), 2) 

the Gulf of California (January-April), and 3) the Costa Rica 

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

°N53°N53

°N63°N63

°N73°N73

°N83°N83

°N93°N93

2

2

0

0

00

0

m

m

0 25 50Km

5

3

2

Blue whale Balaenoptera musculus

Sightings

(Number of whales)

1

Survey Effort

> 3000.00

1500.01 - 3000.00

1000.01 - 1500.00

500.01 - 1000.00

100.01 - 500.00

(km of trackline)

0.01 - 100.00

DRAFT

Source Data: See text.

115
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Dome (Mate et al., 1999). And although blue whales are often 

present in parts of the National Marine Sanctuary waters from 

June through November, their occurrence and distribution 

during this feeding period is highly variable. Due to insufficient 

sightings in the data set (49 sightings of 77 individuals) for 

the study area, seasonal maps of blue whale density were 

not generated. Additional sighting data for blue whale will be 

integrated in Phase 2, and seasonal maps may be generated 

at that time.

Blue whales feed on seasonally abundant and dense euphausiid 

(krill) schools in discrete depths in the water column (Benson 

et al., 2002), concentrated in the deep scattering layer along 

canyon and shelf-break edges, and in daytime surface swarms 

of krill (Schoenherr, 1991; Croll et al., 1998; Forney and Barlow, 

1998). Spatially, they were widely distributed in shelf-break 

and slope habitats, as well as seaward of National Marine 

Sanctuary boundaries, and to a lesser extent, over the shelf. 

Although not directly shown on this map, blue whales also occur 

in the Cordell Bank National Marine Sanctuary and off Bodega 

Bay (Calambokidis et al., 1990b; Calambokidis et al., 1998), 

as well as in waters around the Farallon Islands (C.Keiper, 

pers.comm). 

There is considerable interchange and interregional movements 

between Blue whales that occur off southern California (from 

the Santa Barbara Channel and Southern California Bight) to 

areas in the Monterey Bay, Gulf of the Farallones, Bodega Bay, 

and northern California (Calambokidis et al., 1998). In a study 

of the Monterey Bay area (Benson et al., 2002), occurrence 

of Blue whales in Monterey Bay was related to seasonal 

upwelling patterns that affect seasonally abundant, dense (and 

ephemeral) patches of euphausiids that occur during summer 

and fall (Benson et al., 2002). See map of SWFSC survey data 

for blue whale (Figure 77) for greater geographic extent of the 

range and interannual variations for this species.

116
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 74. Maps for humpback whale: seasonal at-sea densities and high use areas.

ABOUT THESE MAPS

Figures 74a, b and c show the density (animals/km2) of 

humpback whales in the Upwelling, Oceanic, and Davidson 

Current seasons, displayed in 10’x10’ cells. Densities are based 

on combined data of several studies (see “Methods” and “Data 

Sources”). The color and mapping intervals were customized to 

show the most structure and highlight significant areas, while 

allowing comparisons among marine mammal species. Cells 

that were surveyed but which had no humpback whales have 

a density of zero; unsurveyed areas appear white. Blue lines 

indicate the National Marine Sanctuary boundaries of Cordell 

Bank, Gulf of the Farallones, and Monterey Bay; bathymetric 

contours for the 200m and 2,000m isobaths are also shown 

in blue.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence in the study 

area, map d shows seasonal high use areas, displayed in 

10’x10' cells. This map provides a further synthesis of densities 

presented in maps a, b and c (see “Methods” for details), and 

portrays the relative importance of various areas to the species. 

Areas with consistent high use are highlighted on this map. To 

provide a relative reference for the “high use” areas, cells are 

also shown where the species were absent (i.e., the cell was 

sampled but the species was not recorded there), or present 

but at lesser concentrations in any particular season.

DATA SOURCES

At-sea densities for cetaceans are based on data from eight 

survey programs conducted in 1980-2001. These data were 

combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, five aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See section introduction for details on 

individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (MMS, 

2001) and California Department of Fish and Game Office of 

Spill Prevention and Response (CDF&G-OSPR), unpublished 

data. Early data were collected using methods described by 

Bonnell et al. (1983) and Dohl et al. (1983); more recent data 

were collected using updated technology but with the same 

general method. Data sources for ship-based survey data 

include David Ainley, unpublished data (see Oedekoven et al., 

2001 for details on methods). Although the at-sea data span 

the years 1980-2001, data are not available for all seasons in 

all years. For the Upwelling Season, data are from 1980-1982 

and 1985-2001. For the Oceanic Season, data are from 1980-

1982, 1991 and 1994-2001. For the Davidson Current Season, 

data are from 1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources”). Cetacean 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into 

10’x10’ cells using CDAS, a custom geographic information 

system for analyzing marine bird and mammal surveys (MMS, 

2001). The length and width of the survey trackline in a given 

cell (estimated trackline width varied by platform, depending on 

speed and height above water) were used to estimate the area 

sampled. The number of cetaceans of each species seen in a 

cell was then divided by the area sampled in the cell to estimate 

density. If a cell was censused more than once, densities were 

averaged, with adjustment made for effort.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and to 

exclude observations with winds greater than 25 knots (smaller 

or less obvious species are often less detectable even at wind 

speeds of less than 25 knots). Additional corrections are 

planned for Phase 2 of this project and are briefly discussed 

below. 

For example, no adjustments or corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies. Additional data, mapping 

and analysis in Phase 2 may provide more definitive spatial 

patterns for this species.

Map d was developed using the same approach as for maps a, 

b and c . For each season, the cells with densities in the top 20% 

of non-zero values were designated “high use” for that season. 

Cells were scored for “high use” in one, two, or three seasons 

and are depicted by color. To provide a relative reference for 

124°W 123°W 122°W 121°W

124°W 123°W 122°W 121°W 124°W 123°W 122°W 121°W

124°W 123°W 122°W 121°W

Humpback whale Megaptera novaeangliae

Upwelling Season

(Mar. 15 - Aug. 14)

20

2

2

2

0

00

0

00

0

0

0

m

m

 m

m

Ocea ic Season n

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

Davidson Current Season 2

2

0

0

0

0

0 

0

0

m

 m

 m

Seasonal High Use Areas

(Nov. 15 - Mar. 14) m

3 Seasons

2 Seasons

1 Season

Whales present

a b

Persistence of

High Use

Whales absent

c d

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

0.00

°N53 °N63 °N73 °N83 °N93

°N53 °N63 °N73 °N83 °N93°N53 °N63 °N73 °N83 °N93

°N53 °N63 °N73 °N83 °N93

Source Data: See text.

DRAFT

117
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

the “high use” areas, cells are also shown where the species 

were absent (i.e., the cell was sampled but the species was not 

recorded there) or present (but densities were never in the top 

20% for any season). Further detail on methods is provided in 

the "Data and Analysis" section.

RESULTS AND DISCUSSION 

The humpback whale is federally listed as endangered under 

the Endangered Species Act. The eastern North Pacific 

stock of the humpback whale that occurs in the study area, 

feeds off California, Oregon, and Washington and migrates 

from its breeding and calving areas off coastal Mexico and 

Central America (Calambokidis et al., 2000). In this study, the 

humpback whale was the most numerous pelagic baleen whale 

sighted and was primarily distributed over the shelf, upper slope 

and some lower slope habitats. Humpback whales are sighted 

from the Farallon Islands in all months (Pyle and Gilbert, 1996), 

though they are more frequently sighted off central California 

from March through November, with peaks in the summer 

and fall (Calambokidis et al., 1996), a pattern reflected in the 

seasonal distribution maps. 

During the Upwelling Season, humpback whales mostly 

occurred in the shelf and slope areas of, and adjacent to, 

the Gulf of the Farallones (GFNMS) and the northern part 

of Monterey Bay National Marine Sanctuary (MBNMS); see 

map for other areas. During the Oceanic Season, the CDAS 

map shows the Humpback whales more concentrated in 

the areas of the GFNMS, the Cordell Bank National Marine 

sanctuary (CBNMS), the northwest corner of the MBNMS, and 

the adjacent slope area; the SWFSC Humpback whale map 

(Figure 77) shows concentrations over the shelf and slope 

throughout the study area extent. Densities and sightings for 

the Davidson season were lowest, but like the other seasons, 

most occurrences were over the shelf and slope. 

A major food type for humpback whales is euphausiids (krill). 

The Upwelling Season and beginning of the Oceanic Season 

is characterized by a seasonal peak in euphausiid density 

that occurs in July/August but can extend into the Oceanic 

Season (8/15-11/14). Krill abundance increases one to four 

months after seasonal peaks in primary production (Croll et 

al. 1998). One of the dominant species of krill (Thysanoessa 

spinifera) forms dense shoals in the shelf region from Fort 

Ross south to the Channel Islands (Kieckhefer 1992). Primary 

feeding sites of humpback whales are located at Monterey 

Bay (Benson et al., 2002), Bodega Canyon, Cordell Bank, and 

the Farallon Islands (Kieckhefer, 1992). There is considerable 

interchange and inter-regional movement of humpback whales 

within a feeding season between the Santa Barbara Channel, 

Monterey Bay, and to the north off Eureka (Calambokidis et al., 

1996, Calambokidis et al., 1998). During the Davidson Current 

Season, most humpback whales are in breeding/calving areas, 

hence the relatively few sightings in the study area (1980, 1982, 

and 1993) during this season. 

The NOAA/SWFSC stock assessment sightings maps 

(Figure 78) indicate humpback whales occurred off northern 

California, and south to Point Conception, with sightings in 

the CBNMS, GFNMS, and MBNMS during 1993, 1996, and 

2001. During the 1996 and 2001 surveys (when effort extended 

north to Washington), humpback whales were also sighted 

off Washington and Oregon. Based on CDAS data shown in 

these maps, most high use areas occurred over the shelf and 

slope. 

Humpback whales feed on seasonally abundant, small 

schooling fishes (e.g. northern anchovy, Pacific sardine, 

Pacific herring) and euphausiids (primarily T. spinifera and E. 

Pacifica; Kieckhefer, 1992). See map of SWFSC survey data 

for humpback whale (Figure 78) for additional geographic extent 

of the humpback whale range and interannual variations for 

this species.

118
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

ABOUT THESE MAPS

Figures 75a, b and c show the density (animals/km2) of gray 

whales in the Upwelling, Oceanic, and Davidson Current 

seasons, displayed in 10’x10’ cells. Densities are based on 

combined data of several studies (see “Methods” and “Data 

Sources”). The color and mapping intervals were customized 

to show the most structure and highlight significant areas, 

while allowing comparisons among marine mammal species. 

Cells that were surveyed but which had no gray whales have 

a density of zero; unsurveyed areas appear white. Blue lines 

indicate the National Marine Sanctuary boundaries of Cordell 

Bank, Gulf of the Farallones, and Monterey Bay; bathymetric 

contours for the 200m and 2,000m isobaths are also shown 

in blue.

In order to provide one map for the species that integrates the 

patterns of its spatial and temporal occurrence in the study 

area, map d shows seasonal high use areas, displayed in 

10’x10’ cells. This map provides a further synthesis of densities 

presented in maps a, b and c (see “Methods” section for details), 

and portrays the relative importance of various areas to the 

species. Areas with consistent high use are highlighted on this 

map. To provide a relative reference for the “high use” areas, 

cells are also shown where the species were absent (i.e., the 

cell was sampled but the species was not recorded there), or 

present but at lesser concentrations in any particular season.

DATA SOURCES

At-sea densities for cetaceans are based on data from eight 

survey programs conducted in 1980-2001. These data were 

combined using CDAS software into the MMS-CDAS data 

system (MMS, 2001), developed for Minerals Management 

Service and expanded for this project. Of the data sets on the 

original CD-ROM, five aerial survey data sets contained data 

in the study area from Point Arena to Point Sal. Of these, the 

OSPR survey program was still ongoing and data from recent 

years were added to this data set. In addition, data from three 

ship-based survey programs were converted to a compatible 

format for analysis. See "Data and Analyses" subsection in 2.3 

for details on individual data sets.

Data sources for aerial at-sea data include MMS-CDAS (2001) 

and California Department of Fish and Game Office of Spill 

Prevention and Response (CDF&G-OSPR), unpublished data. 

Early data were collected using methods described by Bonnell 

et al. (1983) and Dohl et al. (1983); more recent data were 

collected using updated technology but with the same general 

method. Data sources for ship-based survey data include David 

Ainley, unpublished data (see Oedekoven et al., 2001 for details 

on methods). Although the at-sea data span the years 1980-

2001, data are not available for all seasons in all years. For the 

Upwelling Season, data are from 1980-1982 and 1985-2001. 

For the Oceanic Season, data are from 1980-1982, 1991 and 

1994-2001. For the Davidson Current Season, data are from 

1980-1986 and 1991-2001. 

METHODS

At-sea densities are the result of a synthesis of data from eight 

shipboard and aerial survey programs conducted in the study 

area in the years 1980-2001 (see “Data Sources”). Cetacean 

observation data and trackline data from these studies were 

converted to a common format. All aerial data were continuous; 

ship-based data were converted separately into a continuous 

transect to the extent possible. From the digitized survey data, 

the distributions of effort and of species were mapped into 

10’x10’ cells using CDAS, a custom geographic information 

system for analyzing marine bird and mammal surveys (MMS, 

2001). The length and width of the survey trackline in a given 

cell (estimated trackline width varied by platform, depending on 

speed and height above water) were used to estimate the area 

sampled. The number of cetaceans of each species seen in a 

cell was then divided by the area sampled in the cell to estimate 

density. If a cell was censused more than once, densities were 

averaged, with adjustment made for effort.

Note that these maps represent either sighting locations or 

densities that used survey strip widths relative to each survey 

platform (e.g., plane, ship); density was calculated on the basis 

of the number of animals sighted and area surveyed. The data 

have only been corrected to normalize for survey effort and to 

exclude observations with winds greater than 25 knots (smaller 

or less obvious species are often less detectable even at wind 

speeds of less than 25 knots). Additional corrections are 

planned for Phase 2 of this project and are briefly discussed 

below. 

For example, no adjustments or corrections have been made to 

account for differences in marine mammal detectability among 

species and differential probability of detecting animals from 

aerial and shipboard platforms. Individual body size, group 

size, and species-specific behaviors, such as proportion of time 

spent submerged, are all factors known to affect detection and 

hence, observed distribution and density estimates as well. 

Because of the very different attributes of aerial and shipboard 

platforms, these factors, and the associated adjustments for 

observations, vary among the studies.

Map d was developed using the same approach as for maps a, 

b and c. For each season, the cells with densities in the top 20% 

of non-zero values were designated “high use” for that season. 

Cells were scored for “high use” in one, two, or three seasons 

and are depicted by color. To provide a relative reference for 

the “high use” areas, cells are also shown where the species 

was absent (i.e., the cell was sampled but the species was not Figure 75. Maps for gray whale: seasonal at-sea densities and high use areas.

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W 124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

124°W 123°W 122°W 121°W

°N53 °N63 °N73 °N83 °N93

Gray whale Eschrichtius robustus

Upwelling Season

(Mar. 15 - Aug. 14)

20

2

2

2

0

00

0

00

0

0

0

m

m

 m

m

Ocea ic Season n

(Aug. 15 - Nov. 14)

Density

(Animals/km2)

0 25 50Km

20

2

0

0

Davidson Current Season 2

2

0

0

0

0

0 

0

0

m

 m

 m

Seasonal High Use Areas

(Nov. 15 - Mar. 14) m

3 Seasons

2 Seasons

1 Season

Whales present

a b

Persistence of

High Use

Whales absent

c d

10.01 - 50.00

5.01 - 10.00

1.01 - 5.00

0.51 - 1.00

0.11 - 0.50

0.06 - 0.10

0.01 - 0.05

DRAFT

0.00

°N53 °N63 °N73 °N83 °N93

Source Data: See text.

119
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

recorded there) or present (but densities were never in the top 

20% for any season). Further detail on methods is provided in 

the "Data and Analysis" section.

RESULTS AND DISCUSSION 

The eastern population of the gray whale migrates from 

summer feeding grounds in the Bering, Chukchi, and western 

Beaufort Seas, south along the west coast of North America 

to its winter breeding and calving areas off the coast of Baja 

California. The southward migration includes (in the order of sex 

and age-class) females in late pregnancy, females that have 

recently ovulated, adult males, immature females, and lastly, 

immature males. In the study area, this southward migration 

generally occurs from December through February and peaks 

in January. The northward migration generally occurs from 

February through May and peaks in March and includes (in 

the order of reproductive condition, sex, age-class,) newly 

pregnant females, adult males, immature females, and last 

in this migration, the females with calves. The latter migrate 

northward through the study area during April and May, and 

sometimes June. The northward migration is reflected in the 

distribution patterns during the Upwelling Season, when gray 

whales are distributed in the coastal and inner/outer shelf 

habitats throughout the study area, en route to their northern 

feeding grounds, a pattern reflected in their virtual absence 

(according to the data set) in the study area during the Oceanic 

Season. 

In the study area and data sets analyszed, the gray whale was 

the second most numerous baleen whale. Concentrations of 

this species were greatest during the Davidson Current Season, 

a period that encompasses both the southward and northward 

migration, with greatest concentrations observed along the 

coast near Cypress Point and south of Point Sur to Lopez 

Point. Relative densities were somewhat greater to the north 

of CBNMS and to the south of MBNMS (likely related to the 

timing of individuals moving north or south). Recent preliminary 

documentation of the southbound migration during 2000 and 

2001 indicated population estimates of 17,414 (CV=10%), well 

below previous (1997/98) estimates of 26,635 (CV=10%; Rugh 

et al., 2002). These low estimates may have been caused by 

an unusual number of whales that did not migrate as far south 

as Granite Canyon (the survey location), or abundance may 

have declined following the high mortality rates observed in 

1999 and 2000 (Rugh et al., 2002). 

Strandings along the coast of North America were six times 

more prevalent than during 1995-1998 (Gulland et al., 2001). 

Factors that may have contributed to the high number of 

strandings include: starvation, anthropogenic and natural 

toxins, infectious diseases, ship strikes, detection effort and 

reporting, and wind and current effects (Gulland et al., 2001). 

Significant declines in calf counts also occurred during this 

same period (Perryman et al., 2002). 

The apparent seasonal high-use areas noted in map d (the 

Farallon Islands, off Año Nuevo, and north of Cordell Bank near 

Point Arena and Fort Ross) are likely related to the timing of the 

migration and may not represent a discrete spatial pattern.

Gray whales feed on benthic invertebrates (e.g. gammarid 

amphipods; Leatherwood and Reeves, 1983), mysid shrimp, 

herring eggs/larvae, crab larvae, ghost shrimp (Darling et al., 

1998), and surface swarms of euphausiids (Benson et al., 

2002). Although most individuals of gray whales in the study 

area were non-feeding migrants, some individuals do feed on 

a regular basis near the South Farallon Islands, at the mouth 

of Tomales Bay and Drakes Bay (S. Allen, 2002, pers. comm.), 

during their northward migration. Gray whales also feed in San 

Francisco Bay (in some years: 1999, 2000,-2001; Oliver et al., 

2001)) and Monterey Bay (Benson et al., 2002). Gray whales 

also have been seen regularly off Point Reyes, Tomales Bay, 

Drakes Bay, and the Farallon Islands during non-migratory 

periods (S. Allen, pers. comm.). 

120
132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W

°N03 °N23 °N43 °N63 °N83 °N04 °N24 °N44 °N64 °N84

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W °N03 °N23 °N43 °N63 °N83 °N04 °N24 °N44 °N64 °N84

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W

°N03 °N23 °N43 °N63 °N83 °N04 °N24 °N44 °N64 °N84

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W °N03 °N23 °N43 °N63 °N83 °N04 °N24 °N44 °N64 °N84

Dall's porpoise Phocoenoides dalli

National Marine Fisheries Service,

Southwest Fisheries Science Center

National Ocean Service,

National Centers for Coastal Ocean Science

1991

5.1 - 27.0

3.1 - 5.0

2.1 - 3.0

1.6 - 2.0

1.0 - 1.5

Effort

1993

5.1 - 27.0

3.1 - 5.0

2.1 - 3.0

1.6 - 2.0

1.0 - 1.5

Effort

1996

5.1 - 27.0

3.1 - 5.0

2.1 - 3.0

1.6 - 2.0

1.0 - 1.5

Effort

5.1 - 27.0

3.1 - 5.0

2.1 - 3.0

1.6 - 2.0

1.0 - 1.5

Average Average

Group Size Group Size

2001

Average Average

Group Size Group Size

Effort

These maps contain data from one source: the NMFS/SWFSC cetacean stock assessment

shipboard surveys, generally conducted during the late summer and fall, mostly from July through

December. These maps do not represent the species complete spatial and temporal distribution.

Group size was estimated independently by all observers on each survey vessel who obtained a

good look at that group. These independent estimates of group size were averaged to give the

average group sized estimate for each sighting.

Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

Figure 76. Maps for Dall’s porpoise: SWFSC stock assessment data: average group size of sightings and survey 

effort.

Introduction to the SWFSC Data Set, to be used in Phase 

II of this Analysis. The following marine mammal maps are 

based on data from NOAA’s marine mammal stock assessment 

program, conducted by NOAA’s Southwest Fisheries Science 

Center. Maps for three species are included below (and 13 more 

are on the CD-ROM) to provide the reader with an idea of some 

of the additional data that will be incorporated into the overall 

mammal data set and analysis in Phase II (Figures 76-78).

These maps show sightings (species group size), and effort 

locations generally for the late summer/fall season (data ranged 

from July-December) for four years: 1991, 1993, 1996 and 

2001, off the coasts of California, Oregon and Washington. 

These maps are the results of broad-scale, ocean ship 

surveys (aerial surveys are not included), and are used in the 

development of stock estimates and trend analyses for most 

marine mammals that occur off the coasts of California, Oregon 

and Washington. These SWFSC maps do not represent the 

distribution of the species, but they do provide an indication 

of the broader spatial extent of the species during the late 

summer/fall season. 

For more information on the marine mammal stock assessment 

survey data, visit: http://swfsc.nmfs.noaa.gov/PRD/CMMP/ or 

contact Dr. Jay Barlow at Jay.Barlow@noaa,gov.

About the SWFSC Dall’s Porpoise Maps (Figure 76). These 

SWFSC maps of surveys conducted in July through early 

December 1991, 1993, 1996, and 2001, (late upwelling and 

Oceanic season) encompass a much larger geographic 

extent and provide an example of the off-shore and northern 

geographic extent of the Dall’s porpoise. A visual comparison 

of the SWFSC maps among years (1991, 1993, 1996, 2001) 

indicates occurrence patterns of Dall’s porpoise varied; number 

of sightings was relatively greater off northern California than 

off central California in 1991, (when survey effort was only off 

California). In the survey of 1996, (when survey effort extended 

north to Oregon and Washington), number of sightings and 

average group size was relatively greater off Oregon and 

northern California than off central California. Sightings that 

occurred within NMS boundaries occurred in Monterey Bay 

and off Point Reyes (when effort extended into these areas). 

See "Map Text" and "Discussion" in CDAS map section for 

additional information on Dall’s porpoise.

About the SWFSC Blue Whale Maps (Figure 77). These 

SWFSC maps of surveys conducted in July through early 

December 1991, 1993, 1996, and 2001, (late upwelling and 

Oceanic season) encompass a much larger geographic extent 

than the study area covered with the CDAS maps and indicate 

concentrations of Blue whales off southern California and 

further off-shore in pelagic, deep ocean habitats (not shown 

in the CDAS maps). A visual comparison of the SWFSC maps 

among years (1991, 1993, 1996, 2001) indicates occurrence 

patterns of blue whales varied; relatively greater concentrations 

of blue whales off southern California were evident in 1991, 

1993, and 1996, however, this species was virtually absent 

(except for a few sightings) in this region during the survey of 

2001. Sightings occurred within NMS boundaries (when effort 

extended into these areas) off Point Reyes in 1991 and 1996, 

within the Gulf of the Farallones National Marine Sanctuary in 

1993, and within Monterey Bay in 1996. See "Map Text" and 

"Discussion" in CDAS map section for additional information 

on blue whales.

About the SWFSC Humpback Whale Maps (Figure 78). These 

SWFSC maps of surveys conducted in July through early 

December 1991, 1993, 1996, and 2001, (late upwelling and 

Oceanic season) encompass a much larger geographic extent 

and indicate concentrations of humpback whales in central 

California relatively closer to shore. (See SWFSC blue whale 

maps for comparison) and distributed off northern California 

and south to Point Conception. A visual comparison of the 

SWFSC maps among years (1991, 1993, 1996, 2001) indicates 

occurrence patterns of humpback whales varied; relatively 

greater concentrations occurred off central California in the 

survey of 1996, compared to the survey of 1991 (when survey 

effort was similar off central California). Sightings within the 

CBNMS, GFNMS, and MBNMS occurred during 1993, 1996, 

and 2001 (when effort extended into these areas). During 

the surveys of 1996 and 2001 (when effort extended north to 

Washington and Oregon), humpback whales also were sighted 

off Washington and Oregon. See "Map Text" and "Discussion" 

in CDAS map section for additional information on Humpback 

whales.

121
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W

30°N 32°N 34°N 36°N 38°N 40°N 42°N 44°N 46°N 48°N

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W 30°N 32°N 34°N 36°N 38°N 40°N 42°N 44°N 46°N 48°N

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W

30°N 32°N 34°N 36°N 38°N 40°N 42°N 44°N 46°N 48°N

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W 30°N 32°N 34°N 36°N 38°N 40°N 42°N 44°N 46°N 48°N

Blue Whale Balaenoptera musculus

National Marine Fisheries Service,

Southwest Fisheries Science Center National Ocean Service,

National Centers for Coastal Ocean Science

1991

3.1 - 5.0

2.1 - 3.0

2.0

1.1 - 1.9

1.0

Effort

1993

3.1 - 5.0

2.1 - 3.0

2.0

1.1 - 1.9

1.0

Effort

1996

3.1 - 5.0

2.1 - 3.0

2.0

1.1 - 1.9

1.0

Effort

3.1 - 5.0

2.1 - 3.0

2.0

1.1 - 1.9

1.0

Effort

2001

These maps contain data from one source: the NMFS/SWFSC cetacean stock assessment

shipboard surveys, generally conducted during the late summer and fall, mostly from July through

December. These maps do not represent the species complete spatial and temporal distribution.

Group size was estimated independently by all observers on each survey vessel who obtained a

good look at that group. These independent estimates of group size were averaged to give the

average group sized estimate for each sighting.

Average

Group Size

Average

Group Size

Average

Group Size

Average

Group Size

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W

30°N 32°N 34°N 36°N 38°N 40°N 42°N 44°N 46°N 48°N

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W 30°N 32°N 34°N 36°N 38°N 40°N 42°N 44°N 46°N 48°N

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W

30°N 32°N 34°N 36°N 38°N 40°N 42°N 44°N 46°N 48°N

132°W 130°W 128°W 126°W 124°W 122°W 120°W 118°W 30°N 32°N 34°N 36°N 38°N 40°N 42°N 44°N 46°N 48°N

Humpback Whale Megaptera novaeangliae

National Marine Fisheries Service,

Southwest Fisheries Science Center

National Ocean Service,

National Centers for Coastal Ocean Science

1991

3.1 - 14.0

2.1 - 3.0

1.9 - 2.0

1.1 - 1.8

1.0

Effort

1993

3.1 - 14.0

2.1 - 3.0

1.9 - 2.0

1.1 - 1.8

1.0

Effort

1996

3.1 - 14.0

2.1 - 3.0

1.9 - 2.0

1.1 - 1.8

1.0

Effort

3.1 - 14.0

2.1 - 3.0

1.9 - 2.0

1.1 - 1.8

1.0

Effort

2001

These maps contain data from one source: the NMFS/SWFSC cetacean stock assessment

shipboard surveys, generally conducted during the late summer and fall, mostly from July through

December. These maps do not represent the species complete spatial and temporal distribution.

Group size was estimated independently by all observers on each survey vessel who obtained a

good look at that group. These independent estimates of group size were averaged to give the

average group sized estimate for each sighting.

Average

Group Size

Average

Group Size

Average

Group Size

Average

Group Size

Figure 78. Maps for humpback whale: SWFSC stock assessment data: average group size of sightings and 

survey effort.

Figure 77. Maps for blue whale: SWFSC stock assessment data: average group size of sightings and survey 

effort.

122
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

SECTION SUMMARY

The marine mammal fauna of the study area include species 

with a variety of spatial and temporal patterns and can be 

generally characterized as: 

• resident, breeding species that occur year-round 

 (e.g. harbor seal, southern sea otter, Steller sea lion); 

• species that breed, pup, and molt in the study area and

 then as adults, feed elsewhere (e.g. northern elephant

 seals); 

• species that are seasonally abundant during their migration

 (e.g. gray whale); 

• seasonally abundant species that have either migrated to 

 these waters to forage during summer and fall 

 (e.g. humpback and blue whales) or to forage during 

 winter (e.g. northern fur seal and California sea lions); and 

• species which, though present year-round, exhibit highly 

variable seasonal shifts in distribution (e.g. several species 

of dolphins and porpoises). 

Preliminary CDAS maps for 13 species were developed for 

this document; this is fewer than half of the mammal species 

in the study area and the maps are draft. No summary 

analyses across mammal species were done, as they would 

be inconclusive, and biased by the limited number and type of 

species mapped (e.g., coastal, offshore).

However, preliminary data products do show that marine 

mammals of the study area are widely distributed from the 

shore to deep ocean, and while some species are found mostly 

over the shelf, or deep offshore, most species occur over a 

variety of bathymetric zones. Given that the data and maps 

are preliminary and most likely incomplete, it is not possible at 

this time to evaluate the importance of smaller, discrete areas 

for the mammal species listed.

The broad-scale spatial coverage of the 16 maps for cetaceans 

from the NMFS/SWFSC marine mammal stock assessment 

program (Barlow, unpublished data), provided additional 

information for 13 species that were distributed in deep ocean 

habitats, and well beyond the range of the current CDAS data 

set. These data will likely be incorporated into the CDAS data 

set and mammal analysis planned for Phase II.

The marine mammal life history information and analytical 

map products were used to develop the summary spatial and 

temporal distributions described below.

Life History Characteristics

Table 25 is an initial summary of life history and management 

information that was identified in the marine mammal mapping 

analyses. This table will be expanded in Phase II. 

Associations with Bathymetric 

Areas

Marine mammal distributions can be 

associated with bathymetrically-defined 

areas and results include: 

• Widely distributed (found throughout 

the study area): Dall’s porpoise and 

northern fur seal (but mostly occurs 

over the slope and in the deep ocean); 

California sea lion, (but mostly occurs 

along the coast and over the inner 

shelf); and northern elephant seal 

and Steller sea lion.

• Coastal: Southern sea otter, gray 

whale (but this species also occurs 

throughout the broad shallow shelf 

of the Gulf of the Farallones and in 

proximity of the Farallon Islands).

• Inner Shelf: Southern sea otter, 

California sea lion, Steller sea lion, 

harbor seal, humpback whale and 

gray whale.

• Outer Shelf: California sea lion, 

Steller sea lion, harbor seal, northern 

elephant seal, northern fur seal, 

Risso’s dolphin, Dall’s porpoise, 

Pacific white-sided dolphin, blue 

whale, humpback whale and gray 

whale.

• Slope: California sea lion, northern 

elephant seal, Northern fur seal, Dall’s 

porpoise, Pacific white-sided dolphin, 

Risso’s dolphin, northern right whale 

dolphin, blue whale and humpback 

whale.

• Deep Ocean

Table 25. Preliminary life history and management information for selected marine mammals off north/central California.

Protection & Population Status Occurrence & Breeding in Study Area Prey Types

Protection Time Period of vn r e et r b t a se

ii sd k( ir l) l

l ga ci In ev tr s'

, d co ot up ) s

et r b t a se

Status in Population Trend of Population in Primary c I

no

su

eP

q i u

V r e

Study Area the Study Area (Increasing, Occurrence in Breeding t i h

t k

ah

r e

s

se

r e

(FE, FT, SE, Decreasing, Relatively Stable, Study Area Time Period ne

na

pu

ht

. . g

hs

ht

Common Name Scientific Name ST) Unknown) Temporal Occurrence (months) (months) B

l P

EO

e(

i F

O

Southern sea otter Enhydra lutris nereis Federally

Threatened 1 Declining Year-round All months June/July -Oct/Nov X X

California sea lion Zalophus californianus 2 Increasing

Present year-round; 

seasonally abundant Aug-Mar May-July X X

Steller sea lion Eumetopias jubatus Federally

Threatened

3 Año Nuevo: possibly stable last 3 yrs ;

4 Farallones: declining

Year-round All months mid-May to

mid-July

X X

Harbor seal Phoca vitulina richardsi

Stable (California net production may 

2 be slowing) Year-round All months Mar-June X X

3 Año Nuevo: Stable, last 5 yrs ;

Northern elephant seal Mirounga angustirostris

Farallones: declining5 ; Pt. Reyes 

6 Headlands: increasing ; California: net 

Present year-round; 

seasonally abundant

At-sea - unknown

at this time;

at rookeries -

mid-Dec thru

mid-Mar X X

2a productivity rate declining ; number Nov-Mar

pups appears to be leveling off2a

Northern fur seal Callorhinus ursinus 2 San Miguel Island stock: increasing ;

Pribilof Is: rate of increase 8.12%7

Present year-round; 

seasonally abundant Feb-May June-July X X

Dall's porpoise Phocoenoides dalli 2 Trends Unknown Year-round No trend apparent 

in data Unknown X X

Harbor porpoise (Northern CA, 

San Francisco/Russian River, 

Monterey stocks)

Phocoena phocoena

N. California stock: No Trends2a;

San

Francisco/Russian River and Monterey 

stock: trends in relative abundance not 

statistially significant.2a

Year-round Unknown at this 

time Unknown X X

Pacific white-sided dolphin Lagenorhynchus obliquidens 2 No Trends Year-round No trend apparent 

in data Unknown X X

Risso's dolphin Grampus griseus 2 Trends Unknown Year-round No trend apparent 

in data Unknown X X

Bottlenose dolphin (California

coastal stock) Tursiops truncatus 2 Stable Year-round No trend apparent in data N/A X X

Short-beaked common dolphin Delphinus delphis

Stock status unknown; likely 

distributional shifts rather than

2 population increase

Not detected in CDAS 

data

No trend apparent 

in data Unknown X X

Northern right whale dolphin Lissodelphis borealis 2 Trends Unknown Year-round No trend apparent 

in data Unknown X X

Killer whale Orcinus orca 2 Trends Unknown Year-round No trend apparent 

in data Unknown X X X

Baird's beaked whale Berardius bairdii 2 Trends Unknown Unknown Insufficient data N/A ? ?

Beaked Whales 

(Mesoplodonts) Mesoplodond spp. 2 Trends Unknown Unknown Insufficient data N/A ? ?

Cuvier's beaked whale Ziphius cavirostris 2 Trends Unknown Unknown Insufficient data N/A ? ?

Sperm whale Physeter macrocephalus Federally

Endangered 2 Trends Unknown Seasonal No trend apparent in data N/A X

Blue whale Balaenoptera musculus Federally

Endangered Increasing?8 Seasonal Aug-Nov N/A X X?

Humpback whale Megaptera novaeangliae Federally

Endangered Increasing 6-7%/yr9 Present year round; seasonally abundant June-Nov N/A X X

Fin whale Balaenoptera physalus Federally

Endangered 2 Trends Unknown Seasonal Aug-Nov N/A X X

Minke whale Balaenoptera acutorostrata

Stock status unknown; no data on

trend 2 s Year-round No trend apparent 

in data N/A X X

Gray whale Eschrichtius robustus Delisted

Federal 1994

Increasing to late 1990's; Decreasing

10 (2002)

Present year round; 

seasonally abundant Dec-Apr

Dec-Jan

(breeds off 

Baja)

X X X

: California sea lion, 

northern fur seal, northern elephant 

seal, Dall’s porpoise, Pacific whitesided dolphin, Risso’s dolphin, 

northern right-whale dolphin, blue 

whale, and humpback whale.

Occurrence by Oceanographic 

Season

The seasonal occurrence patterns of 

marine mammals in waters off north/ Notes

1. This table is preliminary; in Phase II more information will be added and the table will be reviewed by experts.

central California were clearly evident 2. A question mark (?) in the table indicates the entry is a probable entry (e.g., prey type); these items may be further evaluated in Phase II.

for migrating species of large cetaceans 3. Superscripts indicate sources as follows: 1-USGS, 2002; 2-Carretta et al.; 2001; 2a-Carretta et al. 2002; 3-P.Morris pers.comm., credited to B. Le Boeuf; 4-Hastings and Sydeman, 2001; and 5-USFWS, 2000.

 6-Sydeman and Allen, 1999; 7-Gerrodette et al.,1985; 8-Calambokidis pers.comm.; 9-Forney et al., 2000; 10-Rugh et al., 2002

(gray, blue and humpback whales) and 4. All marine mammal species have legal protection under the Marine Mammal Protection Act of 1972; species identified as Federally Endangered (FE), Federally Threatened (FT) are identified.

for the non-breeding pinnipeds that No marine mammal species have designation as state endangered (SE) or state threatened (ST) in the California at this time.

123
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

breed mostly outside the study area (northern fur seal and 

California sea lion). The species occurrences in the three 

oceanographic seasons are described below.

Upwelling Season (~Spring/Summer). This season is 

characterized by an increase in cold, nutrient-rich water 

brought to the surface by persistent northwest wind and the 

Coriolis effect, followed by intermittent relaxation of upwelling. 

Within-season variability during the upwelling process affects 

food web development and the availability of prey to marine 

mammals. 

The Upwelling Season is also characterized by variations and 

fluctuations in seasonal peaks in abundance of small schooling 

fish and relative densities of euphausiids. The humpback whale 

was present in greater abundance during the Upwelling and 

Oceanic seasons. Humpback whales migrate to waters off 

north/central California to feed on seasonally-abundant prey. 

The northern fur seal also was relatively abundant during the 

Upwelling and Davidson Seasons. After the breeding/pupping 

season (June-July), adult females and juveniles migrate from 

rookeries on San Miguel Island in the southern California Bight 

(the San Miguel Island stock) and from the Eastern Pacific stock 

of the Pribilof Islands and are therefore relatively abundant in 

the study area during winter and early spring.

Oceanic Season (~Autumn). During the Oceanic Season, the 

northwest winds subside, warmer offshore water is advected 

onshore, thermoclines strengthen, ocean conditions become 

more stratified and marine mammal prey become more 

stabilized. The following four species were relatively more 

abundant during the Oceanic season (evaluated by the visual 

inspection of the maps): Pacific white-sided dolphin, blue whale, 

humpback whale, and California sea lion. Although the Pacific 

white-sided dolphin occurred during all seasons, it appeared to 

be more numerous during the Oceanic Season. The blue whale 

(like the humpback whale) migrates to north/central California 

to forage on seasonally-abundant euhausiids during summer 

and fall. The California sea lion, the most abundant pinniped 

in the study area was present year-round, however, greater 

numbers of sea lions were present during the Oceanic season 

(just after the breeding season), but also during the Davidson 

Season (before the next breeding season). 

Davidson Current Season (~Winter). The Davidson Current 

Season is characterized by frequent winter storms, downwelling, 

relatively warm uniform temperature to considerable depths and 

a deep mixed layer. During this season, the gray whale was 

relatively abundant because it migrates through the study area 

on its way south (or north) during this period. The northern fur 

seal and California sea lion also were relatively abundant (see 

comments on the Upwelling and Oceanic seasons above).

Additional Observations. No clear seasonal patterns could 

be determined in this preliminary visual assessment for 

the smaller cetaceans: northern right-whale dolphin, Dall’s 

porpoise, Pacific white-sided dolphin and Risso’s dolphin. 

For the latter two species, however, a shift in distribution was 

evident during the Oceanic season; see Figures 69 and 70. 

Given the highly variable distribution of the smaller cetaceans, 

shifts in distribution (as indicated on the maps) may not indicate 

a seasonal pattern. 

Elephant seals, Steller sea lions, and harbor seals were present 

in National Marine Sanctuary waters year-round. And although 

at-sea sightings are relatively infrequent, these species are 

frequently sighted at haulouts and rookeries at specific times 

of the year, as noted in Table 25. Important at-sea time periods 

for these infrequently-sighted species is inconclusive due to 

insuffcient at-sea data and differences in behavior that affect 

sighting frequency and otherwise low abundance. For example, 

some of these sighting issues include: at-sea sightings typically 

consist of single individuals or small groups of two or three; 

elephant seals are rarely at the surface; and Steller sea lions 

are a threatened species and thus occur in small numbers.

Overview of Occurrence Patterns

Cetaceans. Cetaceans were found throughout the study area; 

in coast, shelf, upper/lower slope and deep ocean habitats.

• The humpback whale was the most numerous pelagic baleen 

whale seen in the study area and was seen more frequently 

during the Upwelling and Oceanic Seasons. Seasonal high 

use areas within the Gulf of the Farallones National Marine 

Sanctuary were regions around the Farallon Islands and to 

the west of the islands, on the outer shelf and upper slope, 

regions over Pioneer, Ascension and Monterey canyons. 

Given the highly variable distribution of humpback whales 

in the study area during the feeding season, observed spatial 

distribution may not indicate a general spatial pattern.

• The gray whale was the second most abundant baleen 

whale and was found in coastal and shelf regions; relative 

abundance of the gray whale in the study area was greater 

during the Upwelling and Davidson Current Seasons that 

coincided with the north and south migration of this species. 

Seasonal high use areas were to the north of Cordell Bank 

National Marine Sanctuary near Point Arena. Given the 

variable distribution of the gray whale, relative to the timing 

of the migration, this observed spatial distribution may not 

indicate a general spatial pattern.

• The Pacific white-sided dolphin was the most numerous of 

the small cetaceans and appeared to be more abundant 

during the Oceanic Season in the Gulf of the Farallones and 

Monterey Bay National Marine Sanctuaries; seasonal high 

use areas were upper/lower slope regions in the Monterey 

Bay and Cordell Bank National Marine Sanctuary. Given 

the highly variable distribution of the Pacific white-sided 

dolphin, the observed spatial and temporal distribution may 

not indicate a general spatial/temporal pattern. 

• The northern right whale dolphin was the second most 

numerous of the small cetaceans; concentrations appeared 

to be greater within the Monterey Bay National Marine 

Sanctuary, as well as outside National Marine Sanctuary 

boundaries. Seasonal high use areas were upper/lower slope 

regions in the Monterey Bay National Marine Sanctuary. No 

seasonal pattern in relative abundance was visually detected 

in the maps; however, a seasonal shift in the distribution 

of this species in the study area was apparent during the 

Oceanic Season (concentrations were greater outside than 

within National Marine Sanctuary boundaries); during the 

Davidson Season the greatest concentrations occurred in 

the southern regions of the Monterey Bay National Marine 

Sanctuary. Given the highly variable distribution of the 

northern right whale dolphin, the observed occurrences 

may not indicate a general spatial/temporal pattern.

• Risso’s dolphin was the third most numerous of the small 

cetaceans and occurred in shelf, and upper/lower slope 

habitats. This species was more widespread during the 

Upwelling Season and more concentrated in the southern 

portion of the study area (within and outside National Marine 

Sanctuary boundaries) during the Oceanic and Davidson 

Current Seasons. No clear seasonal shift in relative 

abundance in the study area was detected in a visual 

inspection of maps. Seasonal high use areas were in the 

Monterey Bay National Marine Sanctuary over slope/canyon 

habitats. Given the highly variable distribution of the Risso’s 

dolphin, the observed spatial and temporal distribution may 

not indicate a general spatial/temporal pattern.

• The Dall’s porpoise was the fourth most numerous small 

cetacean and distribution was widespread on shelf, upper/

lower slope, and deep ocean habitats. No clear seasonal 

pattern in relative abundance in the study area was visually 

detected in the maps. Seasonal high use areas were upper 

slope in the Cordell Bank and Gulf of the Farallones National 

Marine Sanctuaries. Given the highly variable distribution 

of the Dall’s porpoise, the observed occurrences may not 

indicate a general spatial/temporal pattern.

Pinnipeds. Pinnipeds were found in the coast, shelf, slope and 

deep ocean habitats of the study area.

• The California sea lion was the most numerous pinniped 

seen in the study area and occurred throughout the region 

in coastal, shelf, and upper slope habitats. This species was 

most abundant during the Oceanic (just after its breeding 

period) and Davidson Current Season (before its next 

breeding period) Seasons. Seasonal high use areas were 

in proximity to major haulout sites near Año Nuevo and the 

Farallon Islands. Seasonal trends in relative abundance and 

attendance at haulout sites were associated with warm-water 

periods (El Niño events); sea lions were more numerous both 

at-sea and on land during these warm-water periods.

• The northern fur seal was the second most numerous 

pinniped seen in the study area and occurred in outer shelf, 

upper/lower slope and deep ocean habitats. Although seen 

in all seasons, this species was most abundant during the 

Upwelling and Davidson Current Seasons (non-breeding 

period), a pattern that coincided with their migration to north/

central California from San Miguel Island and the Pribilof 

Islands. Seasonal high use areas were outside (to the west 

and north) of National Marine Sanctuary boundaries.

• The northern elephant seal was the third most numerous 

pinniped seen in the study area, however, sightings were too 

infrequent to determine seasonal trends in at-sea distribution. 

Sightings occurred throughout the study region in shelf, 

upper/lower slope and deep ocean habitats.

• The harbor seal was the fourth most numerous pinniped seen 

in the study area, however sightings were too infrequent to 

determine seasonal trends in at-sea distribution. Sightings 

occurred in coastal and shelf habitats.

• The Steller sea lion was sighted rarely, therefore no seasonal 

trends in at-sea distribution could be determined. Sightings 

of this species occurred in coastal, shelf and upper slope 

habitats.

A Fissiped. The southern sea otter is the only fissiped included 

in the analysis. This species occurs year-round mostly along 

the coast and inner shelf. Due to insufficient data no spatial/

temporal trends could be determined.

Preliminary Observations of Species Distributions Relative 

to National Marine Sanctuary Boundaries

• Eight of the 13 marine mammals evaluated in this assessment 

are relatively pelagic, far-ranging marine mammals that are 

widely distributed, and are either species that occur mostly 

in deep ocean habitats (northern fur seal, northern elephant 

124
seal, the endangered humpback and blue whales, Dall’s 

porpoise, Risso’s dolphin), or over upper/lower slope habitats 

(northern right-whale dolphin, Pacific white-sided dolphin). All 

occur both in and outside of the National Marine Sanctuary 

boundaries of the study area. 

• The gray whale also occurs outside National Marine Sanctuary 

boundaries, but migrates through sanctuary waters along the 

coast and over the continental shelf. 

• To the north of Cordell Bank (within relatively close proximity 

to that National Marine Sanctuary boundary), the Pacific 

white-sided dolphin, humpback whale, Dall’s porpoise, and 

northern fur seal were present. A relatively high seasonal use 

area for the gray whale also occurred north of Cordell Bank 

National Marine Sanctuary. Given the general variable nature 

of cetacean distributions, these observations are preliminary 

and may not indicate a spatial pattern. 

• Relatively high seasonal use areas of the Dall’s porpoise, 

humpback whale and blue whale were located seaward or 

west of the Gulf of the Farallones National Marine Sanctuary 

over the lower slope. Given the highly variable distribution of 

these species, these observations are preliminary and may 

not indicate a spatial pattern.

• Seasonal high use areas of the northern fur seal, northern 

right whale dolphin, and Risso’s dolphin occurred seaward 

of the Monterey Bay National Marine Sanctuary (western 

areas of the Monterey Canyon and the Shepard’s Meander). 

Given the highly variable distribution of these species, these 

observations are preliminary and may not indicate a spatial 

pattern.

• Seasonal high use areas of Risso’s dolphin, northern fur seal, 

and Pacific white-sided dolphin also were located seaward 

of the southern regions of the Monterey Bay National 

Marine Sanctuary (near Lucia Canyon and to the south). 

Given the highly variable distribution of these species, these 

observations are preliminary and may not indicate a spatial 

pattern.

• Within the study area, haulout sites for the northern 

elephant seal all occurred within National Marine Sanctuary 

boundaries. Haulout sites for the harbor seal, California sea 

lion and Steller sea lion also occurred within National Marine 

Sanctuary boundaries, but also both north (Steller sea lion, 

California sea lion, harbor seal) and south (California sea lion, 

harbor seal) of the boundaries. Harbor seal haulouts occurred 

along the coast from Point Arena to Point Sal. 

Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

• Rookeries for the northern elephant seal, Steller sea lion and 

California sea lion occurred within National Marine Sanctuary 

boundaries of the study area, however, during the El Niño of 

1998, California sea lion rookeries were located at Lion rock 

and Point Sal Rock, to the south of National Marine Sanctuary 

boundaries. Haulout sites (n=3) for the threatened Steller sea 

lion are located along the coast to the north of Cordell Bank 

National Marine Sanctuary.

• Southern sea otters occurred in coastal shelf waters, almost 

exclusively in Monterey Bay National Marine Sanctuary and 

to the south, outside of the study area to San Nicholas Island 

in the southern California Bight.

DISCUSSION

Differences in habitat use relative to large bathymetric features 

are likely related to factors such as the distribution, abundance, 

and availability of various prey (species/sizes). Therefore, the 

importance of the study area must be considered in the context 

of the variability of ocean climate and oceanography, which 

strongly affects prey availability. 

Cordell Bank, the Gulf of the Farallones, and Monterey Bay 

National Marine Sanctuaries encompass some of the most 

productive waters along the California coast. Presence of marine 

mammals in these waters is affected not only by bathymetric 

features, but also changing oceanographic conditions that 

result in fluctuations in abundance and distribution of patchily 

distributed prey. The unique bathymetric features, coupled with 

the complex physical oceanography off central California play 

an important role in the distribution of marine mammal prey 

and, in turn, the distribution of mammals themselves. 

This unique combination of both wide and narrow continental 

shelf, areas of high topographical relief (canyon edges, steep 

slopes, ridges, banks, shelf breaks, seamounts), and the 

distinctive oceanographic features associated with seasonal 

upwelling (e.g., upwelling plumes, fronts, temporal and spatial 

variation in thermocline depth, surface and subsurface currents 

and eddies) affect the distribution patterns of organisms at 

many trophic levels. For example, large concentrations of small 

schooling fishes and euphausiids (krill) that are maintained by 

the seasonally high primary productivity (supported by seasonal 

coastal upwelling), often occur along canyons, shelf-breaks, 

seamounts, and downstream of upwelling centers located at 

Point Arena, Point Reyes, Point Año Nuevo, and Point Sur, 

features that also are important areas for both large and small 

cetaceans.

Marine mammals are highly mobile marine predators that 

feed on a great diversity of prey and are attracted to regions 

of seasonally abundant high prey densities. Resident marine 

mammals (e.g. harbor seals) feed on locally available and 

seasonally abundant invertebrates or fish in relative proximity 

to their breeding/pupping/haulout sites, whereas the seasonal 

migrants (e.g. humpback and blue whales) forage on seasonally 

available krill or fish, a pattern reflected in their relative 

abundance during the Upwelling and Oceanic seasons. 

Response to Short-Term Changes in Climate. Although it 

is likely that short periods of unusually warm or cold waters 

affect migratory species and shorter-ranging more resident 

species, it was not possible to determine effects of these events 

during this preliminary assessment. Distributional responses 

to the extremes of climate (e.g. El Niño vs La Niña) may be 

confounded by: 1) issues associated with comparing different 

data sets without application of correction factors, 2) small 

at-sea populations and therefore small sample size for some 

species (e.g. elephant seals, harbor seals), 3) far-ranging, 

migratory species being affected outside of the study area, 4) 

demographic lags to species’ responses, 5) variable effects on 

different marine mammal prey, and 6) behavioral differences 

among species. 

Nevertheless, the California sea lion provides an example 

of a species shift in distribution in response to changing 

oceanographic conditions. The relative increase in at-sea 

abundance during El Niño 1986-87, 1992-93, and 1997-98 

(not presented in maps; see studies below), likely reflected a 

greater than usual influx of individuals in response to a reduction 

in food off southern California (see Trillmich and Ono, 1991; 

Allen, 1994; Keiper, 2001; Keiper et al., In Review). The greater 

numbers of sea lions at sea coincided with greater numbers 

that occurred at haulout sites in the study area. For example, 

an influx of immature sea lions hauled out at Double Point 

and at Point Reyes Headlands (per. comm S. Allen) during El 

Niño, as was also true at the Farallon Islands (Sydeman and 

Allen, 1999). 

In summary, seasonal and interannual processes in the ocean 

climate affect variability in ocean conditions and food web 

development, and thus, the spatial and temporal occurrence 

patterns of marine mammals are strongly linked to the physical 

and biological processes that affect their prey.

Phase II Marine Mammal Assessment. This section provides 

preliminary results of the mammal analyses. The maps 

presented here provide a preliminary estimate of the mammal 

species spatial and temporal use of the study area. In Phase 

II, additional data and analysis will likely yield revised maps 

for the existing species and additional maps for other species. 

Some of the data sets for marine mammals have only recently 

been received and require further processing before species 

distribution maps can be developed in the GIS. Phase II of this 

analysis will address the following factors:

• differences in survey methodology (e.g. line transect 

 vs. strip transect); 

• differences in the detectability of pinnipeds, small and 

 large cetaceans, and effects of group size; 

• differences in time spent underwater; and 

• differences in environmental conditions (e.g. sea state 

 and other weather conditions). 

Major tasks for Phase II are as follows: 

1. Complete the acquisition of data sets for the marine mammals from institutions already contacted (see partial list in 

No. 2 below). 

2. Continue working with marine mammal experts, and determine appropriate methods required to analyze additional 

data sets and apply appropriate correction factors. At a 

minimum, these data sets will include: sighting data from 

John Calambokidis at Cascadia Research, and the marine 

mammal stock assessment program data from NOAA’s 

Southwest Fisheries Science Center. 

3. Develop a composite marine mammal data set and maps 

of occurrence patterns for additional mammal species, 

as well as summary maps and analyses across species, 

for seasons and other selected time periods. Asemblage 

analyses may be done to identify spatial/temporal species 

groups. 

4. Complete a report on the mammal analyses that will address survey data for 14-23 marine mammal species and 

related summary mammal maps (e.g., a composite rookery 

and haulout map, spatial and temporal summaries of atsea occurrence data across selected mammal groups, and 

assemblage analyses).

5. Conduct an expert review of the maps and report and 

incorporate necessary revisions. 

MAJOR SECTION CONTRIBUTORS

Glenn Ford, Carol Keiper, Janet Casey, David Ainley, Sarah 

Allen, Mark Lowry, Tracy Gill, Ken Buja and Wendy Williams.

REVIEWERS

The following institutes and people participated in the initial 

map review in October 2002:

Sarah G. Allen, Point Reyes National Seashore, Nat'l Park 

Service

Scott Benson, NMFS/Southwest Fisheries Science Center

Jay Barlow, NMFS/Southwest Fisheries Science Center

Nancy Black, Monterey Bay Whale Watch Institute

125
Section 2.3: BIOGEOGRAPHY OF MARINE MAMMALS

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Status, abundance and distribution. Final report prepared by 

Center for Marine Studies, University of California, Santa Cruz, 

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Calambokidis, J., J.C. Cubbage, H.H. Steiger, K.C. Balcomb, 

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Calambokidis, J. G.H. Steiger, K. Rasmussen, J.H. Urban R, 

K.C. Balcomb, P. Ladron de Guevara P, M. Salinas Z, J.K. Jacobsen, C.S. Baker, L.M. Herman, S. Cerchio and J.D. Darling. 

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Calambokidis, J. G.H. Steiger, J.R.Evenson, K.R .Flynn, K.C. 

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Don Croll, University of California, Santa Cruz

Karin Forney, NMFS/Southwest Fisheries Science Center

Mark S. Lowry, NMFS/Southwest Fisheries Science Center

Michelle Staedler, Monterey Bay Aquarium

Jan Roletto Research Coordinator, GFNMS/CBNMS

And several other members of the NOAA project team 

and sanctuary programs.

PERSONAL COMMUNICATIONS 

Sarah Allen, Point Reyes National Seashore, 

 U.S. National Park Service

Jay Barlow, Southwest Fisheries Science Center, NOAA

Joelle Buffa, U.S. Fish and Wildlife Service

John Calambokidis, Cascadia Research

Karin Forney, Southwest Fisheries Science Center, NOAA

Denise Greig, The Marine Mammal Center

Mike Harris, California Department of Fish and Game

Brian Hatfield, U.S. Geological Survey

Mike Kenner, California Department of Fish and Game

Mark Lowry, Southwest Fisheries Science Center, NOAA

Pat Morris, University of California, Santa Cruz

Joe Mortenson, Gulf of the Farallones National Marine 

 Sanctuary, Friends of Marine Sanctuaries Association 

Bob Read, California Department of Fish and Game

Michelle Staedler, Monterey Bay Aquarium 

William Sydeman, PRBO Conservation Science 

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128
Section 3: INTEGRATION OF ANALYSES

• Option 2: A co-occurrence analysis of marine bird density 

and fish density

• Option 3: A co-occurrence analysis of density and diversity 

(options 1 and 2 combined) for both fish and marine birds

In the first of these approaches, only patterns of species 

diversity were analyzed. This index was relatively simple to 

calculate using the data available for birds and fishes, and 

represents a common metric for integration. The second option focuses on spatial patterns of density. Density is a more 

intuitive measure than diversity, and it highlights regions of 

highest marine bird concentrations (abundance). An added 

attraction of density is that it is only weakly influenced by 

effort. The third approach incorporates the two metrics for 

marine birds and fishes simultaneously by combining results 

of options 1 and 2. 

Metrics used in these three options were chosen to best de- INTRODUCTION fine the biogeography for each taxon based on the available The greatest challenge in developing a large-scale bio- data. Once each integration parameter was mapped, patterns geographic assessment is the synthesis and subsequent of community structure were superimposed and interpreted analysis of spatial data collected at different scales for varied in the context of various biological and physical covariates. objectives (Gotway and Young 2002). This is particularly true These spatial covariates were used to better understand gen- when attempting to describe meso-scale (tens to hundreds of eral biogeographic patterns, and through interpretation, sug- kilometers) spatial patterns using data for a range of taxa that gest reasons for the observed spatial trends. For example, were each collected using different sampling techniques. The results indicated that a portion of highest observed bird and taxon-specific sections of this document describe spatial pat- fish diversity occurred adjacent to the shelf/slope interface. It terns of community structure for marine birds, mammals, and is well documented that strong upwelling of deep ocean wa- fishes. The intent of this section is to coalesce these results ters consistently occurs in areas along the slope. Nutrients in and construct a unified and biologically relevant assessment these waters support high phytoplankton productivity, which of the biogeographic patterns observed. stimulates a cascade of productivity at all levels of the marine 

food web (Bolin and Abbott, 1963; Ryther, 1969; Malone, There are a number of ways to address the challenge of inte- 1971; Barber and Chavez, 1983; Chavez 1995, 1996; Bakun, grating results for multiple taxa, and this section contains re- 1996). sults for three (of many) reasonable options. This integration 

effort has been tailored to the NMSP mission of “...enhancing Furthermore, by combining multiple parameters across taxa biodiversity, ecological integrity, and cultural heritage”, and (option 3), it was possible to link results presented in earlier specifically focuses on the notion of biodiversity in describing sections to an integrated composite. This approach provides the overall biogeography of the region. a clear and tractable interpretation that the reader can follow 

as a logical end point to the preceding series of analyses. After a thorough assessment of the spatial data for each The combination of diversity and density presents an inclu- taxon, it was concluded that the marine mammal data were sive view of important areas across taxa, and is less likely to not robust enough in present form to include in the integra- overlook regions of potential importance when compared to tion process. As such, only birds and fish were considered maps depicting a single estimate (e.g., options 1 and 2). This here. Additional efforts to reconcile outstanding issues in the is a critical point as the most diverse patch in a seascape is marine mammal data are ongoing. A final integrated analysis, not necessarily the most productive. In addition to the general including mammal data, will be completed during Phase II of patterns observed for each metric, the spatial coincidence of this assessment. The integration alternatives provided in this hot spots among taxa is emphasized to provide a view into section include: the integrated ecosystem. The metrics used in this section 

are similar to those described in sections 2.1 (fish) and 2.2 • Option 1: A co-occurrence analysis of diversity hot spots for (marine birds); however, data were interpolated to produce marine birds and marine fishes

a continuous modeled surface rather than estimates per 5 

minute grid. This approach takes into consideration the spatial structure in the data to model the gradient of the metric 

between any given pair of sampling points. This results in 

smoothed surfaces that permit easier visualization of biologically significant areas. Resulting large-scale patterns have 

been described in the context of sanctuary boundaries to 

provide insights that may enhance management efficacy in 

these protected areas.

DATA AND ANALYSES

Integration Metrics. There are a number of ways by which 

ecologists measure diversity. The simplest metric is a count of 

the total number of unique species in a community, also called 

species richness (S). This is a straightforward, though potentially misleading, measure of diversity. Sampling must be conducted at all locations with the same amount of effort for this 

estimate to be comparable across a study region or between 

data sets. Unfortunately, this was not the case with any of the 

source data available for integration. For example, marine 

bird observation transects were far more numerous (more effort) near shore, and declined dramatically with distance from 

shore. Because this is often the case with biological sampling, 

a number of diversity indexes have been developed that are, 

in theory, more independent of sample size. These are based 

on the relationship between species richness and the total 

number of individuals observed (n), both of which increase as 

a function of effort, and, ideally, cancel out the effect of effort 

on the resulting index (Ludwig and Reynolds, 1988). Here the 

Shannon index of diversity (Shannon and Weaver, 1949) was 

chosen, as this index is the most widely used in community 

ecology and has relatively small statistical bias when sample 

sizes are large (as is the case with this source data).

Diversity may be thought of as being composed of two distinct 

components: 1) species richness, and 2) species evenness. 

Evenness is defined as how the number of individuals is distributed among the species. For example, for a community 

comprised of five species with 70% of the individuals belonging to one species and 30% distributed among the remaining 

four species, the evenness component would be lower than if 

there were a more even distribution of individuals among the 

five species (Ludwig and Reynolds. 1988) (Figure 79). Maximum diversity for a given number of species and individuals is 

achieved where equal numbers are found for each species in 

a community. For consistency, data for all taxa included in this 

section were summarized by five minute grids (see sections 

2.1, 2.2, 2.3). Total diversity was estimated within each grid cell 

using the Shannon index (H’);

where n is the number of individuals belonging to the species i

(S) in the sample (5 minute grid), and n is the total number of 

individuals in the sample (Ludwig and Reynolds 1988). Diversity was calculated independently for birds and fishes using all 

species observed within a grid cell. 

Figure 79. Pictogram of species diversity. Both fish communities are comprised of 5 species and 14 individuals. In the community on the left side, there are 9 individuals of species 1, 1 

of species 2, 2 of species 3, 1 of species 4, and 1 of species 

5. Using the distribution of abundance within this community, 

Shannon’s Index of diversity is 1.12. The community on the 

right also consists of 5 species with 14 individuals; however, the 

distribution of abundance is more even (2, 3, 3, 4, and 2 individuals), and consequently Shannon’s Index is higher (1.57).

Once diversity was calculated for each taxon in each sample, 

a continuous map surface was interpolated to predict diversity 

patterns throughout the study area. The same process was 

used to model density (see below for detailed methods). 

Spatial Modeling. This section details the procedure used to 

process input data for the integration analyses. While technical in nature, it provides the information necessary for NMSP 

and others to generate results identical to those presented 

here using data provided in the appendix to this document 

(CD-ROM), and to explore results of alternate modeling options. The observed patterns in diversity and density were 

found to be robust to changes in model parameters; however, 

calculations of the aerial extent of persistent patterns may be 

more sensitive. For example, the location of areas of high bird 

diversity tends to be relatively constant, regardless of model 

parameters. The quantity (e.g., square kilometers) of these 

high areas that fall inside sanctuary boundaries, however, 

may change. 

S  n  H ∑    n  ′ = −  i  ln  i  i =1  n   n 

129
Section 3: INTEGRATION OF ANALYSES

For interpolation and calculation of spatial autocorrelation sta- on the pattern of the empirical variograms and the lack of data 

tistics, data for each 5 minute grid cell were assigned to the at short lag distances (due to the five minute minimum sepacell centroid. All data were analyzed in the Universal Trans- ration between points), which are necessary to differentiate 

verse Mercator (UTM) projection. Projection is necessary to between spherical and Gaussian models.

ensure that the value of x and y units is equivalent and constant across the study region. The spatial modeling process 4) Surface Interpolation: The interpolation method used 

to generate an interpolated surface consisted of the following is termed ‘ordinary kriging’. Kriging is a linear interpolation 

sequence of operations: method that allows predictions of unknown values of a random function from observations at known locations (Kaluzny 

1) Checking for Spatial Autocorrelation: Prior to interpola- et al., 1998). Ordinary kriging is the kriging method genertion, all data were tested for the presence of spatial autocorre- ally used for interpolation of a single continuous variable of 

lation. Positive autocorrelation (where values for neighboring unknown mean. Kriging is preferred over other interpolation 

pairs of points are more similar to one another than are distant methods because: 1) weights are based on an empirical asones) is important for accurate interpolation. Moran’s I and sessment of the data’s spatial structure (the variogram), 2) 

Geary’s C statistics were calculated for each interpolated vari- kriging is an unbiased predictor, and 3) for many variables, 

able to test for the presence of significant spatial autocorrela- kriging has been shown to outperform other interpolation 

tion using CrimeStat (Levine, 2002). Moran’s I is the standard methods, such as inverse distance weighting (IDW) and trian- ** indicates significance at p = 0.001, * indicates significance at p = 0.05

autocorrelation statistic and provides a global (i.e. across the gulated irregular networking (TIN) (Guan et al., 1999). Before 

study area) test of spatial autocorrelation. Geary’s C is more kriging can be applied, two assumptions must be checked. 

sensitive to autocorrelation within small neighborhoods. Con- The first is stationarity; the mean (and ideally the variance) 

firmation of statistically significant spatial autocorrelation sug- must be constant across the spatial extent of the data. That a correlation exists, maps of diversity may simply reflect the birds. Areas of high marine bird diversity that overlap with low 

gests that point data are suitable for interpolation. As such, is, any large scale trend must be removed (see #2 above). distribution of effort. In order to correct for differences in effort residuals should be interpreted with caution, as these hot 

interpolation was performed only where this was true for both The second assumption is isotropy of the variogram. The co- across the study region, the following technique was applied: spots may simply reflect areas of unusually high effort. Since 

autocorrelation statistics. variance between any two points is assumed to be a function A second order polynomial regression of diversity on effort bird and fish density were only weakly correlated with effort, 

only of the distance between the points, not of their location was conducted and the residuals were interpolated as de- no attempt was made to correct the density maps.

2) Detrending: Detrending is done to ‘standardize’ the es- or angle. This assumption can be examined and, if necessary, scribed above. The interpolated map of residuals depicts artimate across the analysis extent, and is a prerequisite for corrected for during the variogram modeling stage (see #3 eas of higher or lower diversity relative to that expected given ANALYTICAL MAP PRODUCTS

the interpolation procedure used here. After interpolation, the above). Trend analysis was conducted using JMP statistical the amount of local effort. This map was overlayed on the Spatial Statistics. Table 26 summarizes the results of 

removed trend is added back into the model results. Each in- software (SAS Institute), while detrending, variogram mod- interpolated map of diversity to visualize the impact of effort spatial autocorrelation tests, variogram fitting, and kriging 

terpolated variable was plotted against Northing and Easting, eling, and kriging were conducted using the ArcView (GIS) on the observed patterns in diversity. Although significantly cross validation. All variables were found to be significantly 

and a linear trend was fit to each plot. When significant trend Geostatistical Analyst Extension (ESRI Inc.). correlated with effort, fish diversity showed nearly identical positively spatially autocorrelated (p < 0.05) by both the 

(p < 0.05) was present for either Northing or Easting, the data patterns as the map of fish diversity residuals. Fish diversity is Moran’s I and Geary’s C statistics, for fish and marine birds. 

were detrended (first order) before variogram modeling and The kriging neighborhood was set to the twenty nearest therefore not shown with the overlay of residuals. Patterns of Spatial autocorrelation was more pronounced in the marine 

kriging. neighbors with a minimum of five neighbors for each 90 de- marine bird diversity, however, differed substantially from pat- bird data than in the fish data resulting in better model fit and a 

gree angular sector for the fish data, and reduced to eight and terns of the bird diversity residuals, indicating that differences higher cross-validation r-squared value for the bird data sets.

3) Variogram Modeling: Empirical variograms show the de- five for birds in order to capture small scale variability. Cross in effort are responsible for some of the observed pattern. Macrease in relatedness between pairs of points as a function of validation was conducted to assess model accuracy by re- rine bird diversity hot spots, as represented by the top 20% of 

distance. In order to calculate the empirical variogram, pairs gressing observed versus predicted values. Maps of the krig- diversity cell values, are therefore presented, along with an 

of points must be binned by distance, and an average value ing standard error were also generated and used to restrict overlay of the lower third of the diversity residuals for marine 

(diversity, density) calculated for all pairs within a given bin. the analysis extent. In order to avoid unsupported extrapolaThe size of the bin is referred to as the lag size. A variogram tion into poorly sampled areas, the interpolated maps were 

model is fit to the empirical variogram and its parameters clipped to remove areas of higher standard error. Interpolated 

are later used in interpolation. Empirical variograms were maps were clipped so that only grid cells for which the stancalculated using the default lag size and number, as well dard error was in the lowest 20% were used for subsequent 

as for 1km, 5km, and 10km lag sizes. The appropriate lag display and analysis.

size and number of lags were chosen to optimize variogram 

coherence. Directional variograms were then plotted to inves- 5) Correcting for Effort: Total effort was calculated as the totigate possible anisotropy not removed by detrending. Strong tal length of trawls falling within a grid cell for the NMFS trawl 

anisotropy was found only for the fish density data, and ac- data and as the total area surveyed within a grid cell for the 

cordingly a geometrically anisotropic variogram model was fit marine bird survey data. Although diversity is less related to 

to this data set. Spherical variogram models were fit to the effort than other metrics, some significant correlation (p<0.05) 

empirical variograms. A spherical model was chosen based between the two was found for both fish and birds. When such 

Gulf of the Farallons National Marine Sanctuary

Table 26. Summary statistics and parameter estimates for spatial models.

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Bird diversity 1,163 0.141** 0.830** Yes 20.451 12 99.851 0.25 0.117 0.541 8,2

Bird diversity residual 1,163 0.067** 0.893** Yes 9.966 12 88.062 0.199 0.125 0.407 8,2

Bird density 1,403 0.058** 0.891** Yes 5 30 149.54 1,189.30 1,189.50 0.253 20,5

Fish diversity 301 0.018** 0.973* No 5 20 29.595 0.148 0.046 0.025 20,5

Fish diversity residual 301 0.013* 0.975* No 5 10 18.394 0.11 0.061 0.076 20,5

37.929

Fish density 301 0.020** 0.969* No 5 8 (16.802) 0.0046 0.001 0.074 20,5 Sample size Moran's I (significance) Geary's C (significance) Detrending Lag size (km) Lags Range (km) Nugget Partial sill Cross Validation r 2 Neighbors

Bird diversity 1163 0.141** 0.830** Yes 20.451 12 99.851 0.25 0.117 0.541 8, 2

Bird diversity residual 1163 0.067** 0.893** Yes 9.966 12 88.062 0.199 0.125 0.407 8, 2

Bird density 1403 0.058** 0.891** Yes 5000 30 149.54 1189.3 1189.5 0.253 20, 5

Fish diversity 301 0.018** 0.973* no 5 20 29.595 0.148 0.046 0.025 20, 5

Fish diversity residual 301 0.013* 0.975* no 5 10 18.394 0.11 0.061 0.076 20, 5

130
Section 3: INTEGRATION OF ANALYSES

Hot Spots

0 25 50 100

Kilometers

Top 20% Diversity

Top 20% Density

Overlap of both

Diversity and Density

4000 m

50 m

3

10

2

0

00

0

0

20

m 0

0

00

m

m

m

Diversity

0 50 100

Kilometers

High

Low

Top 20%

Density

Residual

Mask

High

Low

Top 20%

a b

c

ABOUT THESE MAPS

Figure 80a depicts interpolated marine bird diversity throughout the study region. 

The top 20% of predicted diversity is bounded by a thin black line. Because bird 

diversity was significantly correlated with survey effort, we have also provided a 

mask (cross hatched area) indicating where residual estimates provided evidence 

that diversity was lower than expected given the amount of effort spent there (residuals were among the lowest third). Interpret with caution in this area, as the 

expression of high diversity under the mask may actually be an artifact of high 

sampling effort. Figure 80b depicts interpolated bird density. Again, the top 20% of 

this estimate is bounded by a thin black line. No statistical relationship was found 

between density and effort; therefore, no residual mask is provided for this model. 

Figures 80a and b have both been clipped using the standard error estimate for 

the interpolated surfaces (access these data on the CD-ROM). This was done to 

avoid unsupported extrapolation into poorly sampled areas. Figure 80c depicts the 

top 20th percentile for diversity and density and the overlap between them.

DATA SOURCES

R.G. Ford and J.L. Casey. 2003. CDAS Density Maps for Marine Birds off North/

Central California, developed for NOAA’s National Centers for Coastal Ocean Science. Portland, Oregon.

METHODS

See "Data and Analysis" section.

RESULTS AND DISCUSSION

Species Diversity. The interpolated maps of marine bird diversity show one continuous area of high diversity along the continental slope, and, to a lesser extent, 

along the shelf between Point Arena and Point Sur. Within this area, diversity appears highest on, and seaward of, the Farallon Escarpment in the northwestern 

corner of the Monterey Bay NMS (Pioneer Canyon), and off of the region between 

Point Lobos and Point Sur (refer to locator map). Since marine bird diversity was 

correlated with survey effort, much of the hot spot region coincides with areas of 

high survey effort. The Farallon Escarpment, in particular, received a disproportionate amount of survey effort. When the map of interpolated residuals was overlayed on marine bird diversity, some parts of the diversity hot spot (top 20%) fell in 

a region of low (bottom third) residual diversity (the masked portion of Figure 79a). 

This indicates that the high estimated diversity in the Farallon Escarpment is due, 

at least in part, to high sampling effort. The portion of the marine bird diversity hot 

spot between Point Lobos and Point Sur coincides with a region of high residual 

diversity. This indicates that diversity in this region was both high and higher than 

expected given relatively moderate sampling effort.

Overall, a total of 62,000 square kilometers were modeled for bird diversity. Of 

that, roughly 12,000 square kilometers were classified as a hot spot (top 20% of 

estimated diversity). Approximately 28% of the entire modeled surface, and 58% 2 (7,158 km ) of the hot spot, fell inside the boundaries of the three National Marine 

Sanctuaries. This disproportionate allocation of high diversity inside sanctuaries 

indicates that current boundaries generally incorporate areas of high regional diversity. A considerable area of high diversity can be found seaward of the northern 

Monterey Bay NMS, and seaward of the entire Gulf of the Farallones and Cordell 

Bank NMS boundaries. As mentioned in section 2.2, the persistence of high species diversity along the shelf break may be attributed to this natural physiographic 

feature acting as a biogeographic boundary, where oceanic and shelf species of 

birds show maximum overlap. The region seaward of the Farallon Islands displays 

high diversity not only because of its proximity to the shelf break, but also because 

many species of birds breed on these islands and would not otherwise be found so 

far offshore. 

Density. A large region of high (top 20th percentile) marine bird density exists adjacent to and shoreward of the marine bird diversity hot spot. This density hot spot 

covers most of the shelf waters of all three sanctuaries, from Point Sur in the south 

to midway between Bodega Head and Point Arena in the north. The density hot 

spot extends into Monterey Bay. Major regions of overlap between marine bird diversity and density occur along the shelf break. An additional density hot spot exists 

off of Morro Bay to the south of the Monterey Bay NMS. There is some indication of 

high marine bird diversity in this region as well. 

A total of 60,000 square kilometers were modeled for bird density, with approximately 10,000 square kilometers classified in this analysis as a hot spot. Approximately 28% of the entire modeled surface fell inside the boundaries of the three 

National Marine Sanctuaries; however, 84% (8,962 km ) of the high marine bird 2

density hot spot was found in the sanctuaries. The proportion of high density inside 

sanctuaries suggests that the boundaries include most areas of high density.

Summary. Patterns of bird diversity and density exhibited distinct spatial patterns, 

with diversity concentrated from the slope seaward, and density from the slope 

shoreward. The overlap of these estimates mainly occurs along the shelf break; an 

area of high meso-scale bathymetric complexity. It is interesting to note that marine 

bird diversity exhibited a statistically significant positive correlation (r=0.33, p<0.0001) 

with bathymetric variance (Figure 81a)(see section 2.1.1 for details on this estimate). 

Density, on the other hand, exhibited a strong negative correlation (r=0.65, p<0.0001) 

with depth rather than bathymetric variance (Figure 81b).

Figure 81. The left graphic (a) shows the strong positive relationship observed between bird diversity and bathymetric variance, while the right graphic (b) shows a 

strong negative relationship between bird density and depth. In both cases, the estimate (diversity and density) have been classified into 20th percentiles.

Figure 80. Estimated diversity (a), density (b), and hot spots (top 20%) (c) for 

marine birds.

a b

131
Section 3: INTEGRATION OF ANALYSES

ABOUT THESE MAPS

Figure 82a depicts estimated demersal fish diversity throughout the study region. 

Unlike the mean diversity mapped in section 2.1.1, this surface was generated using estimates of total diversity for each 5 minute grid cell. The top 20% of predicted 

diversity is bounded by a thin black line. Though fish diversity was significantly 

correlated with survey effort in this model, high residual values overlapped areas 

of highest (top 20%) estimated diversity. This indicates that interpolated areas of 

highest diversity showed little effect of effort. As such, no residual mask is provided. Figure 82b depicts fish density, and, like the diversity map, is based on an 

interpolation of total density (individuals per area swept (km2)) within each 5 minute grid cell. The top 20% of this estimate is bounded by a thin black line. Figures 

82a and 82b were clipped using the standard error estimates for the respective 

interpolated surfaces (access these data on the CD-ROM). This was done to avoid 

unsupported extrapolation into poorly sampled areas. Figure 82c depicts the top 

20% for diversity and density, and the overlap between the two.

DATA SOURCES

Species diversity was calculated using NMFS shelf and slope trawl data collected 

at depths between 50-1280 meters, between June and November, every third 

year from 1977-2001. For details on trawl methods see Lauth (2001), Shaw et al. 

(2000), Turk et al. (2001), and Williams and Ralston (2002).

METHODS

See "Data and Analysis" section.

RESULTS AND DISCUSSION

Diversity. Interpretation of the interpolated maps of fish diversity is hindered by 

the lack of available data west of the sanctuary boundaries and the high spatial 

variability within the data. Despite these limitations, three hot spots (top 20%) of 

fish diversity are apparent: The northernmost hot spot is centered on Cordell Bank 

within the northwestern corner of the Cordell Bank NMS, and extends northward 

along the continental slope outside of sanctuary boundaries to Point Arena. Its 

northern and western extent cannot be determined with the available trawl data 

as sampling stopped along the edge of high predicted diversity. Extrapolation to 

the north and west of this area indicates that high diversity may continue beyond 

the available data. A second area of high diversity is centered at the boundary 

between the Gulf of the Farallones NMS and the Monterey Bay NMS. The area 

extends in a southeasterly direction past Point Año Nuevo and ends off northern 

Monterey Bay. The southernmost hot spot is located between Point Sur and Lopez 

Point and covers the inshore portions of Sur and Lucia Canyons. Portions of this 

last hot spot, however, were poorly sampled. There is some evidence of an additional hot spot in the shallow waters (<200m) straddling the southern boundary of 

the Monterey Bay NMS and extending into Morro Bay.

Overall, a total of 27,000 square kilometers were modeled for fish diversity. Of 

that, roughly 5,400 square kilometers were classified as a hot spot (top 20th percentile of estimated diversity). Approximately 53% of the entire modeled surface 

fell inside the boundaries of the 3 National Marine Sanctuaries, with 67% (3,675 2 km ) of the hot spot contained within the sanctuaries. Much of the remaining 33% 

of high diversity extends along the shelf break north of the Cordell Bank NMS to 

Point Arena.

Density. Interpretation of the fish density maps suffers from the same problems 

(i.e. lack of data to the west of sanctuary boundaries and high spatial variability) as 

those encountered for diversity. In addition, densities tend to emphasize the distribution of common numerically dominant species. High density areas of the map 

can be divided into four major hot spots (top 20%). One hot spot occurs on and to 

the southeast of Cordell Bank. A second hot spot is found off of Point Reyes. The 

largest density hot spot covers a large portion of the shelf to the north of Monterey 

Canyon, the entire area of Monterey Bay, and near shore waters south to Point Sur. 

Although portions of this hot spot are found over Monterey Canyon, this fact should 

be incorporated with caution since the deep canyon waters themselves were not 

sampled. The fourth hot spot is found to the south of Monterey Bay NMS and covers a substantial area of the shelf from Point Estero to Point Sal. This final hot spot 

is the largest region of high fish density within the mapped area that falls outside of 

Sanctuary boundaries and overlaps with a much smaller fish diversity hot spot to 

the north. 

A total of 27,000 square kilometers were modeled for fish density, with approximately 5,200 square kilometers classified in this analysis as a hot spot. Approximately 

54% of the entire modeled surface fell inside the boundaries of the three National 

Marine Sanctuaries; however, 76% (4,041 km ) of the hot spot was contained 2

within the sanctuary boundaries. 

Summary. Patterns in both fish diversity and density appear in many cases to be 

linked to known oceanographic features already mentioned in previous sections. For 

example, the northernmost diversity hot spot, and some parts of the density hot spot, 

straddle the shelf break, an area known to concentrate a variety of marine fauna (Kim, 

2000; Adams et al., 1995; Yoklavich et al., 2000). The quickly changing depths of the 

shelf break and slope may also increase diversity by allowing fish with overlapping 

bathymetric preferences to coexist. Both diversity and density also appear high near 

well known upwelling regions, including Point Sur, near Point Año Nuevo, and near 

Cordell Bank. Although the majority of the fish diversity and density hot spots fall 

within sanctuary boundaries, this fact should be interpreted with caution since the 

sanctuary area represents approximately half of the mapped region for both of these 

variables. Areas of high diversity and density outside of the sanctuary boundaries 

exist to the north and south. Diversity and density to the west of sanctuary boundaries cannot be adequately assessed with the available data. 

Hot Spots

0 25 50 100

Kilometers

Top 20% of Diversity

Top 20% of Density

Overlap of both

Diversity and Density

4000 m

50 m

3

10

2

0

00

0

0

20

m 0

0

00

m

m

m

Diversity

0 50 100

Kilometers

High

Low

Density

Top 20%

High

Low

Top 20%

Figure 82. Estimated diversity (a), density (b), and hot spots (top 20%) (c) for fish.

132
Section 3: INTEGRATION OF ANALYSES

ABOUT THIS MAP

Figure 83 shows the overlap of diversity hot spots for birds 

and fishes. As described previously, hot spots were defined 

as the top 20% of diversity estimated through the spatial 

modeling process (kriging). Also shown is the most recent 

estimated distribution of kelp beds within the study area. 

Although no specific analysis of biodiversity was done for 

kelp communities, it is well documented that these habitats 

support a rich and diverse faunal assemblage (Abbott and 

Hollenberg, 1976; VanWagenen, 2001; McLean, 1962; Foster and Schiel, 1985; Harrold et al., 1988; Thorson 1950; 

Randall 1965; Dayton 1984; Dean et al., 1984; Ebeling et al., 

1985; Harrold and Reed, 1985; Miller and Geibel 1973; King 

and DeVogelaere, 2000; Van Blaricom and Estes, 1988). 

Because of this, we have chosen to include kelp distributions 

in all of the integrated hot spot maps. The kelp distributions 

depicted here represent only a "snapshot" view of a highly 

dynamic feature.

DATA SOURCES

Species diversity for fishes was estimated using NMFS shelf 

and slope trawls data collected at depths between 50-1280 

meters, between June and November, every third year from 

1977-2001. For details on trawl methods see Lauth (2001), 

Shaw et al. (2000), Turk et al. (2001), and Williams and 

Ralston (2002). Species diversity for birds was estimated using data provided by R.G. Ford Consulting and H.T. Harvey 

and Associates. 1999 kelp distribution data were provided by 

California Department of Fish and Game.

METHODS

See "Data and Analysis" section.

RESULTS AND DISCUSSION

All three regions of high fish diversity show some overlap 

with the regions of high bird diversity. An interesting result 

of this analysis is that all regions of overlap occur near well 

known upwelling centers (Huyer and Kosro, 1987; Brink 

and Cowles, 1991; Kelly, 1985; Breaker and Mooers, 1986; 

Breaker and Gilliland, 1981; Tracy, 1990; Schwing et al., 

1991; Breaker and Broenkow, 1994; Rosenfeld et al., 1994); 

including the area surrounding Cordell Bank, the area south 

of the Farallones (off point Año Nuevo), and directly adjacent 

to point Sur. The northernmost fish diversity hot spot overlaps 

the marine bird diversity hot spot from Cordell Bank north 

to approximately midway between Bodega Head and Point 

Arena. The seaward half of the central fish diversity hot spot 

overlaps with the area of high marine bird diversity within the 

Gulf of the Farallones NMS and the Monterey Bay NMS. The 

northern half of the southernmost fish hot spot overlaps the 

southern tip of the marine bird hot spot. There is a small portion of the Northern overlap of diversity that continues along 

the slope for 40-50 km beyond the northern boundary of 

Cordell Bank National Marine Sanctuary.

Overlap in diversity hot spots occurs in both slope and shelf 

waters. The northernmost hot spot is clearly associated with 

the slope. The southernmost hot spot is also found in an area 

of rapidly changing bathymetry off of Point Sur. A large portion 

of the central diversity hot spot, however, occurs over primarily soft bottom shelf regions. The ecological linkages report 

(see CD-ROM) cites a considerable volume of literature that 

describes slope communities as diverse, with well documented trophic interactions between birds and fishes. The authors 

report that spatial and temporal distribution of plankton is 

thought to affect the distributions of many fishes and marine 

birds. In particular, marine birds aggregate in regions with extremely high plankton density, such as Cordell Bank, the Gulf 

of the Farallones, and parts of Monterey Submarine Canyon 

(Croll et al., in press). Each of these areas were identified in 

this analysis as being biodiverse. Furthermore, squid, a primary food source for numerous fishes and birds, concentrate 

in areas of high plankton productivity (Mais, 1972; Roper and 

Young, 1975; Anderson, 1977; Pearcy et al., 1977; Anderson 

and Morel, 1978; Cailliet et al., 1979), where they consume 

euphausiids and copepods (Karpov and Cailliet, 1979; Chen 

et al., 1996). This provides further evidence that trophic setting might be partially responsible for the expression of high 

diversity in areas of upwelling. 

Summary

1) Diversity overlap between birds and fishes appear to be 

correlated to known centers of coastal upwelling.

2) Overlap occurs in slope and shelf waters.

3) Much of the expression of high diversity may be related to 

the trophic setting in these areas rather than directly to the 

physical factors that characterize these areas.

Figure 83. Integration option 1, diversity hot spots (top 20%) for fish and marine birds. Coastal kelp bed areas are also shown.

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

N°53N°53

N°63N°63

N°73N°73

N°83N°83

N°93N°93

Integration: Option 1

Legend

0 10 20 40 60 80

Kilometers

Fish - Top 20% Diversity

Birds - Top 20% Diversity

Overlap of both

Fish and Birds

Species Diversity

Kelp Beds (1999)

4000 m

2

5

0

2

0

3

0

1

0

0

0

0

m

00

0

m

0

m

m

0 m

133
Section 3: INTEGRATION OF ANALYSES

ABOUT THIS MAP

Figure 84 shows the overlap of density hot spots for fish and 

birds. As described previously, hot spots were defined as the 

top 20% of density estimated through the spatial modeling 

process. Also shown is the most recent estimated distribution of Kelp beds within the study area. Although no specific 

analysis of density was done for kelp communities, it is well 

documented that these habitats support a productive faunal 

assemblage (Abbott and Hollenberg, 1976; VanWagenen, 

2001; McLean, 1962; Foster and Schiel, 1985; Harrold et al., 

1988; Thorson, 1950; Randall, 1965; Dayton, 1984; Dean et 

al., 1984; Ebeling et al., 1985; Harrold and Reed, 1985; Miller 

and Geibel, 1973; King and DeVogelaere, 2000; Van Blaricom 

and Estes, 1988). Because of this, we have chosen to include 

kelp distributions in all of the integrated hot spot maps. The 

kelp distributions depicted here represent only a "snapshot" 

view of a highly dynamic feature.

DATA SOURCES

Species density for birds was estimated using data provided 

by R.G. Ford Consulting and H.T. Harvey and Associates. 

1999 Kelp distribution data were provided by California Department of Fish and Game.

METHODS

See "Data and Analysis" section.

RESULTS AND DISCUSSION

Nearly all of the fish density hot spot is coincident with the two 

areas of high bird density. The distributions for both metrics 

are generally confined to the shelf (<200m) with the notable 

exception of Monterey Canyon which appears as a density 

hot spot for both groups. Although the majority of the hot spots 

for fish and bird density fall within sanctuary boundaries, it is 

notable that overlapping hot spots for both groups exist to the 

south of Monterey Bay NMS. The pattern of marine bird density is dominated by the distributions of the Common Murre 

(Uria aalge) and Sooty Shearwater (Puffinus griseus) because they are so abundant. Fish density reflects a somewhat 

more balanced species composition. Among the most numerically dominant fish species are shortbelly rockfish (Sebastes 

jordani) and Pacific hake (Merluccius productus). 

Because the modeled distribution of bird density is dominated 

by two species and all density maps emphasize common species, these maps should be interpreted with caution. While 

the density interpolation for birds closely approximates what 

is generally observed in the wild, it is heavily biased towards a 

few numerically dominant species. This fact may tend to overshadow the density distribution for rare and/or endangered 

species.

Summary

1) There is considerable overlap between areas of high bird 

and fish density.

2) Density maps should be interpreted with caution due to 

their inherent biases toward numerically dominant species.

Figure 84. Integration option 2, density hot spots (top 20%) for marine birds and fish. Coastal kelp bed areas are also shown.

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

N°53N°53

N°63N°63

N°73N°73

N°83N°83

N°93N°93

Integration: Option 2

Legend

0 10 20 40 60 80

Kilometers

Fish - Top 20% Density

Birds - Top 20% Density

Overlap of both

Fish and Birds

Species Density

Kelp Beds (1999)

4000 m

2

5

0

2

0

3

0

1

0

0

0

0

m

00

0

m

0

m

m

0 m

134
Section 3: INTEGRATION OF ANALYSES

ABOUT THIS MAP

Figure 85 shows the overlap of options one and two. The top 

20% for bird diversity and density were combined, as were the 

top 20% of fish diversity and density. This is the most inclusive 

view of marine bird and fish hot spots and the areas they overlap. Also shown is the most recent estimated distribution of 

kelp beds within the study area. Although no specific analysis 

of biodiversity was done for kelp communities, it is well documented that these habitats support a rich and diverse faunal 

assemblage (Abbott and Hollenberg, 1976; VanWagenen, 

2001; McLean, 1962; Foster and Schiel, 1985; Harrold et al., 

1988; Thorson, 1950; Randall, 1965; Dayton, 1984; Dean et 

al., 1984; Ebeling et al., 1985; Harrold and Reed; 1985, Miller 

and Geibel; 1973, King and DeVogelaere, 2000; Van Blaricom 

and Estes, 1988). Because of this, we have chosen to include 

kelp distributions in all of the integrated hot spot maps. The 

kelp distributions depicted here represent only a "snapshot" 

view of a highly dynamic feature.

DATA SOURCES

Species diversity for fishes was estimated using NMFS shelf 

and slope trawls data collected at depths between 50-1280 

meters, between June and November, during every third 

year from 1977-2001. For details on trawl methods see Lauth 

(2001), Shaw et al. (2000), Turk et al. (2001), and Williams 

and Ralston (2002). Species diversity and density for birds 

was estimated using data provided by R.G. Ford Consulting 

and H.T. Harvey and Associates. Kelp distribution data were 

provided by California Department of Fish and Game. 

METHODS

See "Data and Analysis" section.

RESULTS AND DISCUSSION

The majority (71%) of the fish hot spot is coincident with the 

much larger bird hot spot. The greater area of the bird hot spot 

(~19,000 km2

 for birds compared to ~10,000 km2 for fish) is 

due to the greater spatial extent of the bird survey data. Major 

areas of overlap occur in the following regions:

1) from Cordell Bank and the northwest corner of the Gulf of 

the Farallones NMS north to approximately midway between 

Bodega Head and Point Arena,

2) off Point Reyes,

3) shelf waters from the southern boundary of the Gulf of the 

Farallones NMS south to Point Sur, including Monterey Bay, 

and

4) near shore waters off of Point Buchon.

Although the majority of the regions that were identified as 

hot spots for fish and birds occur within Sanctuary waters, 

there are hot spots beyond Sanctuary boundaries to the 

north and south. The westward extent of important areas for 

fish cannot be determined from the available trawl data, and 

may extend beyond the pictured hot spots. Since Option 3 is 

simply a combination of Options 1 and 2, all of the concerns 

and results for those two sections apply here as well.

Summary

1) The sanctuary boundaries incorporate much of the highest 

diversity and highest density areas within the region.

2) Many of these biologically important regions coincide with 

known oceanographic and bathymetric features, such as upwelling regions, areas of high bathymetric variance, and the 

continental shelf break.

3) Regions of high diversity and high density outside of the 

current sanctuary boundaries exist to the north, across much 

of the shelf and slope, and to the south, in near-shore waters.

4) Uneven sampling effort across the study region and lack 

of trawl samples to the west of the sanctuary boundaries limit 

the scope of any integrated biogeographic assessment.

5) Known limitations and biases of the two metrics (diversity and 

density) exist and are discussed elsewhere within this section 

(Section 3 – Integration).

Figure 85. Integration option 3, diversity and density, hot spots (top 20%) for fish and marine birds. Coastal kelp bed areas are also 

shown.

124°W

124°W

123°W

123°W

122°W

122°W

121°W

121°W

N°53N°53

N°63N°63

N°73N°73

N°83N°83

N°93N°93

Integration: Option 3

Legend

0 10 20 40 60 80

Kilometers

Fish - Top 20%

Diversity and Density

Birds - Top 20%

Diversity and Density

Overlap of both

Fish and Birds

Diversity and Density

Kelp Beds (1999)

4000 m

2

5

0

2

0

3

0

1

0

0

00

0

0

0

m

m

0

m

m

0 m

135
Section 3: INTEGRATION OF ANALYSES

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area trawls. Fishery Bulletin 93: 446-455. sea surface temperature patterns over the northern California Roper, C. F. E., and R. E. Young. 1975. Vertical Distribution of 

Dayton, P. K., V. Curries, T. Gerrodette, B. Keller, R. Rosen- slope. Journal of Geophysical Research 90: 11783-11798. Pelagic Cephalopods. Smithsonian Contributions to Zoology 

Bakun, A. 1996. Patterns in the Ocean: Ocean processes thal, and D. Van Tresca. 1984. Patch dynamics and stability 209. 51 pages.

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Dean, T. A., S. C. Schroeter, and J. Dixon. 1984. Effects of Ecosystem Change: Natural or Human? March 18, 2000. Co- for Monterey Bay. Continental Shelf Research 14: 931-964.

Barber, R. T., and F. P. Chavez. 1983. Biological consequenc- grazing by two species of sea urchins (Strongylocentrotus conut Grove, Santa Cruz, CA

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survival of two species of kelp (Macrocystis pyrifera and King, A., and A. DeVogelaere. 2000. Monterey Bay National sea. Science 166: 72-76.

Bolin, R. I., and D. P. Abbott. 1963. Studies on the marine Pterygophora californica). Marine Biology 78: 301-313. Marine Sanctuary final Kelp Management Report. Backclimate and phytoplankton of the central coast area of Cali- ground, Environmental Setting, and Recommendations. Oc- Schwing, F. B., D. M. Husby, N. Garfield, and D. E. Tracy. 

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midwater trawl catches in Monterey Bay and their affinities in the structure of kelp forest communities along a wave expo- and netplankton as primary producers in the California Curwith the market squid, Loligo opalescens. California Coopera- sure gradient. Marine Ecology 9(2): 131-156. rent system. Fisheries Bulletin 69: 799-820. Turk, T. A., T. Builder, C. W. West, D. J. Kamikawa, J. R. Waltive Oceanic Fisheries Investigations Reports 20: 21-30. lace, R. D. Methot, A. R. Bailey, K. L. Bosley, A. J. Cook, E. 

Huyer, A., and P. M. Kosro. 1987. Mesoscale surveys over the McLean, J. H. 1962. Sublittoral ecology of kelp beds of the L. Fruh, B. H. Hormess, K. Piner, H. R. Sanborn, and W. W. 

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136
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100: p. 836-855.

137
Section 4: DATA SOURCES AND GAPS

INTRODUCTION

This section addresses a secondary objective 

of the project: the acquisition and assessment 

of available comprehensive data for the study 

area and the identification of data gaps in such 

information. In addition, suggestions are made 

for prioritizing future research efforts to generate 

data that would be especially valuable for future 

biogeographic analyses.

Throughout the project, members of the Biogeography Program contacted numerous 

academics, scientists, and agency personnel 

who were likely to have knowledge of data 

relevant to the study area, compiling a contact 

list of over 160 people. Additionally, staff consulted the impressive compendium of studies 

compiled by Monterey Bay Sanctuary staff for 

their Sanctuary Integrated Monitoring Network 

(SIMoN) program, which provides a “blueprint for 

a comprehensive, integrated monitoring network 

to detect natural and human induced changes 

to the Monterey Bay National Marine Sanctuary 

and its resources” (http://montereybay.noaa.gov/

). Through extensive consultation with contacts, 

approximately 62 data sets were investigated 

for incorporation into this study. Data sets were 

considered in terms of sampling objective, the 

extent of their spatial and temporal coverage, the 

existing format and ability to be converted into a 

GIS layer, the utility of the data compared to the 

work involved in its incorporation into the project, 

and whether or not the Biogeography Program 

was granted access to the data. In general, team 

members acquired only accessible data sets that 

had broad spatial extents covering a significant 

portion of the study area, a large number of 

samples that could be georeferenced, and high 

confidence in data quality. 

Data sets that met the above criteria were 

requested and obtained if possible. Once inhouse, data were further evaluated in how well 

they served the objectives of the study, and the 

most useful data were synthesized into a working 

GIS library. This involved conversion into GIS 

format, standardization of geographic projection, 

and when possible, the aggregation of smaller 

data sets into a master data layer.

Data Set Target Info. Source Org

and/or PI

Strengths of Data for Biogeographic Dates Samples Depth Range AssessmentConstraints of Data for Biogeographic 

Assessment

NMFS Long time-series, wide spatial extent, Sampling only in summer season, some

Triennial Shelf 

Trawl Data

Fish,

Invertebrates

(Alaska & 

Northwest

1977-1998 every 3 fairly good depth range, abandoned n=994 55-500m years, June-Aug only trawl areas suggest areas of hightrawls suspected of being off-bottom, 

rocky areas undersampled due to threat 

FSC) rugosity of gear damage.

Slope Trawl

Data

Fish,

Invertebrates NMFS

1991, 1997, 1999, 10+ years of data, wide spatial 2000, 2001, July-Nov n=454 190-1280m extent, good depth range only

Sampling for only 5 months (July-Nov.); 

identification of common inverts only

NMFS

Midwater Trawl

Data

Rockfish

juveniles

NMFS / 

SWFSC

1986-2001, May-June 6-32m n=1548 1500+ tows only mean=26mSampling only in May & June, along

transects, targets juv. rockfish

Recreational

Fish Data Rockfish CDF&G 1987-1998, 2-360 fm (3-650 n=4357 continuous m)

provides information about 

nearshore areas, wide range of 

depths.

No effort data (presence/absence only), 

effort targets Rockfish only

Laidig Data

KelpAssociated

Species

Tom Laidig/ 

NMFS

1983-1995 (Sonoma)

year-round but to max extent of 

sparse, 1984, 1997, n=43 surveys scuba or kelp

2001 (Monterey) May- (<130 ft.)

Oct only

provides year-round look at kelp in

Sonoma 1983-95, quick look at 

Monterey in 84, 97, 2001; 

differentiates juveniles and adults.

Sampling is sparse, presence/absence

data only, very limited spatial extent

Commercial

Fishing Data

Commercially

Valuable

Fishes

CDF&G

n=117,176

1988-2000, year- (records grouped shoreline to

round by species, not trip 4810m

or boat)

All gear types, data can be sorted by 

gear, long time series.

Variable reliability re: locations of fishing, 

summarized to 10-minute grids (large

scale), fisheries-dependent, can't sort by 

boat or trip/effort

5 categories, provides the most 

comprehensive view of benthic 

substrates for the study area; in

Sediment Substrate

Composition

Greene et. al., 

National Sea

Grant College

Project

sampling dates shoreline to unknown, received unknown number ~3500m 12/2002

some places very detailed, high

resolution; Original data consisted of 

seismic-reflection profiles and

sediment/rock sample data collected

by California Division of Mines and

Geology, USGS, and California

Based on surface extrapolation of point 

data, most of the map is low resolution

1:250,000.

Coastal Commission. New data

include multibeam data from MBARI, 

and Center for Habitat Studies at 

Moss Landing Marine Laboratories

Bathymetry200mDepth,

Topography

CDF&G shoreline to unknown unknown 4810m

best available at the start of the

project Medium resolution

Bathymetry30mDepth,

Topography

NOAA /

NGDC & 

MBARI

shoreline to unknown unknown 4810m

provides higher resolution which

increases ability to identify smaller

areas of high bathymetric variance, 

ie. pinnacles and drop-offs

Better resolution, late availability for this 

project

Kelp Data Kelp Location CDF&G many, polygon 1989, 1999 surface data

Polygons generated from aerial

photos provide literal 'snapshot' of 

kelp along long stretch of coast.

Changes since 1999, missing sections, 

doesn't differentiate species

Monthly composites will smooth out 

Sea Surface

Temperature

Sea Surface

Temperature

NOAA / 

Coastwatch monthly composites satellite data surface Monthly composites available foryears 1992 - current.

important temporal fluctuations, ie. short 

upwelling and relaxation events; corrected

for best surface.

MMS High

Altitude Aerial

Surveys

Cetaceans & 

turtles

Dohl,

Minerals

Management

Service

(MMS)

1980-1983, in all three

ocean seasons

1,057 cells visited; 

76,888km of 

trackline; 10,014

cell-study-day

visits

surface survey 

of the shelf, 

slope and deep

ocean beyond

Relatively large spatial coverage; 

cost-effective, year-round synoptic 

surveys for cetaceans over the shelf 

and slope. 

Data from early 1980s may not represent 

current status and distribution of species; 

high altitude surveys may not provide

good characterization of smaller, less 

visible species.

MMS Low

Altitude Aerial

Surveys

Marine Birds 

and Mammals

Bonnell-PI for

mammals,

Briggs-PI for

birds; MMS

1980-1983, in all three

ocean seasons

870 cells visited; surface survey 

70,114km of of the shelf, 

trackline; 9,306 cell-slope and deep

study-day visits ocean beyond

Relatively large spatial coverage; 

cost-effective, year-round synoptic 

surveys for species over the shelf 

and slope. 

Data from early 1980s may not represent 

current status and distribution of species; 

low altitude surveys may not provide good

characterization of rare cetacean species.

EPOCS

Shipboard

Surveys

Marine Birds 

and Mammals Ainley

1984-1994, in all three

ocean seasons

76 cells visited; 

1,033km of 

trackline; 77 cellstudy-day visits

surface survey 

of the deep

ocean

Includes outer Calif Current surveys; 

better species sightability on a ship

than an airplane.

Spatial coverage is not as robust as with

the aerial surveys, but sightability for

some species is better.

Table 27. Matrix of data sets and their associated characteristics that were used or referenced in the biogeographic assessment. Within this library of data, some sets emerged as 

primary data sources, while others contributed 

to the project in terms of providing contextual 

information, reference or validation.

The data sets that ultimately proved most useful in this undertaking are summarized in Table 

27 below, which provides information about the 

source of the data, target information, dates of 

collection, number of samples, and depth range 

when available. Additionally, comments about 

the general strengths and constraints of the data 

sets in the context of this analysis are noted in 

separate columns. Full citation information for 

each data set is provided in the list of references 

that appears at the end of each section utilizing 

the data.

CONCLUSIONS AND RECOMMENDATIONS 

FOR FUTURE ACTIVITIES

During the course of this project, Biogeography 

Program staff gained a unique familiarity with 

the data available and the data necessary to 

undertake the analysis. This position enables 

project team members to make observations 

about the types of data that, if acquired, could 

improve the biogeographic assessment in the 

future. Some of the data sets may exist, but in 

a format that could not, in their current state, 

be incorporated into the project. For example, 

historical benthic infauna data exists, but has not 

yet been converted to digital format or updated 

to reflect current taxonomy. Several important 

data sets do not, to our knowledge, exist at all 

or at the necessary spatial scale, but should be 

considered priorities for future analytical efforts. 

They appear in the following list. 

•Resolution. Finer thematic and spatial resolution on the substrate and bathymetric maps will 

be highly advantageous to the analyses based 

on Habitat Suitability Modeling. Improving the 

resolution for the bathymetry map will help 

identify more small areas of high relief, such as 

rocky pinnacles, that are known to be important 

habitat for some species.

•Spatial Data for Additional Species. Because 

of sampling limitations (i.e. mesh or hook size) 

or a lack of published life history information, 

some ecologically important species are not 

represented in this study. More information 

138
should be collected on these species through other means. 

One example is the pygmy rockfish (Sebastes wilsoni), a small 

but abundant species, that does not show up in any of the 

fisheries-dependent data sets. S. wilsoni can be surveyed via 

submersible, as documented in various studies (Yoklavich et. al, 

2002; Yoklavich et. al., 2000; Hixon et al., 1991). Other species 

of interest include white shark, pelagic fishes, intertidal species, 

krill, marine birds, marine mammals and sea turtles.

•Survey Methods. Sampling fish communities using a consistent 

sampling method over all substrate/habitat types, based on 

stratified random sampling. Multiple survey methods should be 

employed to ensure representation of important fish species 

that are not susceptible to current sampling methods.

•Sampling Strategies. Sampling strategies should be tailored 

to include more life history stages of fish, especially larval 

stages. 

•Sampling Strategy. Sampling should also be better spread 

spatially and temporally to:

•Reduce Effort Disparity. Increased sampling in certain areas would help equalize the distribution of sampling effort 

across the study area. Some analyses were confounded 

by the wide range of sampling effort. 

•Target Important and Under-Sampled Areas. Increasing sampling in important areas that are currently under 

sampled (e.g. the entire near-shore region and the slope 

area west of Cordell Bank) or in areas of particular management interest (e.g. boundary regions) would help to 

better characterize these areas. The techniques used in 

the integration section can accommodate preferential (i.e. 

non-random) sampling in areas of interest.

•Describing Effort. Increase consistency in recording effort-related parameters for fisheries trawls (e.g. recording start and 

end coordinates of trawls) and naturalists’ surveys.

•Expert Knowledge. Incorporate additional expert knowledge 

and data from the fishing community, naturalists (e.g. Monterey Bay Whale Watch cruise data), and recognized experts, 

especially for areas and time periods where there is little or 

no data.

•Data Compatibility. Achieve consensus on the best way to 

merge aerial and ship-based survey data for birds and mammals.

•Location Verification for Fisheries Data. Verification of the spatial reporting from commercial fishing logbooks would enable 

the full incorporation of this valuable data source.

•Abandoned Trawls. Incorporation of NMFS’s study of abandoned trawl locations from the Triennial Surveys. Such information indicates areas that are difficult to trawl or ‘untrawlable’ 

due to the fact that the nets repeatedly became caught or torn 

during trawl attempts. These locations may indicate areas with 

rocky substrates and high rugosity, which, though still targeted 

by hook and line and recreational fishers, are generally protected from trawl fishing methods.

•Oceanographic Influences. Incorporation of more oceanographic features and parameters into the analyses, especially 

for birds and mammals. Ephemeral features such as currents, 

the San Francisco plume, and sources of upwelling could be 

represented in probability maps or by aggregating empirical 

data by various temporal categories (e.g. by week, event, 

month, season, warm/cold period, etc.).

•Kelp Surveys. Increased frequency of surveys to better monitor changes in kelp distribution; differentiation between kelp 

species.

•Life History/Trophic Linkages. Expanded knowledge of life 

history characteristics, habitat affinities, distribution and 

abundance of pelagic prey species, and links between predators and prey species (i.e. hake, krill, and plankton) will help 

describe distributional changes based on trophic linkages and 

foraging behavior.

•Life History/Spawning Areas. Incorporation of known spawning 

areas will help identify important areas and seasonal changes 

in distribution for fish.

•Data QA/QC. Data quality assurance would allow the incorporation of some existing data sets that were discarded due to 

inconsistencies in species coding (e.g. the fisheries data set 

targeting salmon), taxonomic changes (e.g. benthic infauna 

data) or other reasons.

•Expansion of Scope

Section 4: DATA SOURCES AND GAPS

. The scope of this analysis could be 

broadened to include adjacent habitats. For example, the interaction between marine and estuarine habitats could possibly 

be addressed using network analysis of energy flows between 

ecosystems. As part of the Estuarine Living Marine Resources 

(ELMR) series, a 2-volume comprehensive data base on the 

distribution of estuarine fishes and invertebrates in West Coast 

estuaries was completed in 1990-91 (Emmett, et al., 1991; 

Monaco, et al., 1990; Nelson and Monaco, 2000). If updated, 

the resource could be used to couple estuarine, coastal and 

marine ecosystems. 

•Wider Regional Context

Yoklavich, M.M., G.M. Caillet, R.N. Lea, H.G. Greene, R.M. 

Starr, J. de Maringnac, and J. Field. 2002. Deepwater habitat 

and fish resources associated with a marine reserve: impli-

. Expansion of the scope of the study cations for marine fisheries in marine ecological reserves 

to include the biogeography of the entire west coast of North research program research results. 1996-2001. California 

America to better understand how the north/central California College Sea Grant Program CD-ROM. La Jolla, CA. 63 pp.

region fits into the wider biogeographic context. A precedent 

exists in the West Coast Atlas produced by NOAA’s SEA Divi- Yoklavich, M.M., H.G. Greene, G.M. Caillet, D.E. Sullivan, 

sion. Such a document could serve as a blueprint for defining R.N. Lea, and M.S. Love. 2000. Habitat associations of deepspecies distributions along the west coast of the continental water rockfishes in a submarine canyon: an example of a 

U.S. (SAB/NWAFS 1988, SAB 1990). natural refuge. Fish Bulletin, U.S., Vol. 98, pp. 625-641.

REFERENCES

Emmett, R.L., S.L. Stone, S.A. Hinton, and M.E. Monaco. 

1991. Distribution and abundance of fishes and invertebrates 

in west coast estuaries, Volume II: Species life history 

summaries. ELMR Rep. No. 8. NOAA/NOS/Strategic 

Environmental Assessments Division. Rockville, MD. 329 pp.

Hixon, M.A., B.N. Tissot, and W.G. Pearcy. 1991. Fish Assemblages of Rocky Banks of the Pacific Northwest [Coquille, 

Daisy, and Heceta Banks]. A final report by the Department 

of Zoology and College of Oceanography of Oregon State 

University for the U.S. Department of the Interior, Minerals 

Management Service Pacific OCS Office. Contract No. 14-12-

0001-30445. Camarillo, CA. 410 pp.

Monaco, M.E., R.L. Emmett, D.M. Nelson, and S.A. Hinton. 

1990. Distribution and abundance of fishes and invertebrates 

in west coast estuaries, Volume I: Data summaries. 

ELMR Rep. No. 4. NOAA/NOS/Strategic Environmental 

Assessments Division. Silver Spring, MD. 332 pp.

Nelson, D.M, and M.E. Monaco. 2000. National overview 

and evolution of NOAA’s Estuarine Living Marine Resources 

(ELMR) Program. NOAA Tech. Memo. NOS NCCOS CCMA 

144. Silver Spring, MD. 60 pp.

SAB (Strategic Assessment Branch). 1990. NOAA’s west 

coast of North America data atlas: Invertebrate and fish 

volume. National Oceanic and Atmospheric Administration. 

Rockville, MD. 111pp.

SABNAFC (Strategic Assessment Branch, and Northwest 

and Alaska Fisheries Center). 1988. West coast of North 

America strategic assessment: data atlas: Marine mammal 

volume. National Oceanic and Atmospheric Administration. 

Rockville, MD. 33 pp.

139
BACKGROUND

The mission of NOAA National Ocean Service’s (NOS) National 

Marine Sanctuary Program (NMSP) is to serve as the trustee 

for a system of marine protected areas, to conserve, protect, 

and enhance their biodiversity, ecological integrity, and 

cultural legacy. To assist in accomplishing this mission, the 

NMSP has developed a partnership with NOAA’s National 

Centers for Coastal Ocean Science (NCCOS) to conduct 

biogeographic assessments of living marine resources in all 

National Marine Sanctuaries to characterize and assess the 

distribution of marine resources that occur within and adjacent 

to the sanctuaries. The NMSP and NCCOS’s Biogeography 

Program have developed a five-year plan to implement the 

assessments across the system of National Marine Sanctuaries 

(Kendall and Monaco 2003). The biogeographic assessment 

process as defined in the plan is used to conduct studies that 

are designed to address research needs and support a wide 

array of sanctuary management decisions. In general, the 

priority to implement the biogeographic assessments is based 

on the need to update sanctuary management plans. Thus, the 

joint efforts are systematically proceeding to work with each 

sanctuary to provide assessments of species’ distributions and 

their associated habitats in a region.

Since establishment, many of the sanctuaries have witnessed 

increased pressure on marine resources from natural and 

anthropogenic phenomena, including climatic variation and 

degradation of habitats. In order for the NMSP to increase 

management capabilities, it is imperative that the spatial and 

temporal distributions of biota and habitats within sanctuaries 

be delineated. Biogeography provides a framework to integrate 

species distributions and life history data with information on 

the habitats of the region to characterize marine resources 

in a sanctuary. When the biogeographic data are integrated 

into a Geographic Information System (GIS), it enables users 

to visualize species’ spatial and temporal distributions and 

conduct ecological forecasts to assess potential changes in 

species distributions that may result from a variety of natural 

and anthropogenic perturbations. In addition, based on specific 

ecological metrics (e.g., diversity), biologically significant 

areas can be delineated. This document provides the results 

of the GIS-based assessment conducted for the National 

Marine Sanctuaries off north/central California to initiate 

development of a biogeographic assessment capability for 

the sanctuaries.

BIOGEOGRAPHIC ASSESSMENT OFF NORTH/CENTRAL 

CALIFORNIA

The initial biogeographic assessment outlined in the five-year 

NCCOS/NMSP plan was implemented in the spring of 2001 

to conduct a 24-month investigation to assess biogeographic 

patterns of selected marine species found within and adjacent 

to the boundaries of three contiguous West Coast National 

Marine Sanctuaries. These sanctuaries, Monterey Bay, Gulf 

of the Farallones, and Cordell Bank, are conducting a joint 

review to update sanctuary management plans. To support 

the management plan review process, the Biogeography 

Program is leading a partnership effort to conduct a robust 

analytical assessment to define important biological areas and 

time periods within the region. This document represents the 

results of the first of two assessment phases. Phase I provides 

data, analytical results, and descriptions of ecosystems and 

their linkages; it also identifies data gaps, and suggests future 

activities to be addressed in Phase II.

Phase I of this effort was a biogeographic assessment of existing 

data on the distribution and abundance of marine fishes, marine 

birds, marine mammals and their associated habitats. The study 

did not attempt to define biogeographic patterns along the entire 

U.S. West Coast nor in very near-shore environments (e.g., 

estuaries). Rather, the study area was restricted to the marine 

area from Point Arena in Mendocino County (38 ̊54’32” N, the 

northern bound) to Point Sal in northern Santa Barbara County 

(34 ̊54’05” N, the southern bound). The entire study area and 

regional maps of the area are depicted in Figures 2-5. This 

relatively large study area enabled the assessment to extend 

beyond the limits of current sanctuary boundaries to place 

study results in the context of north/cental California Coast 

biogeographic patterns. The biogeographic analyses are based 

on a synthesis of many data sources that were provided by 

project partners and contributors. Results of this assessment 

are being used to assist the NMSP in addressing issues such as 

evaluating potential modification of sanctuary boundaries and 

changes in management strategies or administration, based 

on the principles of biogeography.

The biogeographic assessment was formulated around three 

closely integrated study components: (1) an Ecological Linkages 

Report, (2) biogeographic analyses, and (3) development of GIS 

data for incorporation into NMSP’s Marine Information System 

(MarIS). The majority of the results from the assessment are 

presented as a suite of GIS maps to visually display species’ 

biogeographic patterns across the study area. The body of the 

document provides examples of the entire suite of digital map 

products found on the companion CD-ROM and located on 

the Web at http://biogeo.nos.noaa.gov/products/canms_cd/. 

The spatial data and additional information, such as digital 

species distribution maps and additional details on analytical 

methodologies, are also presented on the CD-ROM.

Section 5: SUMMARY OF BIOGEOGRAPHIC ASSESSMENT

Ideally, biogeographic assessments utilize significant amounts 

of data that have been collected over the entire spatial extent of 

the study area over a long time period. However, such a wealth 

of data is rarely available. In many instances, little information 

exists to accurately characterize the study area or associated 

living marine resources. This paucity of comprehensive data 

can limit the efficacy of biogeographic assessments, but 

additional analytical methods can be employed to complement 

the assessment. In addition to analysis of databases, two 

additional tasks were used to conduct the assessment. 

First, a synthesis of existing information was compiled and 

presented in the Ecological Linkages Report to incorporate 

qualitative information about species, habitats and ecological 

characterization of marine ecosystems and linkages within 

the study area. Second, species habitat suitability modeling 

efforts were conducted for fishes to define potential species’ 

distributions based on known habitat affinities and physiological 

limitations. The potential species distribution maps are displayed 

as a series of digital maps found on the CD-ROM.

In addition, a critical component of the assessment process was 

the extensive effort to have the data, analytical approaches, 

and results peer reviewed. Initial results from the suite of 

biogeographic analyses were presented to experts familiar 

with the marine ecosystem off north/central California, as 

well as to the originators of the data sources, in an attempt 

to improve the analyses. The role of expert review and input 

was considerable, and the contributions made by experts have 

significantly enhanced the assessment. In June 2002, project 

team members traveled to Seattle, WA and Santa Cruz, CA to 

discuss and present the results of the Interim Product to West 

Coast experts (NOAA, 2002). Suggestions were incorporated 

and a Web site was created to further disseminate analytical 

products prior to an additional series of meetings. The final 

suite of review meetings was held in October 2002 in San 

Francisco and Monterey, CA and in Seattle, WA. At that time, 

NOS staff invited members of the scientific community to 

review the preliminary results of the biogeographic analyses. 

Comments from the October meetings were compiled and 

reviewed by project personnel, who either incorporated the 

experts' suggestions or provided explanations as to why they 

did not. Thus, the integration of the synthesis of ecological 

linkage information, statistical analyses of existing databases, 

species habitat suitability modeling, and peer review, resulted 

in this biogeographic assessment product.

ECOLOGICAL LINKAGES REPORT

Section 1 of the document presents a synopsis of the Ecological 

Linkages Report and provides the context to understand overall 

biogeographic product results, relative to the ecosystems 

along the California Coast. The bulk of the report describes 

ecosystems in the region, key species associated with these 

140
Section 5: SUMMARY OF BIOGEOGRAPHIC ASSESSMENT

ecosystems, and linkages between and among them. In 

addition, the report presents latitudinal range distributions of 

species groups, including algae, invertebrates, fish, marine 

birds and marine mammals. These maps provide an overview 

of marine species’ distributions and biogeographic transitions 

along the entire west coast of North America. The report also 

includes important information on ecosystems not easily 

studied at this large scale via GIS, particularly near-shore 

communities. The complete report (163 pp.) is on the CD-ROM 

that accompanies this document (Airamé et al., 2003).

Key West Coast Biogeographic Transitions

• Benthic algae exhibit three major biogeographic transitions 

at Point Conception, Puget Sound, and the Gulf of Alaska. At 

all latitudes, the average number of algal species increased 

with depth from high to low intertidal and subtidal zones.

• Five major transitions occur in distributions of marine 

invertebrates found in California waters: at Point Conception, 

Monterey Bay, Puget Sound, and off the coasts of British 

Columbia and southeastern Alaska. At all latitudes, greater 

numbers of gastropod species occur in the euphotic zone and 

on the continental shelf than on the continental slope.

• Pacific coast fishes exhibit two major biogeographic transitions. 

A biogeographic transition at the Bering Sea is relatively 

abrupt, corresponding to the northern limit of distributions 

of over 100 fish species. A broader biogeographic transition 

occurs along the southern coast of California between Baja 

California and Point Conception. A few minor shifts in fish 

species composition occur between Point Conception and 

the Bering Sea, particularly at Monterey Bay.

BIOGEOGRAPHIC ANALYSES

Section 2 introduces the methods used to conduct the 

assessment and the results of the biogeographic analyses 

of selected marine biota off the north/central California coast. 

This component of the assessment is the cornerstone of the 

overall biogeographic product to support the NMSP joint 

management plan review process. The data, analyses, and 

supporting information are linked using statistical and GIS tools 

to portray in space and time significant biological areas or “hot 

spots.” The term “hot spot” is defined based on specific criteria 

or metrics (e.g., species diversity, high species abundance). 

The vast majority of the analytical results are displayed as a 

series of maps to identify biologically significant areas in the 

study area. 

There are many different ways to analyze and organize 

biogeographic information; however, to efficiently support the 

management plan process, only a limited number of analytical 

options were invoked. These analyses were selected based 

on reviewers' comments on the Interim Product (NOAA 2002), 

feedback from technical review meetings, and peer review 

workshops. Thus, a very difficult step in the project was to 

select and rely on the most appropriate data and analyses to 

characterize the various components of the marine ecosystem 

that exist in the study area. The inclusion of the GIS-based 

products on the companion CD-ROM will enable NOAA staff, 

advisory councils, and research partners to query data and 

information relevant for questions and issues that are not 

specifically addressed in this product.

The first analyses focused on a suite of assemblages analyses 

to assess the biogeography of fishes and a few macroinvertebrates. Primary data included fisheries-independent 

data, such as those collected by researchers from the National 

Marine Fisheries Service (NMFS), and fisheries-dependent 

data, such as those collected by the California Department of 

Fish and Game (CDF&G) for recreational fisheries. These data 

sets, although not spatially or temporally comprehensive, are 

the most robust data sets that exist for the entire region, and 

provide considerable information on the distribution of several 

hundred fish and invertebrate species. 

Key Assemblage Analysis Results for Fishes

• Species assemblages and site groups were distinguished 

through 1-Pearson correlation coefficients with average 

means clustering technique. Species assemblages from 

CDF&G recreational, NMFS shelf, and NMFS slope data 

sets were more resilient than assemblages from the NMFS 

midwater data set, emphasizing the ephemeral nature 

of the midwater environment and the smaller midwater 

data set. The site groups were displayed spatially in a 

GIS and the average frequency of occurrence of species 

assemblages was calculated to show the interaction between 

species assemblages and site groups (i.e., where species 

assemblages were caught).

• The interaction of the site groups with environmental 

parameters that were not used to create the groups can 

be informative about what conditions are affecting species 

distribution. Depth was highly significant between site 

groups in all data sets, emphasizing the importance of 

depth in structuring marine biological communities. Analyses 

comparing the site groups to other environmental parameters 

(latitude, sediment size, and bathymetric complexity) were 

inconclusive, as these parameters often had significant 

interactions with depth. Latitude was found to have a 

significant effect only on the midwater assemblages in 1999; 

there were no discernible latitudinal breaks within the other 

four assemblages.

• Diversity and richness can be used to delineate fish hot 

spots. While little variation in diversity and richness were 

explained by depth (r2 =0.04 between both richness and depth 

and diversity and depth), trawls with high diversity tended to 

be deeper than trawls with high richness. Trawls with high 

species richness of rockfish (Sebastes and Sebastolobos) 

followed the 200-meter contour, which approximates the 

break between the shelf and slope. 

• Even though richness and diversity are correlated, the 

maps showed different results. Hot spots in either richness 

or diversity were identified in all three sanctuaries. In Cordell 

Bank NMS, there was a group of trawls with high richness 

near the center of the sanctuary, and another group of 

trawls with high diversity in the region around the northwest 

boundary. There was also a large collection of trawls with 

either high richness or diversity straddling the boundary 

between Gulf of the Farallones and Monterey Bay NMS. 

There were lines of high diversity along the 200-meter depth 

contour north of CBNMS boundary and from Lopez Point 

south to the southern edge of the study area. 

• Starr (1998) addressed the implementation of rockfish no-take 

areas with two important recommendations. First, in order 

to properly manage marine ecosystems, fish assemblages 

must be better understood. Starr stated that once these 

assemblages are delineated, steps can be taken to ensure 

that each assemblage receives proper management. 

This study defined assemblages of fishes for near-shore, 

shelf, slope and midwater ecosystems. The results of the 

community metrics and species assemblages are displayed 

in this document as a series of maps and tables.

• The second recommendation by Starr (1998) was to delineate 

rectangular no-take areas that cover 20-50 km of the coast 

and extend west to the edge of the continental shelf. From a 

biogeographic viewpoint, the results of the spatial analyses 

coincided with that recommendation, and also identified that 

deep-slope communities significantly contribute to ground 

fish biogeographic patterns. Because assemblages follow 

bathymetry at the scale of this analysis, setting aside an area 

from the coast through the continental slope could protect all 

demersal species assemblages identified in this study. 

Key Species Habitat Suitability Model Results

Due to limitations in the spatial and temporal extent of data and 

to complement the assemblage analyses of fishes, species 

habitat suitability index (HSI) models were developed (Brown 

et al., 2000). This was done primarily to accommodate the 

paucity of empirical data in near-shore areas and to target 

species of special significance to the sanctuaries. An extensive 

literature review of the life history characteristics of individual 

species resulted in information on species’ habitat affinities 

that were converted into quantifiable habitat suitability index 

values (Monaco et al., 1997). The life history information and 

associated species habitat suitability index values are found on 

the CD-ROM. These derived values were input into an equation 

and used to predict potential species’ distributions based on 

their affinity for the mosaic of bathymetry and bottom habitats 

found throughout the region. The species habitat suitability 

models were validated through statistical and spatial analyses, 

using fishery-independent survey data. 

• Bottom substrate and water depth were statistically significant 

variables used to predict the potential distribution of species 

based on their habitat affinities.

• Habitat suitability models for an assemblage of rockfish 

were developed and results indicated that rocky habitats 

located on the shelf were identified as potential hot spots 

for adults; whereas mud and sand substrates on the shelf 

were delineated as potentially important habitats for subadult 

rockfish.

• Map overlays of all species’ HSI models resulted in the 

delineation of a broad range of important areas that cover 

the majority of the continental shelf within and adjacent to 

the three sanctuary boundaries.

Key Marine Bird Analytical Results

The Biogeography Team contracted principal investigators 

David Ainley and Glenn Ford (of H.T. Harvey and Associates 

and R.G. Ford Consulting Co.) to work with the NOAA project 

team to define and assess biogeographic patterns and 

important areas for marine birds (and mammals) found within 

the study area. These experts used regression analysis, GIS 

and over eight spatial data sets to develop over 50 maps that 

display marine spatial and temporal patterns, and estimated 

densities and diversity for selected marine birds in the study 

area. The resulting maps and discussion summarize important 

locations, time periods, and life history information for marine 

birds in the study area. Phase II of the assessment may include 

a technical report on the methods and results summarized in 

the Phase I map and tabular products.

• In general, the marine birds of the three sanctuaries are 

dominated in number and biomass by seasonally resident, 

nonbreeding species, such as sooty shearwater, pink-footed 

shearwater, northern fulmar and black-legged kittiwake. The 

richness of the food web is the primary factor that attracts 

these species to the region.

• Seasonal, interannual and decadal variation of the regional 

biogeography of marine birds is influenced by the vagaries 

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Section 5: SUMMARY OF BIOGEOGRAPHIC ASSESSMENT

of marine climate, which is driven by the California Current 

System and local upwelling centers. Therefore, the 

biogeographic patterns of marine birds are not static and 

exhibit a dramatic spatial and temporal variation, both in 

species composition and species abundance.

• The Gulf of the Farallones, the area lying inside a triangle 

defined by Point Reyes, the Farallon Islands and Año 

Nuevo Island, is the most important area for marine birds 

in California. The reasons are: (1) large and taxonomically 

diverse, demographically related populations breed at the 

three afore-mentioned sites; and (2) an unparalleled diversity 

of habitat (e.g., San Francisco Bay tidal plume, shallow 

sandy shelf, rocky reefs, submarine peaks, and the upper 

continental slope) attracts a variety of migrant and seasonally 

resident species.

• A "halo" of individuals was apparent around important 

breeding sites, such as the Farallon Islands and Año Nuevo 

Island. This pattern is the result of breeding individuals 

searching for food, but going only as far as necessary to 

provide for their young. The Farallon "halo" for ashy stormpetrel, western gull, common murre, rhinoceros auklet and 

Cassin’s auklet, extends substantially west of the Gulf of the 

Farallones National Marine Sanctuary.

• The marine birds of the Gulf of the Farallones/Cordell Bank 

NMS (as defined above) and the birds of the Monterey Bay 

NMS are associated with different habitat features. The Gulf of 

the Farallones has islands and a relatively broad shelf, while 

Monterey Bay has a relatively narrow but sheltered shelf, cut 

by an immense, deep submarine canyon. The greater oceanic 

influence and lack of breeding islands in the Monterey Bay 

NMS drive the marine bird species groups there.

Preliminary Marine Mammal Analytical Results

The Biogeography Team contracted principal investigators 

David Ainley and Glenn Ford (of H.T. Harvey and Associates 

and R.G. Ford Consulting Co.) to work with the NOAA 

project team and local marine mammal experts to identify 

biogeographic patterns and important areas and time periods 

for marine mammals occurring in the study area. NOAA/NMFS 

scientists provided additional marine mammal sightings data 

along the entire West Coast to aid in analyzing marine mammal 

biogeographic patterns relative to the study area. The "bird and 

mammal team" used a GIS to develop a preliminary series of 

maps that show occurrence patterns and important areas and 

time periods for 13 marine mammals in the study area. Phase 

II of this assessment will: incorporate additional data, develop 

additional marine mammal species and species group maps, 

and attempt to develop selected community metrics analyses 

across species and time periods. A technical report on this 

work is also planned.

Spatial Patterns. The spatial occurrence of marine mammals 

relative to large bathymetric features (e.g., shelf, upper 

slope, lower slope) and discrete physiographic features (e.g., 

seamounts, banks, canyons, points and islands) varied by 

species and ocean condition. The occurrence patterns of 

most marine mammals are strongly linked to the highly variable 

ocean conditions of the study area, which significantly affect the 

distribution of prey availability. In Phase II of this work, when the 

data sets are more spatially and temporally robust, summary 

analyses will be conducted to identify important areas and time 

periods across marine mammal groups. 

Large Cetaceans. Important areas for the large cetaceans 

varied by species: the coast and inner shelf were important 

for the gray whale; the outer shelf, slope, and deep ocean 

were important for the humpback and blue whales; and many 

important areas for large cetaceans were identified seaward 

of the sanctuary boundaries. 

Small Cetaceans. Review of the maps indicated that important 

areas for the relatively abundant small cetaceans were the 

outer shelf and upper slope, Monterey Canyon, Sur and Lucia 

Canyons (west and south of the Monterey Bay NMS), Pioneer 

Canyon (west of the Monterey Bay NMS), Ascension, Cabrillo, 

Año and Carmel canyons, Cordell Bank (and to the north of 

the Cordell Bank NMS boundary), and the San Francisco Bay 

tidal plume area (e.g., harbor porpoise). Smaller cetaceans 

were also relatively abundant in areas that include canyons, 

and in locations beyond sanctuary boundaries, but within the 

study area.

Pinnipeds. Important areas for resident breeders (e.g., harbor 

seal, Steller sea lion) were inner and outer shelf habitats, and for 

northern elephant seal, pelagic deep ocean habitats seaward 

of sanctuary boundaries. Seasonal visitors (e.g., northern fur 

seals) occurred mostly in slope and deep ocean habitats, 

seaward of sanctuary boundaries. 

Temporal Patterns. The patterns of seasonal occurrence for 

marine mammals varied by species. In Phase II of this work, 

when the data sets are more complete, summary spatial and 

temporal analyses across marine mammal groups will be 

conducted. 

Large Cetaceans. The seasonal occurrence of the larger 

cetaceans in the study area reflected their migrations. The 

Davidson Current season was important for the gray whale, 

a period when this species is migrating either south or north. 

Several species of the large cetaceans migrate to forage 

seasonally in the study area, a pattern reflected in the relative 

abundance of the humpback and blue whales during the 

Upwelling and Oceanic seasons. 

Small Cetaceans. An important time period for the Pacific 

white-sided dolphin (the most abundant small cetacean in 

this study) was the Oceanic season. Important time periods 

for the other relatively abundant smaller cetaceans (northern 

right-whale dolphin, Risso’s dolphin, Dall’s porpoise) could not 

be determined in this preliminary assessment.

Pinnipeds. The seasonal occurrence of pinnipeds was 

associated with the breeding cycles of the species. Important 

time periods for the relatively abundant northern fur seal were 

winter and early spring (Davidson Current and early Upwelling 

seasons), which reflected the pelagic offshore distribution along 

the West Coast during the nonbreeding season. The relatively 

abundant California sea lion was present year-round in the 

study area, with densities greater during the Oceanic season 

(just after breeding) and Davidson Current season (before the 

breeding season). Elephant seals, Steller sea lions, and harbor 

seals were present in sanctuary waters year-round in relatively 

low numbers; and important time periods for these infrequently 

sighted species were inconclusive due to differences in 

behavior and low abundance (e.g., at-sea sightings typically 

consist of single individuals or small groups of two or three, 

elephant seals are rarely at the surface, and Steller sea lions 

are a threatened species).

INTEGRATION OF ANALYSES

The integration of analyses across taxa occurs in Section 3. 

Many possible combinations of the data layers could be integrated for the biogeographic assessment. Because of differences in sampling design, it was not appropriate to combine 

data from different taxa (e.g. birds and fish) in order to calculate 

community metrics. Therefore, to minimize confounding results 

and to focus on the “protection of biodiversity” component of 

the NMSP mission, diversity and density were calculated separately for each taxon and the resulting patterns were overlayed 

to identify biologically important areas across species groups. 

Spatial interpolation methods were applied to survey data to 

provide a clearer picture of the distribution of diversity and density within the study area. Hot spots were defined as regions 

in which diversity or density were estimated to be in the top 

20% for a particular taxon. These hot spots were mapped for 

fish and birds individually and then combined to show areas 

of overlap. These areas of significant biological importance 

contributed to defining and assessing biogeographic patterns 

within the study area and are discussed in the context of known 

oceanographic features and Sanctuary boundaries. All of the 

conclusions listed below should be considered with an understanding of the inherent limitations of the available data and 

the approaches used to analyze it. A detailed discussion of 

these concerns is presented in Section 3.

Key Findings of Integration of Analyses

Fish Diversity (Trawl data). Three major areas of relatively 

high fish diversity (i.e., hot spots) were delineated, as noted 

below. 

• The northernmost hot spot is centered on Cordell Bank, 

within the northwestern corner of the Cordell Bank NMS, 

and extends northward along the continental slope to Point 

Arena.

• The central hot spot is centered at the boundary between 

the Gulf of the Farallones NMS and the Monterey Bay NMS. 

The area extends in a southeasterly direction past Point Año 

Nuevo and ends offshore, north of Monterey Bay. 

• The southernmost hot spot is located between Point Sur and 

Lopez Point and covers the inshore portions of Sur and Lucia 

Canyons. Portions of this last hot spot, however, were poorly 

sampled. There is evidence of an additional hot spot straddling the southern boundary of the Monterey Bay NMS.

Marine Bird Diversity

• The interpolated maps of marine bird diversity show one continuous area of high diversity along the continental slope, and, 

to a lesser extent, along the shelf between Point Arena and 

Point Sur. Within this area, diversity appears to be highest on, 

and seaward of, the Farallon Escarpment, in the northwestern 

corner of the Monterey Bay NMS (Pioneer Canyon), and in 

the marine region between Point Lobos and Point Sur. 

• The Farallon Escarpment in particular received a disproportionate amount of survey effort. The high estimated marine 

bird diversity for the Farallon Escarpment is, in part, due to 

high sampling effort. 

• A marine bird diversity hot spot was found in the region between Point Lobos and Point Sur. The high residual diversity 

in this area supports the interpretation that this is a real hot 

spot and not an artifact of survey effort.

• Marine bird diversity was correlated with survey effort, so 

some of the “hot spot” diversity areas coinciding with areas 

of high survey effort may, in part, be influenced by high levels of effort. However, the general patterns of marine bird 

diversity are robust, and were largely unchanged by methods 

designed to correct for effort.

Overlap of Marine Bird and Fish (Trawl) Diversity

• Fish diversity shows overlap with the areas of high bird diversity. The northernmost fish hot spot overlaps the marine 

bird hot spot from Cordell Bank north to approximately mid142
way between Bodega Head and Point Arena. The seaward 

half of the central fish hot spot overlaps with the area of 

high marine bird diversity within the Gulf of the Farallones 

NMS and the Monterey Bay NMS. The northern half of the 

southernmost fish hot spot overlaps the southern tip of the 

marine bird hot spot. 

Fish Density (Trawl Data)

Four major hot spots of fish density were found:

• The northernmost hot spot is found on and to the southeast 

of Cordell Bank. 

• A small hot spot is found off of Point Reyes.

• The largest fish density hot spot covers a large portion of 

the shelf to the north of Monterey Canyon, the entire area of 

Monterey Bay, and the near shore waters south to Point Sur. 

Although portions of this hot spot are found over Monterey 

Canyon, this fact should be interpreted with caution since the 

deep canyon waters themselves were not sampled.

• The fourth hot spot is found to the south of Monterey Bay 

NMS and covers a substantial area of the shelf from Point 

Estero to Point Sal. This final hot spot is the largest region 

of high fish density within the mapped area that falls outside 

of Sanctuary boundaries.

Marine Bird Density

• Marine bird density patterns should be interpreted with 

caution since they largely reflect the distribution of the two 

numerically dominant species.

• A large region of high (top 20th percentile) marine bird density 

exists adjacent to and shoreward of the marine bird diversity 

hot spot. This density hot spot covers most of the shelf waters of all three sanctuaries, from Point Sur in the south to 

midway between Bodega Head and Point Arena in the north. 

The density hot spot extends into Monterey Bay.

• An additional density hot spot exists off of Morro Bay to the 

south of the Monterey Bay NMS.

Overlap of Marine Bird and Fish (Trawl) Density

• Nearly all of the fish density hot spots are coincident with 

the two areas of high bird density. 

• The hot spots for both metrics are generally confined to the 

shelf (<200m) with the notable exception of Monterey Canyon 

which appears as a density hot spot for both groups. The 

deep Canyon, however, was not sampled in the fish trawl 

surveys. 

Section 5: SUMMARY OF BIOGEOGRAPHIC ASSESSMENT

• Although the majority of the hot spots for fish and bird density 

fall within sanctuary boundaries, it is notable that overlapping hot spots for both groups exist to the south of Monterey 

Bay NMS. 

Overall Integration Summary

•The current Sanctuary boundaries incorporate much of 

the highest diversity and highest density areas within the 

region.

• Many of these biologically important regions coincide with 

known oceanographic and bathymetric features, such as 

upwelling regions, areas of high bathymetric variance, and 

the continental shelf break.

• Regions of high diversity and high density outside of the 

current sanctuary boundaries exist to the north, across 

much of the shelf and slope, and to the south, in nearshore waters.

• Uneven sampling effort across the study region and a lack 

of trawl samples to the west of the Sanctuary boundaries 

limit the scope of any integrated biogeographic assessment.

• Known limitations and biases of the two metrics (diversity 

and density) exist and are discussed in greater detail within 

Section 3. 

DATA SOURCES AND GAPS

Recognizing that any analysis is only as good as the data 

upon which it is based, the project team undertook a qualitative 

evaluation of the data used in this project and identified relevant 

data gaps. This information is presented in Section 4: Data 

Content and Gaps. This section describes the process used 

to select key databases for analyses and briefly addresses 

strengths and limitations of each database. This information was 

used to aid in the interpretation of the biogeographic analyses to 

minimize confounding of results due to information gaps. Also 

provided are recommendations for future research activities 

that would enhance biogeographic assessment products.

PHASE II BIOGEOGRAPHIC ASSESSMENT

Section 6 suggests potential next steps to augment the 

Phase I analyses. Phase II, however, will not be completely 

designed until a review of Phase I products has occurred. The 

NMSP and NCCOS project team members will meet to define 

the additional suite of activities that will comprise Phase II. 

Nevertheless, a few priority activities are expected to occur in 

Phase II, including expanding the analytical products for fishes, 

marine birds, and marine mammals. Special emphasis will be 

placed on the biogeographic analyses of marine mammal data, 

REFERENCES

Airamé, S., S. Gaines, and C. Caldow. 2003. Ecological Linkages: Marine and estuarine ecosystems of central and northern 

California. NOAA, National Ocean Service. Silver Spring, MD. 

163 pp.

Brown, S.K., K.R. Buja, S.H. Jury, M.E. Monaco, and A. Banner. 2000. Habitat suitability index models for eight fish and 

invertebrate species in Casco and Sheepscot Bays, Maine. 

North American Journal of Fisheries Management, Vol. 20, 

pp. 408-435. 28 pp.

Kendall, M.S. and M.E. Monaco. 2003. Biogeography of the 

National Marine Sanctuaries: A partnership between the NOS 

Biogeography Program and the National Marine Sanctuary 

Program. NOAA. Silver Spring, MD. 8 pp.

Monaco, M.E. and J.D. Christensen. 1997. Biogeography Program: Coupling species distributions and habitat. In: Changing 

oceans and changing fisheries: Environmental data for fisheries 

research and management. G.W. Boehlert and J.D. Schumacher (Eds.). National Marine Fisheries Service Technical 

Memorandum NOAA-TM-NMFS-SWRSC-239, Pacific Grove, 

California. 7 pp.

NOAA's National Centers for Coastal Ocean Science and 

National Marine Sanctuary Program. 2002. Interim Product: 

A Biogeographic Assessment off North/Central California: To 

Support the Joint Management Plan Review for Cordell Bank, 

Gulf of the Farallones and Monterey Bay National Marine 

Sanctuaries. Silver Spring, MD. 38 pp.

Starr, R.M. 1998. Marine harvest refugia for West Coast rockfish: A workshop. Pacific Grove, California. NOAA-TM-NMFSSWFSC-255. La Jolla, CA. 14 pp.

as that component of the study was not completed in Phase 

I. The marine mammal analyses are one of the first efforts to 

assess biogeographic patterns of marine mammals in the study 

area; thus, additional analyses and peer review are required 

to complete this component of the study.

Phase II activities may include publishing technical reports 

and peer-reviewed articles that complement the results of the 

Phase I assessment, as well as additional analyses to further 

define biological areas and time periods important to marine 

fishes, birds, and mammals found throughout the study area.

CD-ROM

A digital version of this document, the Ecological Linkages 

Report, all GIS-compatible files used to conduct the 

biogeographic analyses, metadata for GIS files, and a complete 

suite of digital species maps, are found on the CD-ROM located 

on the back cover of this document. 

All appropriate digital data and analytical products are found on 

the CD-ROM. The products come in several formats, including 

this document (in .pdf format), map products in a browsable 

web format (HTML), GIS shapefiles and grids for use with 

MarIS or ArcView (GIS) software, tables in Excel format (.xls), 

and descriptive text files. Metadata for each shapefile or grid 

accompanies each file and appears in .xml format. 

To support the NMSP and others in making maximum use of 

the spatial data generated from this study, along with other 

products (e.g., economic assessments) that support the 

joint management plan review, the NMSP is developing a 

GIS tool, the Marine Resource Information System (MarIS). 

MarIS has been designed to facilitate the organization, 

analysis and display of spatial data to support analysis of 

NMSP management questions and issues within and across 

sanctuaries. All applicable spatial data will be integrated into 

MarIS to enable NMSP staff and partners to conduct additional 

biogeographic analyses in Phase II.

CONCLUDING COMMENTS

This spatially explicit assessment provides a robust set of 

analytical results and GIS data to strengthen the sustainable 

management of marine resources within and adjacent to the 

sanctuaries. A primary use of the biogeographic assessment 

will be to support the NMSP as it continues to conduct the joint 

management plan review for the three sanctuaries. In addition, 

the Biogeography Program will assist the NMSP in further 

analyses and presentations of the data and analytical results 

to address specific research and management questions. 

This Phase I product provides the foundation to continue the 

development of a biogeographic assessment capability to 

support the Cordell Bank, Gulf of the Farallones, and Monterey 

Bay National Marine Sanctuaries.

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Section 6: PHASE II BIOGEOGRAPHIC ASSESSMENT

Phase II of the biogeographic assessment of north/central California to support the research and management needs of Cordell Bank, Gulf of the Farallones, and Monterey Bay National Marine Sanctuaries will build on the information and analytical results 

presented in Phase I. Phase II, however, will not be completely designed until a review of Phase I products has occurred. Most important, the NMSP and NCCOS project team members will meet to define an additional suite of activities that may comprise 

Phase II. Nevertheless, a few priority activities are expected to occur in Phase II, including expanding the analytical products for fishes, marine birds, and marine mammals. A special emphasis will be placed on the biogeographic analyses of marine 

mammal data, as that component of the study was not completed in Phase I. The marine mammal analyses are one of the first efforts to assess biogeographic patterns of mammals in the study area, thus additional analyses and peer review are required 

to complete this section of the study.

Phase II activities may include publishing technical reports and peer reviewed articles that complement the results of the Phase I assessment and further define areas and time periods important to fishes, marine birds, and marine mammals found 

throughout the study area. Also, discussions will be held between project partners to determine if additional assessments should be implemented to study near-shore and estuarine ecosystems and associated key species groups such as marine and coastal 

invertebrates. These ecosystems and species were only qualitatively addressed in the Ecological Linkages Report due to data limitations, and time and resource constraints to complete the first phase of the project. In addition, to continue to implement 

the 5-year Biogeography Program plan developed by NCCOS in consultation with the NMSP, additional habitat and environmental maps under various temporal climate regimes could possibly be addressed to support future biogeographic analyses. For 

example, climatic regime shifts and associated influences on the distribution of living marine resources may provide additional insight into natural or anthropogenic perturbations on regional biogeographic patterns.

For now, project partners and colleagues are encouraged to provide comments on the information and analytical results provided in this document and on the CD-ROM. Also, please provide suggestions on how best to address Phase II proposed activities 

and new biogeographic assessment studies that may complement or improve Phase I analyses. For further information or to provide comments on the Phase I product and Phase II activities, please contact:

Dr. Mark E. Monaco, Biogeography Team Leader

NOAA/NCCOS/CCMA

1305 East West Highway, N/SCI1

Silver Spring, MD 20910

p. 301-713-3028 x 160

f. 301-713-4384

mark.monaco@noaa.gov

or

Mr. Charles E. Alexander, National Programs Branch Chief

NOAA/NMSP

1305 East West Highway, 

Silver Spring, MD 20910

p. 301-713-3125 x 147

f. 301-713-0404

charles.alexander@noaa.gov

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ACKNOWLEDGEMENTS

A project of this magnitude would not have been possible without the cooperation, time, data and effort of numerous people and institutions. We would like to thank everyone who participated in this significant undertaking. The following is a list of those 

who have contributed to this work.

Sarah Allen

Tara Anderson

Jay Barlow

Lillian Becker

Heather Beeler

Scott Benson

Carol Bernthal

Nancy Black

Laurence Breaker

Joelle Buffa

Tonya Builder

Gregor Cailliet

John Calambokdis

James Caretta

Mark Carr

Harry Carter

Josh Churchman

Elizabeth Clarke

Steve Copps

Natalie Cosentino

Don Croll

Brad Damitz

Chris Essert

Megan Ferguson

Doug Forsell

Fathey Fosmark

Michael Gallagher

Jim Glock

Gary Greene

Denise Greig 

Deirdre Hall

Rick Hanks

Michael Harris

Chris Harvey

Jim Harvey

Brian Hatfield

Laird Henkel

Michelle Hester

Tom Hourigan

Ruth Howell

David Hyrenbach

Todd Jacobs

Brian Jarvis

Roxanne Jordan

Mike Kenner

Stacy Kim

Chad King

Howatt King

Jamie Kum

Tom Laidig

Mark Lampinen

Bob Lauth

Bob Leeworthy

Phil Levin

Steve Lonhart

David Lott

Mark Lowry

Gerry McChesney

Huff McGonigal

Nazila Merati

Richard Methot

Pat Morris

Joe Mortenson 

Hannah Nevins

Kelly Newton

Jim Nybakken

Jim Oakden

Mike Parker

John Pearse

Brady Phillips

Holly Price

Stephen Ralston

Bob Read

Paul Reilly

Dale Roberts

Nora Rojek

Kaustuv Roy

Mary Jane Schramm

Michelle Staedler

Rick Starr

William Sydeman

Mario Tamburri

Christine Taylor

Julie Thayer

Teresa Turk

W. Breck Tyler

Tiffany Vance

Kerstin Wasson

Mark Wilkins

Deb Wilson-Vandenberg

Lisa Wooninck

Nancy Wright

Levon Yengoyan

Mary Yoklavich

Mark Zimmermann

Federal Government

National Centers for Coastal Ocean Science, National Ocean Service (NOS), NOAA

National Marine Sanctuaries National Program Office, NOS, NOAA 

Cordell Bank National Marine Sanctuary Office, NOS, NOAA 

Gulf of the Farallones National Marine Sanctuary Office, NOS, NOAA 

Monterey Bay National Marine Sanctuary Office, NOS, NOAA 

Channel Islands National Marine Sanctuary Office, NOS, NOAA 

Special Projects Office, NOS, NOAA 

Coastal Services Center, NOS, NOAA 

Southwest Fisheries Science Center, National Marine Fisheries Service (NMFS), NOAA 

Northwest Fisheries Science Center, NMFS, NOAA 

Alaska Fisheries Science Center, NMFS, NOAA 

U.S. Geological Survey, Department of Interior 

Minerals Management Service, Department of Interior 

U.S. Fish and Wildlife Service, Department of Interior 

Point Reyes National Seashore, National Park Service, Department of Interior 

State/Local Government

California Department of Fish and Game, Marine Region 

University of California, Santa Barbara 

California State University, Monterey Bay 

California State University, Moss Landing Marine Laboratories 

San Francisco Public Utilities Commission 

Non-Governmental Organizations

Alliance of Communities for Sustainable Fisheries

H.T. Harvey and Associates 

R.G. Ford Consulting Company 

Monterey Bay Aquarium Research Institute 

PRBO Conservation Science 

Diablo Canyon Power Plant 

145