National Park Service

U.S. Department of the Interior

Natural Resource Program Center

San Francisco Bay Area Network Pinniped Monitoring

Protocol

Version 3.02

Natural Resource Report NPS/SFAN/NRR—2009/170
ON THE COVER

Volunteer monitoring harbor seals at Drakes Estero, Point Reyes National Seashore.

Photograph by: Judith Fitzpatrick
______________________________________________________________________________

San Francisco Bay Area Network Pinniped

Monitoring Protocol

Version 3.02

Natural Resource Report NPS/SFAN/NRR—2009/170

Dawn Adams1

David Press1

Michelle Hester2

Hannah Nevins2

Dale Roberts3

Ben Becker3

Heather Jensen3

Erin Flynn3

Marcus Koenen1

Sarah Allen3

1National Park Service

San Francisco Bay Area I&M Network

Building 1063, Fort Cronkhite

Sausalito, California 94965

2Oikonos

P.O. Box 1932

Benicia, California 94510

3National Park Service

Point Reyes National Seashore

One Bear Valley Road

Point Reyes Station, California 94956

December 2009

U.S. Department of the Interior

National Park Service

Natural Resource Program Center

Fort Collins, Colorado
ii

The National Park Service, Natural Resource Program Center publishes a range of reports that

address natural resource topics of interest and applicability to a broad audience in the National

Park Service and others in natural resource management, including scientists, conservation and

environmental constituencies, and the public.

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precedent-setting nature. Peer review was conducted by highly qualified individuals with subject

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Views, statements, findings, conclusions, recommendations, and data in this report are those of

the author(s) and do not necessarily reflect views and policies of the National Park Service, U.S.

Department of the Interior. Mention of trade names or commercial products does not constitute

endorsement or recommendation for use by the National Park Service.

The National Park Service shall not be held liable for improper or incorrect use of the data

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It is the responsibility of the reader to use the data appropriately and consistent within the

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graphics as data. The National Park Service gives no warranty, expressed or implied, as to the

accuracy, reliability, or completeness of these data.

This report is available from the San Francisco Area Network Inventory and Monitoring website

(http://science.nature.nps.gov/im/units/sfan) and the Natural Resource Publications Management

website (http://www.nature.nps.gov/publications/NRPM).

Please cite this publication as:

Adams, D., D. Press, M. Hester, H. Nevins, D. Roberts, B. Becker, H. Jensen, E. Flynn, M.

Koenen, and S. Allen. 2009. San Francisco Bay Area Network pinniped monitoring protocol.

Natural Resource Report NPS/SFAN/NRR—2009/170. National Park Service, Fort Collins,

Colorado.

NPS 962/100743, December 2009
iii

Revision History Log

Prev. Version # Revision Date Author Changes Made Reason for

Change

New

Version #

August 2004 M. Hester,

S. Allen,

D. Adams,

H. Nevins

Initial protocol

submitted for peer

review.

1.00

1.00 June 2008 D. Adams,

S. Allen,

B. Becker,

D. Roberts,

M. Koenen,

D. Press,

H. Jensen,

E. Flynn

See Appendix SOP

5A for specific

changes made.

Addressed

recommendations

of two peer

reviewers.

2.25

2.25 September

2009

D. Adams,

S. Allen,

B. Becker,

D. Roberts,

M. Koenen,

D. Press

See Appendix SOP

5B for specific

changes made.

Addressed

recommendations

of two peer

reviewers, the peer

review manager,

and the PWR

Regional I&M

Coordinator.

3.00

3.00 November

2009

K. Freeman Formatting edits.

Removed citations

that were only

referenced in the

SOPs.

To meet NRPM

guidelines.

3.01

3.01 December

2009

D. Press Minor grammatical

and formatting edits.

Added a version

number to protocol

title. Added this

revision history log.

Comments from

Penny Latham and

Jason Bennett.

3.02

v

Contents

Page

Figures...................................................................................................................................... ix

Tables .........................................................................................................................................x

Standard Operating Procedures (SOPs) ..................................................................................... xi

Appendices .............................................................................................................................. xii

Executive Summary ................................................................................................................ xiii

Acknowledgements..................................................................................................................xiv

1.0 Background and Objectives.................................................................................................. 1

1.1 Background .................................................................................................................. 1

1.2 History of Monitoring................................................................................................... 4

1.3 Pinniped Management .................................................................................................. 9

1.4 Rationale for Selecting this Resource to Monitor .......................................................... 9

1.4.1 Legal Mandates.................................................................................................11

1.4.2 Enabling Legislation .........................................................................................11

1.4.3 Indicator of Ecosystem Condition......................................................................12

1.5 Measurable Objectives.................................................................................................13

1.5.1 Monitoring Questions........................................................................................14

1.5.2 Monitoring Objectives.......................................................................................14

1.5.3 Management Objectives ....................................................................................15

1.5.4 Currently Funded Monitoring Objectives ..........................................................17

2.0 Sampling Design .................................................................................................................19

2.1 Rationale for Selecting this Sampling Design...............................................................19

2.1.1 Parameters Monitored .......................................................................................20

2.2 Study Area and Site Selection......................................................................................21
vi

2.3 Sampling Frequency ....................................................................................................22

2.3.1 Harbor Seal Monitoring.....................................................................................22

2.3.2 Northern Elephant Seal Monitoring ...................................................................22

2.4 Number and Location of Sample Sites .........................................................................23

2.4.1 Harbor Seal Study Sites.....................................................................................23

2.4.2 Northern Elephant Seal Study Sites ...................................................................23

2.5 Level of Change That Can Be Detected .......................................................................26

2.5.1 Harbor Seal Population Monitoring ...................................................................26

2.5.2 Northern Elephant Seal Population Monitoring .................................................26

3.0 Field Methods .....................................................................................................................29

3.1 Site Access ..................................................................................................................29

3.2 Harbor Seal Monitoring ...............................................................................................29

3.2.1 Field Season Preparation and Equipment Setup .................................................29

3.2.2 Details of Taking Measurements .......................................................................29

3.3 Northern Elephant Seal Monitoring..............................................................................30

3.3.1 Field Season Preparation and Equipment Setup .................................................30

3.3.2 Details of Taking Measurements .......................................................................30

3.4 End of Season Procedures............................................................................................31

4.0 Cooperation with Other Monitoring and Research ...............................................................33

4.1 Dye-Marking, Tagging and Resighting Tags................................................................33

4.2 All Species Pinniped Monitoring – Point Reyes Headlands..........................................34

4.3 Scat Collection ............................................................................................................34

4.4 Statewide Surveys........................................................................................................35

4.5 Volunteer and Docent Programs ..................................................................................35

4.6 Stranding Network Program.........................................................................................35
vii

4.7 Disease Monitoring......................................................................................................36

4.8 University Research.....................................................................................................36

4.9 Collaborative Products.................................................................................................37

5.0 Data Management, Analysis, and Reporting ........................................................................39

5.1 Overview of Database Design......................................................................................39

5.2 Data Entry, Verification, and Editing ...........................................................................40

5.3 Data Archival Procedures ............................................................................................40

5.4 Metadata Procedures....................................................................................................41

5.5 Data Distribution .........................................................................................................41

5.6 Data Analysis ..............................................................................................................42

5.6.1 Harbor Seal Monitoring Program ......................................................................42

5.6.2 Northern Elephant Seal Monitoring Program.....................................................43

5.7 Reporting Schedule and Formats..................................................................................44

6.0 Personnel Requirements and Training .................................................................................47

6.1 Roles and Responsibilities ...........................................................................................47

6.1.1 Project Manager ................................................................................................47

6.1.2 Biological Technicians ......................................................................................47

6.1.3 Data Manager....................................................................................................47

6.1.4 Volunteers.........................................................................................................47

6.2 Qualifications ..............................................................................................................47

6.3 Training Procedures.....................................................................................................47

7.0 Operational Requirements ...................................................................................................49

7.1 Annual Workload ........................................................................................................49

7.2 Annual Field Schedule.................................................................................................49

7.3 Facility and Equipment Needs .....................................................................................49
viii

7.4 Budget.........................................................................................................................51

7.5 Permitting and Compliance..........................................................................................51

8.0 Literature Cited ...................................................................................................................53
ix

Figures

Page

Figure 1. Northern elephant seal breeding and molting locations along the coast of

western North America (Carretta et al. 2007). .............................................................................3

Figure 2. Map of the western coast of North America indicating northern elephant seal

foraging areas..............................................................................................................................4

Figure 3. Maximum harbor seal pup counts for 2000–2008 at Marin County locations. ...............6

Figure 4. Maximum counts of harbor seal adults and immatures during the breeding

season (March-May) at Marin County locations. .........................................................................7

Figure 5. Harbor seal haul out monitoring locations within Point Reyes National

Seashore and Golden Gate National Recreation Area. ...............................................................24

Figure 6. Northern elephant seal monitoring locations at Point Reyes National Seashore...........25
x

Tables

Page

Table 1. Point Reyes National Seashore northern elephant seal population and

productivity counts for 2005–2007 breeding seasons at each colony site .................................... 8

Table 2. Summary of reporting and communication products. ...................................................46

Table 3. Annual SFAN harbor seal monitoring field schedule. ..................................................50

Table 4. Annual SFAN northern elephant seal monitoring field schedule. .................................50

Table 5. Annual budget for the SFAN harbor seal monitoring program. ....................................52

Table 6. Annual budget for the SFAN northern elephant seal monitoring program. ...................52
xi

Standard Operating Procedures (SOPs)

Page

SOP 1. Harbor Seal Surveys......................................................................................................61

SOP 2. Northern Elephant Seal Surveys ....................................................................................89

SOP 3. Data Management .......................................................................................................117

SOP 4. Data Analysis and Reporting .......................................................................................175

SOP 5. Revising the Protocol ..................................................................................................193

SOP 6. Safety Procedures........................................................................................................225
xii

Appendices

Page

Appendix A: Power Analysis for the NPS San Francisco Bay Area Network Harbor

Seal (Phoca vitulina) Monitoring Program. .............................................................................235

Appendix B. Power Analysis for the NPS San Francisco Bay Area Network Northern

Elephant Seal (Mirounga angustirostris) Monitoring Program ................................................243

Appendix C. Program Products ...............................................................................................255
xiii

Executive Summary

The purpose of this document is to describe the National Park Service’s monitoring program for

pinniped populations that occur within the San Francisco Bay Area Network (SFAN) of parks in

central California. Protocols document standardized objectives, methods, and data management

to enable high quality evaluation of pinniped population status in the region. Oakley et al. (2003)

provided guidance in the development of this protocol. The main purpose of the program is to

monitor pinniped population status and trends and to adaptively guide management actions.

Within the order Carnivora, the Pinnipedia sub-order is a group of marine mammals that includes sea

lions, fur seals, true seals, and walruses. The numerically dominant pinniped species that breed,

haul out, and molt in the region include the Pacific harbor seal (Phoca vitulina richardii) and

northern elephant seal (Mirounga angustirostris). Survey effort focuses on species that breed in

the parks because this information contributes significantly to the regional and stock-wide

understanding of these species required under the Marine Mammal Protection Act (1972).

The SFAN Inventory and Monitoring Program is committed to long-term, full-funding of the

harbor seal monitoring program within Point Reyes National Seashore and Golden Gate National

Recreation Area. As funding permits, the SFAN will reconsider funding for the northern

elephant seal monitoring program. The SFAN will continue to provide logistical and technical

support to the northern elephant seal monitoring program. For this reason, this protocol and

associated standard operating procedures (SOPs) encompass both monitoring programs. For

simplicity’s sake, although this protocol only addresses harbor seals and northern elephant seals,

it is known and referred to as the pinniped monitoring protocol.

Specific objectives of the long-term harbor seal monitoring program are to:

1. Determine the long-term trends in population size and seasonal distribution of harbor seal

populations at primary sites in the SFAN parks during the breeding and molt seasons.

2. Determine long-term trends in reproductive success of harbor seals through annual

estimates of pup production at PORE and GOGA.

3. Determine the long-term trends in sources, frequency and level of effects of natural and

anthropogenic disturbances on harbor seal haul out use and productivity.

General guidelines for field methods, data analyses, reporting requirements, and project budgets

to meet these objectives are provided in the protocol and detailed in the SOPs. The protocol and

SOPs will be updated as methods are revised or as new analytical methods are adapted. Data are

housed in a Microsoft Access database with front-end files available for data entry and analyses.

The document outlines ongoing collaborations with other agencies and researchers. Coordination

with other agencies is necessary to protect these species because their movements during

migration, foraging, and molting range outside park boundaries. Protocols will be integrated with

other resource agencies for compatible population analyses. The SFAN monitoring program

contributes to regional and national efforts to assess pinniped population status and trends.
xiv

Acknowledgements

Key persons who have contributed to this program and methods over the years include J. Adams,

P. Boveng, K. Fehring, H. Huber, R.E. Jones, M. Lowry, D. Nothelfer, J. Nusbaum, J. Pettee, L.

Ptak, C. Ribic, W. Sydeman, and S. Waber. We thank the hundreds of volunteers who have

contributed thousands of hours to pinniped monitoring at Point Reyes. B. Sommerfeldt, J.

Manna, K. Truchinski, E. Flynn, S. Codde, and E. Wheeler have capably managed the harbor

seal and northern elephant seal monitoring programs over the last several years. We are also

grateful to various federal and state agencies and their representatives that have collaborated to

analyze population status, including R. DeLong, D. DeMaster, and J. Barlow of NOAA

Fisheries; F. Gulland and D. Greig of the Marine Mammal Center; E. Ueber, J. Roletto and J.

Mortenson of NOAA; H. Markowitz, E. Grigg and D. Green of SFSU; and D. Hanan and D.

Miller of CDFG. D. Ainley and J. Harvey have contributed to the program over the years and

reviewed the protocol providing many helpful comments. R. Zeno contributed to sections of the

protocol by addressing reviewer comments. B. Merkle also provided valuable comments to help

improve this document and the overall monitoring program. We also thank P. Latham and two

anonymous reviewers for their comments on earlier drafts of this document.
1

1.0 Background and Objectives

1.1 Background

Point Reyes National Seashore (PORE) and Golden Gate National Recreation Area (GOGA) are

situated north and south of San Francisco Bay in Marin, San Francisco and San Mateo Counties,

California. PORE was established in 1962 and has one of the most accessible congressionally

designated wilderness areas in the United States (71,046 acres with 80 miles of coastline).

GOGA was established in 1972 as part of the “parks to the people” program, and includes

approximately 95,000 acres and 20 miles of coastline. Marine boundaries are shared with the

Gulf of the Farallones National Marine Sanctuary, the Monterey Bay National Marine Sanctuary,

and Tomales Bay State Park. In 1988, UNESCO Man in the Biosphere program designated the

Central California Coast Biosphere Reserve (CCCBR) under the International Biosphere

Program; CCCBR includes PORE and GOGA and other public lands in the region. The state of

California designated four "Areas of Special Biological Significance" within the study area in the

1970’s: Tomales Point, Point Reyes Headlands, Duxbury Reef, and Double Point. In 1990, under

implementation of the California Marine Life Protection Act, the California Department of Fish

and Game (CDFG) designated four marine protected areas within PORE boundaries, Point Reyes

Headlands, Drakes Estero, Limantour Estero and Duxbury Reef.

Because of its agricultural character, much of the coastline north of San Francisco Bay has

remained largely undeveloped, even prior to inclusion in the 1960’s and 70’s in PORE and

GOGA. The inaccessibility of much of the area has historically afforded some protection from

human disruption during seal terrestrial resting periods; however, most pinniped populations in

California are still recovering from a long period of exploitation that did not end until the

passage of the Marine Mammal Protection Act (MMPA; Public Law 92-522) in 1972. Prior to

the MMPA, Pacific harbor seals at PORE were likely disturbed by humans, as throughout their

range, and hunted extensively. Currently, disturbances are likely reduced from those earlier years

with protection provided by National Park status and enforcement of the MMPA. Nevertheless,

with over 2 million visitors to PORE and almost 14.5 million visitors to GOGA in 2008 (NPS

2008), human disturbances to seals do occur within the parks.

Exploitation through hunting was seen in all pinniped species in California, but with varying

long-term effects. Sea lions were hunted in California in the late 1800s for oil, hides, and

“trimmings” that were sold to Chinese markets (Scammon 1874); and were hunted by

commercial fisheries around 1900 to reduce competition for fish (Bonnot 1937). A bounty was

offered for Steller sea lions in the early 1900s in areas north of California (Rowley 1929; Bonnot

1931, 1951). Pacific harbor seals and California sea lions (Zalophus californianus) were hunted

with a bounty fee provided by the CDFG prior to the MMPA and sea lions were hunted for dog

food on the Channel Islands National Park until the 1960s.

Northern elephant seals were over-hunted to the verge of extinction for their blubber, used for

cooking and heating oil (Twiss and Reeves 1999). Scammon described northern elephant seals at

Point Reyes during early sealing voyages in the early 1800s, but by the late 1800s, the species

was extirpated from the region and nearly extinct (Scammon 1874; Allen et al. 1989; Le Boeuf

and Laws 1994). In the late 1800s, the northern elephant seals only occurred on Guadalupe

Island, Mexico. From that small colony of less than a few thousand animals, the population grew
2

to the current level of greater than 170,000 seals after receiving protection from the Mexican and

US governments. Guadalupe fur seals (Arctocephalus townsendi) were hunted for their fur and

currently are listed as a federally and state threatened species and breed on Guadalupe Island,

Mexico.

Harbor seals, California sea lions, northern fur seals (Callorhinus ursinus), and northern elephant

seals have increased in number and distribution at California rookeries over the past two decades

(Sydeman and Allen 1999; Pyle et al. 2001; Carretta et al. 2007). An exception is the Steller sea

lion, whose populations have declined sharply in California in just the last 20 years, and the

population from California to southeastern Alaska is currently classified as threatened under the

Endangered Species Act (ESA; Public Law 93-205; Sydeman and Allen 1999, Hastings and

Sydeman 2002). In California, the Steller sea lion population has slowly declined to about 1,500

individuals with less than 20 at PORE where they had historically bred up until the 1970s (Chan

1980; Sydeman and Allen 1999, Hastings and Sydeman 2002).

Six pinniped species occur in central California to breed, migrate through or rest onshore. The

five numerically dominant species that haul out and molt in the region include harbor seal,

northern elephant seal, California sea lion, northern fur seal, and Steller sea lion. Guadalupe fur

seals have been reported at PORE, although they occur only incidentally. The species that have

been documented breeding within the parks of the San Francisco Bay Area Inventory and

Monitoring Network (SFAN) include the harbor seal (GOGA and PORE) and northern elephant

seal (PORE).

Northern elephant seals breed and molt on islands and remote coastal locations from Baja

California, Mexico north to Point Reyes National Seashore (Figure 1). For most of the year,

northern elephant seals forage in the open ocean, and studies using satellite tags and time-depth

recorders have documented remarkable differences in where female and male northern elephant

seals spend that time. Males generally forage along the continental shelf north to at least Oregon

and often much further north and then west to the Aleutian Islands. Females on the other hand

forage in significantly deeper waters far to the west of the continental shelf (Figure 2).

Harbor seals inhabit the temperate and subarctic waters of the North Atlantic and the North

Pacific oceans. In the northeast Pacific, the Pacific harbor seal ranges from Cedros Island off of

Baja California, Mexico and north along the California, Oregon, Washington, and Canadian

coasts to the Gulf of Alaska, then west to the Aleutian Islands (Figure 2). Harbor seals occur

along the entire nearshore coast of California, but the larger haul-out and breeding colonies are

found in protected estuaries and at river mouths.

Other species (e.g., California sea lions) may breed in the future in the San Francisco region and

some species, particularly northern fur seals, likely dominated these coastal sites historically.

Tens of thousands of northern fur seals forage offshore in central California; however, in 1974, a

small group of fur seals recolonized the Farallon Islands, and the occurrence of fur seals at

PORE may increase in the future (Pyle et al. 2001). In 2003, one California sea lion pup was

born at PORE, and the breeding range of this species has been expanding north over the past

decade, now breeding on the Farallon Islands and Ano Nuevo Island in low numbers (NPS,

unpublished data; Sydeman and Allen 1999).
3

Figure 1. Northern elephant seal breeding and molting locations along the coast of western North

America (Carretta et al. 2007).
4

Figure 2. Map of the western coast of North America indicating northern elephant seal foraging areas.

Female elephant seals primarily forage far offshore in the North Pacific Gyre whereas male elephant

seals forage along the continental shelf. Pacific harbor seals occur along the entire nearshore coastal

area. (Image courtesy of Google Earth).

1.2 History of Monitoring

The CDFG, Minerals Management Service and National Marine Fisheries Service (NMFS) have

independently and collaboratively inventoried and monitored pinnipeds along the Pacific coast of

the continental United States since the 1920s (Bonnot 1928; Bonnell et al. 1983; Miller 1983;

Carretta et al. 2007); however, these studies were limited to aerial surveys, and did not include

ground-based monitoring. The monitoring protocols were developed over several decades by

NMFS and modified to regional conditions and requirements (Eberhardt et al.1979; Le Boeuf

and Laws 1994; Carretta et al. 2007). The regional design is based on the seasonal occurrence of

each species, the data required to assess population condition and the need to adaptively manage

the resource. The program limits the level of invasive methods to maintain low levels of
5

disturbance from research activities. In response to sporadic events, other monitoring may be

conducted and/or efforts shifted (i.e., mass stranding event, disease outbreak, storm damage, and

aberrant interactions among species/individuals).

For harbor seals and northern elephant seals, there are impressive time-series from PORE sites

(25+ years) and nation-wide (Sydeman and Allen 1999, Carretta et al. 2007). Researchers from

the University of California initiated ground-based surveys of harbor seals at PORE in

association with surveys in San Francisco Bay in the mid-1970s (Risebrough et al. 1978). In the

1980s, PRBO Conservation Science (PRBO) conducted an inventory of pinnipeds at PORE.

When northern elephant seals colonized PORE in 1981, PRBO began monitoring pinnipeds in

conjunction with their monitoring program on the Farallon Islands (Allen and Huber 1983, 1984;

Allen et al. 1989). A collective of volunteers from various organizations and agencies continued

monitoring pinnipeds at Point Reyes between 1990 and 1995. In 1995, the National Park Service

(NPS) initiated a standardized pinniped monitoring program (Allen 1995; Sydeman and Allen

1999).

Monitoring methods for northern elephant seals were adopted from existing regional monitoring

programs to allow for comparisons among sites and integration of data. Specifically, northern

elephant seal survey methods were based on those used by the NMFS on Channel Islands

National Park, the U.S. Fish and Wildlife Service on the Farallon Islands, and the University of

California at Santa Cruz at Año Nuevo (Le Boeuf and Laws 1994; Barlow et al. 1993; Sydeman

and Allen 1999). Survey methods over the years were modified as the PORE northern elephant

seal colony grew.

Between 1982 and 1985, researchers conducted a general inventory of pinnipeds in Point Reyes

(Allen and Huber 1983). Beginning in 1995, the park initiated weekly pinniped surveys at Point

Reyes Headlands. Surveys were timed to coincide with weekly surveys on the Southeast Farallon

Islands, to compare population trends of island versus mainland pinniped colonies (Sydeman and

Allen 1999).

In their study on the effects of marine climate variability on pinniped populations following

implementation of the MMPA, Sydeman and Allen (1999) analyzed population survey data from

the long-term monitoring programs (1973-1997) at the South Farallon Islands and PORE. They

found that California sea lions increased over the study period, with peak numbers observed

during and after major El Niño events, but the rate of increase appeared to have decreased in

later years. Steller sea lions decreased at the South Farallon Islands and remained depleted at

PORE. Harbor seal populations increased in a logistic and non-linear fashion at PORE and the

South Farallon Islands, respectively. Northern elephant seal abundance increased in a logistic

fashion over the study period at both the South Farallon Islands and PORE. The authors felt that

oceanographic relationships did not appear to confound interpretations of population recovery

since the MMPA for the species with increasing populations, and may help to explain declines in

the Steller sea lion population.

More recently, Allen et al. (2004) summarized PORE harbor seal data from 1997-2001. The fiveyear time period included data collected prior to, during, and three years following the 1998 El

Niño Southern Oscillation (ENSO) event. During this period, the harbor seal population
6

remained relatively stable. Annual maximum counts for the breeding season ranged between

2,481 and 3,506, and annual average counts ranged from 1,744.6 and 2,511.1 (range of SE =

122.5 to 379.0). The maximum numbers of adult/immature seals and pups were higher in 1997

and 2001 than those observed in 1998 (1998 Lambda = -0.46 and 2001 Lambda = +1.36)

coinciding with the El Niño year. Significantly fewer seals were breeding in 1998 during the El

Niño than in 1997 (-24%). Pup production was also lower (-46%).

From 2000-2008, Drakes Estero and Double Point annually produced the highest numbers of

harbor seal pups (Flynn et al. 2009). Taken together, these two sites produced 57% of the pups

observed in 2008 at PORE and GOGA. Overall, pup counts in 2008 bounced back from a lull in

2006 and 2007 (Figure 3). The authors speculate that this decline may have been related to

changes in marine conditions. Upwelling was much reduced in 2005 and 2006, resulting in

reduced krill production, which in turn may have affected food availability for harbor seals. A

lag effect from this reduced period of upwelling may be reflected in the lower breeding season

adult counts of all sites combined in 2008 (Figure 4). 1338 1232 1194 1233

1265

1106

954

903

1171

0

200

400

600

800

1000

1200

1400

1600

2000 2001 2002 2003 2004 2005 2006 2007 2008

Year

Number of pups

Figure 3. Maximum harbor seal pup counts for 2000–2008 at Marin County locations. The solid line on

the graph represents the mean of the maximum pup counts from 2000–2008 (1155.1), and the dashed

lines represent one standard deviation from the mean (143.9) (Flynn et al. 2009).
7

2576

2617

3272

3082

3622

28382860

2771

2499

0

500

1000

1500

2000

2500

3000

3500

4000

2000 2001 2002 2003 2004 2005 2006 2007 2008

Year

Number of harbor seals

Figure 4. Maximum counts of harbor seal adults and immatures during the breeding season (March-May)

at Marin County locations. The solid line on the graph represents the mean of the maximum adult counts

from 2000–2008 (2904.1), and the dashed lines represent one standard deviation from the mean (364.1)

(Flynn et al. 2009).

Regardless of year, most harbor seal disturbances have occurred at haul outs at Point Bonita,

Bolinas Lagoon, Drakes Estero, and Tomales Bay (Allen et al. 2004; Flynn et al. 2009). Harbor

seal response to disturbance ranged from a simple head alert to flush into the water. The highest

number of disturbances per hour occurred at Point Bonita in 2000, during which time the area

was heavily used for educational tide pooling. The haul out at Double Point also had elevated

disturbances in 2001 related to an aggressive male northern elephant seal. Bolinas Lagoon seals

experience elevated disturbance levels due to their proximity to Highway 1. During the 2008

pupping and molting season, 108 harbor seal disturbances resulting in a seal response were

recorded at PORE.

The PORE northern elephant seal population grew by almost 29% from 2005 to 2007 (Table 1;

Adams et al. 2007). Using a correction factor for animals at sea, the total population size was

estimated at 1,771 and 2,285 seals at PORE in 2005 and 2007, respectively. Almost 50% more

females were counted at North Drakes Beach (NDB) colony sites in 2006 (223) compared with

2005 (147). There also was a smaller increase of 20% at NDB in 2007 (272). The authors

suggest that hazardous coastal weather and tide conditions coinciding with the initial arrival of

females made NDB a more attractive colony site than the Point Reyes Headlands (PRH) colony

in 2006. The other colony sites, PRH and South Beach (SB), showed much smaller increases in

numbers of female seals (10% and 20% respectively) in 2006 and declines (-13% and -30%) in

2007, indicating the movement of seals from these sites to NDB.
8

Table 1. Point Reyes National Seashore northern elephant seal population and productivity counts for

2005–2007 breeding seasons at each colony site (adapted from Adams et al. 2007).

Season Colony

site1

Max #

of

females

Adjusted

max # of

females2

Max # of

pups plus

weaners

Breeding

population size

estimate4

Overall

population

estimate5

Productivity

index6

2005 PRH 384 408 320 677 1120 0.78

SB 29 30 28 73 98 0.93

NDB 147 166 158 322 553 0.95

 Total 560 604 506 1072 1771 0.84

2006 PRH 413 447 352 768 1232.0 0.79

SB 30 36 39 99 136.5 1.08

NDB 223 245 209 463 731.5 0.85

 Total 666 711 600 1330 2100 0.82

2007 PRH 362 387 377 809 1319 0.97

SB 24 25 24 70 84 0.96

NDB 272 293 252 551 882 0.86

 Total 658 705 653 1430 2285 0.93

1

 PRH=Point Reyes Headlands; SB=South Beach; NDB=North Drakes Beach. Census includes all sub-sites.

2

 The adjusted maximum includes the number of females counted 33 days prior and after the maximum count.

3

 The maximum count of pups plus weaners on a single census for each colony site.

4

 The maximum survey count of all seals.

5

 Based on pup count multiplier of 3.5.

6

 Maximum number of young divided by the adjusted maximum number of females.

Beginning in 1988, weaned northern elephant seal pups at all PORE sites were given a minimum

of one flipper tag; a second tag was applied, when possible. Individually numbered pink plastic

Dalton cattle ear tags (Jumbo roto tags) were applied to sleeping or resting seals. These tags were

chosen over the use of PIT (passive integrated transponder) tags for several reasons: the plastic

tags are 6-12 times less expensive, there are no battery operated devices necessary, and the

likelihood of northern elephant seals losing two flipper tags has been calculated to be 0.0031 for

both males and females (Filippo et al. 2000). The NMFS coordinates the national northern

elephant seal tagging program and assigned pink color tags for the PORE colony. NMFS assigns

unique color tags for each of the colonies so that movement between colonies and source

populations for new colonies can be identified. All marking of seals is conducted under a permit

from the NMFS issued to PRBO Conservation Science; current permit is no. 373-1868-00.

Until 1998, the number of weaned northern elephant seal pups tagged each year roughly

approximated the total number of pups surviving to weaning. Due to the high pup mortality and

reduced colony access during the 1998 El Niño storm events, only about 27% of the pups

produced were tagged. Between 1999 and 2004, approximately 55% to 94% of the pups

produced were tagged. Since 2005, the number of pups surviving to weaning has far surpassed

the number researchers were able to tag. The general goal, as outlined in the NMFS permit, is to

tag 200-300 weaned northern elephant seal pups each year. Opportunistically, some sub-adult

and adult male northern elephant seals are tagged and dye-marked to track movement of males

between breeding sites and to identify the alpha and beta males. Tag resighting is done in

conjunction with other research activities.
9

1.3 Pinniped Management

Managers at PORE and GOGA have developed an adaptive pinniped monitoring and

management program. A key focus to any adaptive management program is monitoring to detect

the effects of management actions. The monitoring program is structured to collect long-term

pinniped population data and identify shifts in distribution and haul out use patterns to protect

the species. Through disturbance monitoring, managers can determine if resource protection

measures are effective.

With northern elephant seal populations increasing within the San Francisco Bay Area, the NPS

has had to respond with increased monitoring and management. The northern elephant seal

colony at PORE has grown rapidly since 1981, with seals now using multiple breeding sites. In

response to the increase of seals and associated park visitor interactions, a northern elephant seal

management plan was initiated in 1995 to set guidelines for research, interpretation, and resource

protection measures and their enforcement (Allen 1995). The management plan outlines

management actions and programs for issues such as disturbance, conflicts with other sensitive

animals and plants, and safety for both the seals and the public. This plan replaces an earlier plan

for PORE on marine mammal management that recommended inventories and research (Ainley

et al. 1979).

PORE and GOGA have adaptively managed harbor seals based on the results of monitoring of

population numbers and annual productivity at several seal colonies. Harbor seal numbers have

changed at each site because of various stressors including predation by coyotes, human

disturbance and climatic events. The NPS and the Gulf of the Farallones National Marine

Sanctuary (GFNMS) have responded adaptively and collaboratively with different strategies for

management specifically related to reducing human disturbance at haul outs ranging from noaction to seasonal closures.

Additional past and current management strategies have included:

1) The initiation of a baseline study of disease in harbor seals in conjunction with The

Marine Mammal Center.

2) Annual restriction of kayaks and other watercraft in Drakes Estero during the

breeding season March 15 – June 30.

3) A study of the dispersal of weaned pups and feeding habits of harbor seals at Point

Reyes in collaboration with Moss Landing Marine Lab.

4) Proposed delineation of marine protected areas at Point Reyes to further protect seal

colonies.

5) A year-round public access closure to the tide pools at Point Bonita.

6) Educational opportunities to inform the public about pinnipeds and their sensitivity to

human activities, implemented in collaboration with the Marine Mammal Center and

the Gulf of the Farallones National Marine Sanctuary.

1.4 Rationale for Selecting this Resource to Monitor

SFAN is one of eight networks in the Pacific West Region (PWR) and one of 32 throughout the

NPS. The NPS National Inventory and Monitoring Program (I&M) in 1998 created “networks”

or groupings of parks in order to develop common methodologies for data comparability, to
10

reduce the level of effort, and to share resources. The units in the SFAN that encompass

resources utilized by pinnipeds (seals and sea lions) include PORE and GOGA. One other park

unit in the PWR has a pinniped monitoring protocol, Channel Islands National Park (DeMaster et

al. 1988).

In 1992, the NPS I&M Program developed a national policy “to better understand their dynamic

nature and condition” of natural resources, to detect or predict changes that may require

intervention, and to serve as reference points for more altered parts of the environment. By

integrating this information into NPS planning, management and decision-making, scientific

knowledge of natural resources will improve NPS stewardship of our heritage lands (NPS 1992).

Marine mammals, particularly pinnipeds, were selected by the SFAN to monitor and were

ranked as the 10th priority vital sign. The ecosystem conceptual models developed for the SFAN

include pinnipeds as an indicator of the marine ecosystem (Adams et al. 2006). Pinnipeds are one

of the few species that inhabit both marine and terrestrial ecosystems; they forage and travel in

the coastal waters of the parks but come onshore to rest, breed and molt. They reside in estuaries

such as Drakes Estero, in rocky intertidal zones such as Point Bonita, along pocket beaches in

wilderness areas such as Tomales Point, in research natural areas such as Point Reyes Headland

and on islands such as Alcatraz. Pinnipeds are sensitive to changes in the marine ecosystem and

respond quickly to changes in prey abundance and distribution, and to human disturbance (Allen

et al. 1985; Trillmich and Ono 1991; Thompson et al. 1998; Sydeman and Allen 1999;

Thompson and Miller 1990).

The pinniped assemblage was specifically selected for monitoring because:

1. Pinnipeds come under the legal mandates related to the Endangered Species Act

(1973) and Marine Mammal Protection Act (1972),

2. Marine mammals and their habitat are specifically identified in the general

management plan and management objectives of PORE.

3. The data collected under the pinniped monitoring program can be directly applied to

key management decisions, particularly in regards to the protection of breeding

pinnipeds (see 1.3 Pinniped Management).

4. Pinnipeds are good indicators of the condition of the marine ecosystem because they

respond quickly to oceanic conditions, and

5. There is a long history of monitoring pinnipeds at PORE and GOGA in collaboration

with other agencies and organizations.

Seals are also charismatic species that are of great interest to the public. Tens of thousands of

visitors come to the parks every year just to observe marine mammals, including seals.

General pinniped conservation concerns include effects of climate change, human disturbance,

oil spills, or fishing activities (operational and biological). Additionally, other important
11

concerns include natural and anthropogenically enhanced toxic blooms, preservation of haul out

habitats, biomagnified contaminants, and disease.

1.4.1 Legal Mandates

The NPS shares a mandate with National Oceanic and Atmospheric Administration (NOAA)

Fisheries to protect marine mammal populations. Several federal laws and executive orders

provide legal direction and support for expending funds to determine the condition of pinniped

populations in national parks:

x Coastal Zone Management Act (1972)

x Endangered Species Act (16 USCA 1531 et seq., 1973, amended in 1982)

x Executive Order 11900 (Protection of Wetlands)

x Fish and Wildlife Act (16 USCA 742a et seq., 1956)

x Fish and Wildlife Coordination Acts (16 USCA 661 et seq., 1958, 1980)

x Magnuson Fishery Conservation and Management Act (16 USCA 1801 et seq., 1977)

x Marine Mammal Protection Act (16 USCA 1361 et seq.; amended 1972 and 1994)

x Marine Protection, Research and Sanctuaries Act (33 USCA 1401 et seq., 16 USCA 1431

and 1431 et seq., 1972)

x Natural Resource Protection Act (1990)

x National Environmental Policy Act (PL 91-190 as amended 1969)

The National Parks Omnibus Act of 1998 includes a congressional mandate for national parks to

provide information on the long-term trends in the condition of their natural resources.

The ESA mandates the protection of all threatened, endangered, or candidate species as well as

their critical habitats within park boundaries. The MMPA supplements the ESA, providing

special protection for all marine mammals. MMPA states that it is unlawful to "harass, hunt,

capture or kill, or attempt to harass, hunt, capture or kill" marine mammals. The law places much

emphasis on protecting species and population stocks in danger of extinction or depletion above

a level (to be determined) at which they cease to be a significant functioning element of the

ecosystem. Particular emphasis was placed on protecting rookeries, mating grounds and areas of

similar significance. NMFS (1994) proposed guidelines on closest approach distances to avoid

disturbing marine mammals.

1.4.2 Enabling Legislation

In 1972, GOGA was authorized by Congress as an NPS unit (Public Law 92-589). The enabling

legislation of the park stated that the new park’s purpose was, "to preserve for public use and

enjoyment certain areas on Marin and San Francisco Counties, California, possessing

outstanding natural, historic, scenic, and recreational values..."

In September 1962, PORE was authorized by Congress as a unit of the National Park Service

(Public Law 87-657) and was officially established in October 1972 (Public Law 92-589). The

statement of purpose for the park in this law calls for the preservation and protection of the

diminishing seashore of the United States for "public recreation, benefit and inspiration."
12

The Wilderness Act of 1976 (Public Law 95-544) established 25,370 acres of Wilderness and

8,003 acres of potential wilderness in PORE, thereby adding special protection. The Wilderness

Act also amended the PORE enabling legislation (Public Law 87-657) to include:

“...without impairment of natural values, in a manner which provides for such

recreational, educational, historic preservation, interpretation, and scientific research

opportunities as are consistent with, based upon, and supportive of the maximum

protection, restoration, and preservation of the natural environment within the area.”

A primary objective of resource management stated in the PORE General Management Plan

(NPS 1980) is "to protect marine mammals...and other sensitive resources found within the

Seashore. The revised PORE Statement of Management (NPS 1993) specified several natural

resource management objectives including, but not limited to:

“To identify, protect and perpetuate the diversity of existing ecosystems which are found

at Point Reyes National Seashore and are representative of the California seacoast.”

“To enhance knowledge and expertise of ecosystem management through research and

experimentation programs relating to wildlife,... regulation and control of resource use,

and pollution control.”

As noted in the 1993 PORE Statement for Management, the enabling legislation “affects

seashore management in the ocean shore areas by: 1) requiring personnel and funding to monitor

populations and activities within the Seashore; 2) generating meetings and discussions and action

plan coordination between different agencies and organizations; 3) suggesting the inclusion of

information in interpretive programs and handouts; and 4) requiring the fabrication and

installation of regulatory and informational signs.”

The 1999 GOGA Resources Management Plan identifies the need to monitor and protect natural

resources and the ecosystems upon which they depend (NPS 1999). This plan highlights threats

and challenges from GOGA’s location at the urban interface of the San Francisco Bay Area, with

a regional population of over eight million people. “This Natural Resources Management Plan

identifies GOGA’s natural resources and their condition. It describes a program to preserve,

monitor, maintain, and restore, where necessary, the natural California habitats, and ecosystems

on which they depend. The ever-growing metropolitan population adjacent to these natural areas

exerts a great pressure to over-utilize the fragile natural systems that remain. This plan identifies

these pressures and provides strategies for protecting the natural systems and resources (NPS

1999).”

1.4.3 Indicator of Ecosystem Condition

Pinnipeds are apex predators of the marine ecosystem, and numerous dynamic processes

interacting together have the potential to affect their abundance, species composition and

distribution. The collective knowledge gained about the recovery of pinnipeds since passage of

MMPA has been possible due to long-term monitoring programs that provide information at

temporal and spatial scales and that allow accurate interpretation of measured trends and

responses to environmental change. Information gained at PORE and GOGA contributes to
13

predicting how recovered or disappearing populations will influence the ecosystem structure and

productivity of this region.

Analysis of the monitoring data collected through this program will allow changes in pinniped

abundance, species composition, distribution, and phenology to be detected. These changes may

be influenced by a combination of variables such as changes in food supply, disease, pollution,

disturbance by park visitors (commercial and recreational users), interspecies interactions, or

environmental factors on multiple scales from localized storm events to decadal shifts in climate

(Allen et al. 1985; Harvey 1990; Francis and Hare 1994; Pettee 1999; Sydeman and Allen 1999;

Sholin et al. 2000; Dierauf and Gulland 2001; Edwards and Richardson 2004; Keiper et al. 2005;

Neale et al. 2005; Womble and Sigler 2006; Laidre et al. 2008; Ragen et al. 2008). Additional

research and data analysis involving data collected outside this monitoring program (e.g., climate

data) will be needed to determine some of these effects.

Pinniped monitoring has applications and links to other monitoring programs conducted by

SFAN, parks, and other agencies. Incorporating data and analyses from these other programs

may help in the interpretation of changes in pinniped populations observed through the SFAN

pinniped monitoring program. Many of these other monitoring programs target pinniped prey

species, but also long-term trends in climate change and ocean conditions. SFAN supports a

stream fish assemblage vital sign monitoring program, which includes collecting fish

productivity data on salmonids (seal prey) at Lagunitas, Redwood, Pine Gulch, and Olema

Creeks. Lagunitas Creek and Olema Creek flow into Tomales Bay, whereas Pine Gulch Creek

flows into Bolinas Lagoon, both of which are estuaries monitored for harbor seals. CDFG

conducts annual Pacific herring population assessment and manages herring stocks in Tomales

Bay and San Francisco Bay. NMFS and CDFG, through the Nearshore Fishery Management

Plan, collect productivity and stock assessments for rockfish and other nearshore groundfish.

Through a multi-agency partnership, the Central and Northern California Ocean Observing

System (CeNCOOS) collects and provides regional information on ocean conditions and water

quality.

At a regional scale, long-term studies can also help interpret potential population responses to

management strategies. Bolinas Lagoon is rapidly changing in shape due to siltation, which

alters haul out space and prey availability. Fisheries management by state and federal agencies

has altered activities in the region with preliminary designation of Marine Protected Areas

(MPA) by the CDFG and with restrictions on gillnetting, trawling and take of certain species of

rockfish. New studies in Tomales Bay are illuminating concerns of contamination from the

Gambonini mercury mine and land use changes (U.S. Environmental Protection Agency,

administrative history).

1.5 Measurable Objectives

Based on past monitoring, pinniped breeding populations within the SFAN appear to be at a

stable or increasing state in terms of abundance and productivity. While those two parameters are

the easiest to monitor and have been selected as the primary metrics for monitoring objectives,

other questions remain regarding the overall long-term viability of populations. In particular,

managers need to understand the potential effects of natural and anthropogenic factors that range

from loss of breeding and molting habitat due to sea level rise and global climate change, El
14

Niño events, increasing recreation and commercial activity around haul outs, and disease

transmission.

1.5.1 Monitoring Questions

In the SFAN Vital Signs Monitoring Plan (Adams et al. 2006), specific monitoring questions

were identified for pinnipeds. They include:

x What are the status and trends of the population size and distribution of pinniped

assemblage?

x What is the natural level of variation in the pinniped population size and productivity?

x Are northern elephant seals and harbor seals reproducing successfully?

x How do natural and anthropogenic disturbances affect seal haul out use and productivity?

x Are there long-term trends in the phenology of pupping and molting by pinnipeds at

SFAN?

The above monitoring questions are central to the SFAN Pinniped Monitoring Program, but as

mentioned above, other questions exist related to pinnipeds such as prey availability, dispersal,

effects of pollution, effects of disease and survivorship. Some of these other questions have been,

or are being, pursued by university research projects regionally and at PORE and are investigated

at larger spatial scales than is possible for the SFAN monitoring program.

1.5.2 Monitoring Objectives

Monitoring of pinnipeds will address the overall goals and objectives for vital signs monitoring

as described in the SFAN Monitoring Plan (Adams et al. 2006). There are several critical

sampling design criteria that will allow for the program to meet the monitoring objectives: 1) the

survey frequency captures the normal range of variability during the season of importance (i.e.,

breeding and molt); 2) the survey frequency captures the population maximum during the season

of importance (i.e., breeding and molt); 3) all primary survey sites are included in the analyses;

4) the survey frequency captures the potential effects of natural and anthropogenic stressors; and

5) observers receive consistent training to avoid observer biases in data collection and reporting

(For more explanation, see Elzinga et al. 1998). These criteria are addressed in Section 2.0

Sampling Design of this protocol.

The specific monitoring objectives of the Pinniped Long-Term Monitoring Program are to:

1a. Determine the long-term trends in population size and seasonal distribution of harbor seal

populations at primary sites in the SFAN parks during the breeding and molt seasons.

1b. Determine the long-term trends in population size and seasonal distribution of breeding

northern elephant seal populations at SFAN parks as measured by counts of adult females.

1c. Determine the long-term trends in annual population size and seasonal distribution of

other pinniped populations at SFAN parks.

Understanding the abundance and distribution of pinnipeds during different haul out

periods (pupping/breeding, molting, juvenile haul out) is vital to managing SFAN
15

beaches and intertidal areas where pinniped haul out sites occur. This objective also

supports the next two monitoring objectives, both of which focus on the critical pupping

and breeding season. Changes in pinniped use (abundance and distribution) of SFAN

haul outs can inform interpretation of long-term trends seen in reproductive success and

disturbance levels.

2a. Determine long-term trends in reproductive success of harbor seals through annual

estimates of pup production at PORE and GOGA.

2b. Determine long-term trends in reproductive success of northern elephant seals through

annual estimates of pup production at PORE.

The long-term reproductive success of pinnipeds in the SFAN is a key metric to

determining the overall status of each species within its SFAN habitat.

3. Determine the long-term trends in sources, frequency and level of effects of natural and

anthropogenic disturbances on harbor seal haul out use and productivity.

Harbor seals are sensitive to disturbance. Disturbance at haul out sites can negatively

affect reproductive success and reduce or eliminate harbor seal use of specific haul outs.

Past monitoring has indicated problems with anthropogenic disturbances at harbor seal

haul out areas, and management actions have been applied. The MMPA restricts

harassment or disturbance of pinnipeds, therefore the monitoring plan involves

observation and recording of incidental or intentional disturbance of pinnipeds.

1.5.3 Management Objectives

The overall management objectives, as defined in the SFAN Monitoring Plan (Adams et al.

2006), that relate to marine mammals:

Golden Gate

National

Recreation Area

x Maintain and restore the character of natural environmental lands by

maintaining the diversity of native park plant and animal life,

identifying and protecting threatened and endangered species,

marine mammals, and other sensitive natural resources, controlling

exotic plants and checking erosion whenever feasible.

Point Reyes

National Seashore

x Identify, protect, and perpetuate the diversity of existing ecosystems,

which are representative of the California seacoast.

x Preserve and manage wilderness.

x Protect marine mammals, threatened and endangered species, and

other sensitive natural resources found within the seashore.

x Retain research natural area status for the Estero de Limantour and

the Point Reyes Headlands.
16

x Manage seashore activities in the pastoral and estuarine areas in a

manner compatible with resource carrying capacity.

x Enhance knowledge and expertise of ecosystem management

through research and experimental programs that provide sound

scientific information to guide management relating to wildlife,

prescribed burning techniques, exotic plant and animal reduction,

regulation and control of resource use, and pollution control.

x Monitor mariculture operations, in particular, the oyster farm

operation in Drakes Estero, in cooperation with the CDFG.

Specific management objectives fall into two categories: threshold/target objectives and

condition/trend objectives (Elzinga et al. 1998). These management objectives vary by species

and meet certain assumptions regarding the inherent variability of the data.

The threshold/target management objectives for the pinniped assemblage are as follows:

x Detect any change in the number of primary colony sites of harbor seals between years.

x Detect any change in the number and distribution of breeding/molting sites of northern

elephant seals between years.

x Detect any new breeding sites of Steller or California sea lions between years.

x Determine changes in the type (i.e. cause) and magnitude of harbor seal disturbances at

haul out sites annually during the breeding and molting season.

x Detect mass stranding of any marine mammal species within a year (see NMFS website

http://www.nmfs.noaa.gov/pr/health/ for details)

The condition/trend management objectives for the pinniped assemblage are as follows:

x Detect a 36% decline in harbor seal pup production at six sites over four years.

x Detect a 27% decline in harbor seal abundance at six sites over three years.

x Detect a 41% decline in northern elephant seal pup production over five years.

x Detect a 46% increase in northern elephant seal pup production over four years.

x Detect a 36% decline in the abundance of northern elephant seal cows over four years.

x Detect a 33% increase in the abundance of northern elephant seal cows over three years.

These trend thresholds for harbor seal and northern elephant seal monitoring reflect the results of

power analyses of the long-term NPS pinniped data (see Section 2.5). The threshold levels

represent the number of years to detect 10% compounded annual changes with greater than 80%

power. A 10% annual decline over four years therefore represents a 35% cumulative decline. The

power analyses indicate that our current monitoring design has the ability to detect significant

population changes in short periods of time, thus allowing for timely, reactive management

actions if warranted.

A management action might be initiated if any of the above threshold/target or condition/trend

objectives are realized. For example, if a new northern elephant seal colony forms in a given

year, the parks would close the area to the public in order to protect female seals and pups from
17

human disturbance and exposure to dogs. Monitoring the type and magnitude of northern

elephant seal expansion into recreation areas such as Limantour Beach or endangered species

habitat such as western snowy plover (Charadrius alexandrinus nivosus) critical habitat, will

provide early warning to managers that these situations are occurring and allow for more

informed management decisions. In many cases, the management response to declines that are

greater than the threshold levels would be to initiate further research to better understand the

factors involved. High levels of disturbance at any site might trigger management actions to

reduce the disturbance levels, where appropriate. In the past, these management actions have

included increased outreach, and seasonal or permanent closure of sites.

1.5.4 Currently Funded Monitoring Objectives

In 2007, the SFAN Board of Directors, with guidance from the SFAN Technical Steering

Committee, approved funding for the pinniped monitoring program that would not allow the

program to meet all the monitoring objectives. Based on these funding limitations, a decision

was made to focus the SFAN pinniped monitoring on harbor seals. As such, funding is currently

limited to only meet the following monitoring objectives related to harbor seals:

1a. Determine the long-term trends in population size and seasonal distribution of harbor seal

populations at primary sites in the SFAN parks during the breeding and molt seasons.

2a. Determine long-term trends in reproductive success of harbor seals through annual

estimates of pup production at PORE and GOGA.

3. Determine the long-term trends in sources, frequency and level of effects of natural and

anthropogenic disturbances on harbor seal haul out use and productivity.

PORE will continue the northern elephant seal monitoring program to the greatest extent

possible using volunteers under the direction of the PORE Science Advisor. The SFAN I&M

program will continue to offer data management support for the program and may be able to reinstate funding for the program in the future. For these reasons, sample design, field methods,

and data management specifications for northern elephant seal monitoring are described within

this protocol and associated SOPs in full detail.

19

2.0 Sampling Design

2.1 Rationale for Selecting this Sampling Design

The primary focal species of the monitoring program are harbor seals and northern elephant

seals, during their respective breeding seasons. Ancillary data on other pinniped species are

collected concurrently, but are not the primary targets of this monitoring protocol.

Due to the regional and national interest in the health and protection of marine mammals, many

pinniped monitoring programs exist along the Pacific Coast. The sample design and methods for

this program were developed so that the data could be integrated with other regional surveys,

allowing for the results to be interpreted in a regional context. PORE and GOGA participate in

regional harbor seal breeding season surveys in collaboration with several other agencies and

groups, with the PORE Science Advisor as the coordinator for the surveys. PORE also annually

exchanges northern elephant seal breeding season data with other northern elephant seal

researchers in California and with NOAA Fisheries.

Harbor seals do not make extensive migrations, are susceptible to disturbance, and regularly use

haul out areas throughout the year. Disturbances can affect harbor seal use of SFAN parks, so

disturbance levels have been a key metric to monitor for park managers. The parks have engaged

volunteers in monitoring activities, particularly with harbor seals, because the methods are

relatively easy, there is strong local interest in marine mammals, and there is cost efficiency. The

harbor seal monitoring program is a long-standing program and has the added benefit of visitor

education and enhanced park stewardship through volunteer appreciation and participation.

Northern elephant seals are a wide-ranging species, migrating twice a year annually to pelagic

and continental shelf feeding grounds in Alaska and north of Hawaii, and only spending breeding

and molting seasons, and the fall onshore. Given the broad spatial component to the northern

elephant seal life history and limited monitoring resources, it is important for any monitoring

program to monitor at the spatial and temporal scale at which management actions can have an

effect. Seasonal visitor and beach management of current and potential northern elephant seal

breeding and molting beaches is dependent on data gathered through the long-term monitoring

program.

The current population size and distribution of the harbor seal and northern elephant seal

breeding populations are at a level allowing surveyors to complete timely censuses of all

breeding sites. Thus, spatial stratification or other sampling techniques were not needed to decide

which haul outs to include for monitoring. Survey frequencies and timing capture the beginning

of the breeding season, the peak of the breeding and molting seasons, and have been shown to

have sufficient ability to detect meaningful population changes over time (see Section 2.5).

The sampling design is outlined below and presented in greater detail in the standard operating

procedures (SOPs). If the pinniped populations expand in number and space beyond the current

capacity to census all the animals, the sample design will be reviewed and revised.
20

2.1.1 Parameters Monitored

Reproductive Success: The productivity or reproductive success of a population can be measured

and defined in several ways. At SFAN sites, the most accurate data that can be collected without

disturbance is direct ground counts of pups and females at haul out sites. Using appropriate

correction factors applied to counts of female seals and pups, an index of reproductive success

can be calculated annually by site for harbor seals and northern elephant seals (Eberhardt et al.

1979; Le Boeuf and Laws 1994; Sydeman and Allen 1999; Harvey and Goley 2005; Carretta et

al. 2007). Data are also collected on the week of first pup, the week of the peak pup count, pup

mortality, survivorship to weaning, and lifetime pup production of marked females (Eberhardt et

al. 1979; Huber et al.1985; DeMaster et al. 1988; Sydeman and Allen 1999). Measuring

reproductive success provides important demographic information on understanding pinniped

populations. Reproductive success is strongly associated with population size. In addition,

reproductive success provides additional information above and beyond population counts. For

example, human disturbance at a haul out may be at a level that does not cause the seals to

abandon the site, but may be causing the seals at the site to have reduced reproductive success.

Population Size: Population size is an important parameter to measure, as it shows whether the

population is growing, stable or declining. Assessing the total number of individuals is complex,

given pinniped natural history and vulnerability to disturbance. Not all individuals are hauled-out

and visible at one time, making complete direct counts sometimes impossible. NMFS develops

regional correction factors to account for this problem in assessing population size. Common

methods for censusing pinnipeds include direct counts of a population subsample (e.g., during

the breeding season) or index from ground/boat/aerial observations and mark-recapture methods

to estimate population size (Eberhardt et al. 1979). Standard protocols have been used by the

NMFS for decades to conduct population stock assessments and are the basis for protocol

development on the Channel Islands (DeMaster et al. 1988) and at the Farallon Islands (Sydeman

and Allen 1999), PORE (Allen and Huber 1983; Allen et al.1989; Allen Miller 1988; Sydeman

and Allen 1999), and SFAN.

An index of regional population status at PORE and GOGA based upon the number of

individuals, by age class and gender, if possible, is quantified annually for each species. Status of

northern and Guadalupe fur seals are represented in strandings, as they do not haul out regularly

on coastal beaches at this time. The proportion of the entire “stock”, as determined by NMFS

stock assessments, that utilize SFAN habitats can then be evaluated, and management and

program resource allocation wisely directed (DeMaster et al. 1988; Barlow et al. 1993; Lowry et

al. 2005).

Distribution: Due to inaccessibility of many coastal sites for pinnipeds, shifts in breeding and

non-breeding habitats can go undocumented without regular surveys (Carretta et al. 2007). In

addition to tracking range shifts for protection, these shifts also contribute to our understanding

of how populations contract and expand in response to environmental change or disturbance.

Haul out sites are documented annually, and mapped periodically, to assist in assessing shifts in

distribution. Shifts to new areas within or adjacent to primary monitoring sites are easily detected

by observers through regular monitoring. SFAN is reliant upon other monitoring, for example

GFNMS Beach Watch program or CDFG aerial surveys, and reports from park visitors,

including boaters, kayakers and an avid birding community, to locate new haul outs in remote

areas of the parks.
21

Phenology: Tracking the changes in the timing of seasonal activities of plant and animal species

can provide information on species’ responses to seasonal and climatic changes in the

environment (Visser and Both 2005; Moore 2008). In marine mammals, cyclic events such as the

first arrival and departure dates during the breeding and molt seasons, the birth of the first pup,

and the date of peak pup numbers can be related to seasonal and climatic changes seen and

measured on a broader scale (Laidre et al. 2008). The frequency and timing of our pinniped

censuses is designed to track seasonal arrival, departure, molt, birth of first pup, and peak pup

numbers at each study site.

Disturbance Data: Disturbance data are collected for both natural and anthropogenic disturbances

at haul outs. Observers note potential and actual disturbance sources (e.g., human, dog, cattle,

other) to pinniped colonies or haul out sites. The data recorded include the disturbance source,

time, and effect. The effect is noted as the behavioral response of the seals and the number of

seals that are disturbed. As mandated by NMFS under permit number 373-1868, the NPS is

required to record disturbance events caused by researchers during the course of monitoring

pinnipeds. These data are currently collected routinely during all surveys and submitted with the

annual report to the NMFS.

2.2 Study Area and Site Selection

The coastal topography of PORE is diverse and complex, including long stretches of sandy

beaches, offshore islands, rocky intertidal areas, steep cliff-backed pocket beaches, and bays and

estuaries. Significant and extensive sandy beaches include RCA Beach, Wildcat Beach, Drakes

Beach, the sandspit of Limantour Estero, and Point Reyes Beach. Point Reyes Headlands

encompasses a series of pocket beaches, as does the shoreline extending from Palomarin to Bear

Valley. Pinnipeds use both terrestrial and marine habitats of PORE. Haul out and pupping sites

occur throughout the park, but are limited mostly to remote beaches, estuaries, or rocky

shorelines.

GOGA also has complex topography and is a long, narrow, fragmented park surrounding the

mouth of one of the largest estuaries and ports in the United States. Pinnipeds at GOGA are

limited to haul out sites on islands within San Francisco Bay, including Alcatraz Island, and at

rocky intertidal habitats around Point Bonita, Muir Beach and Seal Rock near the mouth of the

Bay. GOGA is in the process of acquiring additional coastal properties in San Mateo County that

include pinniped haul out sites. Once these properties are acquired, SFAN and GOGA will

determine how to incorporate these sites into the monitoring program.

Primary monitoring sites include the dominant harbor seal and northern elephant seal pupping

and breeding sites within PORE and GOGA. Secondary sites do not have a large and consistent

occurrence of seals during the breeding season, due to habitat availability or other characteristics,

such as high recreation levels (e.g., Ocean Beach at GOGA, Bolinas Point at PORE). Secondary

sites, for example, include the rocky coastline of GOGA between Stinson Beach and Muir Beach

where a handful of harbor seals occur at any given time of the year. For northern elephant seals,

secondary sites include the beaches distant from the Point Reyes Headlands where sub-adult

males may come ashore to temporarily rest during the breeding season. Northern elephant seal

females and pups do not occur at secondary sites. The pinniped monitoring is focused on and
22

designed in regards to primary sites, although data and information from secondary sites may be

collected opportunistically or in regards to management considerations.

2.3 Sampling Frequency

2.3.1 Harbor Seal Monitoring

Shore-based harbor seal surveys are conducted a minimum of twice per week at each site during

the breeding and molting seasons, which run from March 1 to June 1 and June 1 to July 31,

respectively. Volunteers and park biologists survey each site, weather and logistics permitting.

Each survey lasts two hours, if possible, with seal counts occurring every half-hour. Each subsite

is surveyed separately, comprising a grand total for the site on each half-hour count. Regional

surveys are coordinated with other monitoring organizations outside of the study area and occur

bi-weekly during a five day window (Thursday - Monday) between March 1 and July 31. See

SOP 1: Harbor Seal Surveys for additional information.

Factors that might cause variation in the number of seals counted are time of day, tide height,

time of year and number of seals that are in the water at the time of the count (Harvey 1990;

Frost et al. 1999; Ver Hoef and Frost 2003). Therefore, in an effort to rule out some of these

covariates, regardless of season, surveys target low to medium tides (ideally +2.0ft tide or less)

between 10:00 and 16:00; the time when the maximum number of seals haul out in the San

Francisco Bay region (Risebrough et al. 1978; Fancher 1979; Allen and Huber 1984; Stewart and

Yochem 1984; Allen et al. 1989; Grigg et al. 2002).

The survey frequency described above and used in the past are sufficient to capture the peak pup

and total population counts necessary to estimate the population size and productivity at each

site. The surveys begin prior to the start of the pupping season to capture the date of first pup to

track phenology and to begin disturbance monitoring during this critical period. Disturbance

monitoring is done concurrently with the seal population monitoring. All disturbances and

potential disturbances that occur during the survey period are recorded.

2.3.2 Northern Elephant Seal Monitoring

The survey period for the breeding season extends from December 1 to March 31. Surveys for

population size, distribution, productivity, and phenology are conducted a minimum of two times

weekly at all sites during the peak breeding season. This frequency is warranted to capture the

maximum counts and changes in phenology. One count is conducted per survey, with surveys

typically done on the same days each week (i.e., Tuesday and Friday), but that schedule is

weather dependent.

In addition, during the breeding season, since adult females remain in the same location for at

least one month, tags are resighted at each site once every two weeks at minimum. While a more

frequent tag resighting effort would be desirable to assure that the surveyors are capturing the

majority of the tagged animals, factors such as beach access, weather, safety, and limited

personnel availability, must be considered.
23

2.4 Number and Location of Sample Sites

All sites where seal breeding occurs within SFAN parks are included in the current study design.

If seal populations increase in size or distribution, the sample design may need to be reviewed

and number of sites modified.

2.4.1 Harbor Seal Study Sites

The topographic diversity of this coastal zone provides a broad range of substrates upon which

harbor seals haul out: tidal mud flats, rocky intertidal areas, offshore tidal ledges, and sandy

beaches.

There are eight primary monitoring sites: Double Point, Drakes Estero, Tomales Point, Tomales

Bay, Point Reyes Headlands, Bolinas Lagoon, Point Bonita, and Duxbury Reef (Figure 5). Most

sites are in PORE, while Bolinas Lagoon and Point Bonita are in GOGA. Duxbury Reef is

located within Agate Beach (Marin) County Park and adjacent to PORE. These sites are

surveyed during the pupping/breeding and molting season. Additional harbor seal data is

collected during northern elephant seal surveys and park-based “all species” surveys of the Point

Reyes Headlands (see Section 4.2). Counts of harbor seals at Alcatraz Island (GOGA) by park

staff and volunteers have an irregular history. In recent years, however, the data has been

consistent enough to include in regional summaries of harbor seal data.

2.4.2 Northern Elephant Seal Study Sites

There are three main survey sites (Figure 6), all at PORE: Point Reyes Headlands (PRH), North

Drakes Beach (NDB), and South Beach (SB). There are seven subsites at PRH (see SOP 2:

Northern Elephant Seal Surveys): Cove 1, Cove 2, Cove 3, Cove 4, Tip, Loser Beach, and Dead

Seal Beach. There are four subsites at NDB: North Drakes Beach, Lifeboat Station, Gus’ Cove,

and Chimney Rock Cove. At South Beach, there are three subsites: Lighthouse Beach, Nunes

Beach, and Mendoza Beach. Incidental observations occur at other sites including Double Point,

Abbott’s Lagoon, and Point Bonita.
24

Figure 5. Harbor seal haul out monitoring locations within Point Reyes National Seashore and Golden

Gate National Recreation Area.
25

Figure 6. Northern elephant seal monitoring locations at Point Reyes National Seashore.
26

2.5 Level of Change That Can Be Detected

2.5.1 Harbor Seal Population Monitoring

A power analysis was completed for the harbor seal monitoring program based on data collected

from 2000 to 2008 (Appendix A). The analysis was designed to estimate the likelihood that the

existing monitoring program will detect a 25% or 50% decline at individual colonies, and the

number of years it would take to detect a 10% annual compounded decline for the six major

colonies as a group, excluding Duxbury Reef and Point Bonita. The analysis used maximum

counts for adults and pups from surveys during the pupping season for 8 colonies from north to

south: Tomales Bay, Tomales Point, Point Reyes Headlands, Drakes Estero, Double Point,

Duxbury Reef, Bolinas Lagoon, and Point Bonita. Because Duxbury Reef and Point Bonita are

mainly molting sites with few pups, molting season maximum count data was used for this

analysis.

All of the six pupping sites had an 80% chance of detecting a 50% decline in adults at any one

colony within 2-5 years, not including the base year. Detecting an overall 25% decline in adults

would always take at least 14 years, not including base year. 50% declines of pups at each of the

six pupping sites could be detected in 2-7 years, and 25% declines for pups would always take at

least 14 years, except for at Bolinas Lagoon, which would only take 4 years. Tomales Bay and

Bolinas Lagoon had the lowest coefficient of variation.

Power was generally higher for both adults and pups for the six major SFAN pupping sites

pooled (excluding Duxbury Reef and Point Bonita). Current monitoring effort had a 90% chance

of detecting a 27% decline in overall population counts over 3 years. For pups, an 88% chance of

detecting a 36% decline would be realized after 4 years. Thus, after only three years of

monitoring (not including the baseline year) the current program is very likely to detect ~25%

declines in both adults and pups.

Based on these results, the harbor seal monitoring program will focus on detecting a 10% annual

decline (total 27%) of adults in the six major SFAN pupping sites pooled over a period of 3

years. For pups, the focus will be on a 10% annul decline (total 36%) over 4 years. Power for

detecting these trends is 90% for adults and 88% for pups. Colony-specific declines, which take

longer to detect, will be explored at intervals consistent with the results of the power analysis.

The sites not included in the pooled analysis, Duxbury Reef and Point Bonita (low number of

pups each year, with less intercount variance during the molting season), will continue to be

surveyed because of the high disturbance levels at these sites and the need to acquire information

for management even if trend analyses are not possible.

2.5.2 Northern Elephant Seal Population Monitoring

A power analysis was completed for the elephant seal monitoring program based on data

collected from 1998 to 2009 (Appendix B). The analysis was designed to estimate the likelihood

that the existing monitoring program will detect a 25 or 50% decline at individual colonies, and

the number of years it would take to detect a 10% annual compounded decline or increase for

total maximum count. The analysis used maximum counts for adult cows and pups+weaners

from surveys during the breeding season were compiled from 1998 – 2009 for Point Reyes

Headlands, South Beach, and North Drakes Beach, as well as the maximum count day for all

colonies.
27

For cows, Point Reyes Headlands had an 80% chance of detecting a 50% decline in only 2 years,

as well as the population as a whole. However, North Drakes Beach and South Beach would take

8-9 years to detect a 50% decline. Detecting an overall 25% decline in adults would always take

at least 7 years for the population pooled. 50% declines in pups pooled could be detected in 2

years, and 25% declines for pups would take at least 12 years to detect.

For all sites combined, monitoring effort had an 86% chance of detecting a 36% decline in cows

over 4 years. For pups, an 83% chance of detecting a 41% decline would be realized after 5

years. Increases were easier to detect, generally having 0.1 - 0.2 higher power. Thus, after only

4-5 years of monitoring (not including the baseline year) the current program is very likely to

detect 36-41% declines or increases in both adult cows and pups.

29

3.0 Field Methods

3.1 Site Access

Most sites are accessed via trails from park roads. Counting locations are typically off trail and

not in public access areas or in view of the public. The exceptions are North Drakes Beach,

Duxbury Reef, Point Bonita, and Bolinas Lagoon, which are in public access areas. When

observers are in closed areas, such as seal pupping beaches, the park dispatch is notified via radio

of their presence and likely duration of activities. When possible, temporary signs are posted to

alert the public to the official research activities occurring within closed areas. See SOP 1:

Harbor Seal Surveys and SOP 2: Northern Elephant Seal Surveys for maps of sub-sites and

counting locations.

3.2 Harbor Seal Monitoring

3.2.1 Field Season Preparation and Equipment Setup

The field season preparations for the harbor seal monitoring program focus on volunteer

recruitment, training, and coordination. Each year, volunteer recruitment is started in the fall

with advertisements on NPS websites, in local Bay Area newspapers, and in environmental

organization newsletters. Training sessions are scheduled in October for February and March,

and include two-half day classroom sessions, typically in the PORE Red Barn classroom, and

field visits to each survey site. In 2006, a mentor program was established for beginner surveyors

to work on survey skills with long-term volunteers. See SOP 1: Harbor Seal Surveys, for more

details.

3.2.2 Details of Taking Measurements

Population data: Shore-based surveys are conducted from standardized observation points using

binoculars and/or spotting scope. Direct counts of all harbor seals present at sub-sites within a

monitoring location occur from March 1 to July 31. Pups may be identified and are counted

separately from March 1 to May 31. Trained volunteers and park biologists conduct surveys.

This program is currently dependent on an extensive volunteer program. To maintain data quality

and standardization, volunteers are trained by park biologists and surveys coordinated by a

volunteer coordinator. See SOP 1 for training documentation, data forms and monitoring field

methods.

Tagging: Tagging of harbor seals is not a primary task of the monitoring program. However, on

occasion, project staff do assist with tagging efforts by researchers affiliated with universities

and other agencies.

Resighting Tags: The monitoring project does not actively tag or track tagged harbor seals.

However, tagged harbor seals that are incidentally observed during surveys are recorded and the

appropriate research program is notified.

Disturbance data: These data involve the number of potential and actual disturbance sources

(e.g., human, dog, cattle, other) and include both natural and anthropogenic disturbances. For

each potential or actual disturbance, observers record the source, time, and effect of activity,

including the behavioral response of the seals and the number of seals affected. Harbor seals are
30

very reactive to human activities and will flush into the water when disturbed (Allen et al. 1985).

If disturbances are chronic, seals will alter haul out patterns, shifting to nighttime haul out or

abandoning sites completely (Grigg et al. 2002).

Environmental data: Weather data is collected during surveys to provide information on visibility

(fog), precipitation, and wind speed. These three parameters can affect the presence or visibility

of seals. Climate data include ENSO events, La Niña events, North Atlantic Decadal Oscillation,

and Pacific Decadal Oscillation and can help interpret the reproductive results of the season

(DeLong et al. 1999; Sydeman and Allen 1999).

3.3 Northern Elephant Seal Monitoring

3.3.1 Field Season Preparation and Equipment Setup

In October and November, surveyors assemble and inventory equipment needed during the

breeding season and replace or repair any missing or damaged equipment. Flipper tags are drilled

and checked for flaws prior to the start of the season. Temporary beach closure signs are made.

Surveyors follow a signage plan to erect signs to alert the public to beach and cliff closures

during the breeding season. See SOP 2: Northern Elephant Seal Surveys for more details.

3.3.2 Details of Taking Measurements

Population data: Direct counts of breeding sites are conducted from beaches or fixed cliffside

vantage points with the aid of a spotting scope and binoculars. Age class and gender of

individuals are identified and recorded in the following categories: bull, male sub-adult classes 1-

4, other sub-adult male, cow, pup, dead pup, weaned pup, immature of unknown sex, yearling.

Other species noted include number of harbor seals, California sea lions, and other pinnipeds.

See SOP 2 for more detailed information on northern elephant seal monitoring field methods and

data forms.

Tagging: The goal outlined in the NMFS permit is to tag between 200-300 weaned pups at

PORE each year. When the colony was small, >90% of the weaned pups were tagged; however,

since the largest colony at PRH has grown, access is limited, and the number of pups tagged has

declined to around 60-70%. At the newer colonies, access is not limited and 80-90% of pups are

tagged. Opportunistically, some sub-adult and adult males are tagged and/or dye-marked to track

movement of males between breeding sites and to identify the alpha and beta males. Tag

information is recorded in the field on data sheets, including date, location, size, sex, tag color,

number and tag position and presence or absence of other tags. Dye-marking reduces the effort

of resighting the same tagged animal multiple times throughout a season, and aids in

identification of important male seals by park docents and interpreters.

Resighting Tags: Surveys to re-sight tagged individuals occur once every two weeks at a

minimum on the easily accessible beaches (NDB, SB). Re-sight surveys to PRH sites typically

occur only in December, early January and March because of concerns for human safety. The

PRH sites have difficult access, a higher density of seals, and increased seal movement on the

beach. Tag information recorded from animals during re-sight surveys includes location of seal,

flipper tag number, color, side (left or right), and position among the inter-digit webs (round or

square). Also, the presence or absence of tags on the other flipper is recorded. Animals with

freeze brand marks (applied at other breeding colonies) and distinctive scars such as shark bites
31

are recorded in the notes field. Nursing activities and pup size class (P1-4) are recorded if the

animal is an adult-sized female. Dominancy on the beach (alpha, beta, not associated) is recorded

if the animal is a sub-adult 4 or bull male.

Disturbance data: Disturbance data are collected on source (e.g., human, dog, cattle, other) and

on effect to seals including potential versus actual disturbances. Northern elephant seals are not

as reactive to human disturbance as harbor seals; however, females are more sensitive and the

presence of humans can deter colony formation. Additionally, responses of seals to humans can

have indirect effects on productivity due to disruption of nursing or causing males to interact.

Harbor seal disturbances that occur during northern elephant seal surveys are recorded as well.

Environmental data: Weather data is collected during surveys to provide information on visibility

(fog), precipitation, and wind speed. These three parameters can affect the presence or visibility

of seals. Climate data include ENSO events, La Niña events, and Pacific Decadal Oscillation and

can help interpret the reproductive results of the season (DeLong et al. 1999; Sydeman and Allen

1999).

3.4 End of Season Procedures

General end of season procedures are briefly described here, but more detailed descriptions of

data management, reporting, equipment maintenance, and data and report archive procedures are

outlined in the SOPs.

Following the data entry, proofing, and analysis (described in Section 5.0 and SOPs 3 and 4),

program and park staff produce a brief annual monitoring report with basic data summaries and

any natural history items of note using the NPS Natural Resource Technical Report template.

The report provides pertinent updates to the park program managers and I&M Coordinator for

inclusion in other reporting requirements (e.g., Annual Administrative Report and Workplan or

for website updates) as outlined in SOP 4: Data Analysis and Reporting.

The number of volunteers and the total volunteer hours spent on the pinniped program is

summed by program staff and provided to volunteer coordinators at GOGA and PORE for use in

annual volunteers in parks reporting.

All monitoring equipment is cleaned and stored at either PORE or GOGA. At PORE, storage of

monitoring supplies is in the wildlife garage, basement of the Resource Management building or

Science office. At GOGA, equipment is stored in the Resource Management Building (Fort

Cronkhite Building 1061) or in the SFAN I&M Building (Fort Cronkhite Building 1063).

All digital photographs taken during the field season will be labeled with site name and date and

organized on the PORE server within the appropriate directory. High quality photographs (300

dpi) should be submitted to the Network I&M Coordinator for use with the annual reporting

along with a caption or explanation of the photograph.

33

4.0 Cooperation with Other Monitoring and Research

During surveys associated with this monitoring protocol, additional activities may occur in

support of regional or national long-term ecological monitoring programs. These activities are

not represented as part of the protocol but are included to document the activities currently

supported. The information collected contributes to the understanding of the SFAN pinniped

populations in a regional context and may inform the SFAN monitoring program.

Understanding the pattern of relationships between organisms and their environment (abiotic and

biotic, environmental and anthropogenic) is a necessary goal for adaptive management. These

relationships are complex for pinnipeds and patterns vary by species and season. The effort

expended to collect ecological and anthropological data at SFAN sites varies and is often the

outcome of collaborations with other researchers and resource agencies.

The following partners, collaborators, agencies and institutions have expertise and

complementary programs that contribute to the NPS program goals and give a broader context to

the data collected by the NPS.

x California Academy of Sciences

x California Department of Fish and Game

x California State University - San Francisco

x California State University - Sonoma

x California State University – San Jose

x Channel Islands National Park

x The Marine Mammal Center

x Moss Landing Marine Lab

x National Marine Fisheries Service

x National Oceanic and Atmospheric Administration

x National Marine Sanctuary Program

x California Oiled Wildlife Care Network

x PRBO Conservation Science

x University of California at Santa Cruz

x University of California at Davis

x University of California at Bodega Marine Lab

x University of California at Berkeley, Museum of Vertebrate Zoology

4.1 Dye-Marking, Tagging and Resighting Tags

Northern elephant seal tag information is collected during scheduled surveys and

opportunistically. Between 200 and 300 weaned northern elephant seal pups are tagged each

year. Data on tagging and tag resighting are submitted as a component of the annual report to the

NMFS.

Tag resight data within and across seasons may be used to understand mechanisms of dispersal,

colony expansion, and movements between PORE breeding sites. During a single season,
34

temporary dye marks may be applied to tagged and/or dominant males to aid in tracking

individual movements.

Northern elephant seal tag resighting data are shared among researchers from other colonies

including Piedras Blancas, San Miguel Island, Southeast Farallon Islands, and Año Nuevo.

Resight data of northern elephant seal pups tagged at PORE have been provided by other

researchers from Russia, Alaska, Oregon, and Washington. Additionally, The Marine Mammal

Center (TMMC) shares resight data of all rehabilitated seals. Reporting resighted tags aids in

understanding recruitment, seasonal distribution, survivorship, reproductive success, and success

of rehabilitation efforts.

Tagging and tag resighting have been core components of the NPS northern elephant seal

monitoring program for several years due to the minimal effort required to collect the data and

high value to the broader research community. The SFAN I&M program has provided support

for these efforts, and would likely continue to do so should it be able to again fund northern

elephant seal monitoring in the future. As such, tagging and tag resighting are written into this

protocol as core field activities and are addressed both in field methods and data management

sections.

Harbor seals are tagged by various researchers in the region and the data are shared among

researchers. Resight data of tagged harbor seals observed during surveys is recorded and shared

with researchers.

4.2 All Species Pinniped Monitoring – Point Reyes Headlands

Point Reyes staff and volunteers, under direction of the PORE Science Advisor, conduct yearround counts of all pinniped species at all locations at the Point Reyes Headlands every other

week. Winter surveys overlap with and are coordinated with counts of northern elephant seal

breeding sites. The park’s all species monitoring program compliments the harbor seal and

northern elephant seal monitoring programs by documenting the northern elephant seal molts,

harbor seal pupping, and harbor seal molt at the Point Reyes Headlands. The program

additionally collects data on California sea lions, Steller sea lions, and northern fur seals. The

monitoring program contributes to a long-term data set for the Point Reyes Headlands dating

back to 1980. The SFAN I&M program provides data management support for the all species

monitoring program. All data collected at the Point Reyes Headlands are entered into the

pinniped monitoring database. I&M data management staff assists PORE with data entry, data

maintenance, and data summaries.

4.3 Scat Collection

Although scat collection is not a component of the current protocol, some relationships, such as

diet and trophic interactions, are extremely valuable and information in this area would enhance

the monitoring program and pinniped management. To this end, through the pinniped program,

SFAN will examine pinniped diets by opportunistically collecting scat to identify the prey seals

are utilizing. Information on diet also will be obtained by assisting in analyzing carcasses of dead

seals. Standardized protocols for fecal collections and measuring diet may prove valuable for

long-term assessments, but samples are currently collected only opportunistically (Harvey 1987).

Some species, such as harbor seals forage locally, while northern elephant seals, feed mainly in

the north Pacific.
35

4.4 Statewide Surveys

The CDFG and NMFS conduct statewide aerial surveys of harbor seal sites during peak molting

season. Surveys are conducted on an annual basis during June, weather permitting (Hanan 1996;

Lowry et al. 2005). The NMFS annually collects data on northern elephant seal demography

which is used for stock assessments on the number of total seals and the number of pups

produced and pups weaned. SFAN shares survey data from monitoring at PORE with NMFS for

the stock assessments (Carretta et al. 2007).

The year round sea lion survey data are also shared with the NMFS for stock assessments. These

data are also relevant for ground-truthing aerial surveys during the Steller sea lion pupping

season, May through July. Although Steller sea lions no longer breed at PORE, large male sea

lions do appear during May through July, and individuals are present year round. Observations of

marked California sea lions are shared with NMFS and are used to estimate survival for the

population. California sea lions were branded at San Miguel Island to study survival of the

population.

Additionally, data are shared with PRBO for comparison with Southeast Farallon Island colonies

(Sydeman and Allen 1999). The NMFS requires an annual report from the park as part of the

permit authorization. S. Allen and D. Lee of PRBO are co-primary investigators for the NMFS

permit number 373-1868.

4.5 Volunteer and Docent Programs

As needed, the NPS has assisted the GFNMS volunteer stewardship program, SEALS. However,

the SEALS program is no longer active in Tomales Bay or Bolinas Lagoon. The GFNMS

participates in the breeding and molt season region-wide surveys, and provides the results in

their annual reports (Tezak et al. 2004).

PORE has a northern elephant seal docent program with volunteer docents who educate visitors

about northern elephant seals to protect the easily accessible haul out sites from disturbance. The

focus is on interpretive efforts. I&M monitoring data is shared with the docent program to

provide the public with current seasonal breeding summaries.

4.6 Stranding Network Program

The SFAN follows NMFS standard protocols as part of the Stranding Network (see Geraci and

Lounsbury 1993 for protocols and

http://www.nmfs.noaa.gov/prot_res/PR2/Health_and_Stranding_Response_Program/mmhsrp.ht

ml website). Stranding frequency data at SFAN sites is captured from several sources including

1) NPS survey data from breeding and haul out monitoring for northern elephant seals, harbor

seals and Point Reyes Headlands “all species” (see Section 4.2), 2) GFNMS Beach Watch

monthly beach surveys, 3) miscellaneous reports from visitors and NPS staff. Occurrence of

disease is documented based on protocols as noted above and in collaboration with partners.

Regional Stranding Network partners include California Academy of Sciences (CAS), University

of California - Museum of Vertebrate Zoology (MVZ), and TMMC. GFNMS conducts a

monthly regional beach-monitoring program (Beach Watch), and alerts NPS to any stranded
36

marine mammals within PORE and GOGA lands. Additionally, PORE maintains a reporting

form for all marine mammals that visitors or park employees document (digital form located at

u:\science\stranding network\forms).

All specimens collected within the parks are vouchered with an NPS accession number, as well

as a number from the collecting agency. Most specimens are housed at MVZ or CAS because of

limited space at the parks.

4.7 Disease Monitoring

Disease can have large impacts on pinniped populations. As such, SFAN will continue to work

with partners to monitor the presence and effects of disease on pinniped individuals and

populations by documenting affected animals and coordinating investigations with TMMC, other

researchers, and the National Marine Mammal Stranding Network. Currently these data are

collected opportunistically, when seals are captured for research or when an unusual stranding

event occurs (Gulland et al. 1997).

An important component of monitoring the health and status of pinniped populations is

documenting stranded dead, injured, and sick animals. Levels of contaminants in marine

mammals that die and wash ashore often provide a useful indicator of certain pollutants in

coastal marine ecosystems, particularly pollutants that are lipophilic and are bio-magnified in

marine food webs. GOGA and PORE are members of the NMFS, Southwest Region Marine

Mammal Stranding Network (see NOAA website

http://www.nmfs.noaa.gov/prot_res/PR2/Health_and_Stranding_Response_Program/mmhsrp.ht

ml for details). The Stranding Network is linked to the Marine Mammal Health and Stranding

Response Program, which tracks various health parameters across the nation, and PORE

contributes to the National Marine Mammal Tissue bank. Additionally, PORE banks tissue with

the TMMC for future analysis of baseline diseases and pollutant loads.

Two major stranding events have occurred over the past decade at PORE; in 1997 and 2000, sick

and dead adult harbor seals washed ashore. TMMC, UC Davis, NMFS and the National Marine

Mammal Stranding Network documented disease as the reason for the mortality events. In one

case, a newly identified virus was the cause of mortality (Gulland et al. 1997). Opportunistically,

the parks collect blood, tissue and other tissue from stranded or captured (tagged) seals to be

used as reference data on health (Gulland et al. 1997; Neale et al. 2002). Necropsies are

performed on most dead marine mammals, including pinnipeds, found on SFAN beaches by the

stranding network personnel to determine cause of death.

4.8 University Research

The wealth of monitoring data and knowledge about the SFAN pinniped populations have

spurred many university researchers and graduate students to address specific questions related

to pinnipeds, such as disease transmission, dispersal, reproductive success relative to habitat

differences, and El Niño effects. Some of these research areas fall outside the objectives and

scope of the long-term pinniped monitoring program. However, these research projects provide

critical information in effectively managing pinniped populations. The SFAN Network will

continue to support research to address questions that promote a better understanding of pinniped

populations in the region.
37

4.9 Collaborative Products

NPS staff members contribute regularly to products developed by other agencies. The following

section lists examples of contributions made by assisting with data analyses or reviewing

documents.

State (CDFG): Ground-truth data for annual CDFG/NMFS harbor seal aerial surveys.

Federal (NMFS/NOAA): Under the 1994 amendments to the MMPA, the NMFS is required to

publish Stock Assessment Reports for all stocks of marine mammals within U.S. waters, to

review new information every year for strategic stocks and every three years for non-strategic

stocks, and to update the stock assessment reports when significant new information becomes

available. Stock assessments are required for all marine mammals, and the NPS reports for

northern elephant seals, harbor seals and sea lions.

Federal (National Marine Sanctuaries): Data from the NPS harbor seal monitoring program are

included in the annual harbor seal reports of the GFNMS (1998-2002).

International: Collaboration with researchers in other countries occurs on a sporadic basis

regarding resight data from tagged northern elephant seals.

39

5.0 Data Management, Analysis, and Reporting

This section briefly describes the data management, data analysis and reporting aspects of the

SFAN pinniped monitoring program. Two SOPs provide further details:

SOP 3 (Data Management) describes in more detail how the SFAN pinniped monitoring protocol

meets data management objectives through data entry specifications, database design, quality

assurance and control measures, metadata development, data maintenance, data storage and

archiving, and data distribution. Data management procedures are explained for all the

components of the protocol.

SOP 4 (Data Analysis and Reporting) describes in more detail annual data analysis and reporting

procedures.

5.1 Overview of Database Design

The pinniped protocol encompasses two monitoring programs (harbor seal and northern elephant

seal). The pinniped database contains data collected by both programs. There are separate data

entry and editing procedures for the harbor seal and northern elephant seal programs. The

northern elephant seal data entry and editing forms are also used for pinniped surveys at Point

Reyes Headlands conducted by PORE outside of the breeding seasons. While separate data entry

and editing forms are used, data are stored in common tables to facilitate reporting and analysis

across the monitoring programs.

The SFAN staff has developed a relational Microsoft (MS) Access XP database modeled after

the Natural Resource Database Template (NRDT), an application developed by the NPS I&M

Program. The database consists of two separate MS Access .MDB files. The ‘front end’

(Pinniped.mdb) contains forms, linked tables, reports, queries, macros and Visual Basic code

while the ‘back end’ (Pinniped_BE.mdb) houses the data tables. This organization of the

database allows new development and edits of forms and reports (housed in the front end) to

proceed without hindering use of the data (housed in the back end). The two .MDB files are

linked using the ‘Linked Table Manager’ utility of MS Access.

The data organization is based on the concept of surveys (sampling events occurring at a

specified time) recorded in an event table which are conducted at specified locations, that are

geo-spatially described in a locations table. EventID and LocationID codes provide the unique

keys for databases built on the NRDT model. Besides actual counts of pinnipeds, the database is

used to record effects of natural and anthropogenic disturbances to harbor seals and track the fate

of tagged northern elephant seals.

As described above, there are two different data collection protocols, one for harbor seals and the

other for northern elephant seals. The primary information collected by both programs is the

number of pinnipeds observed at a specific time and location. The same tables are used to house

the primary information from both programs, namely, tblEvents, tblLocations, tblObservers and

tblSealCount. Events are linked to counts by an EventID which is automatically generated by

Visual Basic code housed in the data entry forms. EventIDs are the concatenation of the
40

following values: park, project, year, month, day and starting time (i.e., PORE_Pinniped_2005-

Jan-03_12:30:00).

5.2 Data Entry, Verification, and Editing

Data entry is done by field staff within a week of collecting the data. The data entry forms

resemble the field data sheets as closely as possible. Data entry and editing are discrete

operations which cannot be combined. Separate entry and editing forms are provided for each

pinniped program.

Satellite databases are distributed to PORE and GOGA, which enters data just for the Point

Bonita harbor seals. Satellite databases should begin with data collected after Aug 1 and continue

through to the following July 31. This time frame captures the entire northern elephant seal

breeding season (approximately Nov-March), the harbor seal breeding season (March-May), and

the harbor seal molting season (June-July). Field staff must cross check the northern elephant

seal census and northern elephant seal resight data in the database against the paper datasheets

completed in the field. In addition, after the field staff has completed its review, the Network

Data Manager should independently check a random 10% of the records for accuracy.

The harbor seal monitoring program undergoes a higher level of data scrutiny because it is

primarily collected by volunteers and is more subject to difficult field conditions, such as fog and

high winds, that may compromise the accuracy of the data. In addition, data collected by

volunteers are given data reliability ratings based on the amount of experience and evaluation by

project staff. During the course of the season, and again at the end of the season, each survey

should be evaluated and assigned a yes/no for high quality rating, based on factors such as poor

visibility, incomplete survey, and poor observer quality. Following these procedures, data

checking continues as described for the northern elephant seal monitoring program.

The Database Manager incorporates all the satellite databases into a single annual database and

completes additional error-checking queries.

Prior to any major changes to the database design, a back-up copy of the database should be

made. Once the database design changes are complete, the database should be assigned the next

incremental version number. The final copy of the previous database version should be archived

with the version closing date incorporated into the database title. Version numbers should

increase incrementally by hundredths (e.g., version 1_01, version 1_02, ... etc.) for minor

changes. Major revisions should be designated with the next whole number (e.g., version 2_0,

3_0, 4_0, ...). The front-end and back-end databases should be titled with the same version

number, regardless of in which database file modifications are made. Significant database redesign may require approval by the project manager, review by other data management staff, and

revisions to this data management SOP.

5.3 Data Archival Procedures

Before the annual data is uploaded into the master database, a copy of the master is made and

archived with the date incorporated into the file name. The satellite databases are archived after

the data has been uploaded. PORE database archives will be stored at PORE, while GOGA files

will be archived at GOGA. In addition, when changing the database to a new version, the final
41

copy of the previous database version is archived with the version closing date incorporated into

the database title. Both GOGA and PORE servers have regular back-ups that are maintained by

park staff.

At the end of each field season, after error-checking, proofing, and uploading the seasonal data,

all of the field datasheets are organized into a binder for that year. Also included in the binder are

a hardcopy of the annual report, once completed, and a CD containing a copy of the complete

master database and an electronic copy of the annual report. With the exception of the Point

Bonita datasheets, which are stored at GOGA in the Marin Headlands I&M office, all data

binders are stored in the PORE Science office.

5.4 Metadata Procedures

The NPS GIS Committee requires all NPS GIS data layers be described with the NPS Metadata

Profile, which combines the FDGC standard, elements of the ESRI metadata profile, the

Biological Data Profile, and NPS-specific elements. Although no standard has been applied to

natural resource databases and spreadsheets, the SFAN will complete the NPS Metadata Profile

to the greatest extent possible to document the annual and master pinniped back-end databases.

Because the annual Point Bonita harbor seal data is uploaded into the master Point Bonita

database without alteration, it is not necessary to create metadata records for the annual Point

Bonita back-end databases.

Complete metadata records for the SFAN pinniped databases will be generated in compliance

with current NPS standards by the SFAN Data Manager. Because the location data for this

project is stored as UTM coordinates within the MS Access databases, there are no spatial data

products associated with this protocol that require metadata records.

When completed, metadata records, but not the data, will be posted to the NPS Data Store for

public discovery and consumption. Contact information within the metadata records will direct

interested parties to the SFAN Data Manager for further inquiries. Master database metadata

records posted to the NPS Data Store will be updated annually after the annual data has been

uploaded or following database revision to a new version whole number (i.e., v1_3 to v2_0, but

not v2_0 to v2_1).

5.5 Data Distribution

In order for the pinniped monitoring program to inform park management and to share its

information with other organizations and the general public, guidance documents, reports, and

data must be easily discoverable and obtainable. The main mechanism for distribution of the

pinniped monitoring documents and data will be the Internet. The pinniped monitoring protocol,

accompanying SOPs, and all annual reports will be made available for download at the SFAN

website:

http://science.nature.nps.gov/im/units/sfan/

Although the pinniped monitoring database will not be posted for public download, as previously

mentioned, metadata records for the master database will be maintained at the NPS Data Store.
42

The metadata records will direct interested parties to the SFAN Data Manager for further

inquiries.

In addition to the NPS Data Store, the NPS I&M Program maintains an on-line natural resource

bibliographic database known as NatureBib. NatureBib records will be created for all of the

pinniped monitoring documents, including the protocol, annual reports, and any resulting

publications.

5.6 Data Analysis

Each year an annual report is produced that is largely based on the presentation of summary

statistics for the season. Both site specific and aggregate data are presented. Comprehensive

trend analyses will be prepared every five years. Details for the annual and five-year reports are

presented in SOP 4: Data Analysis and Reporting.

5.6.1 Harbor Seal Monitoring Program

Several harbor data summaries are developed each year for each location and for all sites

combined, including:

x breeding season maximum count of adults and immatures combined

x breeding season maximum count of pups

x molting season maximum count of adults, immatures, and pups combined

x summary of disturbance sources (e.g., motorboat, human, vehicle, aircraft, etc.),

presented by reporting, for each source, the number recorded and the percent of the total

number of disturbances for the season

x rate of disturbances (number of disturbances per hour of survey) for each monitoring

location

As an index of the total population size, the maximum counts for each location are summed and

reported separately for the breeding and molting seasons. Graphs of the maximum total count of

pups and adults for each year are developed for the breeding and molting seasons to compare the

data across years (Figures 3 and 4).

During all surveys, some harbor seals are in the water and cannot be counted. Consequently,

aerial and shore-based surveys of seals at their haul out sites measure only a proportion of the

population. The current population estimator is 1.65 times the maximum onshore number of

adults/immatures, pups, and individuals during molting (Lowry et al. 2005; Carretta et al. 2007).

SFAN synthesis and trend reports will apply the appropriate correction factor for long-term

harbor seal population trends.

To determine long-term trends in population size and productivity, the maximum count from

each colony, multiplied by the 1.65 correction factor, is evaluated by regression (linear or nonlinear) analyses (versus year) as described in Sydeman and Allen (1999) and . This results in one

data point per colony per year for the analyses. As recommended in Appendix A, the harbor seal

monitoring program will focus on detecting a SFAN-wide decline over a period of three years

(90% likelihood of detecting a 27% decline) using six of the primary sites (Tomales Bay,

Tomales Point, Point Reyes Headlands, Drakes Estero, Double Point, and Bolinas Lagoon).
43

Both population and productivity trends are analyzed to report the rate of change and whether it

is significantly different from zero (Caughley and Birch 1971; Zar 1984). In addition to the

colony specific regressions, route regressions (Elzinga et al. 1998) will be used to evaluate the

population trend for the entire SFAN harbor seal population. This consists of individual

regressions from each colony being combined to report a mean slope, standard error, and

statistical significance for all the colonies. A report of the statistical power of the regression will

also be presented with the regression results.

Disturbance data are summarized every year using the following measures:

x source of disturbance: annual tally of sources of disturbance (e.g., motorboat, human,

vehicle, aircraft, etc.) for each location and for all locations combined

x rate of disturbance: number of disturbances per hour of survey for each location

Rate of disturbance will be explored for changes through time using binomial tests on human

disturbance sources versus total disturbance sources. In addition, ANOVA or Generalized Linear

Models (GLM) will be applied to test for differences in disturbance rates between years (pooling

all sites and at each individual site), differences in weekday and weekend disturbance rates, and

differences in disturbance between sites.

The effects of disturbance on population size and pup production can be tested using GLMs

following methods developed by Becker et al. (2009). GLMs will be run using factors that may

affect population size and productivity, such as year since the most recent El Niño event, and

density-dependence due to total counts in the region in order to test the relative influence of

disturbances to the harbor seal population.

5.6.2 Northern Elephant Seal Monitoring Program

In 2007, a two-year northern elephant seal report was produced using the NPS Natural Resource

Report Template (Table 1; Adams et al. 2007). Annual and long-term trend reports will likely

remain consistent with this report format, which emphasized northern elephant seal population

and productivity estimates.

Annual and long-term trends of northern elephant seal population size are reported by age and

sex class using direct counts. Breeding population estimates are based on maximum survey

counts for northern elephant seals by sex, age group, and colony (Adams et al. 2007). During the

breeding season, not all age classes are present on the beaches so accurate total population size

counts are not possible. In addition, during surveys, some northern elephant seals, especially subadult males, are in the water and cannot be counted. Consequently, shore-based surveys of seals

at their haul out sites measure only a proportion of the population. If survey methods and timing

are standardized and the proportion of animals counted remains constant; such surveys can be

used as reliable indices of population trends.

The NMFS estimates the elephant seal population size by using raw pup counts multiplied by the

inverse of expected ratio of pups to total animals (McCann 1985). Boveng (1988) and Barlow et

al. (1993) recommend using 3.5 as an appropriate multiplier for a rapidly growing population

such as the California stock of northern northern elephant seals. The PORE population estimates
44

are based on the pup count multiplier (3.5) used with the maximum total of pup and weaned pup

counts by colony or sub-site. NMFS is currently reviewing this multiplier and may provide new

guidelines in the future. SFAN contributes data to NMFS for an annual national population

estimate (Barlow et al. 1993; Carretta et al. 2002; Carretta et al. 2007).

Annual productivity is reported as an index of annual reproductive success using direct counts of

females, pups, and applying correction factors. An example of productivity summary data for the

northern elephant seal monitoring program is in the protocol narrative, Table 1. The productivity

index is calculated from the following formula (Lee 2006):

Maximum count of weaned pups and pups

Adjusted maximum count of females = Productivity Index

The index is calculated for colony sites and the entire PORE population. The total number of

breeding females is estimated using the maximum count of adult females during peak pupping

adjusted to include the adult female counts 33 days prior to and 33 days after the peak count for

each colony site (Adams 1994; Le Boeuf and Laws 1994; Table 1). This adjustment takes into

account females that depart early and those that have not yet arrived at the time of the peak count

(average female stay at colony is 6 days prior to pupping + 27 days nursing period; LeBoeuf and

Laws 1994). The assumptions of this method to determine productivity are that observers are

able to capture the high count of pups plus weaners and adult females during the bi-weekly

surveys and that female natality is unknown but relatively stable across years. The index reflects

productivity only and not mortality (dead pups are included in the total) that occur at the

breeding site.

Rates of change in the northern elephant seal population will focus on adult female counts and

pup production. Cow adults will be used as a proxy for total breeding population size because

northern elephant seal males, particularly sub-adults, are highly mobile during the breeding

season, which can result in them being double-counted. The maximum count of pups plus

weaners for each colony provides an estimate of actual pup production.

A power analysis (Appendix B) indicates that for all sites combined, monitoring effort has an

86% chance of detecting a 36% decline in cows over 4 years. For pups, an 83% chance of

detecting a 41% decline can be realized after 5 years. Increases are easier to detect, generally

having 0.1 - 0.2 higher power. Site specific trends will take longer to detect, but will be explored

for Point Reyes Headlands, North Drakes Beach, and South Beach separately. Methods for

exploring long term trends in the northern elephant seal population will be similar to those

already described for harbor seals.

5.7 Reporting Schedule and Formats

Reporting is an essential component of the pinniped monitoring process. The effectiveness of

pinniped monitoring at GOGA and PORE lies not only in the field work and data management,

but also in how the information gathered is shared throughout the season and how it is

summarized at the end of the season. Reporting within-season allows for the information

gathered to be transferred to managers for the most effective internal support of the program; it

also allows visitors to understand what it is that Resource Management does in a NPS unit; and
45

how resources are protected while providing for visitor enjoyment of those resources. Reporting

at the end of the season allows for consistent scientific thoroughness to be applied to the

pinniped monitoring program, and allows resource managers to identify population and

productivity trends and triggers for management actions and resource protections.

A summary of reports that will be developed is provided in Table 2.

One of the most critical components of updating park staff about ongoing activities is the

Weekly Updates. These reports include updates on maximum numbers documented and any

unique or noteworthy observations (e.g., arrival dates, shifts in beach use). The Weekly Updates

are distributed to all employees via e-mail and are posted to the SFAN website.

The post-season or annual report follows the national guidelines established for NPS Natural

Resource Publications (http://nature.nps.gov/publications/NRPM). The annual report format

includes an abstract, introduction, study area and methods, results, discussion and conclusion.

Recommendations including management, research, and changes in the protocol (changing

monitoring intervals and timing, moving/adding sites, etc.) will also be included in the

discussion. The annual report enables readers to determine if the goals of the project are being

met and provides an administrative and scientific record of monitoring activities. These annual

reports will also be distributed to the SFAN parks, and can be used to report on park

management goals. Portions may be included in the network’s Annual Administrative Report

and Workplan.

A comprehensive data analysis and synthesis will be written every 5 years to summarize general

trends within a context of the park ecosystem. The longer time period for comprehensive

analyses allows for more thorough data analysis and review of protocols and may give greater

opportunity for adaptive management. Details for the annual and five-year reports are presented

in SOP 4: Data Analysis and Reporting.
46

Table 2. Summary of reporting and communication products.

Communication

Product

Lead Audience Schedule Summary

Annual Report Biological

Technician

Park Resource

Managers

Annually - Document monitoring activities

-Describe current condition of the

resources

-Document changes in the monitoring

protocol

-Increase communication within the park

and network

Analysis and Synthesis

Report

Project Lead

and possibly

contractors

Park Resource

Managers

5 years -Determine patterns and trends

-Discover correlations among resources

being monitored

-Analyze data to determine the level of

change that can be detected using the

existing sampling scheme

-Provide context, interpret data for the

park within a multi-park, regional, or

national context

-Recommend changes to management

practices

-Review of protocol design and product to

determine if changes are needed

Executive Briefing Biological

Technician

Program

Managers,

Superintendents,

Interpretation staff

Annually Two-page summary that lists monitoring

objectives and questions, discusses

annual results, and provides a regional

context.

NMFS Report Project Lead NMFS + Partners Annual report

and permit

renewal due

every 5 years.

The NMFS reports include information on

number and species of seals tagged (tag

number, location of tag, location of tagging

event, date, and age-sex of individual),

resighting records of tags from non-PORE

sites, and the number and species of

seals and sea lions disturbed during

research activities. Other health data that

might be collected is also provided.

Stranding Network

Report

Project Lead NMFS + Partners Annually Stranding data (species, date, location,

condition) is shared with NMFS through

the stranding network.

Web Site Internet Data Manager Park Staff, General

Public

Annually or as

needed

Post all Executive Briefings, Report Cards,

Park Presentations Biological

Technician/

Project Lead

Park Staff Annually Provide a presentation to park staff during

senior staff, all employee, or division

meetings at each park upon request.

Gives staff an opportunity to ask questions

about the program.

Weekly Update Biological

Technician

Park Staff Weekly during

the field season.

Brief update listing maximum numbers

and pertinent natural history notes.

Highlights areas where pupping occurs.

Photos Biological

Technician/

Volunteers

For all reports and

publication

Continuous High quality publication quality photos are

needed to support all communication

products. For digital photos that means

300 pixels per inch resolution in a plain or

compressed TIF format. Specialist should

make every effort to document ongoing

work, special incidents, site visits for

communication purposes.

Press Releases PIO Public, park staff Annually Submit to local news media before the

breeding season for northern elephant

seals and harbor seals to remind the

public not to disturb seals and to highlight

the monitoring program.
47

6.0 Personnel Requirements and Training

6.1 Roles and Responsibilities

6.1.1 Project Manager

The Project Manager oversees the monitoring program, trains technicians and volunteers,

conducts field surveys, oversees data management, and submits annual reports. The project

manager responsibilities are currently shared by the PORE Science Advisor (Sarah Allen) and

SFAN Data Manager (David Press).

6.1.2 Biological Technicians

Presently, a full-time Conservation Corps North Bay/AmeriCorps member coordinates

volunteers, conducts field surveys, and enters data for harbor seal program.

Although not currently funded, traditionally a full-time, seasonal GS-7 biological technician has

organized the monitoring schedule, conducted population surveys, and completed data entry

during the northern elephant seal breeding season. In addition, the AmeriCorps member has

provided significant field and office assistance to the program.

6.1.3 Data Manager

The data manager maintains the database, oversees data entry, and generates data summaries for

the project manager.

6.1.4 Volunteers

Volunteers contribute significant amounts of time each year and are considered the backbone of

this monitoring program. Over 30 volunteers per year participate in the harbor seal monitoring.

A few, highly trained volunteers assist in the northern elephant seal monitoring program.

Usually, these volunteers have worked with northern elephant seals at other locations or have

trained extensively in the harbor seal program.

6.2 Qualifications

Observers (both volunteers and program staff) must have an ability to use binoculars and a

spotting scope; ability to record data into a field form; be in excellent physical shape to hike

several miles in rugged terrain and off trail; and carry a backpack with up to 30 lbs. Project staff

and experienced volunteers will mentor new volunteers. Program staff requirements include

either one season of experience doing surveys, including field data collection, or training in seal

survey techniques.

6.3 Training Procedures

The project manager and biological technicians train over 30 volunteers per year who participate

in the monitoring of harbor seals; many of the volunteers have been active for more than three

years. Harbor seal volunteers are trained in two in-class sessions and five field sessions. New

volunteers are asked to go out on surveys with a returning volunteer who will mentor them for

the first few surveys. New volunteers are required to attend all in-class training sessions, and all

five field trips, and to commit to a minimum of 10 surveys per year. See SOP 1: Harbor Seal

Surveys for the summary of volunteer training and an overview of the volunteer training guide.

Training documentation includes background information, papers, tide charts, safety information

and contact information.

49

7.0 Operational Requirements

7.1 Annual Workload

The harbor seal long-term monitoring study requires an average of 270 visits per year, and 30

visits per site during the breeding/molt seasons. This has been accomplished with 25-30

volunteers working from March 1 until July 30. A full-time AmeriCorps member has

traditionally overseen the program, scheduling, and coordinating volunteers with direct oversight

by the two program leads. The AmeriCorps position lasts for one year, with new members

beginning in October.

The northern elephant seal monitoring study requires an average of 70 visits per year. When

funded, this is accomplished with one full-time, seasonal GS-7 biologist, the AmeriCorps

member (part-time), 3-4 volunteers, and the two program leads as needed. The volunteers assist

with field surveys only. The biologists oversee the program, scheduling, coordinating volunteers,

data entry and weekly reporting, and conduct surveys.

7.2 Annual Field Schedule

The annual schedule is presented separately for harbor seals (Table 3) and northern elephant

seals (Table 4). Taken together, however, pinniped monitoring is divided into three major

periods: 1) northern elephant seal breeding season (December 1- March 31), 2) harbor seal

breeding season (March 1-July 30); and 3) data processing and reporting (August 1-November

30). Within each of these periods, there are several tasks both specific to the season and general

to all seasons.

7.3 Facility and Equipment Needs

Program staff members use office space and computers at PORE. Field equipment used by field

staff and volunteers is shared for harbor seal and northern elephant seal monitoring. This

equipment includes binoculars (8x40), spotting scopes with tripods, hand counters, clipboards,

digital camera, and backpacks. Some specialized equipment is also used for tagging northern

elephant seal pups. See SOP 1 and 2 for equipment details. All of the equipment is stored in the

Science office at PORE.

Two vehicles based at PORE are available for use for travel from Bear Valley Headquarters to

the pinniped monitoring sites. The SFAN I&M program pays for one vehicle, while the Pacific

Coast Science and Learning Center (PCSLC) pays for the other. The PCSLC, PORE Science

Advisor, pinniped monitoring programs, and the northern spotted owl program share these two

vehicles on a first-come, first-served basis.
50

Table 3. Annual SFAN harbor seal monitoring field schedule.

Activity Oct Nov Dec Jan Feb Mar April May June July Aug

Harbor Seal Technician

Starts

Volunteer Recruitment

Equipment Prep

Signs posted

Train Volunteers

Press release by PIO

Breeding Season Surveys

Molt Season Surveys

QA/QC and Data Analysis * *

Annual Report Completed *

* Data analysis and completion of the annual report occurs during the fall months following the field season.

Table 4. Annual SFAN northern elephant seal monitoring field schedule.

Activity Oct Nov Dec Jan Feb March Aug Sept

Northern Elephant Seal BioTechnician Starts

Pre-season meeting with park

managers

Equipment Preparation

Contact Volunteers

Train Volunteers

Beach Signs

Adult Dye Marking

Census

Field Work (1x weekly)

Census Field Work (2x weekly)

Re-Sight Survey (2x weekly)

Flipper Tag Preparation

Weaned Pup Flipper Tagging

Annual Report Completed
51

7.4 Budget

The annual budgets for harbor seal monitoring (Table 5) and northern elephant seal monitoring

(Table 6) include costs for personnel, vehicle, travel, equipment, and housing. Every five years,

long-term trend analyses will be developed by park and network staff or through cooperative

agreements with partnering agencies such as PRBO or the California Cooperative Ecosystems

Study Unit (CESU). These reports will incur additional costs.

Harbor seal monitoring is funded primarily through SFAN. Contributions are also made by

PORE and by the Point Reyes National Seashore Association (PRNSA) to cover costs for

equipment replacement and miscellaneous supplies.

The northern elephant seal monitoring was funded by SFAN through FY07. Contributions after

that date were reduced and phased out. Future monitoring will occur with volunteers under the

direction of the PORE Science Advisor.

The SFAN I&M data management staff supports both monitoring projects. Data management

needs include database modifications, training staff and volunteers on data entry, error-checking,

and producing annual data summaries and other data requests.

Volunteers also make significant annual contributions. From 2007 to 2009, for example,

volunteers donated over 1,300 hours to harbor seal monitoring resulting in an in-kind

contribution of $26,325 at a rate of $20.25/hour. Partners contribute additional hours of in-kind

funds in personnel time and supplies by conducting various tasks ranging from tagging seals to

collecting tissue sample.

7.5 Permitting and Compliance

SFAN conducts harbor seal and northern elephant seal monitoring under NMFS permit 373-

1868, in cooperation with PRBO Conservation Science, who conducts research on pinnipeds on

the Farallon Islands National Wildlife Refuge. A permit is required due to northern elephant seal

tagging activities and because both monitoring programs have the potential to disturb seals, even

during censuses. Additional research on harbor seals, such as harbor seals tagged in San

Francisco Bay and at PORE for a study by TMMC, also occurs under this permit. To meet

permitting requirements, this project provides an annual report to NMFS with certain required

information. The permit was reissued in 2007 and is valid for another five years, until 2012.
52

Table 5. Annual budget for the SFAN harbor seal monitoring program.

Category Item Annual Expenses

Project Income

SFAN I&M Program $34,650

PORE Contribution $8,000

Volunteer Support (in-kind contribution) $26,325

Total Income $68,975

Project Expense

Personnel Project Manager GS-13 (2 pp) $8,000

Data Manager GS-11 (2 pp) $7,770

Data Manager GS-9 (2 pp) $6,180

AmeriCorps/CCNB Volunteer $18,000

Volunteer Support (in-kind contribution) $26,325

Cooperative Agreements Data Analyses

Equipment Repair/replacement $500

Supplies Miscellaneous $200

Travel Vehicle $2,000

Total Expense $68,975

Balance -0-

Table 6. Annual budget for the SFAN northern elephant seal monitoring program.

Category Item Annual Expenses

Project Income

SFAN I&M Program $3,090

PORE Contribution $8,000

Volunteer Support (in-kind contribution) $610

 Total Income $11,700

Project Expense

Personnel Project Manager GS-13 (2 pp) $8,000

Data Manager GS-9 (1 pp) $3,090

Bio-Tech GS-6/7 (7 pp) $18,550

AmeriCorps/CCNB Volunteer $4,000

Volunteer Support (in-kind contribution) $610

Cooperative Agreements Data Analyses

Equipment Repair/replacement $500

Supplies Miscellaneous $200

Travel Vehicle $2,000

Total Expense $36,950

Balance -$25,250

Note: The only I&M contribution to this monitoring program will be limited data management

assistance.
53

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vitulina richardsi, in south San Francisco Bay, California. M.S. Thesis, California State

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integrated transponders. Marine Mammal Science 16 (2):500–504.

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of the Northeast Pacific: a case for historical science. Fisheries Oceanography 3:279–291.

Frost, K. J., L. F. Lowry, and J. M. Ver Hoef. 1999. Monitoring the trend of harbor seals in

Prince William Sound, Alaska, after the Exxon Valdez oil spill. Marine Mammal Science

15:494–506.

Geraci, J. R., and V. J. Lounsbury. 1993. Marine mammals ashore: a field guide for strandings.

Texas A&M Sea Grant, Galveston, TX.

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patterns of harbor seals (Phoca vitulina richardsi) at Castro Rocks, San Francisco Bay,

California. California Fish and Game 88 (1).

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Harvey, J. T. 1987. Population dynamics, annual food consumption, movements, and dive

behaviors of harbor seals, Phoca vitulina richardsi, in Oregon. Unpubl. Ph.D. Dissertation,

Oregon State University, Corvallis. 177pp.

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1975–1983. Northwestern Naturalist 71(3):65–71.

Harvey, J. T. and D. Goley. 2005. Determining a correction factor for aerial surveys of harbor

seals in California. Final Report to National Marine Fisheries Service and Pacific States

Marine Fisheries Commission, PSMFC Contracts No. 03-19 and 04-33, NOAA Grant No.

NA17FX1603. 35 pp.

Hastings, K. K. and W. J. Sydeman. 2002. Population status, seasonal variation in abundance,

and long-term population trends of Steller sea lions at South Farallon Islands, California Fish

Bulletin 100:51–62.

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at the Farallon Islands, 1983–1985. Final report to the National Marine Fisheries Service,

U.S. Department of Commerce. 44pp.

Keiper C. A., D. G. Ainley S. G. Allen, and J. T. Harvey. 2005. Marine mammal occurrence and

ocean climate off central California, 1986 to 1994 and 1997 to 1999. Marine Ecological

Progress Series 289:285–306.

Laidre, K. L., I. Stirling, L. F. Lowry, Ø. Wiig, M. P. Heide-Jørgensen, and S. H. Ferguson.

2008. Quantifying the sensitivity of arctic marine mammals to climate-induced habitat

change. Ecological Applications 18(Suppl.):97–125.

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physiology. University of California Press, Berkeley. 414 pp.

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Farallon Islands 2005–2006. Report to U. S. Fish and Wildlife Service Farallon National

Wildlife Refuge, San Francisco, CA. 9pp.

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northern elephant seals. Journal of Mammalogy 90:1–8.

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Southwest Fisheries Science Center, 8604 La Jolla Shores Drive, La Jolla, CA 92037. 38 p
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populations. Pages 1–17 in J. K. Ling and M. M. Bryden, editors. Studies of sea mammals in

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61

SOP 1. Harbor Seal Surveys

Version 1.5

Revision History Log

Prev. Version # Revision Date Author Changes Made Reason for

Change

New

Version #

1.0 March 2008 Marcus

Koenen, D.

Press, Erin

Flynn

General editing. Add

revision history log.

Combined SOP 1, 2,

and 3 to reduce

redundancy.

Update. 1.1

1.1 May 2008 Dawn

Adams,

Sarah Allen

Fix layout, minor edits

General editing

Prep for review 1.2

1.2 September

2009

D. Press, M.

Koenen, S.

Allen

Added directions to

survey sites. Minor

editing.

Peer review

comments.

1.3

1.3 November

2009

K. Freeman,

D. Press

Changed tables and

figures to a modular

numbering system,

added a literature

cited section,

additional minor edits.

Formatting

requirements.

1.4

1.4 December

2009

D. Press Minor grammatical

edits. Added

definition of redpelaged seals.

Comments from

Penny Latham.

1.5
62

Contents

Page

Tables .......................................................................................................................................64

Appendixes ...............................................................................................................................64

1.0 Field Schedule.....................................................................................................................65

2.0 Volunteers...........................................................................................................................66

2.1 Observer Requirements................................................................................................66

2.2 Recruitment .................................................................................................................66

2.3 Training Sessions.........................................................................................................66

2.3.1 In-class training.................................................................................................66

2.3.2 Training Guide ..................................................................................................67

2.3.3 Mentor Program................................................................................................68

3.0 Field Equipment and Preparation.........................................................................................68

4.0 Field Methods .....................................................................................................................69

4.1 Survey Sites.................................................................................................................69

4.1.1 Bolinas Lagoon .................................................................................................69

4.1.2 Duxbury Reef....................................................................................................70

4.1.3 Double Point .....................................................................................................70

4.1.4 Drakes Estero....................................................................................................70

4.1.5 Tomales Point ...................................................................................................71

4.1.6 Tomales Bay .....................................................................................................72

4.1.7 Point Bointa ......................................................................................................72

4.2 Field Visit Schedule.....................................................................................................73

4.3 Field Forms .................................................................................................................73

4.4 Surveys........................................................................................................................73
63

4.4.1 Census Data ......................................................................................................73

4.4.2 Disturbance Events............................................................................................75

5.0 Literature Cited ...................................................................................................................76
64

Tables

Page

Table SOP 1.1. Annual SFAN harbor seal monitoring field schedule.........................................65

Table SOP 1.2. Harbor seal disturbance source groups and specific sources

collected in the field. .................................................................................................................76

Appendixes

Page

Appendix SOP 1A. Harbor Seal Site Maps................................................................................78

Appendix SOP 1B. Harbor Seal Field Datasheets......................................................................85
65

This SOP details field preparation and field methods for monitoring harbor seals at Golden Gate

National Recreation Area and at Point Reyes National Seashore. Data sheets and maps to

observation sites are attached.

1.0 Field Schedule

The field season for harbor seal monitoring begins in March and continues to the end of July

(Table SOP 1.1). Field preparation begins in January and February. Field surveys for the

breeding and molting seasons are conducted March 1 through July 31. Scheduling surveys and

volunteers is coordinated by the lead field biologist or volunteer coordinator for the project.

Each harbor seal colony is surveyed a minimum of two times per week during the season.

Weather can be unpredictable and surveys are occasionally cancelled or rescheduled at the last

minute due to rain or fog. The weekly updated schedule is maintained by the volunteer

coordinator on a website accessible to the volunteers. For each scheduled survey day, the

calendar has the location and observer initials. Project staff and some volunteers continue

monitoring during the non-breeding season and provide survey forms throughout the year.

Although these surveys occur outside of the breeding and molting season and are not included in

the annual summaries and reporting, they do provide important information on colony sites

during the rest of the year.

Signs are placed at the access points to several of the seal colonies to advise park visitors to

avoid disturbing seals before the breeding season begins. The sign template is located on the

PORE server inppore05\Resources\Science\Phoca\Harbor Seal Signs. A press release is also

distributed to the local press before the season begins through the public information officer

(PIO) at PORE.

Table SOP 1.1. Annual SFAN harbor seal monitoring field schedule.

Activity Oct Nov Dec Jan Feb Mar April May June July Aug

Harbor Seal

Technician Starts

Volunteer

Recruitment

Equipment Prep

Signs posted

Train Volunteers

Press release by

PIO

Breeding Season

Surveys

Molt Season

Surveys

QA/QC and Data

Analysis

* * *

Annual Report

Completed

*

*Data analysis and completion of the annual report occurs during the fall months following the field

season.
66

2.0 Volunteers

Each year in December, the park schedules training dates for new volunteers and returning

volunteers. A minimum of 20 volunteers is required to run the program. Typically around 15

volunteers return each year and so 5-10 new volunteers are needed annually.

2.1 Observer Requirements

Observers must have an ability to use binoculars and a spotting scope; ability to record data into

a field form; be in excellent physical shape to hike several miles in rugged terrain and carry a

backpack with up to 30 lbs; and to hike off trail. Experienced volunteers will mentor new

volunteers. See also personnel section of protocol.

2.2 Recruitment

The first step is to advertise in the Sierra Club Yodeler to attract new volunteers. A fee is

required to put an advertisement in the Yodeler. A digital copy of the advertisement is located at

inppore05\Resources\Science\Phoca08\Volunteer recruit\2008 volunteer ad. This ad should be

placed in the Yodeler by December.

Each year in January, a press release recruiting volunteers is sent by the Park Information Officer

(PIO) to be distributed to local media (Point Reyes Light, West Marin Citizen, etc...). A digital

copy of the release is located at inppore05\Resources\Science\Phoca\Phoca08\Volunteer

recruit\harbor seal monitoring press release-08.

Additionally, the Park VIP coordinator posts applications on volunteer.gov/gov, nps.gov/pore,

and other regional volunteer websites. Signs are posted at the Palomarin, Tomales Point, and

Five Brooks trailheads. A digital sign is located at inppore05\Resources\Science\Phoca\Phoca08\

Volunteer recruit\flyer. Other recruitment options include the Park Wavelength volunteer email,

local outdoor recreation businesses, The Marine Mammal Center, and the Gulf of the Farallones

National Marine Sanctuary.

2.3 Training Sessions

Training includes two half-day sessions in the classroom and five field trips. Dates are selected

for mid-late February and March that coincide with medium to low tide levels to maximize the

number of seals onshore at the haul outs. Field trips include one trip to each of the primary seal

haul out sites (Tomales Bay, Drakes Estero, Double Point and Bolinas Lagoon) and a trip in

April to train new volunteers on harbor seal pup identification and behavior. Other optional field

trips include a visit to The Marine Mammal Center. New volunteers are asked to go out on

surveys with a returning volunteer who will mentor them for the first few surveys. New

volunteers are required to attend all in-class training sessions, and all five field trips, and to

commit to a minimum of 10 surveys per year. All of the training materials are located on the

PORE server under inppore\Resources\Science\Phoca\Training.

2.3.1 In-class training

There are two 1⁄2 day training sessions that include presentations on the following topics:

x General marine ecology and Point Reyes
67

-Speaker from the Cordell Bank Marine Sanctuary and/or the Pacific Coast

Science and Learning Center

x General information on marine mammals and pinnipeds

-Speaker from The Marine Mammal Center

-Speaker from the NPS or AmeriCorps

(inppore05\Resources\Science\Phoca\Training Materials\Presentations\

phocamarinemammals08 ppt files a and b)

x Specific information on long-term monitoring of harbor seals at Point Reyes

(inppore05\Resources\Science\Phoca\Presentations\Training Materials\Presentations\

phocaclass08b.ppt)

x Specific information on long-term monitoring of northern elephant seals at Point Reyes

(inppore05\Resources\Science\Phoca\presentations\Training Materials\ phocaeseal08.ppt)

x Data collection and volunteer information (inppore05\Resources\Science\Phoca\Training

Materials\Presentations\Volunteer Information and Data Collection 2008.ppt)

x Specific information on safety in the field including

-Poison oak identification and avoidance

-What to do if you get bitten by a tick

-Facts on West Nile Virus, Avian Flu, and other relevant diseases

-Interactions with park visitors, presented by Park Law Enforcement

All of the presentations are updated each year with new information.

New volunteers are also trained in the field at each of the survey sites and a mentor program

pairs up new volunteers with older volunteers to continue training (see below).

Each year, returning volunteers are provided with a refresher on the survey methods and their

ability to count seals is evaluated to determine if more practice is needed.

2.3.2 Training Guide

A full packet of information for new volunteers is updated each year and is located at

inppore\Resources\Science\Phoca\Training Materials\Training Manual\Harbor Seal Training

Manual 08.doc. The training manual is organized in a binder and includes the following:

x Volunteer service agreement for Natural Resources Agencies

x Natural history of Marine Mammals

x Working in the field at PORE

x Harbor seal survey protocol

x Published articles with background information

x Maps of each location and observation sites

x Data forms

x Examples of field data forms filled out

x Equipment list (see below)

x Equipment care and maintenance

x Tide book (available from visitor center bookstore; for new and returning volunteers)

x Park brochure
68

x Safety issues (Lyme disease, poison oak, West Nile virus)

x Contacts (update annually)

2.3.3 Mentor Program

New volunteers are encouraged to participate in a mentoring program and are paired up with

long-term volunteers that are familiar with the locations and the survey methods. In so doing,

new volunteers are not only trained in the methods but their abilities are evaluated by the mentor

and more intensive training is provided if needed. We recommend that new volunteers

accompany a mentor at least 3 times and at least once to each survey site.

3.0 Field Equipment and Preparation

In January, the equipment needs are reviewed, and missing or damaged items are replaced.

Equipment for observers is housed in the three separate boxes for survey convenience. The boxes

are located at Bear Valley Headquarters, the PRBO Palomarin Field Station, and Fort Cronkhite.

Individual box content may vary by location.

Equipment includes:

x Binoculars (8x40 Eagle Optics or equivalent; 3 available)

x Spotting scopes and tripods (Bushnell Spacemaster or equivalent; 5 available)

x Hand counters (10 available)

x Clipboards (metal to hold forms and maps; 5 available)

x Backpacks (4 available)

Data sheets include:

x Survey form

x Disturbance form

x Map of location being surveyed

Recommended personal equipment:

x Water and snacks

x Sunblock

x Warm clothing

x Sturdy hiking boots

x cellphone

Optical equipment is easily damaged by salt air, wind and dust/sand and should be checked for

damage and corrosion. Equipment is housed in an outside, weatherproof and secure box for

access to volunteers during non-office hours.
69

4.0 Field Methods

Field methods include surveys that are conducted March 1 through July 31 to cover the breeding

season (March 1-May 30) and the molt season (June 1-July 31). Some volunteers continue

monitoring during the non-breeding season and do provide survey forms throughout the year.

Although these surveys occur outside of the breeding and molting season and are not included in

the annual summaries and reporting, they do provide important information on colony sites

during the rest of the year.

4.1 Survey Sites

There are eight distinct survey sites located within the SFAN parks (see Protocol Narrative

Section 2.4.1 and Figure 5). Each survey site is further subdivided into subsites based on habitat

features.

ESRI ArcMap and Arcview files for reproducing or updating maps are located at

inppore07\GIS\vector1\wildlife\marine\pinnipeds. Seal haul out sites and observer positions are

represented as point locations in the maps. In addition, the project MS Access database stores

UTM locations of pinniped haul-out and colony sites within the locations table (see SOP 3. Data

Management).

Maps of each of the study sites are presented in Appendix SOP 1 A. To produce quick maps with

no changes, files are located at inppore05\Resources\Science\Phoca\Fieldmaps. Maps for Point

Reyes Headlands are located in SOP 2 Northern Elephant Seal Surveys.

4.1.1 Bolinas Lagoon

Subsites: HWY1, Kent Island (KI), Pickle Weed Island (PWI).

From San Francisco, take 101N, exit at Mill Valley/Stinson Beach/Hwy1. Follow signs for

Stinson Beach via Hwy1/Shoreline Hwy. Pass through Stinson Beach on Hwy1. Calle Del

Arroyo Rd. will be on your left, 1.6 miles further north, park on the right hand side of the road in

a small dirt parking lot to survey for HWY1 and PWI sites (see below).

From Bear Valley, start from the intersection of Sir Francis Drake Blvd, and Rt. 1, in Olema.

Traveling south on Hwy1, the Hwy1 site is 12 miles from this intersection. It is 1.3mi. past the

sign for the Audubon Canyon Ranch. There will be a small dirt parking lot on your left. At the

back of the lot is a brown sign that says no camping/overnight parking. Park your car here. The

best vantage spot is approximately 100 yards north on Rt. 1 (in the direction that you came

from). Here you are at least a little bit above the seals, and it is easier to count them. There is

very little room on the side of the road, however, so please watch out for cars! The group of seals

right in front of you is the Hwy1 subsite. The group of seals off to the left is PWI.

1.6 miles further south down Rt.1, turn right onto Calle Del Arroyo Rd., at the end of the road

you will come to a guard shack for Sea Drift, a gated community. Tell them you are with Point

Reyes and are here to survey the harbor seals. If no one is at the gate, back up, park, and go

across the road to the Assoc. office and they will open the gate for you. Immediately after the

guard shack, turn right onto Dipsea Rd. Across from house #197, right before the grey/blue
70

boathouse, there is a small pullout. Park your car here. At low tide, a sandbar will be visible from

here (KI). Kent Island is the sandbar across the channel.

4.1.2 Duxbury Reef

Subsites: None

From San Francisco, take 101N, exit at Mill Valley/Stinson Beach/Hwy1. Follow signs for

Stinson Beach via Hwy1/Shoreline Hwy. Pass through Stinson Beach on Hwy1. Go about 3

miles, take a left onto Olema/Bolinas Rd. (this road is not labeled), right at the end of the bay. At

the end of this road, take a left onto Horseshoe Hill Rd, then follow the directions below.

From Bear Valley, start at the intersection of Sir Francis Drake Blvd, and Rt. 1, in Olema.

Go 9.6 miles south on Rt.1, and then turn right onto Horseshoe Hill Rd.

After approximately 3 or 4 miles, at your second stop sign, take a right onto Mesa Rd for 0.6mi.

Take a left onto Overlook Dr for 0.5mi.

Take a right onto Elm Rd for 0.6mi.

Take a left onto Maple Ave (across from BCPUD, Bolinas Community Center)

Drive to the end of the road and park in the small dirt parking lot.

Set up at the bench. The reef is right across the way. The seals tend to haul out at the end beyond

where the tidepoolers can get to, but make sure to check the entire length.

4.1.3 Double Point

Subsites: North Beach (NB), North Beach Rocks (NBR), and Stormy Stack (SS), South Beach

(SB), Tide Pools (TP) and South Point (SP).

Start at the intersection of Sir Francis Drake Blvd, and Rt. 1, in Olema.

Go 9.6 miles south on Rt.1, and then turn right onto Horseshoe Hill Rd.

After approximately 3 or 4 miles, at your second stop sign, take a right onto Mesa Rd.

Continue down the dirt road (Mesa Rd.) to the end and park in the Palomarin parking lot.

Take the Coast Trail to Bass Lake, which is about 2.6 mi. or 3.l (info varies on mileage) from the

start of the Coast Trail.

About a 1⁄2 mile after Bass Lake, on the right side of the trail is a small sign for Crystal Lake, and

a separate trail closed sign, with a minor trail next to the sign. This trail is right before the main

trail starts to descend. Backtrack a few yards and on the left side of the trail is a "trail -opening in

the trees." This is the off-trail route to Double Point.

4.1.4 Drakes Estero

Subsites: Drakes Beach (DB), Drake’s Mouth Sandbars (DEM), Limantour Spit (L), Main

Colony (A), Sandbar to the Right of A (A1), Upper Estero Near (UEN), Oyster Bar (OB), Upper

Estero Far (UEF).

Park at Drakes Beach at the Ken Patrick Visitor Center. Walk down the beach to the left. The

beach is bordered to your left by steep cliffs. Watch out for rock debris. Soon after you climb

over a rock formation, the cliff ends temporarily. This is where Horseshoe Pond exchanges water

with the ocean. Walk across the beach to the end of the pond, and head up the hill using an old
71

abandoned ranch road. Continue on the road until it begins to slope down the other side of the

hill. You will see some cypress tress with a rookery below you. Then leave the road and hike

away from the ocean and towards the Estero and find a spot with good visibility.

If the tide is too high to walk the beach, at the visitor center go left but instead of walking on the

beach, climb the bluff and walk parallel to the beach. Please beware of erosion issues and do not

hike near the cliff edge. You will descend just before Horseshoe Pond. Cross the beach and

follow the directions above. Alternatively, you can park at the abandoned D Ranch, the last ranch

on your left before Drakes Beach, and hike across the field and down to Horseshoe Pond. It is

about equivalent distance to the suggested route above. If you do park at D Ranch, you much

notify dispatch and leave a note in the windshield explaining you are a harbor seal volunteer.

4.1.5 Tomales Point

Subsites: Two Rock Beach (TRB), Rope Beach (RB), Bird Rock (BR)

Follow Sir Francis Drake towards the lighthouse. Turn right onto Pierce Point Rd. towards

Tomales Bay State Park. Follow the road into the Tule Elk reserve and park at the Upper Pierce

Ranch parking lot and take the Tomales Point Trail.

Two Rock Beach: Two Rock Beach is the first subsite you will survey. You will begin to hike up

a large hill about 15-20 minutes into the hike. About three-quarters the way up the hill, you will

pass a fenced enclosure on your right. About 2-3 minutes past this enclosure you will pass the

first rock outcroppings. At this point the path is still uphill. 8-10 minutes after passing the

enclosure you will reach the crest of the hill. About 2-minutes after you have passed the crest of

the hill you will arrive at a large rock outcropping, located about twenty feet from the left side of

the trail. This rock out cropping is an important landmark. It is on your left, twenty feet from the

trail. Forty feet past the rock outcropping is a water bar on the right that points towards Tomales

Bay.

Stand on the trail facing the pile of rocks and pretend that the pile of rocks is at 12 o’clock. Then

hold your right arm out so that it is pointing towards an imaginary 2 o’clock. Walk in this

direction. You will cross a long gully. Keep going towards the coast until you reach the

observation point. From the observation point look back south towards the lighthouse or

McClures Beach, you should be able to see the beach as well as a variety of flat rocks along the

shore. It is on these flat rocks where the harbor seals usually haul out. Two Rock Beach is so

named because each side of the beach has two large rocks, approximately 100m from shore.

Make a count and then return to Tomales Point trail.

The alternative way to get to the observation site for TRB is to walk past the main rock

outcropping landmark. To your left are grasses. After a 4-5 minute walk past the rock

outcropping you will come to several coyote brush bushes that are touching the trail. Turn left at

the second coyote bush on your left and walk directly towards the coast. The rocks should be

directly below you and the beach, south of you.

Rope Beach: After returning to the Tomales Point trail, continue north. You will go down a long

gradual hill. Near the bottom of the hill, on your right will be a pond and ahead will be a line of
72

tall trees. This is Lower Pierce Point ranch. Go around the west side, or ocean side, of the trees

and head for the coast. Walk north along the coast counting as you go. Continue to walk north

along the coast until Bird Rock is easy to survey. Seals can be hauled out on any of the many

rocks and beaches along this segment of the coast, so remember to look down over the cliffs

often to makes sure you are not missing any of them. During breeding season you will need to

hike until you are directly across from Bird Rock, then look back at the beach across from Bird

Rock, in order to see all of the seals.

Bird Rock: Bird Rock is north of Rope Beach. Bird Rock is a large white rock about 400 yards

from shore, where shorebirds nest and seals haul out. Hike north until you are confident in your

ability to count the seals on Bird Rock. Count here twice, then survey RB and TRB on your way

back.

4.1.6 Tomales Bay

Subsites: Seal Island (SI), Clam Island (CI) Hog Island (HI).

Follow Sir Francis Drake towards the lighthouse. Turn right onto Pierce Point Rd. towards

Tomales Bay State Park. Follow the road into the Tule Elk reserve and park at the Upper Pierce

Ranch parking lot and take the Tomales Point Trail.

You will begin to hike up a large hill about 15-20 minutes into the hike. About three-quarters the

way up the hill, you will pass a fenced enclosure on your right. About 2-3 minutes past this

enclosure you will pass the first rock outcroppings. At this point the path is still uphill. 8-10

minutes after passing the enclosure you will reach the crest of the hill. About 2-minutes after you

have passed the crest of the hill you will arrive at a large rock outcropping, located about twenty

feet from the left side of the trail. This rock out cropping is an important landmark. It is on your

left, twenty feet from the trail. Forty feet past the rock outcropping is a water bar on the right that

points towards Tomales Bay. Continue walking 50-100 yards past the rock outcropping then turn

right and cut across the field towards the bay. Hike down towards the bay until you have a good

view of the sandbars down below in the bay. It may take some experimentation to find the best

spot to count from. Seal Island and Clam Island, which are both sandbars, should be in front of

you while Hog Island will be way off to the right. Seal Island is the sandbar closer to you, while

Clam Island is the sandbar further away from you.

4.1.7 Point Bointa

Subsites: # 1–20.

From Hwy 101 take the Alexander Avenue/Marin County exit. Turn right at the stop sign on to

Alexander Avenue. After approximately 100-200 yards, turn left towards the tunnel on Bunker

Road (look for Marin Headlands Visitor Center sign). You will drive through a one-way traffic

tunnel. There may be up to a five minute wait to enter the tunnel. Continue on Bunker Road to its

intersection with Field Road. Turn left onto Field Road. You will pass the Headlands Visitor

Center and the historic Nike Missile Site. Follow signs to the Point Bonita Lighthouse. This site

involves a very short walk and looks down upon a group of rocks on which the harbor seals haul

out.
73

4.2 Field Visit Schedule

A monthly field schedule is maintained by the volunteer coordinator and updated once per week.

The coordinator ensures that each site is covered a minimum of once per week, but ideally twice

per week with one survey during a weekday and one on the weekend. During the peak of the

breeding season (mid-April to mid-May) extra effort is made to ensure that sites are surveyed

twice per week, and surveys are promptly re-scheduled if canceled due to weather. The weekly

updated schedule is emailed to the volunteers weekly.

All surveys are scheduled through an online calendar that is private to the public. This allows the

volunteers to check available survey dates and to notify the volunteer coordinator when they are

available to survey. Most recently, an online Google calendar has been used in which editing

privileges are limited to volunteer coordinators at PORE and GOGA.

At the beginning of the field season, the project managers develop a list of regional survey dates.

The dates occur every other Saturday beginning in early March until the end of July, but occur

every Saturday during the peak breeding season. The volunteer coordinator ensures that all sites

are monitored at least once during the regional surveys. Any survey that occurs within two days

of the selected regional survey date, or Thursday through Monday, is accepted as a regional

survey. The regional survey dates are also distributed to harbor seal researchers and volunteer

groups working in San Francisco Bay, on the Sonoma County coast, and along the San Mateo

County coast. The project managers compile data from outside the NPS study area and manage

this data separately from the I&M program.

4.3 Field Forms

Three field survey forms are presented in Appendix SOP 1 B, including:

x Harbor seal census form

x Harbor seal disturbance form

Digital copies of forms are located at inppore05\Resources\Science\Phoca\Form\PhocaForm.doc

Maps are located at inppore05\Resources\Science\Phoca\Fieldmaps. A separate census form is

designed for Point Bonita with an inset map depicting the numbered sub-sites at the bottom of

the form.

4.4 Surveys

Surveys include collecting census data and recording disturbance events. For each site visit,

volunteers retrieve equipment and survey forms from outside storage containers distributed in the

parks and then go to their assigned survey location. For each survey, volunteers should collect

the needed equipment (listed above) from the storage containers or provide their own. Each

survey site has a specific field map with marked locations for observation site and where the

seals haul-out (Appendix SOP 1A).

4.4.1 Census Data

Observers count all harbor seals onshore at each site by subsite where seals are hauled out and

separate out age class into two categories (adults/immatures and pups). Pups may be documented

as early as mid-February, but after May 31, all seal age classes are combined because pups

cannot be easily distinguished from immature seals. Other data collected include number of red-
74

pelaged seals, number of fresh shark attacked seals, and number of dead pups. Red pelage is

easily identified and results from the deposition of iron oxide precipitates on the hair shaft; it

usually extends from the head down to the shoulder and is of interest due to its rarity outside of

the San Francisco Bay Area (Allen et al. 1993). In the comments section, observers can add

information on dead or stranded seals and any marked seals (radio or flipper tag).

To maximize the number of seals on the haul out site, surveys should be conducted between a

medium (2.5 ft) to a low (-1.0 ft) tide level during mid-day (Allen et al. 1985; Grigg et al. 2002).

The tide time and tide level is standardized to San Francisco, Pacific Standard Time, as

documented in local tide books. During weeks with early morning low tides, survey times should

be adjusted accordingly. For example, if low tide of –1.0 is at 7am, a survey should be conducted

between 8–11 am.

To help plan accordingly, the following tide time adjustments should be taken into account for

each site.

Tomales Bay +30 min

Tomales Point -30 min

Point Reyes Headlands -25 min

Drakes Estero +45 min

Double Point -30 min

Duxbury Reef -25 min

Bolinas Lagoon +37 min

Point Bonita no correction

Survey period lasts at least two hours, with counts occurring every half-hour. The number of

seals in the water and/or moving between sites fluctuates; therefore, multiple counts within a

two-hour period better reflect the maximum number of seals present. Each subsite is surveyed

separately, comprising a grand total for the site. All subsites at each site are visible from one site

location with the exception of Tomales Point and Bolinas Lagoon, where the subsites are a

considerable distance from each other, and are usually counted twice during a survey event

(instead of four times at other sites).

The survey start and end times are intended to capture the time spent on site with the harbor seals

within view. The start time should represent the time that the observer arrives on site and begins

preparing for the survey. The end time should be the time that the observer physically leaves the

survey site.

All harbor seal counts are recorded by subsite, and all subsites with seals must be recorded

during each count. For ease of data entry in the database, only the start time of each count needs

to be recorded on the datasheet and not the exact time that each subsite is counted. In addition,

only subsites where seals are present need to be recorded on the datasheet.

Additional data included in the form are weather and other species of note. Weather data are

limited to visibility that may affect observers’ ability to see the seals and rain, which can cause

seals to haul out in lower numbers (Jemison and Pendleton 2001). Information on white and
75

brown pelicans is included on the form because both species are of interest and often occur in the

same area as the seals. Brown pelicans are a federally threatened species and occur in the parks

most months of the year and white pelicans are a species of concern in the state of California.

Observers should count the number of pelicans roosting within view on rocks or sandbars

following the first harbor seal count.

Finally, the observer must note whether or not all of the subsites were surveyed, yes or no. This

notation is intended to capture whether or not more seals may have been present during the

survey but were not counted, perhaps due to poor visibility. If subsites are underwater during the

survey due to tide height or swell conditions, this does not mean that all of the subsites were not

surveyed.

4.4.2 Disturbance Events

Disturbance data include any potential or actual disturbance of the seals while they are resting

onshore causing them to alter their behavior. Tracking disturbances allows us to monitor the

amount of activity, especially human activity, in an area. By recording the seals’ reactions to

these events we will also be able to observe trends or changes in their reactions or use of haul-out

sites. An example of a trend is chronic flushing, which may lead to the desertion of a site.

Information collected includes source for disturbance (various anthropogenic or nonanthropogenic sources) and seal response (a gradient from no response to flush into water).

Disturbance data is collected as needed during harbor seal surveys.

Actual disturbance events occur when at least one of three harbor seal behaviors are observed:

x Head-Alert (HA): when a resting seal raises its head and clearly looks around. The seal’s

eyes are open, and the seal is not scratching itself. Note Head-Alerts only if > 5 seals

exhibit this behavior.

x Flush (F): seal movement towards the water but not completely in the water. Rising tides

do not constitute approaching the water.

x Flush Water (FW): when, in one continuous movement, seals stampede from their haulout site and completely enter the water.

When a disturbance event occurs, the observer notes the time of the disturbance, identifies the

source of the disturbance, and records the seal response at each affected subsite. Data columns

relating to the number of seals before the disturbance, the number of seals that remain on site,

etc., only relate to FW disturbance events.

One disturbance source may affect multiple subsites with varying responses, all of which should

be recorded on the datasheet. In addition multiple seal responses may be observed for one

subsite; however, only the strongest reaction per subsite is recorded on the datasheet and entered

in the database. For example, if some seals at a subsite head-alert and some flush as the result of

a disturbance, the disturbance should be recorded as “flush” on the datasheet for that subsite.

Single disturbance sources, such as a kayaker, may result in more than one disturbance event.

However, separate disturbance events for the same source should only be recorded if the source

departs from the haulout area of influence, if the seals are observed to return to state of rest, or if
76

a period of greater than 20 minutes passes. For example, a kayaker traveling south through

Drakes Estero may disturb several subsites along the way. These disturbances should be recorded

as one event, even though several minutes may pass from the time the first subsite is disturbed

until the last. If the kayaker returns north later in the day and again disturbs subsites, then this

would be counted as a new disturbance event. It is helpful to note in the comments that this is the

same disturbance source. Following these guidelines will prevent the error of counting single

disturbances events/sources multiple times when summarizing the data.

Table SOP 1.2 lists the specific sources of disturbances collected by the harbor seal monitoring

program from 2000-2007. Observers should reference this table in order to correctly categorize

disturbance source observed in the field. The table follows data entry specifications designed in

the project database, which allows for the disturbance data to be more easily and more correctly

summarized.

In addition, the harbor seal observers record potential disturbances to harbor seal haul-out areas.

Potential disturbances are recorded when a disturbance source is observed that does not appear to

elicit a response from the harbor seals. Examples might include a low-flying aircraft or a nearby

coyote.

Table SOP 1.2. Harbor seal disturbance source groups and specific sources collected in the field.

Categories are standardized to facilitate data entry and summarization.

Vehicular Type Disturbance Sources Human Type Disturbance Sources

Source Source Specific Source Source Specific

vehicle car fisherman

vehicle truck clammer

vehicle motorcycle human hikers

vehicle bus human visitors / tourists

vehicle ambulance human photographers

aircraft small plane human divers

aircraft jumbo jet human surfers

aircraft helicopter human oyster workers

aircraft hang glider human horse riders

aircraft ultralite human joggers

non-motor boat kayak human bicyclists

non-motor boat canoe human other workers

non-motor boat sailboat researcher

non-motor boat row boat school group

non-motor boat wind surfer

motor boat fishing boat Other Disturbance Source Types

motor boat tug boat Source Source Specific

motor boat sailboat w/engine dog

motor boat jet skis coyote

motor boat park ranger boat bobcat

motor boat oyster boat bird sea gull, etc.

motor boat clam boat other rock slide, etc

5.0 Literature Cited

Allen, S. G., D. G. Ainley, G. W. Page, and C. A. Ribic. 1985. The effect of disturbance on

harbor seal haul out patterns at Bolinas Lagoon, California, 1978–1979. U. S. Fishery

Bulletin 82:493-500.
77

Allen, S. G., M. Stephenson, R. W. Risebrough, L. Fancher, A. Shiller, and D. Smith. 1993. Redpelaged harbor seals of the San Francisco Bay Region. Journal of Mammology. 74(3):588–

593.

Grigg, E. K., D. E. Green, S. G. Allen, and H. Markowitz. 2002. Diurnal and nocturnal haul out

patterns of harbor seals (Phoca vitulina richardsi) at Castro Rocks, San Francisco Bay,

California. California Fish and Game 88 (1).

Jemison, L.A. and G.W. Pendleton. 2001. Harbor seal population trends and factors influencing

counts on Tugidak Island, Alaska. Pages 31–52 in: Harbor Seal Investigations in Alaska.

Annual Report for NOAA Award NA87FX0300. Alaska Department of Fish and Game.

Division of Wildlife Conservation, Anchorage, AK. 356 pp.
78

Appendix SOP 1A. Harbor Seal Site Maps.

Map of Bolinas Lagoon haulout sites. Subsites include: KI = Kent Island, HWY1 = Highway 1 sand bars,

PWI = Pickle Weed Island. X = Observation Points.
79

Map of Duxbury Reef haulout site. Subsite DUX notes location of haul out site. X = Observation Point.
80

Map of Double Point haulout sites. Subsites include: SS = Stormy Stack, NBR = North Beach Rocks, NB

= North Beach, SB = South Beach, TP = Tide Pools, SP = South Point.
81

Map of Drakes Estero haulout sites. Subsites include: UEF = Upper Estero Far, OB = Oyster Bar, UEN =

Upper Estero Near, A = A Sandbar, A1 = A1 Sandbar, DB = Drakes Beach, DEM = Drakes Estero Mouth,

L = Limantour Spit.
82

Map of Tomales Point haulout sites. Subsites include: BR = Bird Rock, RB = Rope Beach, TRB = Two

Rock Beach.
83

Map of Tomales Bay haulout sites. Subsites include: SI = Seal Island, CI = Clam Island, HI = Hog Island.
84

Map of Point Bonita haulout site. X = Observation Point. Dotted black line denotes area of harbor seal

haulout. Refer to Point Bonita data sheet (Appendix SOP 1 A) for a diagram of subsites, which for Point

Bonita are predominantly numbered rocks.
85

Appendix SOP 1B. Harbor Seal Field Datasheets.

Harbor seal census data form.
86

Harbor seal disturbance data form.
87

Point Bonita harbor seal census data form.

89

SOP 2. Northern Elephant Seal Surveys

Version 1.5

Revision History Log

Prev. Version # Revision Date Author Changes Made Reason for

Change

New

Version #

1.0 March 2008 Marcus

Koenen,

Dave Press,

Heather

Jensen

General editing.

Combine with SOP 4

and 6. Added

Appendixes A and B.

Update. 1.1

1.1 June 2008 Dawn

Adams,

Sarah Allen

Additional methods

information, format

and layout.

update 1.2

1.2 September

2009

D. Press, M.

Koenen, S.

Allen

Edits to SOP format

and layout.

Preparation for final

protocol

submission.

1.3

1.3 November

2009

K. Freeman,

D. Press

Changed tables and

figures to a modular

numbering system,

added a literature

cited section,

additional minor edits.

Formatting

requirements.

1.4

1.4 December

2009

D. Press Minor grammatical

edits.

Comments from

Penny Latham.

1.5
90

Contents

Page

Figures......................................................................................................................................91

Tables .......................................................................................................................................91

Appendixes ...............................................................................................................................91

1.0 Field Schedule.....................................................................................................................92

2.0 Volunteers...........................................................................................................................93

2.1 Observer Requirements................................................................................................93

3.0 Field Equipment and Preparation.........................................................................................93

3.1 Beach Signs.................................................................................................................94

3.2 Plastic Flipper Tag Preparation ....................................................................................94

4.0 Field Methods .....................................................................................................................95

4.1 Field Forms .................................................................................................................95

4.2 Survey Sites.................................................................................................................96

4.3 Field Visit Schedule.....................................................................................................96

4.4 Surveys........................................................................................................................97

4.4.1 Full Count Surveys............................................................................................97

4.4.2 Resight Surveys ................................................................................................99

5.0 Literature Cited .................................................................................................................102
91

Figures

Page

Figure SOP 2.1. Drill code for flipper tag letters and numbers...................................................94

Figure SOP 2.2. Northern elephant seal aging and sexing chart (Le Boeuf and

Laws 1994). ..............................................................................................................................98

Figure SOP 2.3. Example of northern elephant seal resight observation data. ..........................101

Figure SOP 2.4. Dorsal view diagram of northern elephant seal rear flippers...........................102

Tables

Page

Table SOP 2.1 Annual SFAN northern elephant seal monitoring field schedule. .......................92

Appendixes

Pages

Appendix SOP 2A. Northern Elephant Seal Census, Resight Survey Forms, and Scar

Cards.......................................................................................................................................103

Appendix SOP 2B. Northern Elephant Seal Survey Maps .......................................................106
92

This SOP details field preparation and field methods for monitoring northern elephant seals at

Point Reyes National Seashore. Data sheets and maps to observation sites are attached.

1.0 Field Schedule

The field season for northern elephant seal monitoring begins in November and continues to the

end of March (Table SOP 2.1). Field preparation begins in November and December. Field

surveys for the breeding season are conducted December 1 through March 31. Scheduling

surveys and volunteers is coordinated by the lead field biologist or volunteer coordinator for the

northern elephant seal project. The proposed survey dates for each month are distributed to

volunteers via e-mail usually a month in advance. Weather can be unpredictable and surveys

occasionally get cancelled or rescheduled at the last minute due to rain or fog. The weekly

updated schedule is maintained on a wall-calendar in the Science office. For each scheduled

survey day, the type of survey, observer initials, and low tide time and height are written on the

calendar.

Table SOP 2.1 Annual SFAN northern elephant seal monitoring field schedule.

Activity Oct Nov Dec Jan Feb March Aug Sept

Northern elephant Seal BioTechnician Starts

Pre-season meeting with

park managers

Equipment Preparation

Contact Volunteers

Train Volunteers

Beach Signs

Adult Dye Marking

Census

Field Work (1x weekly)

Census Field Work (2x

weekly)

Re-Sight Survey (2x

weekly)

Flipper Tag Preparation

Weaned Pup Flipper

Tagging

Annual Report Completed
93

2.0 Volunteers

Volunteers assist the field biologist by independently collecting field data. Volunteers receive

hands on training and must meet all of the observer requirements.

2.1 Observer Requirements

Observers should be physically fit, and have experience observing wildlife, particularly seals.

Observers must have the ability to use binoculars and spotting scope; ability to record data into a

field form and computer database; be in excellent physical shape to hike several miles in rugged

terrain and carry a backpack with up to 30 lbs; and to hike off trail and orient using a topographic

map. Training for new observers includes intensive one-on-one field training over one breeding

season with the program manager or someone who has extensive experience studying northern

elephant seals (i.e. lead biological technician). Observers who are volunteers are asked to commit

to one survey every other week. Observers are expected to follow the same rules and signage as

visitors to Point Reyes National Seashore unless accompanied by a uniformed NPS employee or

given permission by NPS administration. An exception to this rule is that the split rail fence at

Chimney Rock must be crossed in order to get a clear view of the colony at Gus’ Cove. Before

new volunteers participate in fieldwork, a volunteer form should be completed.

3.0 Field Equipment and Preparation

In October, equipment needs are reviewed and missing or damaged items are replaced.

Equipment for observers is housed in the Science office.

Equipment includes:

Binoculars (3)

Spotting scopes and tripods (3)

Hand counters (5)

Digital camera

Marking equipment

Hand-held pliers for attaching flipper tags (4; Dalton Veterinary Supplies)

Plastic tags (Dalton Veterinary Supplies; jumbo-roto tags; color pink;

series P, H, R, J, K-0)

Hair dye (Lady Clairol blue-black hair dye- donation)

Rope ladder and 50 feet of climbing rope

5” x 8” field binders with data forms

Field vest for carrying gear and identification as NPS biologist (2)

Laminate and laminator for signage

Optical equipment is easily damaged by salt air, wind and dust/sand and should be wiped down

with a damp cloth after each use. Other optical cleaning products include items such as Eagle

Optics Lenspens or microfiber cloth.
94

3.1 Beach Signs

Beach restrictions go into effect in late November and early December when adult male northern

elephant seals arrive on the colony beaches. A total of 14 laminated signs are posted at

prominent beach access points in the Point Reyes Headlands and on the edges of the northern

elephant seal colonies where northern elephant seals breed. The purpose of the signs is to warn

park visitors of the temporary beach closures to prevent visitors from entering or walking above

the colonies. All signage should be in place by December 15th. Facilities Management and

Visitor Services staff assist in the placement of signs.

Signage should be strategically placed in highly visible locations. In some locations, the area

may need to be roped off (i.e., Lifeboat Station and north end of North Drakes Beach). Each sign

requires: a sign post, a 9x12” plywood sign board, 8x11 1⁄2” laminated sign or map based on

location, 2 bolts, 2 nuts, and 2 washers. A post pounder will be needed for installation of the

signs.

Several templates and guidance documents have been prepared and stored on the PORE server to

streamline sign creation and placement, including:

Signage maps: inppore07\GIS\vector1\wildlife\marine\pinnipeds\arcview

Signage templates without map: inppore05\Resources\Science\ESeal\SealSigns

Signage placement images: inppore05\Resources\Science\ESeal\SealSigns\Sign

Location Images.ppt

Signage placement guidance: inppore05\Resources\Science\ESeal\SealSigns\

ESsignplan.doc

3.2 Plastic Flipper Tag Preparation

Annually, approximately 250 northern elephant seals are flipper tagged, the majority of which

are weaned pups. Tags are prepared at the beginning of each season. Each flipper tag is drilled

with a dremel tool using an established drill pattern (Figure SOP 2.1) for letters (P, R, H, J, and

K) and the numbers (0-9). The letter “M” does not have a drill pattern.

Figure SOP 2.1. Drill code for flipper tag letters and numbers.
95

Tags ready to be drilled should be placed on a small wooden board with a layer of cardboard on

the top to avoid the premature wearing of the drill bits. Safety glasses should be worn during

drilling.

As a result of the drilling process, plastic will need to be scraped from the tag using a pocket

knife so that the surface of the tag is relatively smooth. The final step of tag preparation is to

match the corresponding male and female ends of each individual tag and then string and label

the tag sets numerically in groups of ten using masking tape. If any tags are destroyed during the

drilling process include them with the other tags on the string, but place a large “X” on either

side of the masking tape to indicate it is unusable. When a tag with an “X” is encountered in the

field while tagging, the data recorder should record the tag letter/number sequence in the left or

right tag number box and place a “9” in the code box on the resight data form.

By January, the drilling and stringing of flipper tags should be completed and ready for the

tagging of weaned pups. Equipment used for tag drilling includes:

Dremel tool (extra bits)

Three prong extension cord

Safety glasses

Key to drill patterns

Pocket knife

Masking Tape and sharpie

Small wooden board with cardboard on top

4.0 Field Methods

Field methods include full count surveys and re-sight surveys, which may include all or some of

the following activities: flipper tagging, dye-marking, and tag re-sighting. All field work is

conducted during the breeding season (December through March). Early northern elephant seal

arrivals are captured in the all pinniped species monitoring surveys. A complete census of

northern elephant seals is conducted a minimum of once per week at all breeding sites and

subsites within Point Reyes National Seashore (PORE) beginning in December. Surveys to resight tagged individuals occur once every two weeks at a minimum on the easily accessible

beaches (NDB, SB). Re-sight surveys to Point Reyes Headlands (PRH) sites typically occur only

in December, early January and March because of concerns for human safety. The PRH sites

have difficult access, a higher density of seals, and increased seal movement on the beach.

4.1 Field Forms

There are three survey forms, one for Full Count (Census) Surveys and two for Resight Surveys

(Appendix SOP 2A). Digital copies of forms are located at inppore05\Resources\Science\Eseal\

Forms and SOPs\Data_Forms.

Northern elephant seal survey form (Full Count/Census)

Northern elephant seal resight form (Resight)

Northern elephant seal mark form (Scar Card)
96

Always use one of the three standardized data forms to ensure all essential information has been

collected. Observational data that should be collected during census and resight surveys include

number of seals with fresh shark bites, number of dead seals, and any marked seals (dye mark,

brand, radio, or flipper tags).

4.2 Survey Sites

Northern elephant seals breed at three sites in PORE including North Drake’s Beach (NDB),

Point Reyes Headland (PRH), and South Beach (SB) (Protocol Narrative, Figure 6). To facilitate

a more accurate census, the three main breeding sites are further subdivided based on proximity

to one another. There are four sub-sites within NDB: North Drakes Beach (NDB), Lifeboat

Station (LBS), Gus’s Cove (GUS), and Chimney Rock Cove (CRC). There are seven sub-sites at

PRH: Cove 1 (C1), Cove 2 (C2), Cove 3 (C3), Cove 4 (C4), Tip Beach (TIP), Loser Beach (LB),

and Dead Seal Beach (DSB). At SB, there are three sub-sites: Lighthouse Beach (LTH), Nunes

Ranch Beach (NUN), and Mendoza Ranch Beach (MEN). Maps of the northern elephant seal

breeding sites are in Appendix SOP 2B.

Appendix SOP 2B consists of one general map of all survey locations with positional

information on the northern elephant seal haul out sites, and specific location maps with the

observation points. Additional maps will be provided as new locations are established.

ESRI ArcMap and Arcview files for reproducing or updating maps are located at

inppore07\GIS\vector1\wildlife\marine\pinnipeds. Seal haul out sites and observer positions are

represented as point locations in the maps. In addition, the project MS Access database stores

UTM locations of pinniped haul-out and colony sites within the locations table (see SOP 3: Data

Management).

To produce quick maps with no changes, files are located at inppore05\Resources\Science\Eseal\

Forms and SOPs\Maps.

4.3 Field Visit Schedule

In December and March, full counts are conducted once per week on Tuesdays with Wednesdays

as a back-up day in case of inclement weather conditions. During January and February, during

the height of the season, counts are conducted twice per week on a Monday and Thursday

schedule. Tuesdays and Fridays are used as back-up survey days in case of rain or fog.

Resight surveys depend on safe access to the northern elephant seal colonies and the timing of

resight surveys coincides with low tide. Allow enough time to exit the beach safely. Resight

surveys can be completed on the same day the full count is completed.

If very large storms with large ocean swell are predicted during any given week, extra effort

should be made to conduct a survey immediately before and immediately after the storm in order

to document any losses due to wash out by storm waves. Documenting storm effects on the

colony during a large storm is also important to determining the extent of mortality and the

movement of females to new colony sites.
97

4.4 Surveys

4.4.1 Full Count Surveys

During December to March of each breeding season, full count (census) surveys of northern

elephant seals are conducted a minimum of once per week at all breeding sites and associated

subsites within PORE. From mid-January to the end of February, two censuses per week are

conducted to try to capture the peak female and pup/weaned pup counts. Full pinniped surveys,

which include SLO in addition to the northern elephant seal sites and subsites, are completed

once per week.

Seals are counted from fixed vantage points on cliffs with the aid of a 40X spotting scope and 8-

10X binoculars. Counts are completed from pre-determined observation locations to maintain

consistency between observers and data collection (Appendix SOP 2B).

Sex and age groups are tallied within each sub-site; adult female (Cow), bull male (Bull), subadult male classes 1-4 (SA1-4), immature (IMM), yearling (YRLNG), pup, dead pup, and

weaned pup (WNR). Male age classes are distinguished by the extent of the chest shield, the

length of the proboscis, and overall body length (Figure SOP 2.2; Le Boeuf and Laws 1994).

Immature and SA1 age groups are not identified on the aging chart. Immature, SA1, and cow

(female) northern elephant seals are indistinguishable unless a ventral (belly) view is obtained to

positively identify sex. When present, harbor seals and pups, California Sea Lions, and any other

pinniped species are also recorded on the survey data sheet.

At the onset of the breeding season (November-December), large numbers of young northern

elephant seals are hauled out on the breeding beaches and it is not time efficient or realistic to

identify the sex of all animals. A concerted effort is made to identify adult females early in the

breeding season, but the immature classification encompasses both male and female sexes and is

used when sexes can not be determined. SA1 can be used when a young male lacking any sign of

a proboscis can be positively sexed, but a large amount of effort should not be placed in making

this determination. Overall, SA1 is used infrequently for age classification.

Seals in the water are not counted as a part of the census surveys; however, any unusual activities

in the nearshore waters should be added to the comments section. To maximize the number of

seals on the haul out sites, surveys should be conducted between a medium (3.0 ft) to a low (-1.0

ft) tide level. Time of day is not a limiting constraint when conducting surveys since northern

elephant seals are hauled out all day long.

Time commitment for each survey is a minimum of four hours. Full count surveys should be

completed in a single day. It is acceptable (although not ideal) to stretch the survey out over two

day and finish the full count within 24 hours or by the close of the subsequent survey day only if

weather prohibits survey completion within a single day.

To avoid disturbance of roosting or nesting Common Murres (Uria aalge), the TIP subsite of

PRH should not be accessed when murres are present on the offshore rocks. A rough count of

murres should be completed and added to the comments section of the data form.
98

Figure SOP 2.2. Northern elephant seal aging and sexing chart (Le Boeuf and Laws 1994).
99

4.4.2 Resight Surveys

Dye Marking: Temporary dye-marking is used in some years to identify individual breeding

adults, and to document adult and sub-adult male movement. Alpha and Beta bulls are the

primary target for marking, and if the animal does not have a tag, they are also flipper tagged

along with the dye mark. Dye marking occurs early in the breeding season (NovemberDecember). Dye marks allow individual identification without needing to read the tags each visit

during a season. Dyes are applied with “Lady Clairol, Natural Blue-Black” human hair dye using

the applicator bottle and using a series of individual alpha-numeric codes. Each dye mark

includes the first letter of the name of the breeding site (i.e.: “M”= Main Colony, “S”= South

Beach, “D”= Drakes Beach, etc.) where the animal was dye marked and is followed by a unique

number based on a consecutive numbering system. Finally, the dye mark is underlined to avoid

number confusion (i.e. 6 vs 9). For example, the first animal dye marked at South Beach would

be S1 and the second individual dye marked would be S2 and so on. If possible, marks are placed

on the back and side of the animal to insure good visibility of the mark from a distance. Any

flipper tags present on the animal should be recorded when dye marking occurs. The orientation

and shape of the dye-mark is recorded on a “scar card” to help field staff identify difficult to read

dye marks during subsequent observations. The hair dye is innocuous to the seals and the mark

goes away after the annual fur molt. In addition, marked males increase the ability of volunteer

northern elephant seal docents to track individuals from the Northern Elephant Seal Overlook

above the North Drakes Beach population and educate park visitors about the monitoring study.

Flipper Tagging: Individually marking animals allows researchers to estimate survivorship, site

fidelity, and emigration rates. Colony-specific tag color and serial numbers allow researchers to

track individuals over many years, with the potential to also study individual animal

productivity. Similar to the procedures at other northern elephant seal colonies, we apply

individually numbered plastic tags (Dalton brand) to the hind flipper of weaned pups born at

PORE under National Marine Fisheries Service (NMFS) permits 373-1868-00.

Beginning in 1988, weaned pups have been tagged at PORE and each year the number tagged

ranged between 150-300, as the colony grew. Until 1998, the number of weaned pups tagged

each year roughly approximated the total number of pups surviving to weaning. Due to the high

pup mortality and reduced colony access during the 1998 El Niño storm events, only about 27%

of the pups produced were tagged. Between 1999 and 2004, approximately 55% to 94% of the

pups produced were tagged. Since 2005, the number of pups surviving to weaning has far

surpassed the number researchers were able to tag. Since 2000, the general goal as outlined in the

NMFS permit is to tag 200-300 weaned pups each year. Double-tagging (tagging both hind

flippers) is done to estimate tag loss and to increase the chance of resighting an animal, since

both flippers are not always visible. At PORE, double-tagging is done opportunistically only

because we do not restrain the seals when tagging as occurs at other colony sites. When possible,

we also tag a few adult males to track inter-site movement.

Ideally, tags are applied when seals are sleeping and done using a Dalton brand tag and tag

applicator in the fleshy, inter-digit webbing of the hind flippers. Two researchers are required

during any tagging event, with one tagging and one as a safety lookout for other seals. The

resight survey form is used to record data (Appendix SOP 2A). Location of seal, flipper tag

number, color, side (left or right), and position among the inter-digit webs (round or square) are

recorded for each tagged animal. Nursing activities and pup size class (P1-4) are recorded if the
100

animal is an adult-sized female. Dominancy on the beach (alpha, beta, not associated) is recorded

if the animal is a sub-adult 4 or bull male.

Tag Resighting: Surveys to resight tagged seals are not currently part of the monitoring

objectives for the pinniped monitoring program, but continue as part of the Seashore

commitment to NMFS and other researchers that tag weaned northern elephant seals. SFAN is

not analyzing the tag resight data collected yearly, but PORE is participating in a range-wide tag

resight analysis with researchers working at other northern elephant seal monitoring sites through

the University of California, Santa Cruz.

The resight surveys occur one to two times per week during the breeding season. The first resight

survey of the breeding season usually occurs in mid-December with the purpose of dye marking

large, dominant males and reading flipper tags. Due to ease of access, weekly resight surveys can

occur at GUS, NDB, DSB, or SB. If biweekly resight surveys are completed, resight efforts are

spread out between the breeding locations although NDB takes more effort due to the high

density of animals and can be covered twice in one week. Resight surveys at PRH are restricted

to early and late in the breeding season due to safety concerns (i.e., high seal density and access

issues).

Resight surveys require a minimum of two persons for efficient and accurate data collection and

for safety reasons. Observers can usually only access sites during medium to low tide levels to

conduct these surveys. Seals are hauled out regardless of time of day. Surveys usually require 2-

4 hours to complete. Researchers should radio into dispatch indicating their location and number

of observers prior to and upon completion of each survey.

Resight Data Form: The resight survey form is used for all flipper tagging, dye marking, and

tag resighting activities. Observers record all seals with flipper tags or dye markings applied or

identified at each site surveyed. When possible, the unique letter and/or number sequence of each

flipper tag and/or dye mark should be confirmed with a second view of the tag/dye mark or by

another observer. The mark (dye or tag number) should be recorded, along with the sex, age

class and the reproductive status of the seal. Categories include Bull, Male Sub-adult 4, Male

Sub-adult 3, Male Sub-adult 2, Male Sub-adult 1, Other Sub-adult Male, Cow, Pup, Dead Pup,

Weaned Pup, Immature of unknown sex, Yearling. Only record what is “positively” seen on

resight surveys. Leave sex unknown for immatures, yearlings, and weaned pups unless the sex

can be positively determined with ventral view of animal. Tag/dye determinations should be

checked for quality and accuracy by comparing hardcopy field data with historical database

information. All corrections to hardcopy data should be completed in red pencil or ink.

For each northern elephant seal resight survey, the minimum amount of information must be

recorded including, but not limited to Date, Time (beginning and ending), Observers, and

Visibility. For each resight observation during the survey, record the Site, Sub-site, Size (age

class), Sex, Dye mark (if present), L (Left) Tag Number, and R (Right) Tag Number (Figure

SOP 2.3).

Left and right tag number information should always be recorded and may include an actual tag

number/letter sequence or other information such as NR (tag present, but not read), NS (no tag

seen, but may be present), or NT (no tag). If an observer is only able to positively determine a
101

portion of the tag, the partial tag read can be recorded to the level of information known and an

underscore (_) can be placed under unknown or uncertain tag information. It may be possible to

determine the individual’s identity based on partial information with a search of the database.

For example (Figure SOP 2.3, line 1), an observer applied a dye mark of S6 to an SA4 male on

the lower right side of body and determined there was a green tag present in the left square

flipper position (Figure SOP 2.4), but was unable to read the tag. The observer also recorded a

partial tag read of a green tag in the right round flipper position (Figure SOP 2.4) with an L in

the first position, possibly a 1 in the 2nd position (not confirmed), a 2 in the 3rd position, and 3 in

the 4th position. A dye code of “2” indicates that the dye mark was newly applied. A tag code of

“1” indicates a questionable or incomplete tag read. All codes used on the resight form are noted

on the bottom of the datasheet (Appendix SOP 2A)

Figure SOP 2.3. Example of northern elephant seal resight observation data.

A second example (Figure SOP 2.3, line 2) is of a female with a pink flipper tag of K145 on the

left round flipper position (Figure SOP 2.4) and no view of a tag on the right flipper, but there

could be an unseen tag present. The female (cow) was associated with a newborn pup who was

nursing at the time of the observation.

Seal mark data form (Scar Card): Some individual seals are tracked throughout the breeding

season and for multiple years based on flipper tags, scars, and dye marks. Individual data forms

track the histories of these individuals (Appendix SOP 2A). A scar card should accompany each

dye marked animal to aid in resight efforts. These cards are especially useful with hard to read

dye marks. A scar card identifies where the animal was dye marked and records a realistic sketch

of the dye mark. The scar cards are used for reference only during the breeding season and are

not entered into the project database.
102

Figure SOP 2.4. Dorsal view diagram of northern elephant seal rear flippers. Square (S) and round (R)

lobes of flippers are noted. Flipper tag locations are (1) Left Square – LS (2) Left Square Bar – LSB (3)

Left Round Bar – LRB (4) Left Round - LR (5) Right Round - RR (6) Right Round Bar - RRB (7) Right

Square Bar - RSB (8) Right Square - RS.

5.0 Literature Cited

Le Boeuf, B. and R.M. Laws (eds.). 1994. Elephant seals: population ecology, behavior, and

physiology. University of California Press, Berkeley. 414 pp.
103

Appendix SOP 2A. Northern Elephant Seal Census,

Resight Survey Forms, and Scar Cards.
 104

*Actual resight data form contains 20 rows per page.
 105

Male and female northern elephant seal scar cards.
 106

Appendix SOP 2B. Northern Elephant Seal Survey Maps
107

LTH

NUN

MEN

End of cliffs

Creek outlet

Elephant seal breeding sites:

March 2008

South Beach

Photo taken from counting location near benchmark and cement block below

lower overlook accessed from lighthouse parking lot.

Parking lot

Counting location

Copyright © 2002-2005 Kenneth & Gabrielle Adelman,

California Coastal Records Project, www.californiacoastline.org
108

Cove 2

Cove 3 Cove 4

Tip

Cove 1

Elephant seal breeding sites: Point Reyes Headlands

Photo taken from cliff site which is one of the counting locations for the coves.
109

Copyright © 2002-2005 Kenneth & Gabrielle Adelman, California Coastal Records Project, www.californiacoastline.org

TIP Locations

Cove 1

Cove 2

Ridge splits coves 1 and 2

Elephant seal breeding sites: Point Reyes Headlands

Saddle (Cove 2, LB

Counting Location)

Loser Beach

(LB)
110

Copyright © 2002-2005 Kenneth & Gabrielle Adelman, California Coastal Records Project, www.californiacoastline.org

Loser Beach

(LB)

Dead Seal Beach (DSB)

Elephant seal breeding sites: Point Reyes Headlands
111

Elephant seal breeding sites: Chimney Rock Loop
112

 Copyright © 2002-2005 Kenneth & Gabrielle Adelman, California Coastal Records Project, www.californiacoastline.org

N

CRC

Elephant seal breeding sites: Chimney Rock Cove

Counting location
113

Copyright © 2002-2005 Kenneth & Gabrielle Adelman, California Coastal Records Project, www.californiacoastline.org

GUS

LBS

Elephant seal breeding sites: Gus’s Cove and Lifeboat Station

Counting location on hill below fenced overlook, at end of trail
114

LBS

LBS

Elephant seal breeding sites: Lifeboat Station

Alternate counting location for beach near actual

Lifeboat Station if you do not drive down to building.

This stretch of beach between is not regularly counted unless surveyors are hiking to Gus’ Cove

via the beach. Area currently contains no breeding sites, just subadult haul out sites.

Copyright © 2002-2005 Kenneth & Gabrielle Adelman, California Coastal Records Project, www.californiacoastline.org

This stretch of beach is not regularly counted unless surveyors are hiking to Gus’ Cove via the beach.

Area currently contains no breeding sites, just subadult haul out sites.
115

NDB

Elephant seal breeding sites: North Drakes Beach

Other animals

visible from the overlook

but beyond the NDB

colony can also be

counted in NDB

Photo taken from Overlook platform which is the counting location.
116

Copyright © 2002-2005 Kenneth & Gabrielle Adelman, California Coastal Records Project, www.californiacoastline.org

NDB

California Seal Lion haul out site: Seal Lion Overlook (SLO)

Overlook counting location

Area to be counted, including seals hauled out on

offshore rocks, but not including seals swimming

offshore.
117

SOP 3. Data Management

Version 1.5

Revision History Log

Prev.

Version

#

Revision

Date Author Changes Made Reason for Change

New

Version

#

September

2007

D. Roberts Used SFAN stream

flow data management

plan as template

1.0

1.0 March 2008 David Press,

Marcus Koenen

Review, edits, and

additions to version

1.0, Format

1.1

1.1 July 2008 David Press Added Figure 26.

Annual pinniped data

work flow.

1.2

1.2 September

2009

D. Press, M.

Koenen

Edits to SOP format

and layout. Added

descriptions of new

database features.

Preparation for final

protocol submission.

1.3

1.3 November

2009

K. Freeman,

D. Press

Changed tables and

figures to a modular

numbering system,

added a literature cited

section, additional

minor edits.

Formatting requirements. 1.4

1.4 December

2009

D. Press Minor grammatical

edits. Revised Table

SOP 3.9.

Comments from Penny

Latham.

1.5
118

Contents

Page

Figures....................................................................................................................................120

Tables .....................................................................................................................................122

1.0 Overview...........................................................................................................................123

1.1 Scope and Applicability.............................................................................................123

2.0 Description of Pinniped Monitoring Database ...................................................................123

2.1 Harbor Seal Monitoring .............................................................................................125

2.1.1 Harbor Seal Census Data Entry .......................................................................125

2.1.2 Harbor Seal Census Data Verification and Editing ..........................................129

2.1.3 Harbor Seal Disturbance Data Entry................................................................131

2.1.4 Harbor Seal Disturbance Data Verification and Editing ...................................132

2.2 Northern Elephant Seal and All Species Pinniped Monitoring....................................133

2.2.1 Northern Elephant Seal Census Data Entry......................................................134

2.2.2 Northern Elephant Seal Census Data Verification and Editing.........................136

2.2.3 Northern Elephant Seal Resight Data Entry.....................................................138

2.2.4 Northern Elephant Seal Resight Data Verification and Editing ........................140

2.3 Lookup Tables...........................................................................................................140

2.4 Data Reporting Tools.................................................................................................145

2.4.1 Summary Reports............................................................................................145

2.4.2 Summary Graphs.............................................................................................151

2.4.3 Summary Queries............................................................................................155

2.5 Data Export Functions ...............................................................................................156

3.0 Annual Data Work Flow....................................................................................................157

3.1 Annual Satellite Databases.........................................................................................157
119

3.2 Northern Elephant Seal and All Pinniped Count QA/QC............................................159

3.3 Harbor Seal QA/QC...................................................................................................159

3.4 Annual Data Integration with Master Pinniped Database............................................160

3.5 Master Point Bonita Database ....................................................................................160

4.0 Version Control Guidelines and Database History.............................................................162

5.0 Data Archival Procedures..................................................................................................162

6.0 Metadata Procedures .........................................................................................................163

7.0 Data Distribution...............................................................................................................163

8.0 Literature Cited .................................................................................................................164

Appendix SOP 3A. Pinniped Database Data Dictionary ..........................................................165
120

Figures

Page

Figure SOP 3.1. Relationships of tables which house harbor seal data. ....................................125

Figure SOP 3.2. Main menu which is displayed when the pinniped database is started. ...........126

Figure SOP 3.3. Enter and verify data menu............................................................................127

Figure SOP 3.4. Harbor seal data entry form and example of harbor seal count data

storage. ...................................................................................................................................128

Figure SOP 3.5. Harbor seal data verification and editing form. ..............................................130

Figure SOP 3.6. Harbor seal disturbance data entry form.........................................................132

Figure SOP 3.7. Harbor seal disturbance data verification and editing form.............................133

Figure SOP 3.8. Relationships of tables which house northern elephant seal data. ...................134

Figure SOP 3.9. Northern elephant seal data entry form and example of pinniped count

data storage.............................................................................................................................135

Figure SOP 3.10. Analyze Seal Data Menu. ............................................................................137

Figure SOP 3.11. Northern elephant seal data verification and editing form. ...........................138

Figure SOP 3.12. Northern elephant seal resight data entry form. ............................................139

Figure SOP 3.13. Northern elephant seal resight data verification and editing form. ................141

Figure SOP 3.14. Switchboard menu for accessing lookup tables. ...........................................142

Figure SOP 3.15. Viewing and editing form for the location table. ..........................................143

Figure SOP 3.16. Viewing and editing form for the listing of project observers.......................143

Figure SOP 3.17. Viewing and editing form for the listing of destroyed tags. ..........................144

Figure SOP 3.18. Report of harbor seal annual maximum daily count by location. ..................146

Figure SOP 3.19. Report of harbor seal disturbance count by year, location and

disturbance type. .....................................................................................................................147

Figure SOP 3.20. Report of harbor seal disturbance rate (first page of report)..........................148

Figure SOP 3.21. Daily northern elephant seal census report, all species. ................................150
121

Figure SOP 3.22. Daily northern elephant seal census report, northern elephant seals

only.........................................................................................................................................151

Figure SOP 3.23. Harbor seal maximum abundance by location..............................................152

Figure SOP 3.24. Harbor seal daily abundance for a single location. .......................................153

Figure SOP 3.25. Northern elephant seal daily abundance for all subsites combined. ..............154

Figure SOP 3.26. Export seal data form...................................................................................156

Figure SOP 3.27. Annual pinniped data work flow..................................................................158
122

Tables

Page

Table SOP 3.1. Forms and tables used for harbor seal data entry. ............................................129

Table SOP 3.2 Forms and tables used for harbor seal data verification. ...................................131

Table SOP 3.3. Forms and tables used for harbor seal disturbance data entry. .........................132

Table SOP 3.4. Forms, query and tables used for harbor seal disturbance data

verification..............................................................................................................................133

Table SOP 3.5. Forms and tables used for northern elephant seal data entry. ...........................136

Table SOP 3.6. Forms and tables used for northern elephant seal data verification. .................138

Table SOP 3.7. Forms and tables used for northern elephant seal resight data entry.................140

Table SOP 3.8. Forms and tables used for northern elephant seal resight data

verification..............................................................................................................................141

Table SOP 3.9. Queries and tables used for harbor seal annual summary report.......................146

Table SOP 3.10. Queries and tables used for harbor seal annual disturbance count

report. .....................................................................................................................................147

Table SOP 3.11. Queries and tables used for harbor seal disturbance rate report......................148

Table SOP 3.12. Reports and queries used for daily northern elephant seal census

reports.....................................................................................................................................149

Table SOP 3.13. Queries and tables used for harbor seal abundance by location

histogram. ...............................................................................................................................152

Table SOP 3.14. Queries and tables used for harbor seal daily abundance histogram. ..............153

Table SOP 3.15. Queries and tables used for northern elephant seal daily abundance

histogram. ...............................................................................................................................154

Table SOP 3.16. Queries and tables used to export data sets in Microsoft Excel format

from the database. ...................................................................................................................157

Table SOP 3.17. Annually distributed pinniped database files. ................................................159

Table SOP 3.18. Master pinniped database files. .....................................................................161

Table SOP 3.19. Data components and process for transferring annual harbor seal count

data to the master pinniped database........................................................................................161
123

1.0 Overview

Two critical long-term goals of the SFAN I&M Program are to:

 Integrate natural resource inventory and monitoring information into National Park

Service planning, management, and decision making.

 Share National Park Service accomplishments and information with other natural

resource organizations and form partnerships for attaining common goals and objectives.

For the pinniped monitoring program to meet I&M Program goals, a detailed management plan

is needed to ensure data quality, interpretability, security, longevity and availability. The

pinniped monitoring program has a long history at SFAN parks. Since the late 1970s, staff

scientists and volunteers have monitored seal colonies to determine population status, detect

changes in population numbers and reproductive success and to identify factors such as human

disturbance that might affect population trends. The pinniped database was designed to house

legacy data as well as data taken by contemporary surveys. The database currently houses data

back to 1997. Older legacy data will be added as staff time permits.

1.1 Scope and Applicability

The procedures below cover routine data management activities for the SFAN pinniped

monitoring program. This Standard Operating Procedure describes how the SFAN pinniped

monitoring protocol meets data management objectives through data entry specifications,

database design, quality assurance and control measures, metadata development, data

maintenance, data storage and archiving, and data distribution. Data management procedures are

explained for all the components of the protocol.

The pinniped protocol encompasses three separate programs:

 Harbor Seal Monitoring (SFAN I&M Program)

 Northern Elephant Seal Monitoring (PORE Science Division)

 All Species Monitoring (PORE Science Division) (see Sections 1.5.4 and 2.6.2)

The pinniped database contains data collected by all three of these programs. There are separate

data entry and editing procedures for the harbor seal and northern elephant seal programs. The

census forms for northern elephant seal data entry and editing are also used for the all species

pinniped program. While separate data entry and editing forms are used for harbor seals, data are

stored in common tables to facilitate reporting and analysis across the three programs.

2.0 Description of Pinniped Monitoring Database

The SFAN staff has developed a relational Microsoft (MS) Access XP database compliant with

the Natural Resource Database Template (NRDT), an application developed by the National

Park Service’s (NPS) Natural Resource Inventory and Monitoring Program (I&M). The database

consists of two separate MS Access .MDB files. The ‘front end’ (Pinniped.mdb) contains forms,

linked tables, reports, queries, macros and Visual Basic code while the ‘back end’
124

(Pinniped_BE.mdb) houses the data tables. This organization of the database allows new

development and edits of forms and reports (housed in the front end) to proceed without

hindering use of the data (housed in the back end). The two .MDB files are linked using the

‘Linked Table Manager’ utility of MS Access.

The data organization is based on the concept of surveys (sampling events occurring at a

specified time) recorded in an event table which are conducted at specified locations, that are

geo-spatially described in a locations table. EventID and LocationID codes provide the unique

keys for databases built on the NRDT model. Besides actual counts of pinnipeds, the database is

used to record effects of natural and anthropogenic disturbances to harbor seals and track the fate

of tagged northern elephant seals.

As described above, there are three separate pinniped programs but only two different data

collection protocols, one for harbor seals and the other for northern elephant seals. The data

collection and entry methodology for the all species pinniped program is identical to that used

for northern elephant seal census data. The primary information collected by all programs is the

number of pinnipeds observed at a specific time and location. The same tables are used to house

the primary information from all programs, namely, tblEvents, tblLocations, tblObservers and

tblSealCount. Events are linked to counts by an EventID which is automatically generated by

Visual Basic code housed in the data entry forms. EventIDs are the concatenation of the

following values: park, project, year, month, day and starting time (i.e. PORE_Pinniped_2005-

Jan-03_12:30:00).

Ancillary event tables, equivalent to tblEventDetails in the NRDT model, which contain

information unique to each program (such as weather information and survey number) are linked

to tblEvents in a one-to-one relationship. These tables are:

TABLE PROGRAM

TblPhocaEvents Harbor Seal (counts)

tblElephantEvents Northern Elephant Seal (counts)

tblDisturbanceSource Harbor Seal (disturbances)

tblResightEvents Northern Elephant Seal (tag resights)

Harbor seal disturbance responses are tracked by tblDisturbanceBehav while northern elephant

seal tag resights are kept in tblResight. tblPhocaSealCount contains the number of harbor seals

which had red fur as well as the number of harbor seals with shark bites and is linked to

tblSealCount by EventID, LocationID and SubsiteTime.

In the following narrative, Section 2.1 describes the structure and operation of the harbor seal

portion of the database while Section 2.2 describes the northern elephant seal portion of the

database. Tables which are common to both programs are referenced in both sections.

A complete data dictionary for the pinniped database is included as Appendix SOP 3A.
125

2.1 Harbor Seal Monitoring

Relationships of tables in the pinniped database which house harbor seal data are shown in

Figure SOP 3.1.

Figure SOP 3.1. Relationships of tables which house harbor seal data.

Note that harbor seal and northern elephant seal data are commingled in the primary data tables

such as tblEvents, and tblSealCounts. Ancillary tables such as tblPhocaEvents and

tblElephantEvents house event data specific to the harbor seal and northern elephant seal projects

respectively. Data are differentiated as belonging to the harbor seal or the northern elephant seal

program by values stored in the SubProject field of tblEvents.

2.1.1 Harbor Seal Census Data Entry

Project staff and volunteers regularly visit a standard suite of seal haul-out locations from early

March through the end of July (see SOP 1: Harbor Seal Surveys). At each location, harbor seal

adults/immatures and pups are counted. Dead harbor seal pups, harbor seals with red fur and

seals which have obvious shark bites are tallied separately. Other less common pinniped species

are also enumerated when observed, including:

 California Sea Lion

 Northern Elephant Seal
126

 Northern Fur Seal

 Steller Sea Lion

 Guadalupe Fur Seal

The database accommodates counts of these less common species.

frmMainMenu (Figure SOP 3.2)

The main menu is displayed automatically when the database is opened. A start-up or welcome

form allows the user to navigate to one of three switchboard forms each of which control access

to different database functions. To access the data entry forms the user selects the ‘Enter and

Verify Data’ button which opens frmEnterDataMenu.

Figure SOP 3.2. Main menu which is displayed when the pinniped database is started.

frmEnterDataMenu (Figure SOP 3.3)

This switchboard menu allows the selection of data entry and editing forms for both the harbor

seal and northern elephant seal projects. To add newly collected harbor seal data to the database,

select the ‘Add Harbor Seal Data’ button which opens frm_PhocaObservation1.
127

Figure SOP 3.3. Enter and verify data menu.

frm_PhocaObservation1 (Figure SOP 3.4)

Data recorded on the field data sheets can be entered into the database through this form which

contains three subforms that are bound to temporary tables. When entries in the form are

committed to the database by selecting the ‘Submit’ button at the bottom of the form, Visual

Basic code is executed to move data from the frm_PhocaObservation1 and the temporary tables

to permanent tables. After the data are moved, the forms and temporary tables are cleared.

Temporary data tables are required during initial data entry because of the desire to store the

entire pinniped project’s count data in one table, tblSealCount, regardless of which data form is

used. In this table, each record represents a single count of a pinniped species and age class, at a

specific subsite and at a specific time. Because of many problems with organizing a datasheet in

this manner, the database instead accommodates what is most convenient from a data collection

stand-point, organizes the data entry form based on the datasheet, and then transfers and stores

the data in a manner appropriate for the database.
128

tblSealCount

tblPhocaSealCount

Figure SOP 3.4. Harbor seal data entry form and example of harbor seal count data storage.
129

The counts of red fur seals and shark bitten seals are maintained in a separate table because the

field protocol specifies that these counts be taken as a subset of the total number of harbor seals.

Keeping red fur and shark bite seals in a separate table reduces the risk of tabulating the same

individual twice when data summaries are prepared.

Dead harbor seal pups are also tallied in the field as a subset of the total number of pups. When

dead pup data are committed to the database, the number of dead pups is subtracted from the

total number of pups and the value of ‘DEAD’ is placed in the ‘Qualifier’ field of tblSealCount.

Table SOP 3.1 lists the data entry forms and their associated temporary and permanent tables.

Figure SOP 3.4 illustrates how pinniped count data is stored once the data has been submitted to

the database.

When data entry is complete the data technician should initial and date the field data sheet in the

upper right hand corner.

Table SOP 3.1. Forms and tables used for harbor seal data entry.

Form Temporary Table Permanent Table Table Contents

frmPhocaObservation1 None tblEvents Event fields common to

all projects.

frmPhocaObservation1 None tblPhocaEvents Event fields specific to

harbor seal surveys.

frmObserversSUB tblObservers_Tmp tblObservers Observers performing

survey

frmMiscTaxaCountSUB tblMiscTaxaCount_TEMP tblMiscTaxaCount Counts of select bird

species

frm_harborsealCount_SUB tblSealCount_TEMP tblSealCount Location and time

specific adult, pup and

dead pup counts

frm_harborsealCount_SUB tblSealCount_TEMP tblPhocaSealCount Red fur and shark bitten

seal counts

Important notes for harbor seal data entry include:

x The regional survey check box should be checked for all surveys that occur within a five

day window (Thurs-Mon) of the scheduled regional survey date, which is always a

Saturday. Each regional count date, its respective regional count code, and the five day

range of dates is stored in tlu_Regional_Counts.See also SOP 1: Harbor Seal Surveys.

x Data entry of ‘Pups’ includes live plus dead pups.

x ‘All Subsites Surveyed’ is a mandatory data entry field.

2.1.2 Harbor Seal Census Data Verification and Editing

Data verification is performed as an independent step after the data have been entered into the

database. Data should be regularly verified and corrected by two individuals, one who reads the

field data sheet and a second who verifies each record which is displayed in the harbor seal data

editing form and subforms. Errors in the field data sheets should be corrected using a red pen.

The correction should be signed and dated by the individual who made the change. Once the data

in the database have been verified as correct, the field data sheet should be initialed and dated in

the upper right hand corner by the data technician.
130

frmEditPhocaObservation (Figure SOP 3.5)

Access to the data editing form is through form frmEnterDataMenu (Figure SOP 3.3) and button

“Edit Harbor Seal Data”. The main form and three subforms are related to seven different data

tables as shown in Table SOP3.2. “Subset by Date” and “Subset by Site” utilities have been

included in the data editing form to filter records and eliminate the necessity of scrolling through

the entire data set to locate records.

Figure SOP 3.5. Harbor seal data verification and editing form.
131

Table SOP 3.2 Forms and tables used for harbor seal data verification.

Form Query Permanent Table Table Contents

frmEditPhocaObservation qryEditPhoca tblEvents Event fields common to all

projects.

frmEditPhocaObservation qryEditPhoca tblPhocaEvents Event fields specific to harbor

seal surveys.

frmObserversSUB tblObservers Observers performing survey

frmMiscTaxaCountSUB3 tblMiscTaxaCount Counts of specific bird species

frmSealCountSUB tblSealCount Location and time specific adult,

pup and dead pup counts

frmPhocaSealCountSUB tblPhocaSealCount Red fur and shark bitten seal

counts

frmSubPoorQuality tblPoorQualitySurvey Reasons for when

HighQualitySurvey? is selected

as “no”.

Important notes for the harbor seal data editing form include:

x The regional count code, which is based on the year and survey number (ie. 2008_03),

should be set in the editing form. If a site is visited more than once during a regional

count weekend, the survey with the maximum count should be given the regional count

code. This will identify the survey as the one to use for analytical purposes.

x The quality of the survey is noted in this form by selecting “yes” or “no” in the

“HighQualitySurvey?” field. Poor quality surveys are given reason in the provided

subform. See also Harbor Seal QA/QC.

2.1.3 Harbor Seal Disturbance Data Entry

In addition to population censuses, biologists observe seal behavior, particularly with regard to

factors which could disturb seals while they are resting onshore. Disturbance data include any

potential or actual disturbance of the seals causing them to alter their behavior. Information

collected includes the source of the disturbance and seal responses (a gradient from no response

to flush into water). The database also tracks the fate of seals flushed into the water. Disturbance

data are recorded on a separate data sheet in the field (see SOP 1: Harbor Seal Surveys).

frmDisturbance (Figure SOP 3.6)

The disturbance form is opened by selecting the ‘Disturbed’ check box on the harbor seal data

entry form (Figure SOP 3.4). The disturbance form and the associated subform are bound to two

tables which log the time, nature of the disturbance and subsites affected (Table SOP 3.3).

The disturbance source is recorded in two fields, “source” and “source specific”. The source field

is a general category, such as “human”, where as the source specific field is more detailed, such

as “hikers” or “surfers”. The table tluSource lists source values and related source specific

values. The data entry form is designed to restrict data entry for source specific values based on

the previously entered source value.
132

Figure SOP 3.6. Harbor seal disturbance data entry form.

Table SOP 3.3. Forms and tables used for harbor seal disturbance data entry.

Form Permanent Table Table Contents

frmDisturbance tblDisturbanceSource General description of disturbance

source.

frmDisturbanceSub tblDisturbanceBehav Subsite specific observations.

A disturbance may affect more than one subsite, and seals at a subsite may have more than one

response. The subform should note all disturbed subsites and subsite responses to a single

disturbance source.

Since disturbances are observed during regular harbor seal censuses, general information about

the census such as the date, location, and field survey team members don’t have to be entered in

the disturbance form. The EventID for the census and the disturbance are the same.

If disturbance data is not entered in consort with the associated seal census data, the harbor seal

disturbance data verification and editing form (Figure SOP 3.7) must be used.

2.1.4 Harbor Seal Disturbance Data Verification and Editing

Data verification takes place as an independent step performed after the data have been entered

into the database. Data should be verified and corrected by two individuals, one who reads the

field data sheet and a second who verifies each record which is displayed in the harbor seal

disturbance data editing form and subform. Once the data in the database have been verified as

correct, each field data sheet should be initialed and dated in the upper right hand corner by the

data technician.

frmEditDisturbance (Figure SOP 3.7)

Access to the data editing form is through frmEnterDataMenu (Figure SOP 3.3) and button “Edit

Harbor Seal Disturbance Data”. A “Subset by Date” utility has been included in the data editing

form to filter records and eliminate the necessity of scrolling through the entire data set to locate

records. The control source for the main form is qryEditDisturbance which joins tblEvents to
133

tblDisturbanceSource. The subform frmEditDisturbanceSub is bound to tblDisturbanceBehav

which houses subsite specific disturbance data (Table SOP 3.4).

Figure SOP 3.7. Harbor seal disturbance data verification and editing form.

Table SOP 3.4. Forms, query and tables used for harbor seal disturbance data verification.

Form Query Permanent Table Table Contents

frmEditDisturbance qryEditDisturbance tblEvents Event fields common to all

projects.

frmEditDisturbance qryEditDisturbance tblDisturbanceSource General description of

disturbance source.

frmEditDisturbanceSub tblDisturbanceBehav Subsite specific observations.

2.2 Northern Elephant Seal and All Species Pinniped Monitoring

Census data collected by the all species pinniped program conducted year-round at Point Reyes

Headlands is identical to that collected for the northern elephant seal program. In this section,

references to the handling of data collected by the northern elephant seal program also apply to

the all species pinniped program. The database differentiates between the two programs by

assigning different values to the Survey_Type field in tblElephantEvents. Northern elephant

seals have an additional monitoring component built into the database regarding the tagging and

resighting of tagged animals. Relationships of tables in the pinniped database which contain

northern elephant seal data are shown in Figure SOP 3.8.

Note that harbor seal and northern elephant seal data are commingled in the primary data tables

such as tblEvents and tblSealCounts. Ancillary tables such as tblPhocaEvents and

tblElephantEvents contain event data specific to the harbor seal and northern elephant seal

projects respectively. Data are differentiated as belonging to the harbor seal or the northern

elephant seal program by values stored in the SubProject field of tblEvents.
134

2.2.1 Northern Elephant Seal Census Data Entry

Many of the same locations are surveyed during the northern elephant seal (late November

through March) and the all species pinniped program (year-round). While northern elephant seals

are the target species of this program, the database will accommodate incidental counts of other

pinnipeds, including harbor seals.

Figure SOP 3.8. Relationships of tables which house northern elephant seal data.
135

frmSealObservation (Figure SOP 3.9)

tblSealCount

Figure SOP 3.9. Northern elephant seal data entry form and example of pinniped count data storage.
136

Data from the field data sheets is entered into the database using this form. The form is opened

by selecting the ‘Add Elephant Seal or Pinniped Data’ button on frmEnterDataMenu. which can

be accessed from the main menu (frmMainMenu) as described above. The form accommodates

the entry of a number of northern elephant seal maturity categories as well as other pinniped

species including harbor seal adults and pups. Harbor seal disturbances can also be recorded by

selecting the ‘Phoca Disturbed’ check box which opens the disturbance form (Figure SOP 3.6).

As explained for harbor seal survey data entry, the survey data is initially written to series of

temporary tables. When the ‘Submit’ button on frmSealObservation is selected, Visual Basic

code is executed to permanently write data to the appropriate data tables (Table SOP3.5). When

data are committed to tblSealCount they are transposed and normalized so they are no longer in

the non-normalized data entry format. After the data are moved, the forms and temporary tables

are cleared. Figure SOP 3.9 illustrates how pinniped count data is stored once the data has been

submitted to the database.

Table SOP 3.5. Forms and tables used for northern elephant seal data entry.

Form Temporary Table Permanent Table Table Contents

frmSealObservation None tblEvents Event fields common to all

projects.

frmSealObservation None tblElephantEvents Event fields specific to

elephant seal surveys.

frmSealObservation None tblSealCount Location specific counts of

pinniped species and

maturities.

frmObserversSUB tblObservers_TEMP tblObservers Survey observers

When data entry is complete the data technician should initial and date the field data sheet in the

upper right hand corner.

Important notes for the northern elephant seal survey data form include:

x You must check the box below each subsite for each subsite surveyed.

x It is not necessary to enter zero for species and/or age categories not observed at the

subsites.

x When a full northern elephant seal survey must be completed during two field days, the

data should be entered as one record, using the first day as the survey date and a note in

the comments about when the survey was completed and why.

x Only select a survey type of “S” (full survey) when all northern elephant seal subsites

have been surveyed, with the exception of the TIP.

2.2.2 Northern Elephant Seal Census Data Verification and Editing

Data verification is performed as an independent step after the data have been entered into the

database. Data should be verified and corrected by two individuals, one who reads the field data

sheet and a second who verifies each record which is displayed in the northern elephant seal data

editing form and subforms. Errors in the field data sheets should be corrected using a red pen.

The correction should be signed and dated by the individual who made the change. Once the data

in the database have been verified as correct, the field data sheet should be initialed and dated in

the upper right hand corner by the data technician.
137

Northern Elephant Seal Census Report

Since northern elephant seal counts are stored in tblSealCount,which is a normally formatted

data table, display of northern elephant seal census data does not resemble the field data sheets

and is difficult to check. To aid data checking, a report can be generated which presents the data

in a format similar to the original field data sheet. This report can be printed or viewed on the

computer screen and used to verify the data displayed by the data editing form (frmEditE_Seal)

against the field data sheets. The northern elephant seal census data report is accessed from the

Analyze Seal Data form (Figure SOP 3.10) which can be opened by selecting the “Analyze

Data” button in the main menu (Figure SOP 3.2). The report can not be used to edit data, but can

instead be used to identify errors to fix using frmEditE_Seal. Reports are further described in

Section 2.4 Data Reporting Tools.

Figure SOP 3.10. Analyze Seal Data Menu.

frmEditE_Seal (Figure SOP 3.11)

Changes to the northern elephant seal data can be made using this form. Access to the data

editing form is through form frmEnterDataMenu (Figure SOP 3.3) and button “Edit Elephant

Seal or Pinniped Data”. Errors identified during the data verification step can be corrected by

entering changes in this form. The main form and two subforms are related to the four tables

containing northern elephant seal data as shown in Table SOP 3.6.
138

Figure SOP 3.11. Northern elephant seal data verification and editing form.

Table SOP 3.6. Forms and tables used for northern elephant seal data verification.

Form Query Permanent Table Table Contents

frmEditESeal qryEditESeal tblEvents Event fields common to all projects.

frmEditESeal qryEditESeal tblElephantEvents Event fields specific to elephant seal

surveys.

frmObserversSUB None tblObservers Observers performing survey

frmSealCountSUB None tblSealCount Location specific counts of pinniped

species and maturities

2.2.3 Northern Elephant Seal Resight Data Entry

In addition to population censuses, biologists tag weaned pups by placing Dalton cattle ear tags

in their hind flippers. Subsequent resighting of tagged northern elephant seals is performed by

biologists on resight surveys using binoculars and spotting scopes. A log of tag numbers attached

to northern elephant seals as well as a resight record is maintained on a daily field data sheet (see

SOP 2: Northern Elephant Seal Surveys). Observations of dye-marked northern elephant seals
139

are also recorded on the resight field data sheet. A log of damaged tags is maintained separately

(see Section 2.3). Resight surveys are independent of northern elephant seal census surveys and

are therefore assigned unique EventIDs. The database differentiates between census and resight

surveys by assigning different values to the SubProject field of tblEvents. Censuses are assigned

a value of ‘E_Seal’ and resight surveys are assigned a value of ‘Seal_Resight’. If resight surveys

happen to coincide with census surveys different starting times must be assigned by the field

team to avoid creating duplicate EventIDs.

frmResight (Figure SOP 3.12)

Data from the resight data sheets are entered into the database using frmResight. The form is

opened by selecting the ‘Add Tag Resight Data’ button on frmEnterDataMenu which can be

accessed from the main menu (frmMainMenu) as described above. The form lists tag color,

number and position as well as northern elephant seal location and maturity. When the ‘Submit’

button is selected, Visual Basic code is executed which writes data to the appropriate data tables

(Table SOP 3.7). Upon the completion of data entry, the data technician should initial and date

the field data sheet in the upper right hand corner.

Figure SOP 3.12. Northern elephant seal resight data entry form.
140

Table SOP 3.7. Forms and tables used for northern elephant seal resight data entry.

Form Temporary Table Permanent Table Table Contents

frmResight None tblEvents Event fields common to all

projects.

frmResight None tblResightEvents Event fields specific to

elephant seal resights

frmResightSUB None tblResight Log of elephant seals

tagged or observed

frmObserversSUB tblObservers_TEMP tblObservers Observers performing

survey

2.2.4 Northern Elephant Seal Resight Data Verification and Editing

Data verification takes place as an independent step performed after the data have been entered

into the database. The resight editing form was designed to closely resemble the data entry form

to facilitate the data verification process. Data should be verified and corrected by two

individuals, one who reads the field data sheet and a second who verifies each record which is

displayed in the northern elephant seal resight editing form and subform. Errors in the field data

sheets should be corrected using a red pen. The correction should be signed and dated by the

individual who made the change. Once the data in the database have been verified as correct, the

field data sheet should be initialed and dated in the upper right hand corner by the data

technician.

frmEditResight (Figure SOP 3.13)

Access to the data editing form is through frmEnterDataMenu (Figure SOP 3.3) and button “Edit

Tag Resight Data”. Specific individual field values can be changed or entire records can be

removed from the database using the “Delete Record” button. The resight editing form and the

associated subform are bound to four tables which contain date, time, and location of the tagged

or resighted seal as well as information about the life history stage of the seal and the location

and number of tags (Table SOP 3.8).

2.3 Lookup Tables

Lookup tables are included in the pinniped database for the purpose of tracking and controlling

information about sampling locations and field observers. The pinniped data entry forms will not

allow input of locations or observers which are not listed in tblLocations or tluVolunteerNames.

Additions of new locations and observers can be made through forms accessible from form

frmEditLookupTables (Figure SOP 3.14) which can be opened by selecting ‘Edit Lookup Tables’

on the ‘Main Menu’ (Figure SOP 3.2). A table for tracking the fate of damaged northern elephant

seal tags which were never deployed can also be accessed through this form.
141

Figure SOP 3.13. Northern elephant seal resight data verification and editing form.

Table SOP 3.8. Forms and tables used for northern elephant seal resight data verification.

Form Query Permanent Table Table Contents

frmEditResight qryEditResight tblEvents Event fields common to all

projects.

frmEditResight qryEditResight tblResightEvents Event fields specific to

elephant seal resights

frmResightObserversSUB2 None tblObservers Observers performing survey

frmEditResightSUB2 None tblResight Log of elephant seals tagged

or observed
142

Figure SOP 3.14. Switchboard menu for accessing lookup tables.

frmEditLocations (Figure SOP 3.15)

The table which lists all sampling locations (tblLocations) can be viewed and edited using form

frmEditLocations. Each of the harbor seal and northern elephant seal subsite locations are

represented as separate records in tblLocations. Each of the sampling sites (ie. Drakes Estero,

Double Point, etc) are also represented in tblLocations, with default subsite names such as

“DE_All” (Drakes Estero – All Subsites). UTM coordinates represent the center point of each

location.

frmVolunteerNames (Figure SOP 3.16)

The table which contains the list of all pinniped observers is tluVolunteerNames. The control

source for frmVolunteerNames is qryVolunteerNamesDisplayForm which sorts the table by the

‘LastName’ field. Each year seal observers are assigned a ‘GoodQuality’ rating of “Yes” or

“No” by the program staff. Ratings are based on experience and familiarity with the pinniped

program and allow us to filter out surveys from inexperienced staff or volunteers prior to

analysis. Ratings are displayed in the subform frmObserverQualitySub which is linked to table

tblObserverQuality.
143

Figure SOP 3.15. Viewing and editing form for the location table.

Figure SOP 3.16. Viewing and editing form for the listing of project observers.
144

frmDestroyedTags (Figure SOP 3.17)

The table containing records of destroyed northern elephant seal tags is tblDestroyed_Tags. The

code numbers of destroyed tags are kept for reporting purposes to the National Marine Fisheries

Service. Tags may be destroyed in the office or in the field when the tag code drilling or

application process fails (see SOP 2: Northern Elephant Seal Surveys). Tags destroyed in the

field are recorded on the field resight form with a tag code of ‘9’. Upon data entry, the

appropriate ‘Resightid’ value from the resight form may be given to tags which are destroyed in

the field. To minimize confusion between tag numbers which were actually deployed and those

which were not, destroyed tag numbers are kept in a separate table. This table is not directly

related to any other table in the database.

Figure SOP 3.17. Viewing and editing form for the listing of destroyed tags.
145

2.4 Data Reporting Tools

The pinniped database employs the reporting features of MS Access to produce summary figures

and tabular queries and reports. All summary figures, reports, and queries can be viewed by

selecting the appropriate button on the “Analyze Seal Data” menu (Figure SOP 3.10) which can

be opened by selecting the “Analyze Data” button in the main menu (Figure SOP 3.2). All

figures and tables can be printed using the File>Print pull-down menu located on the MS Access

menu bar. All figures, reports, and queries were designed so that no changes to the reporting

software are required to display new data when it is added to the database.

2.4.1 Summary Reports

The pinniped database provides different tabular reports which can be accessed through the

“Analyze Seal Data” menu (Figure SOP 3.10). The reports summarize harbor seal census and

disturbance data. A listing of survey specific northern elephant seal census data is also available.

Report of harbor seal annual maximum daily count by location (Figure SOP 3.18).

Report rpt_H_Seal_Max_Counts is based on qry_Seal_Count_FindMax3 which identifies the

maximum harbor seal abundance by year and sampling location from qry_Seal_Count2, which

joins red fur and shark bitten seal counts in tblPhocaSealCount with harbor seal adult and pup

counts from qrySealCount_Crosstab1. Query qrySealCount_Crosstab1 selects harbor seals from

tblSealCount and transposes the row major count data to column major format. Poor quality

counts are excluded from the report. The report lists results for all locations and years for which

there are data in the database. Maximum values for each column in the report may have occurred

on separate surveys within a given year. Queries and tables employed for report generation are

shown in Table SOP 3.9.

Report of harbor seal disturbances by year, location and disturbance type (Figure SOP

3.19).

Report rpt_H_Seal_Disturbance_Ann_Smry lists tallies of harbor seal disturbances by type,

location and year. The primary control source for the report is qryNewDisturbance3, the last of a

multi-step query process. The queries sum the number of disturbances and transpose the

disturbance sources in tblDisturbancesSource to column major format. Only disturbances

sources from the breeding or molting season that result in a Head Alert, Flush, or Flush Water

event are included in the report. Queries and tables employed for report generation are shown in

Table SOP 3.10.

Report of harbor seal disturbance rate by year, location and day (Figure SOP 3.20).

Report rpt_H_Seal_Disturbance_Rate lists the number of harbor seal disturbances per hour.

Disturbance rate data are tabulated by location and year. Only disturbances sources from the

breeding or molting season that result in a Head Alert, Flush, or Flush Water event are included

in the disturbance rate calculations. The primary control source for the report is

qryDisturbanceRate40, the final of a series of four queries that calculate the total survey time by

year and location and tally associated disturbance events observed during the surveys. Queries

and tables employed for report generation are shown in Table SOP 3.11.
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Figure SOP 3.18. Report of harbor seal annual maximum daily count by location.

Table SOP 3.9. Queries and tables used for harbor seal annual summary report.

Query Table Table Contents or Query Function

tblEvents EventID is used to count number of surveys

tblPhocaSealCount Counts of red and shark bitten harbor seals

tluPhocaLocation Lookup containing location names

tblSealCount Adult and pup harbor seal counts by location

qry_Seal_Count2 Filters for breeding and molting season harbor

seal counts

qry_Seal_Count_FindMax3 Identifies maximum counts by location for

breeding and molting seasons.

qrySealCount_Crosstab1 Transposes harbor seal adult and pup data.
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Figure SOP 3.19. Report of harbor seal disturbance count by year, location and disturbance type.

Table SOP 3.10. Queries and tables used for harbor seal annual disturbance count report.

Query Secondary Query

or Lookup Table

Table Table Contents or Query

Function

qryNewDisturbance3 qryNewDisturbance2

tluPhocaLocation Translates location code to full

name.

qryNewDisturbance2 qryNewDisturbance1 Transposes disturbance source

data by year, location, and

source type

qryNewDisturbance1 qryNewDisturbance0 Groups records of disturbances

that affected multiple sub-sites

into single source records.

qryNewDisturbance0 qryNewDisturbance0 tblEvents Event table, provides survey date

tblDisturbanceSource Table of disturbance events and

sources

tblDisturbanceResponse Table of related disturbance

responses
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Figure SOP 3.20. Report of harbor seal disturbance rate (first page of report).

Table SOP 3.11. Queries and tables used for harbor seal disturbance rate report.

Query Query Secondary or

LookupTable

Table Table Contents or Query Function

qryDisturbanceRate40 qryDisturbanceRate30

tluPhocaLocation Translates location code to full name.

qryDisturbanceRate30 qryDisturbanceRate20 Links survey date/time data to

disturbance counts

tblEvents Event table, provides survey date

tblPhoceEvents Event fields specific to harbor seal

surveys – provides survey length

qryDisturbanceRate20 qryDisturbanceRate10 Groups disturbance event records

qryDisturbanceRate10 tblEvents Event table, provides survey date

tblDisturbanceSource Table of disturbance events and

sources

tblDisturbanceResponse Table of related disturbance

responses

Reports of daily northern elephant seal counts

Daily northern elephant seal survey data can be viewed in two different formats, and for each

format, the user can report a specific survey date or the entire set of census data. The reports are

intended to aid the data verification process, as previously described, and to summarize northern

elephant seal counts for reporting purposes (see SOP 4. Data Analysis and Reporting). The
149

primary control source for each report is a query which joins tblEvents with tblElephantEvents

providing descriptive information about survey date and time with detailed northern elephant

seal counts from qry_E_Seal_Crosstab2. Qry_E_Seal_Crosstab2 transposes the seal count data

from row major to column major format so that the appearance of the data display resembles the

field data sheet. The macro mcrE_Seal_rawdata_report runs the command buttons associated

with these reports. Report titles, descriptions, and their respective underlying query titles are

listed in Table SOP 3.12.

Table SOP 3.12. Reports and queries used for daily northern elephant seal census reports.

Query Report Report Description

qryE_Seal_Raw_Report_ALL rptDisplayE_Seal_Rawdata_ALL All survey dates, listed in

descending order, and all

pinniped species counted.

Includes row totals.

qryE_Seal_Raw_Report_ALL_MIAN rptDisplayE_Seal_Rawdata_ALL_MIAN All survey dates, listed in

descending order, and only

elephant seal counts. Includes

row totals.

qryE_Seal_Raw_Report_Date rptDisplayE_Seal_Rawdata_Date Survey date specified on

frmAnalyzeData and all pinniped

species counted. Includes row

and column totals.

qryE_Seal_Raw_Report_Date_MIAN rptDisplayE_Seal_Rawdata_Date_MIAN Survey date specified on

frmAnalyzeData and all only

elephant seal counts. Includes

row and column totals.

From the Analyze Seal Data form (Figure SOP 3.10), selecting the “QA/QC Elephant Seal Data”

command button opens rptDisplayE_Seal_Rawdata_ALL (Figure SOP 3.21), which should be

used for error-checking northern elephant seal census data. Selecting the “Summarize Elephant

Seal Data” command button opens rptDisplayE_Seal_Rawdata_ALL_MIAN (Figure SOP 3.22),

which only displays northern elephant seal counts and is best used for producing quick summary

counts for reporting purposes (see SOP 4. Data Analysis and Reporting). Both reports display all

surveys in the database unless a date is first entered before selecting the command buttons.
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Figure SOP 3.21. Daily northern elephant seal census report, all species.
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Figure SOP 3.22. Daily northern elephant seal census report, northern elephant seals only.

2.4.2 Summary Graphs

The pinniped database provides three different graphs which can be accessed via the Analyze

Seal Data form (Figure SOP 3.10). The graphs summarize harbor seal or northern elephant seal

adult and pup abundances using bar histograms. The time period displayed in each of the graphs

is specified by the user through a start-up form which is opened when the appropriate button is

selected on the Analyze Seal Data form. The date range specified by the user is displayed in the

title of the graph.

Graph of harbor seal abundance by location. (Figure SOP 3.23)

Form frmH_Seal_Location_Chart displays the maximum harbor seal counts by location for a

specified time period. The maximum number of adult harbor seals and harbor seal pups per

location may have been observed on separate surveys. The control source for the figure is query

qryH_Seal_Chart2 which employs the MAX function to identify the maximum seal count. The

control source joins the initial query qryH_Seal_Chart1 to the lookup table tluPhocaLocation.

QryH_Seal_Chart1 extracts harbor seal counts from tblSealCount based on the date range

specified by the user in frmStartChart. Poor quality surveys are not included in the graph.

Queries and tables used by the figure are shown in Table SOP 3.13.
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Figure SOP 3.23. Harbor seal maximum abundance by location.

Table SOP 3.13. Queries and tables used for harbor seal abundance by location histogram.

Query Query Secondary Table Table Contents or Query Function

qryH_Seal_Chart2 qryH_Seal_Chart1 tblEvents Event table provides survey dates and

times.

qryH_Seal_Chart1 tblSealCount Adult and pup harbor seal counts by

location

tluPhocaLocation Lookup table which translates location

codes

Graph of harbor seal daily abundance for a single location. (Figure SOP 3.24)

Form frmH_Seal_Daily_Chart3 displays the number of harbor seals counted at a given location

by survey date for a specified time period. The control source for the graph is query

qryH_Seal_Location_Chart2, which joins the initial query qryH_Seal_Location_Chart1 to the

lookup table tluPhocaLocation. Query qryH_Seal_Location_Chart1 extracts harbor seal counts
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at a specified location from tblSealCount based on the date range and location specified by the

user in frmStartChart_Seal_Daily. Poor quality surveys are not included in the graph. Queries

and tables used by the graph are shown in Table SOP 3.14.

Figure SOP 3.24. Harbor seal daily abundance for a single location.

Table SOP 3.14. Queries and tables used for harbor seal daily abundance histogram.

Query Query Secondary Table Table Contents or Query Function

Query1 qryH_Seal_Location_Chart2 tblEvents Event table provides survey dates.

qryH_Seal_Location_Chart2 tblSealCount Adult and pup harbor seal counts by location

tluPhocaLocation Lookup table which translates location codes

Graph of northern elephant seal daily abundance. (Figure SOP 3.25)

Form frmE_Seal_Daily displays the number of northern elephant seals counted at all Point Reyes

Headlands subsites by survey date for a specified time period. Only surveys of type “S” (full

survey) are included so that partial counts are not included in the graph. The control source for

the graph is qry_E_Seal_Daily_Chart which sums counts for surveys extracted by the initial
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query qry_E_Seal_Weekly_Chart. Dates to be analyzed are specified by the user on

frmStartChart_E_Seal_Daily. Queries and tables used by the graph are shown in Table SOP

3.15.

Figure SOP 3.25. Northern elephant seal daily abundance for all subsites combined.

Table SOP 3.15. Queries and tables used for northern elephant seal daily abundance histogram.

Query Query Secondary Table Table Contents or Query Function

Qry_E_Seal_Daily_Chart Qry_E_Seal_Weekly_Chart tblEvents Event table provides survey dates.

Qry_E_Seal_Weekly_Chart tblSealCount Elephant seal counts by maturity
155

2.4.3 Summary Queries

Four queries are available from the Analyze Seal Data form (Figure SOP 3.10) that summarize

harbor seal monitoring data. The queries are predominantly designed to assist with the

development of regular monitoring updates that are distributed to park staff and project

volunteers (see SOP 4: Data Analysis and Reporting). Each query only displays high quality

rated surveys.

A notable difference between these queries and the annual maximum daily count by location

report (Figure SOP 3.18) is that, in the report, the maximum pup value may occur on a different

day than the maximum adult/immature count. In these queries, however, pup values are reported

as a component of a total harbor seal maximum count, and therefore always occur on the same

day as the reported adult/immature count.

Regional survey maximum counts

The query titled qryH_Seal_Update_ViewRegionalSurveys is opened from the “Regional Survey

Max Counts” command button. The query displays the maximum count of all harbor seals,

including pups, for each survey in the data that occurred during a regional count five-day

window. At times, a site may be surveyed more than once during a regional count window. For

reporting purposes, the survey with the higher maximum count will be displayed. This query

helps to identify which regional survey should be used and therefore assigned a value in the

“Regional_Count_Code” field.

Regional count totals

The query titled qryH_Seal_Update_RegionalCountTotals is opened from the “Harbor Seal

Regional Count Totals” command button. The query reports the sum of the maximum counts of

harbor seals from each site surveyed during a regional count. The count data is split between

adults/immatures and pups. The date value is the assigned regional count date and does not

necessarily represent the date that all sites were surveyed. The query is designed to help develop

the regional count graph that is produced for harbor seal monitoring updates (Figure SOP 4.4).

Regional count totals by site

The query titled qryH_Seal_Update_RegionalCountTotals_BySite is opened from the “Regional

Counts by Site” command button. The query reports the maximum count of harbor seals for each

site surveyed during a regional count. The query differs from the regional survey maximum

count query described above in that the count data is split between adults/immatures and pups

and only surveys used for regional count summaries are displayed. The date value is the assigned

regional count date and does not necessarily represent the date that the site was surveyed. The

query is useful for reporting regional count data by site for the harbor seal monitoring annual

report.

Weekly maximum counts by site

The query titled qryH_Seal_Update_WeeklyMaxBySite_Final is opened from the “Weekly Max

Counts By Site” command button. The macro mcr_Run_Phoca_WeeklyMax_Query runs the

command button associated with this query. The query reports the maximum count of harbor

seals for each site surveyed during the date ranges specified below the command button. The

maximum count is split between adults/immatures and pups. The date on which the maximum

count occurred at each site during the specified date range is also reported. The query is designed
156

to help develop the weekly maximum count graphs that are produced for harbor seal monitoring

updates (Figure SOP 4.3).

2.5 Data Export Functions

A simple feature built into the pinniped monitoring database is the ability to export large datasets

in Microsoft Excel format. This feature was designed for users that want to explore and analyze

the data further but do not have the skills to develop their own queries in Microsoft Access. The

export data form (Figure SOP 3.26) is accessible from the database main menu. The four

command buttons on the form are run from the macro mcr_Export_Counts. The command

buttons export data compiled in queries are by default saved to the user’s “My Documents”

folder. Table SOP 3.16 lists the queries, source tables, and exported products associated with the

export data form.

Figure SOP 3.26. Export seal data form.
157

Table SOP 3.16. Queries and tables used to export data sets in Microsoft Excel format from the

database.

Command Button Query Tables Export File

Elephant Seal Counts qryE_Seal_Export tblEvents E_Seal_Counts.xls

tblElephantEvents

tblSealCount

Elephant Seal Resights qryResight_Export tblEvents E_Seal_Resights.xls

tblResight

Harbor Seal Counts qryH_Seal_Export tblEvents H_Seal_Counts.xls

tblPhocaEvents

tblSealCount

Harbor Seal Disturbances qryDisturbance_Export tblEvents H_Seal_Disturbance.xls

tblDisturbanceSource

tblDisturbanceBehavior

3.0 Annual Data Work Flow

The pinniped monitoring program is based at Point Reyes National Seashore, includes sites at

Golden Gate National Recreation Area, utilizes a large volunteer contingent, and has

traditionally employed AmeriCorps interns that serve for one-year appointments only. As such, it

is critical that the program have a detailed and well-organized data work flow to ensure that

annual data is thoroughly error-checked and then uploaded into the master pinniped database.

The annual data work flow and integration into the master pinniped databases is illustrated in

Figure SOP 3.27.

3.1 Annual Satellite Databases

Rather than enter pinniped data directly into the master pinniped database, field staff are

provided with satellite databases with identical front-end and back-end database structure for

annual data entry. Satellite databases should begin with data collected after Aug 1 and continue

through to the following July 31. This time frame captures the entire northern elephant seal

breeding season (approximately Nov-March), the harbor seal breeding season (March-May), and

the harbor seal molting season (June-July). In addition, the time frame nearly matches the

AmeriCorps appointments, which run from October through to August. After July 31, the

AmeriCorps for that year should not enter any new field data, and should instead focus on errorchecking and finalizing the satellite database. Satellite databases are distributed to PORE and

GOGA, which enters data just for Point Bonita harbor seal data. Table SOP 3.17 identifies the

names and locations of the annual database files.
158

Figure SOP 3.27. Annual pinniped data work flow.

Data upload

Annual

Database

Master

Pinniped

Database

Point Reyes NS

Acquire data

Raw

Data

Data entry

Archives

Datasheets

final annual

databases

final version master

databases

NR Data Store

(update and/or

post metadata)

Raw

Data

Annual

Database

Point

Bonita

Database

Certified

Annual

Database

Golden Gate NRA

(Point Bonita Harbor Seals)

Acquire data

Data entry

Certified

Annual

Database

QA/QC QA/QC

Data upload

(max counts

harbor seal)
159

Table SOP 3.17. Annually distributed pinniped database files.

Park File Name Example Description Location

PORE Pinniped_2008.mdb Front-end annual pinniped

database

Inppore05 \ Resources \ Natural \

_Databases \ Pinniped

PORE Pinniped_BE_2008.mdb Back-end annual pinniped data

tables

Inppore05 \ Resources \ Natural \

_Databases \ Pinniped \ BE

GOGA GOGA_PINN_PB2008.mdb Annual pinniped database, Point

Bonita harbor seals only

Inpgogamahe1 \ Divisions \

Network I&M \ Individual Vital

Signs \ Pinniped \ data

3.2 Northern Elephant Seal and All Pinniped Count QA/QC

As previously described above, field staff must cross check the northern elephant seal census, all

pinniped counts, and northern elephant seal resight data in the database against the paper

datasheets completed in the field. In addition, after the field staff has completed its review, the

Network Data Manager should independently check a random 10% of the records for accuracy.

If the Network Data Manager discovers less than 95% accuracy in the data, the data should be

error-checked a second time by the field staff.

3.3 Harbor Seal QA/QC

The harbor seal monitoring program undergoes a higher level of data scrutiny because it is

primarily collected by volunteers and is more subject to difficult field conditions, such as fog and

high winds, that may compromise the accuracy of the data.

As previously described, each volunteer is given a “GoodQuality” ranking of “yes” or “no” for

each year that they participate in the program. Generally, “no” values are applied to a volunteer’s

first year with the program or at the project staff’s discretion based on the perceived quality of

the data collected by the volunteer. The rankings may be applied in the form frmVolunteerNames

(Figure SOP 3.16).

During the course of the season, and again at the end of the season, each survey should be

evaluated and assigned a “HighQualityCount?” value of “yes” or “no”. A survey may be of poor

quality and assigned a value of “no” for the following reasons:

x poor visibility

x not all subsites were surveyed

x poor observer quality of all survey participants

x other comments noted on the datasheet, ie.

o “too windy to distinguish pups from rest of seals”

o “can't see DEM seals well - far undercounted”

o “lots of glare and haze - difficult count”

o “too rainy”

The form frmEditPhocaObservation (Figure SOP 3.5) is used to assign the “HighQualityCount?”

value, with the reason(s) for a rating of “no” listed in the subform frmSubPoorQuality.

As previously described above, field staff must cross check the harbor seal survey and

disturbance data in the database against the paper datasheets completed in the field. In addition,
160

after the field staff has completed its review, the Network Data Manager should independently

check a random 10% of the records for accuracy. If the Network Data Manager discovers less

than 95% accuracy in the data, the data should be error-checked a second time by the field staff.

3.4 Annual Data Integration with Master Pinniped Database

Once data in the satellite databases have been completely error-checked against the paper

datasheets, the Network Data Manager should perform a final review of each of the field data

tables. As examples, the Network Data Manager should check for:

x erroneously generated records with no actual data

x orphaned records within the sub-tables (ie. no link back to tblEvents)

x data outliers

x logic errors (ie. start time is after the end time, more than one pup count record for the

same species, subsite, and time)

x accurate generation of automated fields (ie. LocationID, MatureCode, SpeciesCode)

x correct values for fields with fixed domains (ie. Visibility = 1, 2, or 3 ; Response = HA,

F, FW, Unk, or None)

Once satisfied, the Network Data Manager uploads the annual data into the master pinniped

database. All data is uploaded with no alterations, with the exception of the harbor seal count

data. Due to limited staff time, only summarized harbor seal data was entered into the master

database for many years. Beginning in 2008, all subsite data is entered into the annual satellite

database, but only the maximum count per survey is uploaded into the master database. This

process of summarizing annual harbor seal data before uploading it to the master database will

continue until we are able to return to the legacy datasheets and re-enter the raw data by subsite

in its entirety. The master database file names and locations are listed in Table SOP 3.18.

Table SOP 3.19 describes harbor seal data elements that are queried prior to upload. Before the

annual data is uploaded into the master database, a copy of the master should be made and

archived with the date incorporated into the file name. The satellite databases should be archived

after the data has been uploaded. PORE database archives will be stored at PORE, while GOGA

files will be archived at GOGA.

3.5 Master Point Bonita Database

At the request of GOGA natural resource managers, who originally maintained the Point Bonita

harbor seal data themselves, the Network staff maintains a master Point Bonita database hosted

on the GOGA Marin Headlands server. Because the Point Bonita data was always entered as is

with no summarization, the annual harbor seal data is transferred directly to the master Point

Bonita database with no alterations after the Network Data Manager has reviewed and approved

the data. The master database file name and location is listed in Table SOP 3.18.
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Table SOP 3.18. Master pinniped database files.

Park File Name Example Description Location

PORE Pinniped.mdb Front-end pinniped database Inppore05 \ Resources \ Natural \

_Databases \ Pinniped

PORE Pinniped_BE.mdb Back-end pinniped data tables Inppore05 \ Resources \ Natural \

_Databases \ Pinniped \ BE

GOGA GOGA_PINN_Master_.mdb Point Bonita harbor seals only Inpgogamahe1 \ Divisions \

Network I&M \ Individual Vital

Signs \ Pinniped \ data \

Master_PB

Table SOP 3.19. Data components and process for transferring annual harbor seal count data to the

master pinniped database.

Data Type Source Table Summarization Process

Adult / Immature Harbor

Seal Count

tblSealCount Per survey, identify the subsite count time with the single maximum

harbor seal count, including pups, across all subsites. From this

maximum count, transfer the adult / immature component and

maximum count time to the master database.

Pup Harbor Seal Count tblSealCount Per survey, identify the subsite count time with the single maximum

harbor seal count as above. From this maximum count, transfer the

pup component and maximum count time.

Dead Pup Harbor Seal

Count

tblSealCount Per survey, identify and transfer the maximum dead pup count with

the subsite time set to that for harbor seals.

Other Pinniped Counts tblSealCount Per survey, identify and transfer the maximum counts of other

pinniped species, with the subsite time set to that for harbor seals.

Red Fur Harbor Seal

Counts

tblPhocaSealCount Per survey, identify and transfer the maximum red fur count with the

subsite time set to that for harbor seals.

Shark Bite Harbor Seal

Counts

tblPhocaSealCount Per survey, identify and transfer the maximum shark bite count with

the subsite time set to that for harbor seals.

Version control guidelines for the MS Access pinniped monitoring databases will follow those

presented in the SFAN’s Data Management Plan (Press 2005). Prior to any major changes to the

database design, a back-up copy of the database should be made. Once the database design

changes are complete, the database should be assigned the next incremental version number. The

final copy of the previous database version should be archived with the version closing date

incorporated into the database title. Version numbers should increase incrementally by

hundredths (e.g. version 1_01, version 1_02, ...etc) for minor changes. Major revisions should

be designated with the next whole number (e.g., version 2_0, 3_0, 4_0 ...). With proper controls

and communication, versioning ensures that only the most current database version is used for

queries and analyses. The front-end and back-end databases should be titled with the same

version number, regardless of in which database file modifications are made. Significant

database re-design may require approval by the project manager, review by other data

management staff, and revisions to this data management SOP.

The Network Data Manager maintains a history of the pinniped database in a Microsoft Word

document titled Pinniped_Database_History located at:

Inppore05\Resources\Natural\_Databases\Pinniped\word
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All front-end and back-end design modifications to the database files are tracked within this

document and are referenced to changes in database version numbers. Major changes to the data

themselves are also noted in this document, such as when a new set of annual data is uploaded. It

is especially important to note edits to the data that will result in changes to final data summaries

previously published in annual reports or other mediums. Edits to all database files are

maintained in the database history document, including the GOGA Point Bonita master database

and the annual satellite databases.

4.0 Version Control Guidelines and Database History

Version control guidelines for the MS Access pinniped monitoring databases will follow those

presented in the SFAN’s Data Management Plan (Press 2005). Prior to any major changes to the

database design, a back-up copy of the database should be made. Once the database design

changes are complete, the database should be assigned the next incremental version number. The

final copy of the previous database version should be archived with the version closing date

incorporated into the database title. Version numbers should increase incrementally by

hundredths (e.g. version 1_01, version 1_02, ...etc) for minor changes. Major revisions should

be designated with the next whole number (e.g., version 2_0, 3_0, 4_0 ...). With proper controls

and communication, versioning ensures that only the most current database version is used for

queries and analyses. The front-end and back-end databases should be titled with the same

version number, regardless of in which database file modifications are made. Significant

database re-design may require approval by the project manager, review by other data

management staff, and revisions to this data management SOP.

The Network Data Manager maintains a history of the pinniped database in a Microsoft Word

document titled Pinniped_Database_History located at:

Inppore05\Resources\Natural\_Databases\Pinniped\word

All front-end and back-end design modifications to the database files are tracked within this

document and are referenced to changes in database version numbers. Major changes to the data

themselves are also noted in this document, such as when a new set of annual data is uploaded. It

is especially important to note edits to the data that will result in changes to final data summaries

previously published in annual reports or other mediums. Edits to all database files are

maintained in the database history document, including the GOGA Point Bonita master database

and the annual satellite databases.

5.0 Data Archival Procedures

Before the annual data is uploaded into the master database, a copy of the master is made and

archived with the date incorporated into the file name. The satellite databases are archived after

the data has been uploaded. PORE database archives will be stored at PORE, while GOGA files

will be archived at GOGA. In addition, when changing the database to a new version, the final

copy of the previous database version is archived with the version closing date incorporated into

the database title. Both GOGA and PORE servers have regular back-ups that are maintained by

park IT staff.
163

At the end of each field season, after error-checking, proofing, and uploading the seasonal data,

all of the field datasheets are organized into a binder for that year. Included in the binder are a

hardcopy of the annual report once completed and a CD containing a copy of the complete

master database and an electronic copy of the annual report. With the exception of the Point

Bonita datasheets, which are stored at GOGA in the Marin Headlands I&M office, all data

binders are stored in the PORE Science office.

6.0 Metadata Procedures

The NPS GIS Committee requires all NPS GIS data layers be described with the NPS Metadata

Profile, which combines the FGDC standard, elements of the ESRI metadata profile, the

Biological Data Profile, and NPS-specific elements. Although no standard has been applied to

natural resource databases and spreadsheets, the SFAN will complete the NPS Metadata Profile

to the greatest extent possible to document the annual and master pinniped back-end databases.

Because the annual Point Bonita harbor seal data is uploaded into the master Point Bonita

database without alteration, it is not necessary to create metadata records for the annual Point

Bonita back-end databases.

Complete metadata records for the SFAN pinniped databases will be generated in compliance

with current NPS standards by the Network Data Manager. The metadata records are based on

the FGDC standard, are formatted in XML, and can thus be imported or accessed by other

standard metadata software programs (ie. ArcCatalog). Because the location data for this project

is stored as UTM coordinates within the MS Access databases, there are no spatial data products

associated with this protocol that require metadata records.

The metadata records for the pinniped databases will initially be developed in Dataset Catalog

v3.0, an MS Access metadata development and catalog tool developed by the NPS I&M

Program. Dataset Catalog is currently the preferred tool to begin metadata records for MS

Access databases because of its ability to harvest entity and attribute information from this

database format.

The metadata records will be exported from Dataset Catalog as XML files and completed in NPS

Metadata Tools and Editor v1.1 (NPS MTE), thus allowing for all NPS-specific elements in the

metadata records to be completed. When completed, metadata records, but not the data

themselves, will be posted to the NPS Data Store for public discovery and consumption. Contact

information within the metadata records will direct interested parties to the Network Data

Manager for further inquiries. Metadata records posted to the NPS Data Store will be updated

annually after the annual data has been uploaded or following database revision to a new version

whole number (ie., v1_3 to v2_0, but not v2_0 to v2_1).

7.0 Data Distribution

In order for the pinniped monitoring protocol to inform park management and to share its

information with other organizations and the general public, guidance documents, reports, and
164

data must be easily discoverable and obtainable. The main mechanism for distribution of the

monitoring documents and data will be the Internet. The pinniped monitoring protocol,

accompanying SOPs, and all annual reports will be made available for download at the SFAN

website:

http://science.nature.nps.gov/im/units/sfan/

Although the pinniped monitoring database will not be posted for public download, as previously

mentioned, metadata records for the master database will be maintained at the NPS Data Store.

The metadata records will direct interested parties to the SFAN Data Manager for further

inquiries.

In addition to the NPS Data Store, the NPS I&M Program maintains an on-line natural resource

bibliographic database known as NatureBib. NatureBib records will be created for all of the

pinniped monitoring documents, including the protocol, annual reports, and any resulting

publications. The public version of NatureBib is in development by the NPS I&M program.

All documents produced by the pinniped monitoring program will be published in either the

Natural Resource Report Series or the Natural Resource Technical Report Series following

guidance from the NPS Natural Resource Program Center in Fort Collins, CO. The Natural

Resource Publications Management home page hosts a list of all documents published in the

NRR and NRTR Series. The home page can be found at:

http://www.nature.nps.gov/publications/NRPM/

8.0 Literature Cited

Press, D.T. 2005. Data management plan for the San Francisco Area Network Inventory and

Monitoring Program. USDI National Park Service. San Francisco, CA. 113 pp.
165

Appendix SOP 3A. Pinniped Database Data Dictionary

Data Dictionary Report

Data Dictionary for: Pinniped Monitoring Database, SFAN I&M Program

_________________________________________________________________________________________

TABLE NAME: tblDestroyed_Tags

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Destroyed Tag Numbers "9" Codes

FORMAT: Microsoft Access

NO. OF FIELDS: 5

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

Resightid dbText 15 resight ID, if applicable. Link to tblResightEvents

tagColor dbText 5 Tag color.

tagNo dbText 255 Tag code.

tagCode dbLong 4 Tag code fate. 9 = destroyed.

Comments dbMemo 0 Comments related to destroyed tag.

_________________________________________________________________________________________

TABLE NAME: tblDisturbanceBehav

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Disturbances of Harbor Seals Detail Information

FORMAT: Microsoft Access

NO. OF FIELDS: 15

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 50 Sampling event ID code, link to tblEvents.

DisturbanceID dbGUID 16 Disturbance ID code, link to tblDisturbanceSource.

LocationID dbText 50 Unique location ID code, link to tblLocations.

DisturbanceSubsite dbText 255 Subsite where observations took place

Response dbText 255 Response of seals to disturbance

CountBefore dbDouble 8 Count before disturbance began.

RemainOnSite dbDouble 8 Number of seals that remain on the site after the disturbance.

PupsRemain dbDouble 8 Pups remaining on beach.

Flush dbDouble 8 The number of animals that leave the beach and enter the water.

PupsFlush dbDouble 8 The number of pups that leave the beach and enter the water.

PupsAlone dbDouble 8 Pups that were left alone on the beach.

Return dbText 50 Did seals return (yes/no)
166

RehaulTime dbDate 8 Time when seals return to beach or rock.

WhereRehaul dbText 50 Location or subsite where seals return.

Comments dbMemo 0 Comments

_________________________________________________________________________________________

TABLE NAME: tblDisturbanceSource

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Disturbances of Harbor Seals Header Information

FORMAT: Microsoft Access

NO. OF FIELDS: 8

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 50 Sampling event ID code, link to tblEvents.

DisturbanceID dbGUID 16 Disturbance ID code.

Time dbDate 8 Time of observation at subsite

Source dbText 255 Generic disturbance source category.

SourceSpecific dbText 50 Specific source/cause of disturbance

DistNumber dbDouble 8 Number of people, aircraft, etc. causing disturbance.

Comments dbMemo 0 Comments regarding disturbance source.

_________________________________________________________________________________________

TABLE NAME: tblElephantEvents

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Secondary data for elephant seal surveys

FORMAT: Microsoft Access

NO. OF FIELDS: 7

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling event ID code, link to tblEvents.

Visibility dbDouble 8 Visibility Code (1=good, 2=fair, 3=poor)

Survey_No dbText 50 Sequential survey number for the year.

Survey_Type dbText 50 Type of survey (S = full survey, P = partial survey, I = incidental survey)

Phoca_Disturbed dbBoolean 1 Did a harbor seal disturbance occur?

Comments dbText 255 Comments

Date_Entered dbDate 8 Date that record was entered into tblElephantEvents
167

TABLE NAME: tblEvents

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Primary events table

FORMAT: Microsoft Access

NO. OF FIELDS: 8

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling Event ID Code

StartDate dbDate 8 Date (mm/dd/yy) when sampling began

EndDate dbDate 8 Date (mm/dd/yy) when sampling ended

StartTime dbDate 8 Time (hh:mm) when sampling began

EndTime dbDate 8 Time (hh:mm) when sampling ended

SubProject dbText 20 SubProject (Elephant Seal, Harbor Seal)

Project dbText 8 1-10 character Project Code

Old_ID dbLong 4 Unique ID key from old version of database

_________________________________________________________________________________________

TABLE NAME: tblLocations

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Primary Location Table -- UTMs of all Sites

FORMAT: Microsoft Access

NO. OF FIELDS: 28

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

ParkCode dbText 4 4-character Park Code

ProjectCode dbText 6 Code for component of monitoring project (Harbor Seal, Elephant Seal)

LocationID dbText 26 Unique Location ID code (when combined with ParkCode and Program)

Subsite dbText 8 Subsite Abbreviation (Specific Location Where Seals Were Sampled)

Subsite_Name dbText 38 Long Descriptive Name of Subsite

Location dbText 12 General Location (frequently there are multiple subsites per location)

Location_Name dbText 18 Long Descriptive Name of Location

StartUTMX dbDouble 8 UTM X (northing) coordinate for the center of the plot or location OR starting

point of a line or polygon

StartUTMY dbDouble 8 UTM X (northing) coordinate for the center of the plot or location OR starting

point of a line or polygon

StopUTMX dbDouble 8 UTM X coordinate (northing) of ending point of line or polygon

StopUTMY dbDouble 8 UTM Y coordinate (easting) of ending point of line or polygon

UtmZone dbDouble 8 UTM zone

StartLatitude dbDouble 8 Latitude in decimal degrees for the center of the plot or location OR starting point
168

of a line or polygon

StartLongitude dbDouble 8 Longitude in decimal degrees for the center of the plot or location OR starting

point of a line or polygon

StopLatitude dbDouble 8 Latitude in decimal degrees for the ending point of a line or polygon

StopLongitude dbDouble 8 Longitude in decimal degrees for the ending point of a line or polygon

Datum dbText 5 Datum of mapping ellipsoid

EstimatedHorizontalError dbLong 4 Estimated horizontal accuracy error--see users guide for complete details and

AccuracyComments dbMemo 0 Comments about how positional (horizontal) accuracy was estimated

HabitatType dbText 50 Habitat type

Elevation dbLong 4 Elevation in meters

Aspect dbText 5 Elevation in meters

Slope dbLong 4 Slope in degrees

Azimuth dbSingle 4 Compass bearing between start and stop coordinates

EstablishmentDate dbDate 8 Date site was established

Discontinued dbDate 8 Date site was discontinued

UnitName dbText 50 Management unit in which site is located

PLP dbText 10 Indicates whether location is a point, line, or polygon

_________________________________________________________________________________________

TABLE NAME: tblMiscTaxaCount

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Harbor seal bird observations

FORMAT: Microsoft Access

NO. OF FIELDS: 3

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling event ID code, link to tblEvents.

Taxa dbText 25 Code for miscellaneous taxa.

enumeration dbInteger 2 Number counted
169

TABLE NAME: tblObserverQuality

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Quality of Observer Data

FORMAT: Microsoft Access

NO. OF FIELDS: 4

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

ObserverID dbLong 4 Observer ID Number

YearDQ dbInteger 2 Year Ratings Were Developed For

GoodQuality dbText 50 Yes or No

_________________________________________________________________________________________

TABLE NAME: tblObservers

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Field Observers

FORMAT: Microsoft Access

NO. OF FIELDS: 2

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling event ID code, link to tblEvents.

observer dbInteger 2 Unique identification code number for seal observer, link to tluVolunteerNames.

_________________________________________________________________________________________

TABLE NAME: tblPhocaEvents

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Secondary data for harbor seal surveys

FORMAT: Microsoft Access

NO. OF FIELDS: 13

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling event ID code, link to tblEvents, link to tblEvents.

ObsTimeStart dbDate 8 Start of harbor seal observation time.

ObsTimeEnd dbDate 8 End of harbor seal observation time.

Visibility dbDouble 8 Atmospheric Visibility (Miles)

Tide_Level dbDouble 8 Level of Low Tide (Feet)

Low_Tide_Time dbDate 8 Time low tide occurred

All_Sites_Surveyed dbText 10 Were all Subsites Surveyed? If Location was visited and weather precluded

sampling Say 'UNABLE'

Comments dbMemo 0 Comments

Old_ID dbLong 4 Unique ID key from old version of database

Date_Entered dbDate 8 Date record was entered into database
170

Regional_Survey dbBoolean 1 Designates this survey as part of a region wide study

Regional_Count_Code dbText 50 Survey code of regional count, if applicable.

High Quality Count? dbText 50 Is this survey data of high quality and useful for data analyses (yes/no) ?

_________________________________________________________________________________________

TABLE NAME: tblPhocaSealCount

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Secondary counts for harbor seals (red,shark bite)

FORMAT: Microsoft Access

NO. OF FIELDS: 6

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling event ID code, link to tblEvents.

LocationID dbText 50 Unique Location ID code, link to tblLocations.

SubsiteTime dbDate 8 Time observations were made at a subsite

RedFurPhoca dbLong 4 Number of seals observed with red fur

SharkBitePhoca dbLong 4 Number of seals observed which had shark bites

Old_ID dbLong 4 Unique ID key from old version of database

_________________________________________________________________________________________

TABLE NAME: tblPoorQualitySurvey

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Harbor seal poor quality surveys

FORMAT: Microsoft Access

NO. OF FIELDS: 2

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling event ID code, link to tblEvents.

PoorQualReason dbText 50 Reason why survey is considered of poor quality (may be many reasons).

_________________________________________________________________________________________

TABLE NAME: tblResight

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Resights of Tagged Seals

FORMAT: Microsoft Access

NO. OF FIELDS: 20

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 50 Sampling event ID code, link to tblEvents.

LocationID dbText 50 Unique Location ID code, link to tblLocations.

Resightid dbText 15 Resight survey ID. Rmm/dd/yy-# (#=resight survey #). Link to tblResightEvents.

Subsite dbText 50 Subsite Abbreviation (specific location where seal observation occurred)

MatureCode dbText 10 Maturity of seal
171

Sex dbText 5 Sex of seal

Condition dbText 5 Condition of seal

Dye dbText 10 Number as read, use "-" for place holder

Dye_Code dbText 5 1 = Dye mark partially read, 2 = Newly applied dye mark, use first time animal is

marked, 4 = Data edited

LtagColor dbText 5 Left tag color

LtagNo dbText 10 Left tag number

LtagPosn dbText 5 Left tag position

LtagCode dbLong 4 1 = Tag partially read, 2 = Newly applied tag, use first time animal is marked,

4 = Data edited, 8 = tag recovered

RtagColor dbText 5 Right tag color

RtagNo dbText 10 Right tag number

RtagPosn dbText 5 Right tag position

RtagCode dbLong 4 1 = Tag partially read, 2 = Newly applied tag, use first time animal is marked,

 4 = Data edited, 8 = tag recovered

Bull_Cow_Status dbText 10 A=Alpha Male, B=Beta Male, P=Periphery, NA=Not Associated, PG=Pregnant,

NU=Nursing, NP=No Pup

Pup_Size dbText 5 Pup size

Comments dbMemo 0 Comments on seal observation.

_________________________________________________________________________________________

TABLE NAME: tblResightEvents

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Secondary data for seal resights surveys

FORMAT: Microsoft Access

NO. OF FIELDS: 6

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling Event ID Code, link to tblEvents.

Resightid dbText 15 Reisht survey ID. Rmm/dd/yy-# (#=resight survey #).

ResightSurvey dbLong 4 Resight survey ID number for year.

Visibility dbByte 1 Atmospheric Visibility (Miles)

Comments dbMemo 0 Comments on resight survey.

Date_Entered dbDate 8 Date record was entered in this table.
172

TABLE NAME: tblSealCount

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Primary table for pinniped count data

FORMAT: Microsoft Access

NO. OF FIELDS: 9

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

EventID dbText 45 Sampling event ID code, link to tblEvents.

LocationID dbText 50 Unique Location ID code, link to tblLocations.

Subsite dbText 255 Subsite code.

SubsiteTime dbDate 8 Time observations were made at a subsite

MatureCode dbText 10 Pinniped maturity code.

SpeciesCode dbText 10 Pinniped species code, link to tluPhocaMature.

qualifier dbText 10 Qualifier describing condition of the pinniped.

enumeration dbDouble 8 Number of pinnipeds counted.

Old_ID dbLong 4 Unique ID key from old version of database

_________________________________________________________________________________________

TABLE NAME: tluPhocaMature

FILENAME: Pinniped_BE.mdb

DESCRIPTION: All Seal Names and ITIS Codes

FORMAT: Microsoft Access

NO. OF FIELDS: 6

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

MatureCode dbText 50 Maturity Code

SpeciesCode dbText 6 Species Code

Scientific_Name dbText 50 Scientific name

Common_Name dbText 50 Common Name

ITIS dbLong 4 ITIS Number

Maturity_Description dbText 50 Meaning of Maturity Code
173

TABLE NAME: tluRegional_Counts

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Regional count dates and codes -- Lookup

FORMAT: Microsoft Access

NO. OF FIELDS: 5

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

Year dbLong 4 Survey year.

Regional_Count dbText 50 Regional count sequential code, ie. 2008_09

Date dbDate 8 Scheduled date of regional count.

MinDate dbDate 8 Date minus two days.

MaxDate dbDate 8 Date plus two days.

_________________________________________________________________________________________

TABLE NAME: tluResponse

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Seal response to disturbance -- Lookup

FORMAT: Microsoft Access

NO. OF FIELDS: 2

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

Response dbText 255 Code to describe response of seals to disturbance events.

_________________________________________________________________________________________

TABLE NAME: tluSource

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Harbor Seal Disturbance Sources -- Lookup

FORMAT: Microsoft Access

NO. OF FIELDS: 2

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

Source dbText 50 A list of the posible sources of disturbance simplified to match the original

reports.

SourceSpecific dbText 50 A list of specific disturbance sources.
174

TABLE NAME: tluVolunteerNames

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Names and Addresses of Seal Observers

FORMAT: Microsoft Access

NO. OF FIELDS: 14

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

ObserverID dbLong 4 Observer ID Number

First Name dbText 50 Observer's First Name

Last Name dbText 50 Observer's Last Name

also_known_as dbText 50 Other names (such as maiden names) the observer has used

observer_initials dbText 50 Observer's Initials

Active dbText 50 Are they still participating in surveys? yes/no

Phone Number dbText 50 Observer's Phone Number

E-mail dbText 50 Observer's Email Address

Street Address dbText 255 Observer's Street Address

City,State,Zip dbText 50 Observer's City of Residence

Year started in program dbLong 4 Year volunteer started in program.

Project Participant dbText 10 Project Which the Observer works on (E_Seal or H_Seal)

Comments dbMemo 0 Comments about the observer record

GOGA_ObserverID dbDouble 8 ObserverID in GOGA database (if applicable).

_________________________________________________________________________________________

TABLE NAME: tluWeatherCodes

FILENAME: Pinniped_BE.mdb

DESCRIPTION: Weather Condition -- Lookup

FORMAT: Microsoft Access

NO. OF FIELDS: 2

FIELD NAME FIELD TYPE FIELD WIDTH FIELD DESCRIPTION

Weather Code dbLong 4 Numeric weather code

Weather Description dbText 50 Weather description
175

SOP 4. Data Analysis and Reporting

Version 1.5

Revision History Log

Prev. Version # Revision Date Author Changes Made Reason for

Change

New

Version #

1.0 March 2008 Marcus

Koenen

General editing. Add

revision history log.

Update. 1.1

1.1 June 2008 Dawn

Adams,

Sarah Allen,

David Press,

Marcus

Koenen

Revised format,

added and clarified

analyses, clarified

reports and contents.

1.2

1.2 September

2009

D. Press, M.

Koenen

Revised by adding

updated graphics and

new information from

power analyses.

Removed

unnecessary text.

Final protocol

submission.

1.3

1.3 November

2009

K. Freeman,

D. Press

Changed tables and

figures to a modular

numbering system,

added a literature

cited section,

additional minor edits.

Formatting

requirements.

1.4

1.4 December

2009

D. Press Minor grammatical

edits.

Comments from

Penny Latham.

1.5
176

Contents

Page

Figures....................................................................................................................................177

Tables .....................................................................................................................................177

1.0 Peer-Reviewed Harbor Seal Reports..................................................................................178

1.1 Annual Harbor Seal Report........................................................................................178

1.2 Five-Year Trend Report.............................................................................................181

1.2.1 Census Data ....................................................................................................181

1.2.2 Disturbance Data.............................................................................................183

1.2.3 Data Synthesis.................................................................................................183

1.3 Report Formats ..........................................................................................................184

2.0 Other Harbor Seal Reports.................................................................................................184

2.1 Harbor Seal Weekly Breeding Summary....................................................................184

2.2 NMFS Reports...........................................................................................................184

2.3 I&M Updates.............................................................................................................184

2.4 Executive Briefing.....................................................................................................185

2.5 Regional Population Trends.......................................................................................185

3.0 Northern Elephant Seal Reports.........................................................................................186

3.1 Northern Elephant Seal Weekly Breeding Summary ..................................................186

3.2 Northern Elephant Seal Reports.................................................................................187

3.2.1 Population Estimates .......................................................................................187

3.2.2 Productivity Estimates.....................................................................................188

3.2.3 Trend Analyses ...............................................................................................189

4.0 Literature Cited .................................................................................................................190
177

Figures

Page

Figure SOP 4.1. Rates of disturbances per hour at Marin County locations from March

through July in 2008................................................................................................................181

Figure SOP 4.2. Example of harbor seal trend analysis from Sydeman and Allen (1999).........182

Figure SOP 4.3. Example graph from the harbor seal monitoring program weekly

updates reporting maximum counts per location......................................................................185

Figure SOP 4.4. Example graph from the harbor seal monitoring program weekly

updates reporting total counts of all sites combined during the course of the monitoring

season. ....................................................................................................................................186

Figure SOP 4.5. Example graph of northern elephant seal cows produced for the weekly

updates....................................................................................................................................188

Tables

Page

Table SOP 4.1. Example of survey summary data of harbor seal colonies for the 2008

season. ....................................................................................................................................179

Table SOP 4.2. Identified sources of disturbances (head alert, flush, flush into water) for

Marin County locations, from March 1st to July 31st, 2000—2008...........................................180
178

This SOP details annual and long-term reporting requirements for the pinniped monitoring

program. Data summary descriptions and long-term analytical methods are described for each of

the documented report types.

1.0 Peer-Reviewed Harbor Seal Reports

1.1 Annual Harbor Seal Report

The annual report is a summary of the field season and includes direct counts of seal population

numbers (maximums), number of pups produced, mortality events, disturbances, and any natural

history items of note. Because harbor seal monitoring is currently funded by the I&M program,

we provide details of data summaries that will be produced annually for this program. The data

summaries are presented as they apply to the monitoring objectives.

Details for generating the harbor seal summary survey and disturbance measures using the

project database are described in SOP 3 (Data Management). See especially Section 2.4 Data

Reporting Tools. Examples of recent harbor seal annual reports are posted to the SFAN internet

site: http://science.nature.nps.gov/im/units/sfan/vital_signs/pinnipeds/HarborSeals.cfm .

Objective 1a. Determine the long-term trends in population size and seasonal distribution of

harbor seal populations at primary sites in the SFAN parks during the breeding and molt seasons.

Annual measures produced for each monitored location include (see Table SOP 4.1):

x breeding season maximum count of adults and immatures combined

x breeding season maximum count of pups

x molting season maximum count of adults, immatures, and pups combined

As an index of the total population size, the maximum counts for each location are summed and

reported separately for the breeding and molting seasons (Table SOP 4.1). Graphs of the

maximum total count for each year are developed for the breeding and molting seasons to

compare the data across years (Protocol Narrative, Figure 4).

Reporting the maximum count data for each location monitored (Table SOP 4.1) will provide an

understanding of how the harbor seals are distributed throughout PORE and GOGA during the

field season. In addition, the narrative text of the annual report will highlight changes in how the

harbor seals are distributed within a location and will identify significant new areas that harbor

seals are utilizing during the breeding and molting season. Overtime, this information will show

the expansion and contraction of colonies and will allow for adaptive management as needed.

Objective 2a. Determine long-term trends in reproductive success of harbor seals through annual

estimates of pup production at PORE and GOGA.

For each location monitored, the maximum pup count is reported from the breeding season

surveys (Table SOP 4.1). As an index of annual pup production of the entire study area, the

maximum pup counts for each location are summed to create a maximum total of harbor seal

pups (Table SOP 4.1). Annually, a graph is developed that displays the maximum pup count per

location for all monitoring years.
179

Additional reporting that relates to harbor seal reproductive success includes the maximum dead

pup count per location (Table SOP 4.1) and the first reported date of harbor seal pupping for the

year.

Objective 3. Determine the long-term trends in sources, frequency and level of effects of

natural and anthropogenic disturbances on harbor seal haul out use and productivity.

An annual summary of disturbance sources (e.g., motorboat, human, vehicle, aircraft, etc.) is

presented by reporting, for each source, the number recorded and the percent of the total number

of disturbances for the season (Table SOP 4.2). This data is presented for all monitoring years for

comparison purposes. The average values across all years are also reported (Table SOP 4.2).

Table SOP 4.1. Example of survey summary data of harbor seal colonies for the 2008 season. All

reported numbers reflect the maximum number seen during a single census (Flynn et al. 2009).

Location

Max #

adults in

breeding

season1

Max #

Pups in

breeding

season

Max #

seals in

molting

season2 # Surveys

Max #

Reds3

Max #

Shark

Bites3

Max #

Dead

Pups3

Weekday: 27

Bolinas Lagoon 272 153 405 Weekend: 9 12 2 2

Weekday: 18

Double Point 496 328 904 Weekend: 21 7 4 6

Weekday: 24

Drakes Estero 627 341 1342 Weekend: 17 11 5 5

Weekday: 32

Duxbury Reef 32 3 96 Weekend: 10 0 0 0

Point Reyes Weekday: 6

Headlands 142 64 97 Weekend: 1 0 0 0

Weekday: 21

Tomales Bay 382 118 380 Weekend: 12 15 1 1

Weekday: 17

Tomales Point 384 154 577 Weekend: 12 6 2 1

Weekday: 21

Point Bonita 164 10 152 Weekend: 6 7 2 0

TOTAL 2499 1171 3953 254 58 16 15

1Max # Breed = adults and immatures during the breeding season, March 1 to May 31.

2Max # Molt = all age classes during the molting season, June 1 to July 31.

3

The Max # Red, Shark Bites, and Dead Pups are the maximum number observed March 1 to July 31.
180

Table SOP 4.2. Identified sources of disturbances (head alert, flush, flush into water) for Marin County locations, from March 1st to July 31st,

2000—2008 (Flynn et al. 2009).

Motorboat

Non-Motor

Boats Vehicle Dog Aircraft Human Bird Unknown Other Total

# % # % # % # % # % # % # % # % # %

2000 14 11.3 9 7.3 0 0.0 0 0.0 14 11.3 23 18.5 19 15.3 43 34.7 2 1.6 124

2001 14 10.8 12 9.2 2 1.5 1 0.0 4 3.1 45 34.6 9 6.9 28 21.5 15 11.5 130

2002 19 12.1 15 9.6 9 5.7 0 0.0 9 5.7 48 30.6 11 7.0 39 24.8 7 4.5 157

2003 13 9.8 20 15.0 3 2.3 0 0.0 10 7.5 38 28.6 10 7.5 32 24.1 7 5.3 133

2004 2 2.2 9 9.7 7 7.5 1 1.1 2 2.2 35 37.6 7 7.5 23 24.7 7 7.5 93

2005 9 7.3 14 11.4 1 0.8 2 1.6 10 8.1 43 35.0 10 8.1 31 25.2 3 2.4 123

2006 14 8.9 16 10.2 5 3.2 1 0.6 8 5.1 57 36.3 13 8.3 35 22.3 8 5.1 157

2007 29 13.8 21 10.0 14 6.7 2 1.0 14 6.7 70 33.3 13 6.2 45 21.4 2 1.0 210

2008 11 10.2 10 9.3 5 4.6 0 0.0 4 3.7 51 47.2 5 4.6 18 16.7 4 3.7 108

Average 13.9 9.6 14.0 10.2 5.1 3.6 0.8 0.5 8.3 5.9 45.6 33.5 10.8 7.9 32.7 23.9 6.1 4.7 137
181

A bar graph is developed to report the rate of disturbances (number of disturbances per hour of

survey) for each monitoring location (Figure SOP 4.1). The disturbance rate data is also

presented for all monitoring years for each location.

Additionally, the narrative text of the annual reports highlights specific disturbance events and

management issues that were cause for concern during the field season for each monitored

location.

0.18

0.25

0.38

0.04

0.41 0.39

0.04

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0.45

Bolinas

Lagoon

Double

Point

Drakes

Estero

Duxbury

Reef

Point

Bonita

Tomales

Bay

Tomales

Point

Location

Rate (disturbances/hour)

Figure SOP 4.1. Rates of disturbances per hour at Marin County locations from March through July in

2008. Only actual disturbances (head alert, flush, flush water) were used, and survey time is based on

observation time for all complete surveys (with or without disturbances) (Flynn et al. 2009).

1.2 Five-Year Trend Report

Every five years, a longer report will be developed to provide information and interpretation on

population trends. In addition, the reports are designed to evaluate the current monitoring efforts

and make recommendations for protocol changes if they are needed. An example of a five-year

report (Allen et al. 2004), summarizing the status and trends of the breeding populations of

harbor seals, is posted to the SFAN internet site:

http://science.nature.nps.gov/im/units/sfan/vital_signs/pinnipeds/HarborSeals.cfm

1.2.1 Census Data

As noted for the harbor seal annual reports, several data summaries are developed each year for

each location and for all sites combined, including:

x breeding season maximum count of adults and immatures combined

x breeding season maximum count of pups

x molting season maximum count of adults, immatures, and pups combined
182

During all surveys, some harbor seals are in the water and cannot be counted. Consequently,

aerial and shore-based surveys of seals at their haul out sites measure only a proportion of the

population. If survey methods and timing are standardized and the proportion of animals counted

remains constant, such surveys can be used as reliable indices of population trends. The current

population estimator is 1.65 times the maximum onshore number of adults/immatures, pups, and

individuals during molting (Harvey and Goley 2005; Lowry et al. 2005; Carretta et al. 2007).

This correction factor is also used in statewide surveys. National Marine Fisheries Service

(NMFS) is developing a new estimator for California based on mark-recapture of harbor seals

statewide in California (M. Lowry, NMFS, pers. com). The I&M five year reports will apply the

appropriate correction factor for long-term harbor seal population trends.

To determine long-term trends in population size and productivity, the maximum count from

each colony, multiplied by the 1.65 correction factor, is evaluated by regression (linear or nonlinear) analyses (versus year) as described in Sydeman and Allen (1999) (Figure SOP 4.2). This

results in one data point per colony per year for the analyses. As recommended in Appendix A,

the harbor seal monitoring program will focus on detecting a 27% decline in adults over a period

of three years using six of the primary pupping sites (Tomales Bay, Tomales Point, Point Reyes

Headlands, Drakes Estero, Double Point, and Bolinas Lagoon). For harbor seal pup production,

the program will focus on detecting a 36% decline over a period of four years. Trends in harbor

seal counts and pup production will take longer to detect for individual sites (Appendix A).

Nevertheless, the five-year trend reports will consider site-specific changes in the harbor seal

population to see if any trends are apparent.

Figure SOP 4.2. Example of harbor seal trend analysis from Sydeman and Allen (1999).

Both population and productivity trends are analyzed to report the rate of change and whether it

is significantly different from zero (Caughley and Birch 1971; Zar 1984). Because seal count
183

data will likely be non-normal, counts will be log-transformed to induce normality. If logtransforms do not normalize the data, poisson or negative binomial error terms will be used to

control for non-normal data with non-constant variance. In addition to colony specific

regressions, route regressions (Elzinga et al. 1998) will be used to evaluate the population trend

for the entire SFAN harbor seal population. This consists of individual regressions from each

colony being combined to report a mean slope, standard error, and statistical significance for all

the colonies. A report of the statistical power of the regression will also be presented with the

regression results.

1.2.2 Disturbance Data

Five-year reports will summarize changes in distribution over the five year period. This data may

show the expansion and contraction of colonies over time and will allow for adaptive

management as needed. Data will be presented as a map of all SFAN colony sites with time

series and regression results (described in previous paragraph) overlain on the map. This will

allow managers to determine which sites are increasing, decreasing or are stable, and any

potential relationships or patterns that affect groups of sites that are close to one another.

Regressions on the population data over time will be conducted for the five years since the last

analysis and for the entire dataset, thus providing information on recent trends in the data versus

the complete long-term trends.

Disturbance data are summarized every five years using the following measures:

x source of disturbance: annual tally of sources of disturbance (e.g., motorboat, human,

vehicle, aircraft, etc.) for each location and for all locations combined.

x rate of disturbance: number of disturbances per hour of survey for each location.

The analysis will explore changes in both disturbance rates and the composition of disturbance

sources over time. Care will be taken to evaluate the survey effort and site coverage of the

datasets used when interpreting trends. When sample size allows, variability among years will be

evaluated by site. Rate of disturbance will be explored for changes through time using binomial

tests on human disturbance sources versus total disturbance sources. In addition, ANOVA or

Generalized Linear Models (GLM) will be applied to test for differences in disturbance rates

between years (pooling all sites and at each individual site), differences in weekday and weekend

disturbance rates, and differences in disturbance between sites.

The effects of disturbance on population size and pup production can be tested using GLMs

following methods developed by Becker et al. (2009). GLMs will be run using factors that may

affect population size and productivity, such as year since the most recent El Niño event, and

density-dependence due to total counts in the region in order to test the relative influence of

disturbances to the harbor seal population.

1.2.3 Data Synthesis

To the greatest extent possible, trends of key parameters (e.g., population size, disturbance, and

productivity) will be assessed within the context of other biological, oceanographic, or climatic

indicators monitored by the NPS or partners (e.g., El Niño Southern Oscillation (ENSO),

changes in beach profiles, nearshore current patterns). Examples of these types of analyses

include Allen et al. (1989) and Sydeman and Allen (1999) where ENSO effects were

documented in relation to pinniped productivity. Larger scale analyses such as these will not
184

necessarily occur within every trend report, but will occur as needed, as datasets become

available, or as dataset become robust enough to incorporate into these types of analyses.

1.3 Report Formats

The annual and five-year trend reports will follow the format of the Natural Resource Technical

Report (NRTR; http://www.nature.nps.gov/publications/NRPM/index.cfm) series. The series is

used to disseminate the peer-reviewed results of scientific studies in the physical, biological, and

social sciences for both the advancement of science and the achievement of the National Park

Service’s mission. The NRTR typically follows the "Introduction - Methods - Results -

Discussion" type organization that is standard for many scientific journal publications and

technical reports. Reports should be direct and concise.

2.0 Other Harbor Seal Reports

2.1 Harbor Seal Weekly Breeding Summary

Graphs presenting the attendance of harbor seals at PORE and GOGA is produced weekly. The

graphs 1) illustrate the maximum weekly count of adults/immatures combined and maximum

pups for each monitoring location (Figure SOP 4.3), and 2) illustrate the counts of

adults/immatures and pups across all sites combined over the course of the monitoring season

(Figure SOP 4.4). In addition, photos, natural history notes, and monitoring guidance to the

volunteers are included in the weekly update. The purpose of the update is to brief the

superintendents, the park interpretation staffs, volunteer monitors, and the public regarding the

status of the harbor seal monitoring season. The weekly updates are posted to the SFAN internet

site: http://science.nature.nps.gov/im/units/sfan/vital_signs/pinnipeds/HarborSeals.cfm

2.2 NMFS Reports

The parks are monitoring and conducting research under a NMFS Office of Protected Species

permit. The research at the parks is conducted in cooperation with PRBO Conservation Science,

who is conducting research on pinnipeds on the Farallon Islands NWR. Research on harbor seals

tagged in San Francisco Bay in collaboration with The Marine Mammal Center study also occurs

under this permit. Permit reports are due annually and permit renewals are required every five

years. The NMFS reports include information on number and species of seals tagged (tag

number, location of tag, location of tagging event, date, and age-sex of individual), resighting

records of tags from non-PORE sites, any tissue collected, and the number and species of seals

and sea lions disturbed during research activities. The PORE Science Advisor is the NPS lead on

developing the NMFS report and works in collaboration with PRBO Conservation Science and

The Marine Mammal Center.

2.3 I&M Updates

Interesting findings and project highlights are disseminated once or twice per season through the

monthly I&M Update. This one-page monthly report series is distributed throughout the network
185

Weekly Summary of Harbor Seal Max Counts

 04/27-05/03 2008

0

100

200

300

400

500

600

700

800

900

1000

Bolinas

Lagoon

Double Point Drakes

Estero

Duxbury

Reef

Point Bonita Tomales Bay Tomales

Point

Pups

Adults

Figure SOP 4.3. Example graph from the harbor seal monitoring program weekly updates reporting

maximum counts per location.

to summarize ongoing monitoring work. Highlights are presented in short paragraphs (3-4

sentences) with photographs.

2.4 Executive Briefing

At the end of each breeding season (harbor seal and northern elephant seal), an executive

briefing will be updated and reposted to the I&M website. The briefing is a two-page summary

of pinniped monitoring and provides information to internal staff.

2.5 Regional Population Trends

To contribute to statewide surveys and to evaluate the SFAN sites in context of the larger

population, standardized estimates of total population are also calculated. Data (population

counts and population index) collected at PORE and GOGA are combined with surveys

conducted in San Francisco Bay and Sonoma County to produce an annual regional population

estimate. Regional surveys are scheduled by the PORE Science Advisor so that they coincide

with surveys at PORE and GOGA. The PORE Science Advisor is the lead on evaluating regional

trends in the harbor seal population data.
186

Regional Surveys of Marin County

2008

0

500

1000

1500

2000

2500

3000

3500

3/1/2008

3/15/20083/29/20084/12/20084/26/2008

5/3/2008

5/10/20085/24/2008

6/7/2008

6/21/2008

7/5/2008

7/19/20087/26/2008

Number of Harbor Seals

Pups

Adults

Total Harbor Seals

Figure SOP 4.4. Example graph from the harbor seal monitoring program weekly updates reporting total

counts of all sites combined during the course of the monitoring season.

3.0 Northern Elephant Seal Reports

The harbor seal reports listed above are produced using data collected through the I&M program.

Because of limited funding, the northern elephant seal reports below are supported through data

management efforts and technical assistance but are not primary tasks of the I&M program staff.

They are listed here to serve as a documentation of reports that are produced by the parks and

supported by I&M. If I&M funding becomes available to support these monitoring efforts,

additional information will be provided on data analyses and reports.

3.1 Northern Elephant Seal Weekly Breeding Summary

Graphs presenting the attendance of northern elephant seals at PORE during the

pupping/breeding season are produced weekly. The purpose of the updates are to brief the

superintendent, the park interpretation staff, volunteer monitors, and the public regarding the

status of the northern elephant seal breeding season. The digital graphs presents the previous and

current year weekly maximum counts for all northern elephant seals, cows, and pups/weaned

pups (Figure SOP 4.5). One set represents all colony sites and another set is produced for North

Drakes Beach colony where the majority of public interaction and docent work occurs. Any
187

notable natural history observations or resighting of tagged individual northern elephant seals are

included. The weekly updates are posted to the SFAN internet site:

http://science.nature.nps.gov/im/units/sfan/vital_signs/pinnipeds/ElephantSeals.cfm

3.2 Northern Elephant Seal Reports

In 2007, a two-year northern elephant seal report was produced using the NPS Natural Resource

Report Template (Protocol Narrative, Table 1; Adams et al. 2007). Annual and long-term trend

reports will likely remain consistent with this report format, which emphasized northern elephant

seal population and productivity estimates.

3.2.1 Population Estimates

Annual and long-term trends of northern elephant seal population size are reported by age and

sex class using direct counts. Breeding population estimates are based on maximum survey

counts for northern elephant seals by sex, age group, and colony (Adams et al. 2007). During the

breeding season, not all age classes are present on the beaches so accurate total population size

counts are not possible. In addition, during surveys, some northern elephant seals, especially subadult males, are in the water and cannot be counted. Consequently, shore-based surveys of seals

at their haul out sites measure only a proportion of the population. If survey methods and timing

are standardized and the proportion of animals counted remains constant; such surveys can be

used as reliable indices of population trends.

The NMFS estimates the elephant seal population size by using raw pup counts multiplied by the

inverse of expected ratio of pups to total animals (McCann 1985). Boveng (1988) and Barlow et

al. (1993) recommend using 3.5 as an appropriate multiplier for a rapidly growing population

such as the California stock of northern northern elephant seals. The PORE population estimates

are based on the pup count multiplier (3.5) used with the maximum total of pup and weaned pup

counts by colony or sub-site. NMFS is currently reviewing this multiplier and may provide new

guidelines in the future. SFAN contributes data to NMFS for an annual national population

estimate (Barlow et al. 1993; Carretta et al. 2002; Carretta et al. 2007).
188

Figure SOP 4.5. Example graph of northern elephant seal cows produced for the weekly updates.

Details for generating the northern elephant seal maximum population counts using the database

is described in SOP 3: Data Management. See especially Section 2.4 Data Reporting Tools. An

example of population size summary data for the northern elephant seal monitoring program is in

the protocol narrative, Table 1.

3.2.2 Productivity Estimates

Annual productivity is reported as an index of annual reproductive success using direct counts of

females, pups, and applying correction factors. An example of productivity summary data for the

northern elephant seal monitoring program is in the protocol narrative, Table 1. The productivity

index is calculated from the following formula (Lee 2006):

Maximum count of weaned pups and pups

Adjusted maximum count of females = Productivity Index

The index is calculated for colony sites and the entire PORE population. The total number of

breeding females is estimated using the maximum count of adult females during peak pupping

adjusted to include the adult female counts 33 days prior to and 33 days after the peak count for

each colony site (Protocol Narrative, Table 1; Adams 1994; Le Boeuf and Laws 1994). This
189

adjustment takes into account females that depart early and those that have not yet arrived at the

time of the peak count (average female stay at colony is 6 days prior to pupping +27 days

nursing period; Le Boeuf and Laws 1994). The assumptions of this method to determine

productivity are that observers are able to capture the high count of pups plus weaners and adult

females during the bi-weekly surveys and that female natality is unknown but relatively stable

across years. The index reflects productivity only and not mortality (dead pups are included in

the total) that occur at the breeding site.

Other northern elephant seal monitoring programs use site specific natality rates (proportion of

females giving birth) to estimate pup production. The natality rates correspond to reported values

for an expanding (93% at Año Nuevo) and stable (98% at Southeastern Farallon Islands)

population where good estimates were obtained. Expanding or new colonies are thought to have

lower natality because females are younger and therefore have lower birth rates than at more

established colony sites. Until a valid natality rate for the PORE population is estimated, SFAN

has decided to not use a natality rate since not all PORE northern elephant seal colonies are at the

same growth point (e.g., some are expanding and some are stable). We also present raw count

data in reports for which new productivity values can be estimated when more recent data is

available.

3.2.3 Trend Analyses

Rates of change in the northern elephant seal population will focus on adult female counts and

pup production. Cow adults will be used as a proxy for total breeding population size because

northern elephant seal males, particularly sub-adults, are highly mobile during the breeding

season, which can result in them being double-counted. The maximum count of pups plus

weaners for each colony provides an estimate of actual pup production.

A power analysis (Appendix B) indicates that for all sites combined, monitoring effort has an

86% chance of detecting a 36% decline in cows over 4 years. For pups, an 83% chance of

detecting a 41% decline can be realized after 5 years. Increases are easier to detect, generally

having 0.1 - 0.2 higher power. Site specific trends will take longer to detect, but will be explored

for Point Reyes Headlands, North Drakes Beach, and South Beach separately. Methods for

exploring long term trends in the northern elephant seal population will be similar to those

already described for harbor seals.

Long term trends in productivity and weaning success will also be explored over time. Weaning

success can be estimated by comparing the total number of pups born with the total number of

weaned pups remaining at the end of the season. Because pups begin dispersing from the beaches

where they were born near the end of the breeding season and can be washed to other sites by

storms, trends in productivity and weaning success will be evaluated for the entire population

rather than by individual colonies.
190

4.0 Literature Cited

Adams D., H. Jensen, H. Nevins, K. Truchinski, S. Allen, and D. Roberts. 2007. Northern

elephant seal monitoring 2005–2007 report, Point Reyes National Seashore. Natural

Resource Technical Report NPS/SFAN/NRTR – 2008/085. National Park Service, Fort

Collins, Colorado.

Adams, J. 1994. Status of the Northern elephant seal, Mirounga angustirostris (Gill, 1866),

breeding at Point Reyes Headlands, California during 1992–1993. Senior thesis. University

of California, Santa Cruz, California. 29 pp.

Allen, S. G., H. R. Huber, C. A. Ribic, and D. G. Ainley. 1989. Population dynamics of harbor

seals in the Gulf of the Farallones, California. California Fish and Game, 75:224–232.

Allen, S., S. Waber, W. Holter, and D. Press. 2004. Long-term monitoring of harbor seals at

Point Reyes, five year annual report, 1997–2001. National Park Service, Point Reyes

National Seashore.

Barlow, J., P. Boveng, M. S. Lowry, B. S. Stewart, B. J. Le Boeuf, W. J. Sydeman, R. J.

Jameson, S. G. Allen, and C. W. Oliver. 1993. Status of the northern elephant seal population

along the U.S. west coast in 1992. Administrative Report LJ-93-01. Southwest Fisheries

Science Center, National Marine Fisheries Service, P.O. Box 271, La Jolla, CA. 32 pp.

Becker, B., S. Allen, and D. Press. 2009. Modeling the effects of El Niño, density-dependence,

and disturbance on harbor seal (Phoca vitulina) counts in Drakes Estero, California: 1997-

2007. Marine Mammal Science 25(1):118.

Boveng, P. 1988. Status of the northern elephant seal population on the U.S. west coast.

Administrative Report LJ-88-05. Southwest Fisheries Science Center, National Marine

Fisheries Service, La Jolla, CA. 35pp.

Carretta, J. V., M. M. Muto, J. Barlow, J. Baker, K. A. Forney, and M. Lowry. 2002. U.S. Pacific

marine mammal stock assessments: 2002. U.S. Department of Commerce, NOAA Technical

Memorandum, NMFS-SWFSC-346. 286 p.

Carretta, J. V., K. A. Forney, M. S. Lowry, J. Barlow, J. Baker, B. Hanson, and M. M. Muto.

2007. U.S. Pacific marine mammal stock assessments: 2007. U.S. Department of Commerce,

NOAA Technical Memorandum, NMFS-SWFSC-414. 320 p.

Caughley, G., and L. C. Birch. 1971. Rate of increase. Journal of Wildlife Management 35:658–

663.

Elzinga, C., D. Salzer, and J. Willoughby. 1998. Measuring and monitoring plant populations.

U.S. Dept. of the Interior. Bureau of Land Management. 492 pp.
191

Flynn, E., D. Press, S. Codde, D. Roberts, and S. Allen. 2009. Pacific harbor seal (Phoca vitulina

richardsi) monitoring at Point Reyes National Seashore and Golden Gate National

Recreation Area: 2008 annual report. Natural Resource Technical Report

NPS/SFAN/NRTR—2008/267. National Park Service, Fort Collins, Colorado.

Harvey, J. T. and D. Goley. 2005. Determining a correction factor for aerial surveys of harbor

seals in California. Final Report to National Marine Fisheries Service and Pacific States

Marine Fisheries Commission, PSMFC Contracts No. 03-19 and 04-33, NOAA Grant No.

NA17FX1603. 35 pp.

Le Boeuf, B. and R.M. Laws (eds.). 1994. Elephant seals: population ecology, behavior, and

physiology. University of California Press, Berkeley. 414 pp.

Lee, D. 2006. Population size and reproductive success of Northern elephant seals on the South

Farallon Islands 2005–2006. Report to U. S. Fish and Wildlife Service Farallon National

Wildlife Refuge, San Francisco, CA. 9pp.

Lowry, M.S., J.V. Carretta, and K.A. Forney. 2005. Pacific harbor seal, Phoca vitulina richardsi,

census in California during May–July 2004. Administrative Report LJ-05-06, available from

Southwest Fisheries Science Center, 8604 La Jolla Shores Drive, La Jolla, CA 92037. 38 p

McCann, T. S. 1985. Size, status and demography of southern elephant seal (Mirounga leonina)

populations. Pages 1–17 in J. K. Ling and M. M. Bryden, editors. Studies of sea mammals in

south latitudes. South Australian Museum, Adelaide, Australia. 132 pp.

Sydeman, W. J. and S. G. Allen. 1999. Pinniped population dynamics in central California:

Correlations with sea surface temperature and upwelling indices. Marine Mammal Science

15(2):446–461.

Zar, J. H. 1984. Biostatistical analysis. Prentice-Hall, Inc., Englewood Cliffs, NJ. 718 pp.

SOP 5. Revising the Protocol

Version 1.4

Revision History Log:

Previous

Version #

Revision

Date

Author Changes Made Reasons for Change New Version

#

Sept. 2007 Marcus

Koenen

Adapted from SFAN

Water Quality Protocol

1.0

1.0 Sept 2007 Dawn Adams Added App. A with

reviewers comments

and response

In prep for submitting

to PWR.

1.1

1.1 June 2008 Dawn Adams,

Marcus

Koenen

Remaining comments

addressed

In prep for submitting

to PWR.

1.2

1.2 September

2009

D. Press, S.

Allen

Completed Appendix. B

with reviewers

comments and

response. Updated

MVT.

In prep for final

submission to PWR.

1.3

1.3 November

2009

K. Freemam,

D. Press

Changed tables and

figures to a modular

numbering system.

Additional minor edits.

Formatting

requirements.

1.4
194

Contents

Page

1.0 Revision Procedures..........................................................................................................195

Appendix SOP 5A. 2004 Peer Review Comments and Response from Protocol

Authors. ..................................................................................................................................197

Appendix SOP 5B. 2009 Peer Review Comments and Response from Protocol

Authors. ..................................................................................................................................201

Tables

Page

Table SOP 5.1. Master version table and current SFAN pinniped protocol

documents...............................................................................................................................196
195

This Standard Operating Procedure explains how to make changes to the Pinniped Monitoring

Protocol Narrative for the San Francisco Bay Area Network (SFAN) and accompanying SOPs,

and track those changes. Editors of the Protocol Narrative or any one of the SOPs need to follow

this outlined procedure in order to eliminate confusion in how data is collected and analyzed. All

observers should be familiar with this SOP in order to identify and use the most current

methodologies.

1.0 Revision Procedures

1. The Pinniped Monitoring Protocol Narrative for the SFAN and accompanying SOPs has

attempted to incorporate sound methodologies for collecting and analyzing pinniped data.

However, all protocols regardless of how sound require editing as new and different

information becomes available. Required edits should be made in a timely manner and

appropriate reviews undertaken. The Protocol Narrative is a general overview of the protocol

that gives the history and justification for doing the work and an overview of the sampling

methods, but that does not provide all of the methodological details. The Protocol Narrative

will only be revised if major changes are made to the protocol. The SOPs, in contrast, are

very specific step-by-step instructions for performing a given task. They are expected to be

revised more frequently than the protocol narrative.

2. All edits require review for clarity and technical soundness. Small changes or additions to

existing methods will be reviewed in-house by SFAN staff. However, if a complete change in

methods is sought, than an outside review is required. Regional and national staff of the

National Park Service (NPS) with familiarity in pinniped monitoring and data analysis will

be utilized as reviewers. Also, experts in pinniped research, monitoring, and statistical

methodologies outside of the NPS can be utilized in the review process.

3. Document edits and protocol versioning in the Revision History Log that accompanies the

Protocol Narrative and each SOP. Log changes in the Protocol Narrative or SOP being edited

only. Version numbers increase incrementally by tenths (e.g. version 1.1, version 1.2, etc.)

for minor changes. Major revisions should be designated with the next whole number (e.g.,

version 2.0, 3.0, 4.0, etc.) Record the previous version number, date of revision, author of the

revision, identify paragraphs and pages where changes are made, and the reason for making

the changes along with the new version number.

4. Narrative and SOP updates may occur independently. That is, a change in one SOP will not

necessarily invoke changes in other SOPs; a narrative update may not require SOP

modifications. The program tracks the narrative and SOP version numbers in a Master

Version Table (MVT) (Table SOP 5.1), which is maintained in this document (SOP 5).

Anytime a narrative or an SOP version change occurs, a new Version Key number (VK#)

must be created and recorded in the MVT, along with the date of the change and the versions

of the narrative and SOPs in effect. The VK number increments by whole integers (e.g., 1, 2,

3, 4, 5). The protocol narrative, SOPs, and data should not be distributed independently of

this table.
196

5. Updates to the MVT and changes to the Protocol Narrative or SOP must be provided to the

SFAN Data Manager for inclusion in the master version table database and the metadata

record. In addition, the database may have to be edited by the Data Manager to accompany

changes in the Protocol Narrative and SOPs.

6. Post new versions on the website and forward copies to all individuals with a previous

version of the effected Protocol Narrative or SOP, including pinniped project staff from

Golden Gate National Recreation Area and Point Reyes National Seashore. Archive older

versions of the protocol narrative and SOPs on the network archive server under the pinniped

vital sign folder.

Table SOP 5.1. Master version table and current SFAN pinniped protocol documents.

Document Name Current Version Version Date

SFAN Pinniped Monitoring Protocol 3.01 November 2009

SOP 1: Harbor Seal Field Surveys 1.4 November 2009

SOP 2: Northern Elephant Seal Surveys 1.4 November 2009

SOP 3: Data Management 1.4 November 2009

SOP 4: Data Analysis and Reports 1.4 November 2009

SOP 5: Revising the Protocol 1.3 September 2009

SOP 6: Safety Procedures 1.1 September 2009
197

Appendix SOP 5A. 2004 Peer Review Comments and

Response from Protocol Authors.

A draft of the Pinniped Monitoring Protocol was submitted and reviewed by two researchers in

2004. In 2007, review comments were incorporated into the protocol. This appendix summarizes

the major deficiencies and suggested corrective actions noted by the reviewers. This summary

does not include layout, grammatical, spelling or table/figure change edit recommendations. The

text in italics represents the changes made to the document based on the reviewers’ comments.

Hard copies of reviewer comments are on file.

Review #1: Dr. David Ainley, H.T. Harvey and Associates, 983 University Avenue

Building D, Los Gatos, CA 95032. Phone (408) 458-3200

Indicator of Ecosystem Condition

xNeeds to be better organized to be referred to when justifying the protocols.

xWhat questions can be answered by this protocol? For example, regime shifts data is apparently

going to be collected but not clear how or why. Prey availability is also discussed but issue is

not addressed later. Suggest to expand section.

o Prey availability text expanded within Indicator of Ecosystem Condition section

xUse of term pinniped guild not appropriate. Species discussed are in different ecological guilds.

o Term changed to assemblage within document.

xUse of the terms colony versus rookery vs haul-out. Make consistent and put in glossary.

Monitoring Questions

x Indicated earlier that interested in short- and long-term effects, but didn’t include a question

that addressed changes in phenology, which could change due to food or climate and has

been linked to climate in other vertebrates. Suggest that place importance on phenology as a

parameter to be measured. Could expand on mention of it made in population ecology

section under Sampling Design and Parameters monitored.

o Phenology objective added under Harbor Seal and Elephant Seal-specific

monitoring objectives.

xOther monitoring questions should link directly back to the discussion in the Indicators of

Ecosystem Condition section.

x Pinniped guild section rough and should be placed earlier in document, i.e. before indicators of

ecosystem condition.

o Section moved.

xDiet and tissue analysis for pollutants mentioned in population ecology section under Sampling

Design and Parameters monitored, but no mention of tissue analysis for stable isotopes and

fatty acids. Important and viable technique for the program.

o Not added as a parameter monitored.

Specific Programs Section

xDiscussion for each species begins with reference to monitoring objectives using numbers not

used in the earlier section

o Format has been changed.
198

xNot clear how data are being gathered on climate phenomena.

o Climate data collected on datasheets as indicated. This data is used for qa/qc, not

for data analyses. Climate data for analyses comes from established weather

stations (e.g. NOAA).

x Include trend graphs of certain parameters in species account sections (appendix)

o Species accounts appendix was removed.

Review #2: Dr. James Harvey Review, Moss Landing Marine Lab., 8272 Moss Landing

Rd., Moss Landing, CA 95039 (831) 771-4434:

This is a more substantial review and his notes are 7.5 pages long and referenced to the PWR

checklist.

Overall comments

xNeed more rationale on survey design and periodic analysis to test effectiveness.

xMore citations for the factual statements in text.

o Additional citations added to support statements.

Monitoring Questions and Objectives

xMMPA restricts harassment of marine mammals and should be used as a rational for the harbor

seal disturbance monitoring objective.

o Additional text added to Enabling Legislation section to connect MMPA

restrictions to the protocol objective.

xDiscuss coordination of sampling and data sharing at PORE and GOGA.

xConceptual models represent ecosystem function to understand the components, interactions

and what data is missing. Seems premature to include the model at this point in the

monitoring program.

o Model required for protocol by NPS but moved to an appendix.

xGeneral management issues not useful; include specific issues (i.e. contaminants and effects on

wildlife).

xGood summary of previous monitoring but lacking thorough description of data and findings.

o Additional results added from recent reports and publications.

x Protocol specifies condition/trend and % change threshold, but does not provide rationale for

values and basis for sample design. Some objectives don’t have thresholds.

xCould improve historical perspective discussion of importance in regional and national context.

Methods and Implementation

x Some monitoring questions are complex and specific and not obviously answered by protocol.

o Caveat added that these questions are not addressed by this protocol.

x Sampling disturbance and environmental information does provide some background to assess

changes in pinniped populations, but consider an assessment of prey resources by integrating

fishery data from other sources.

o Brief amount of text added to Indicator of ecosystem condition section that

identifies ways of assessing prey availability.
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x Sample unit is a survey and should be more clearly defined in the protocol. Explain that

sampling is random in time, why it is non-random in space, and how the 2 hour count is

sufficient to count all pinnipeds in area.

xRegarding use of maximum counts, discuss rationale for use of max instead of average (also in

SOP 9) and use of correction factor. Need assessment of quality of counts/measurement

error.

xUse past data to assess power of statistics to resolve effect size and whether stated levels of

change are actually detectable. Look also at variability within a site as well as among sites or

years to establish amount of surveys needed.

xTag sighting protocols should include resight bias, tag loss, and how potential biases will be

minimized or are irrelevant.

o Some discussion of tag loss rate and resight biases added in eseal Methods

section.

xMore detail needed in SOP 10 regarding process to make changes to SOPs and if future sample

design analysis could result in changes to survey scheme.

Data Management and Reporting

xNo clear description of who will enter data.

o Roles and responsibilities are now explained.

xDiscuss audience for annual and 5-year reports, who is responsible for producing reports, when

disseminated and list of recipients.

o This information is now presented in the protocol narrative.

xDiscuss how data may be used in peer-reviewed papers and other communication.

o Reporting section has been expanded. Peer review follows NPS NRPM standards.

x Improve map legibility by producing location maps without topographic information.

o New maps added.

xConsider creating a separate dataset of counts from other surveys conducted by researchers to

be used for comparison (CDFG, MLML, SFSU, etc.).

o This will be incorporated into trend reports and through work by partners as

described.

Personnel and Operations

xDescribe process if had a reduction in volunteer labor.

o This has never been an issue in this area and was not included in the protocol.

x Include training manual in protocol.

o More information on training is presented and is available upon request.

xDescribe facilities, vehicles, and offices needed for project.

o More information on personnel and operations has been included.

xList contributions from partners and cooperative agreements in place.

o Partners are listed. There are no current cooperative agreements.

xExpound on content of periodic reviews – should assess adequacy of frequency and timing of

surveys. Should also be an assessment of quality of counts and attempt to reduce variability

among and within observers.

o This section has been expanded.

xNeed more clarification on the budget and justification.
200

o Much more information on budget has been included.
201

Appendix SOP 5B. 2009 Peer Review Comments and

Response from Protocol Authors.

A draft of the Pinniped Monitoring Protocol was submitted to Dr. James Agee, PWR Protocol

Review Coordinator, and Dr. Penny Latham, PWR Regional I&M Coordinator in June 2008. Dr.

Agee forwarded the protocol to two anonymous peer reviewers (R1 and R2). In 2009, review

comments were incorporated into the protocol. This appendix summarizes the deficiencies and

suggested corrective actions noted by the reviewers. The text in italics represents the authors’

changes to the document based on the reviewers’ comments. Hard copies of reviewer comments

are on file.

PWR Protocol Review Checklist

Protocol Name: Pinnipeds Monitoring Protocol

Science Reviewer: James K. Agee Admin. Reviewer: Joel Siderius

Red Text=extended comments.

Overall Organization and Presentation of Protocol Narrative

YES 1. Is the overall monitoring protocol well-organized with sections clearly delineated?

In-part 2. Does the protocol have a title page with authors’ names, protocol version number and

date? (Protocol version numbers should be constructed to allow for both major and minor

changes.) Is there a Table of Contents, abstract, and the three basic sections: 1-Narrative, 2-

Standard Operating Procedures (SOPs), and 3-Supplementary Materials or Appendices

recommended in the NPS standards published by Oakley et al. 2003

(http://science.nature.nps.gov/im/monitor/protocols/ProtocolGuidelines.pdf).

YES 3. Is there a complete and accurate table of contents with page numbers? (Chapters should

be paginated consecutively, i.e. Chap. 1 (pp. 1-20), Chap. 2 (pp. 21-28), Chap. 3 (pp. 29-

44), etc. to allow for modular updates.)

Mostly 4. Are the tables and figures clearly labeled and understandable?

YES 5. Is the protocol bound so that it lies flat, preferably in a 3-ring binder?

A. Background and Objectives (Chapter 1)

Yes 1. Does the protocol narrative provide a rationale or justification for why a particular

resource or resource issue was selected for monitoring? Is the history and background for

this resource issue well-referenced with supporting literature cited?

In-part 2. Does the protocol narrative discuss the linkages between this and other monitoring

projects?

YES 3. Does the protocol narrative describe how monitoring results will inform management

decisions?

Yes 4. Does the protocol narrative contain careful documentation of the monitoring objectives

or monitoring questions being asked?

Yes 5. Does the protocol narrative identify specific measurable objectives such as thresholds or

trigger points for management actions?

B. Sampling Design (Chapter 2)

Yes 1. Is there a clear and logical rationale for selecting the sampling design over others?

Yes 2a. Were the criteria for site selection clearly discussed including stratification, spatial

design, and whether this monitoring will be co-located and/or integrated with other VS

monitoring protocols? (See Checklist, Section 1A2.)

Yes 2b. Has the target population or “sampling frame”, and the sampling units, been identified?

In other words, is the desired level of inference clear?
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Yes 3. Is the sampling frequency and replication identified?

Yes 4. Is the timing of sampling defined?

In part 5. Are the location of sampling sites clearly identified?

In part 6. Is the level of change that can be detected for the amount or type of sampling being

instituted identified? (See Checklist, Section 1A5.)

C. Field Methods (Chapter 3)

In-part 1. Are preparations for the field season and equipment setup included? Are requirements for

permitting and compliance discussed?

Yes 2. Does the protocol include clear and detailed information on taking measurements with

example survey forms included? (Protocol variables and measurements may be discussed in

detail in a SOP. A complete set of forms should be included in either the supplementary

materials or a SOP.)

In part 3. Is the method of access for sampling sites provided?

NA 4. Is there an overview of procedures for establishing, monumenting, and maintenance of

plots discussed in one or more SOPs?

NA 5. Does the protocol include details for the post-collection processing of samples or

vouchers?

Yes 6. Does the protocol include procedures to be followed at the end of the field season?

D. Data Handling, Analysis and Reporting (Chapter 4)

YES 1. Does the protocol provide an overview of the process for entering, editing, and storing

data, identification of database software, and whether the database is consistent with the

recommended I&M database template structure? (For water quality protocols, see specific

water quality guidance in Part B or WRD’s General Comments 15, and checklist items in

Section 2, items 8-10, below.)

N.A. 2. Are quality assurance (QA) and quality control (QC) procedures presented for the

various levels of data collection and analysis? (See water quality Part B guidance or

General Comments 15 as appropriate.)

Yes 3. Is the data structure clearly presented and sufficient to capture the required information

to meet the stated goal? Is there an overview of the database design?

Yes 4. Are there recommendations for routine data summaries and statistical analysis to detect

change?

YES

5. Is there a recommended reporting schedule?

In-part 6. Is there a recommended report format with examples of summary tables and figures?

Yes 7. Is there a recommendation for long-term trend analysis (e.g. every 5 or 10 years)?

Yes 8. Does the protocol narrative include an adequate description of metadata and data archival

procedures?

Yes 9. Does the protocol narrative describe the frequency of testing and review of protocol

effectiveness?

E. Personnel Requirements and Training (Chapter 5)

YES 1. Does the narrative include a listing of the personnel and describe their roles and

responsibilities, and qualifications?

Yes 2. Does the protocol include a discussion of training procedures for personnel?

F. Operational Requirements (Chapter 6)

In-part 1. Are facility, vehicle and equipment needs identified?

In-part 2. Is there a summary of key partnerships with agencies, organizations and individuals that

are part of the monitoring program and a description of their contribution? Is there a list of

relevant cooperative agreements and other partnership agreements, if applicable?
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YES 3. Is a schedule for the annual fieldwork and administrative needs required to implement

this protocol included?

Yes 4. Is there an overall budget that summarizes the annual and periodic costs of

implementation of the protocol? Does it seem reasonable?

YES 5. Does the staffing plan and budget demonstrate that adequate resources have been

allocated to data management, analysis, and reporting activities (ca. 30% are

recommended)?

G. Literature Cited (Chapter 7)

In part 1. Are the literature citations relevant, sufficient and consistently formatted?

Standard Operating Procedures (Selected essential SOPs in addition to those

mentioned in the narrative outline are identified in the checklist below. For Water

Quality protocols, Part B Guidance or WRD’s General Comments 15 should be

consulted when developing SOPs.)

In-part 1. Is there a table of contents for the SOPs?

YES 2. Are changes to each SOP clearly identified with a title, version number or revision date,

and page numbers? Changes to protocol modules (Chapters or SOPs) should be reflected in

the overall protocol version number and protocol revision history log either through a minor

or major revision; however, you may also wish to develop a numbering scheme for SOPs,

e.g. SOP 1.00, 1.01...

YES 3. Is there a SOP with instructions for revising the protocol and a revision history log?

YES 4. Is there a SOP with instructions for preparation before the field season? Is there a SOP

with instructions for procedures and equipment storage during and after the field season?

(Also see numbers 10 and 11 below.)

Yes 5. Is there a SOP for training field personnel?

Yes 6. Is there a SOP that clearly defines protocol variables and how to measure them? (See

Checklist, Section 1C2.)

In-part 7. Are there clear and detailed driving and other navigational instructions to sampling sites?

Yes 8. Are the details of Data Management identified in one or more SOPs? Topics to be

included are at minimum identified in Section 1D and may include customized data

management routines. Specifically for water quality monitoring data, does the SOP specify

how data will be reported to WRD for entry into the Environmental Protection Agency’s

STORET database?

N.A. 9. For water quality monitoring and other monitoring as appropriate, is there a quality

control SOP associated with each protocol that adequately documents QC objectives for

measurement sensitivity (detection limits), measurement precision, measurement systematic

error (bias as percent recovery), data completeness (including adequacy of planned sample

sizes and statistical power – this topic may be in the SOP on Sampling Design), and (if

applicable for lab measurements only) blank control? Are instrument calibration details

included either in the QC SOP or in a separate calibration SOP?

N.A. 10. For water quality protocols, is there a SOP that includes an explanation of how data

comparability (a quality assurance basic) was considered in choosing which protocols and

chemical labs to utilize? Do protocol SOPs contain enough field and lab method details to

allow others to determine if data produced is comparable enough to other regional data sets

to be considered credible by regulatory agencies interested in the data?

N.A. 11. Do aquatic protocol SOPs adequately describe the details of all Sampling Protocols

(Field and Laboratory), as well as equipment needs and operation, sampling techniques,

sample preservation and handling and logistics?

Yes 12. Are all major procedures required for the protocol sufficiently explained? Are any SOPs

missing?
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Yes 13. Are the literature citations with the SOP relevant, sufficient and consistently formatted?

Supplementary Materials or Appendices

N.A. 1. Is there a table of contents with Section 3 – Supplementary Materials that clearly

identifies the materials provided in this section of the protocol?

N.A. 2. Are the supplementary materials relevant, sufficient and consistently presented?

Consistent formatting is desirable, but not always possible.

Yes 3. Are data collection forms provided either in this section or in an SOP?

No 4. Is there a section for the Administrative Record that provides the history of protocol

development and refinement? A summary event table is highly recommended in addition to

the supporting materials required in the Protocol Review File Checklist, e.g. the initial

study plan or protocol development summary, the results of protocol development studies,

peer review comments and responses during the development phase, and/or any published

protocol on which a major portion of the methodology included in this protocol is based.

(The published protocol may be presented either in Section 2 or Section 3 depending upon

its contribution to the current protocol.)
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Extended Administrative Review Comments

General/Editorial Comments

1. Pg iii-xiii. The only bold text should be the Heading 1’s. i.e “1.0 Background Objectives” on

pg iii should not be bold.

Fixed.

2. The “Table of Contents” should be changed to “Contents” on pg iii. And on pg iv and

henceforth it should read “Contents (continued)”

Fixed.

3. pgs v, vii, ix, xi, xiii, xv, Do not need to be blank, they should be deleted.

Fixed.

4.The Tables of Contents, Figure, Tables, should have “Page” right justified on the top of each

page. See below for example.

Contents

Page

Exhibits..................................................................................................................................... v

Executive Summary................................................................................................................ vii

Fixed.

5. Page 1, should be paginated.

Fixed.

6. Page 1, my non-scientific opinion is that “pinnipeds” should be defined. I guess it is a

suborder? Or is it a superfamily? (PRC Note: this is done in glossary, but it might help the

average reader to put it in the text)

A short definition was added as the first sentence of paragraph 2 in the Executive

Summary.

7. Use Scientific Names only once.

Extra uses of scientific names have been removed.

8. Elephant and Northern Elephant appear to be used interchangeably? I assume they are the

same. Make usage consistent.
206

All references to the species now standardized to “northern elephant seal” in the

protocol narrative and SOPs.

9. A summary table of all the relevant Pinnipeds would be helpful somewhere in Section 1.1 or

1.2. Maybe include name, scientific name, range, status...... etc.

Because we have pared down the protocol to just harbor seals and elephant seals, we do

not feel that a summary table as described is warranted. Paragraphs and two maps were

added to Section 1.1 describing the ranges of northern elephant seals and Pacific harbor

seals.

10. Dovetailing with Comment 9 above, the 2nd to the last paragraph in Section 1.1 is out of

place.

This paragraph fits in nicely with the paragraph before it and after it. The paragraph

identifies the pinniped species that occur at PORE and GOGA, which seems relevant for

this background section.

11. Multiple references should be separated by semicolons, oldest to newest.

Ex. (Wakeley 1954; McManus 1957).

DOUBLE CHECK THROUGHOUT ENTIRE DOCUMENT

Fixed.

12. Pg 8, reference for NPS-75 should be (NPS 1992).

Fixed.

13. pg 10, the quotes should be indented.

Fixed.

14. pg 31. The first two sentences of Section 3.1 are not informative. It seems like 5/9 sites are

on trails. Then 4/9 are off trail, though it says “counting locations are typically located off trail”

This section is in reference to both harbor seal and elephant seal counting locations. Our

tally is that 4 of 12 counting sites are off trail, so we retained the language as is. We

removed Sea Lion Overlook from the list of publicly accessible sites in the second

sentence since this site was in reference to the All Species component of the protocol,

which we have removed.

15. pg 37, should read section 4.5.1 not 4.51

Fixed.
207

16. Table 4, goes for multiple pages so the caption should be included on all pages with the word

“continued”

Fixed. This table is now Table 2.

17. Pg 55. 4th reference does not look right with two last names, Maybe it needs a hypen?

The reference for Allen Miller was left as is at the author’s request.

Chapter 7 should be the literature cited

Fixed.

The glossary should be an appendix.

Fixed.

Overall Organization and Presentation of Protocol Narrative

2. No date is presented in the title page, just XXXX 2008.

Completed on submittal of final protocol.

SECTION 1.A Background and Objective

2. Section 1.4 explains why the NPS selected pinnipeds and how pinniped monitoring is linked

to a larger NPS program. However, there is not mention of any other SFAN vital signs. It would

ideal to mention how pinniped monitoring is linked to other SFAN vital sign monitoring. (PRC

Note: These other signs ARE mentioned on page 11)

As noted by the PRC, links to other monitoring programs, both NPS and non-NPS, are

discussed in Section 1.4.3 Indicator of Ecosystem Change.

SECTION 1.C Field Methods

1. No mention of compliance in Chapter 3. Perhaps since, the volunteers are just observing and

not sampling anything, no permits are needed. But it would behoove the author to address

compliance, likely in Section 3.1. The compliance section 6.5 should be in Chapter 3.

Compliance is relative to the logistics and management of the monitoring program and is

therefore correctly placed in Chapter 6: Operational Requirements rather than Chapter

3: Field Methods. We clarified that a permit is required for both harbor seal and

northern elephant seal monitoring.

SECTION 1.D Data Handling

6. No examples of figures or tables are mentioned or shown. Ideally these would be in Section

4.6.1
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Section 4.6.1 is part of the Reporting section, not Data Handling. Table 4 is referenced in

this section. The reader is directed to SOP 5: Data Analyses and Reports, where more

tables and figures are found.

SECTION 1.F Operation Requirements

1. Vehicle needs are not address in Section 6.3. Though tables 7&7 identify budget line items for

vehicles. Section 6.3 should clarify the vehicle situation.

Added paragraph on the vehicle situation to Section 6.3.

2. Section 5.4 needs to be in Section 6.

As suggested, Section 5.4 Partners and Collaborators is now Section 6.6.

Section 2 SOP’s

SECTION 2

1. An additional list of SOPS would be helpful, especially since page 68 is clearly the end of the

narrative. (PRC Note: I agree here, had a hard time referencing them).

The protocol SOPs have been included with the protocol narrative, thus creating one

large document. The SOPs therefore are now listed within the Table of Contents.

7. I see lots of maps, but I cannot find driving directions to the sites in SOP 1,2,3.

Detailed directions were added to SOP 1 for each harbor seal survey site. The maps and

aerial images in SOP 2, which include the major road names and an inset map, provide

adequate directions to the northern elephant seal monitoring sites. SOP 3 was removed

from the protocol.

I would suggest that the map on page 22 of the narrative be included in each of the Appendixes

B’s for SOP’s 1,2,3. Otherwise the maps in SOP’s 1,2,3 are too localized.

Because the SOP’s have been added to the protocol narrative, thus creating one large

document, the above suggestion would result in repeating the same figures in one

document. Instead, we have provided references to the maps in SOP’s 1 and 2. SOP 3 has

been removed from the protocol.
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PRC Comments

P34: “Digital photos WILL be labeled...”

Sentence changed to read, “Digital photos will be labeled ....”

Many problems with Literature Cited:

P2: Is Hastings et al. 2002 really Hastings and Sydeman 2002? Keep “et al.s” to three or more

authors.

P2: Miller et al. 1983 missing from lit cited.

P2. CDFG 2001 missing from lit cit

P3: Allen et al 1996 missing from lit cit

P11: Sydeman et al. 1999: really Sydeman and Allen?

P11: Keiper 2005 is Keiper et al. 2005

P11: Womble et al. 2006: really Womble and Sigler?

P18: Allen et al. 1983 really Allen and Huber?

P20: Risebrough 1978 is Risebrough et al. 1978

P20 and 31: Allen et al. 1984 not in lit cit

P38: Caughley 1971 and Zar 1984 missing from lit cit

P39: Adams 1993 and LeBoeuf and Laws 1994 missing from lit cit

P55: There are a number of references here that I did not find in the text: Adams 1994, Allen et

al. 1985, Barlow et al. 1994, Epstein et al. 1998, Francis and Hare 1994, Geraci and Lunsbury

1993, Hanan 1996, Harvey 1987, Harvey and Goley 2005, Lowry et al. 2005, Miller 1983, NPS

1980 and 1992.

P56: Becker et al. in press needs a journal listed.

P57: Eberhardt et al needs a issue and page number for Wildlife Monographs

P57; Geraci and Lounsbury (if kept) need initials.

Fixed.

Reviewer #1 (R1)

Background. Pinnipeds have been selected by the NPS as focal species for determining the

condition of PORE and GGNRA as parks, their associated marine habitats, and their ecosystems

in general. Goals of the SFAN Pinniped Monitoring Plan are as follows:

1) Determine pinniped status and trends, using Harbor Seal (HASE) and northern elephant

seal (NESL) as key species

2) Determine the seasonality of pupping events (presumably to look for changes that may be

related to climate change?)

3) Determine the annual reproductive success/productivity of HASE and NESL in PORE

and GGNRA

4) Determine the effects of natural and human disturbance (in particular on HASE) in these

parks.
210

Review. The protocol is based on a long-term research program implemented by the lead author

of the plan (S Allen), and has been in place since the early 1980s. The pinniped program

involves a large group of collaborating organizations and individuals, making it a complex

undertaking. The monitoring will also involve the public as volunteer data collectors. Overall,

the plan is sound, and the methods appropriate, tested and true. I do wonder how effective

volunteers are (and what happens if they drop out?), but probably this has been going for years

and is unlikely. I provide some suggestions and criticisms below in the spirit of improving the

protocols, and thinking “outside the box” a bit. Most of these comments are about some bigger

issues. The work of these authors in preparing the protocol has obviously been substantial, and

they have done an excellent job overall on all the technical details.

1) Data to date (and in the future) is to be stored in a relational ACCESS database. This is

not a particularly sophisticated way to manage these data, but it is a reasonable place to

start. What next? I was also surprised to see no specifics in the protocol about releasing

these data to the public. Certainly, a portion of these data should be made publically

available as soon as possible, and some parameters should be updated and released

annually, presumably on the PORE and GGNRA websites.

Microsoft Access is the current database standard adopted by the NPS Inventory and

Monitoring Program. The reviewer is correct, however, that Microsoft Access will has its

limits, particularly in regard to file size, the ability to track changes to the data, and to

set detailed user controls. In the future, if necessary, the database will be upgraded and

managed in SQL Server. Modifications to the appropriate data management sections of

the protocol will be made if and when the database is upgraded to SQL server or another

database platform.

In regards to public release of the data, SOP 4 Data Management provides information

on data distribution. Although the actual data will not be posted on-line, a database

metadata record will be posted and maintained at the NPS Data Store with the

appropriate contact information. The data will be provided to the public upon request. A

summary of the data distribution section in SOP 4 has been added to the protocol

narrative.

2) Honestly, it is not entirely clear why pinnipeds were selected as focal species, aside from

the fact that solid long-term data exists. As I read about the Vital Signs program, I

wondered about other taxa....indeed, marine mammals are not mentioned. What about

landbirds? Or amphibians? Or, more to the point, why pinnipeds?

Section 1.4 provides explicit rationale for selecting pinnipeds as an I&M vital sign.

However, we did add an additional bullet item to the reasons to monitor pinnipeds listed

in this section, noting the direct application to NPS management decisions. Other marine

mammals (ie. cetaceans) were not selected as vital signs primarily because the NPS does

not have the ability to manage transient cetaceans within their coastal waters. Additional

information can be found in the SFAN Vital Signs Monitoring Plan (Adams et al. 2006),

which notes that cetaceans ranked 60 of 63 vital signs during the SFAN prioritization
211

process. Information about the other vital signs selected for monitoring, including

landbirds and amphibians, can also be found in the SFAN Vital Signs Monitoring Plan

and at the SFAN website. R2 noted that our rationale for selecting pinnipeds for

monitoring was “clearly and completely presented”.

3) The monitoring plan references a long history of many excellent publications. In addition,

apparently some new analyses were conducted, specifically to support aspects of the

monitoring protocols (e.g., a power analysis on the frequency of surveys; Becker 2008).

Becker’s analysis shows no more than an 80% chance of detecting a 40% decline in

HASE abundance over 5 years, and 45%-87% chance of detecting a 50% decline in

NESL over the same period (if I am reading this correctly). This was a bit difficult to

understand as written, but a question remains: is this sufficient in terms of management?

I’m not sure that more surveys could be realistically accomplished (this analysis was

based on 2 surveys/week, which seems like a maximum), so was this an exercise to

determine the power in doing what is being done? If so, that is fine, but it should be

stated as such.

Becker re-ran the analysis for harbor seals for this draft of the protocol. The previous

power analysis incorporated all counts per location during the peak of the breeding

season for each monitoring year. The final harbor seal power analysis (Appendix A)

prepared for this draft of the protocol only uses the maximum counts from each location

per year. And to further clarify, a power analysis for northern elephant seals was not

submitted in the peer-reviewed protocol draft, but was prepared for this draft (Appendix

B).

The harbor seal power analysis indicates that current monitoring efforts have a 90%

chance of detecting a 27% decline in overall population counts over only 3 years. 25%

percent declines take more time to detect for individual colonies, especially pups. In the

case of northern elephant seals, current monitoring efforts have an 86% chance of

detecting a 36% decline in cows over 4 years. For pups, an 80% chance of detecting a

41% decline would be realized after 5 years. As with harbor seals, declines take longer to

detect at individual colonies.

The power analyses were performed to determine if the current monitoring efforts are

sufficient to determine trends in the populations that are meaningful to management and

to identify the limitations of the data. We do not perceive the analyses as simply an

exercise to determine the power in doing what is already being done.

In the end, we feel like the short number of years that it will take to detect significant

population-level changes for all sites combined provides opportunities for timely

responses, either as direct management actions or through additional research. Although

significant trends at individual sites take longer to detect, this is primarily a function of

the variability in the data set rather than a function of effort. In further regards to effort,

the power analyses only employ maximum counts and the monitoring programs are

specifically designed to ensure that frequent surveys occur during the peak of the

breeding seasons.
212

4) Moreover, and more to the point, these populations (NESL especially) are growing like

gangbusters, and pup production (number of pups born) appears to be increasing annually

(these are obviously correlated), so why would the “management objectives” be stated in

terms of population decline? Seemingly, this makes little sense given the welldocumented history of population increases which continue to this day. The interesting

questions from a management perspective (and the ones that might be realistic within the

next 5-10 years for these species/populations, and could be addressed in a power

analysis) have to do with chances of detecting slowing of the population growth rates, not

declines. Indeed, if there was any cessation of population growth in any given year, it

should (and presumably would be) of great interest to park management. Also, perhaps

the power analysis on productivity would be more revealing, but unfortunately it was not

clear whether this analysis was on the number of pups born or the proportion of pups

successfully weaned – the latter would be particularly interesting. If it was on the number

of pups born, I would say the management question is again suspect, as it is for

population abundance as well (and the power analysis does not say much that is

different). Let me also say, I am not a big fan of this kind of power analysis as it is often

based on an untenable assumption regarding the variance structure of dataset. How does

one know that the variance won’t change in time? Given these growing populations, etc.

it is likely that it will, thereby compromising these results.

Times series plots indicate that harbor seal populations within the SFAN have remained

steady over the past decade (Appendix A), and we therefore feel justified in considering

our ability to detect trends in terms of declines. For northern elephant seals however, we

have modified our approach to consider both increases and declines. Positive and

negative trends in northern elephant seals are explored in the power analysis and the

subsequent management objectives have been modified.

The power analyses were conducted on the number of pups born. Determination of

weaning success of harbor seals is beyond the capabilities of this monitoring program as

is would require an intensive tagging/resighting program. Weaning success for northern

elephant seals can be evaluated by comparing the total number of pups born with the

total number of weaned pups remaining at the end of the season. Due to movements of

the weaned pups around the Point Reyes Headlands, we could only look at weaning

success for the entire populations and not for individual colonies. Weaning success will

be evaluated in future annual and trend reports.

The reviewer is correct regarding the limitations of power analyses in general.

Appendices A and B both discuss the pitfalls and assumptions of the power analyses.

Temporal autocorrelation is particularly problematic for the northern elephant seal

analysis. Nevertheless, the analyses provide critical insights into the ability of these two

monitoring programs to track meaningful populations trends.

5) Given the depth of available datasets, I would have liked to see more analysis of the

observations at hand. In particular, a more comprehensive update of the analyses

presented (for the PORE populations) originally presented by Sydeman and Allen (1999)
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would have been appropriate, and could have been used to answer some of the key

questions, such as: what are the current population trajectories for HASE and NESL in

PORE? Are there indications of population stabilization? If there are, at what point may

these populations reach carrying capacity (or an upper inflection point)? These questions

have important implications for the monitoring program, yet were not addressed. Some

basic population modeling would also be useful for designing (and implementing) this

program.

The analyses requested by R1 are more appropriate for an in-depth analysis and

synthesis report, as described in Section 4.6.1. Once the protocol is completed, the SFAN

hopes to begin development of a synthesis report that builds upon Sydeman and Allen

(1999) using the last decade or more of available data.

6) It was stated that all NESL weaners were tagged between 1988 and 1998, and most were

tagged thereafter, but what is the point of this tagging program without a commitment to

re-sighting (no funding means no resighting?), a difficult and costly activity? How will

resighting data be taken and used? If there is no real plan for funding this program and resighting specifically, perhaps it is not necessary to tag as much, unless it is necessary for

determining NESL productivity. I’m not sure if it is, but in any case perhaps this could be

clarified.

Section 2.6.1 discusses the importance of the northern elephant seal (NESL) tagging and

resight data to the broader research community. The data set is available to the NPS to

explore in regards to dispersal, site fidelity, and colony expansion, although no plans for

data analysis are currently in place since this is an unfunded program. Even without

I&M funding, PORE will likely continue to resight and tag NESL weaned pups using

park staff and trained volunteers.

7) It is intended that Information from continuing HASE and NESL surveys will be used in

“adaptive management” and decision making in these parks, as well as, generally

speaking, to proxy the health of the habitats and ecosystems these species inhabit. In

terms of adaptive management, I have no concerns with this – indeed, I am aware of

myriad decisions for park management that on the surface would seem simple enough,

but in reality are quite complex, and often involve difficult value judgments (e.g., to

promote NESL or snowy plover recovery?). Having up to date population data would aid

in making these tough decisions. However, with respect to using these population data as

indicators to the health of park habitats and ecosystems, I am not so convinced. First and

foremost, marine mammals are not nearly as useful as indicators of marine ecosystems as

are, for example, seabirds. There are some data/papers on mammals as indicators of

marine ecosystems, but they were not referenced. More importantly, however, is the fact

that most marine mammals are recovering from exploitation, and thus do not track

environmental and ecosystem variability very well. This is because their populations are

often far below carrying capacity, and are generally increasing (as is the case here).

Second, population-level data generally does not resolve on an annual (or sub-annual)

temporal scale, and yet that is the scale often desired of an indicator. Third, if this is an

important goal, I think the authors should try to be as specific as possible about what the
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indicators are actually indicating...for example, what do HASE population numbers

indicate about marine conditions and/or food web variability? In this regard, in looking at

the time series, I would suggest that HASE pup production numbers and “weaning

success” possibly would be good indicators. AS NESL cows do not feed during the puprearing period, this species/parameter would not be that useful in this context. Moreover

NESL numbers just seem to be increasing, regardless of temporal environmental

variability, so I question the use of this species as an indicator of anything other than

itself. HASE on the other hand clearly do show some responses to the environment. Some

additional research and summaries (as suggested above) might be needed to flush this out

in more detail, but it seems HASE pup production and weaning success (if one could get

at this) would provide information not only on HASE in these parks, but also something

about the ecosystem.

Pinnipeds were selected as indicators of ecosystem condition because 1) they respond

quickly to short term environmental changes such as to El Nino and harmful algal bloom

events (Allen et al. 1989; Sydeman and Allen 1999; Pettee 1999; Sholin et al. 2000;

Dierauf and Gulland 2001); 2) they are sentinels to changes in climate because of

changes in their distribution, abundance and reproductive success which can be

measured locally and regionally (Dierauf and Gulland 2001; Le Boeuf and Crocker

2005; Ragen et al. 2008; Lee and Sydeman 2009); 3) other parks and agencies, including

Channel Islands National Park, the California Department of Fish and Game and

National Oceanic and Atmospheric Administration, monitor pinnipeds as one of several

marine indicators of marine ecosystem condition, providing opportunities for regional

collaboration and analysis; 4) monitoring several colonies at PORE and GOGA has

allowed biologists to distinguish broad-scale environmental effects, such as climatic

events and human-caused disturbances, on individual colonies

During El Nino events in the past 20 years, harbor seal reproduction and population

numbers declined significantly and elephant seal pup mortality increased significantly at

Point Reyes (Allen et al. 1989; Pettee 1999; Sydeman and Allen 1999; Becker et al.

2009). Thus, monitoring reproductive success, pup mortality and population numbers of

apex predators provide ecosystem level effects on the frequency and intensity of El Nino

events and into other climate anomalies that cascade through ecosystems. Monitoring

several marine indicators including prey and predators provide better understanding

about how marine ecosystems function and how resilient they are to disruptions such as

climate change.

The parks also monitor pinnipeds to guide management actions. In addition to changing

population size, a change in the distribution of pinnipeds at the parks may influence

management decisions. For example, new elephant seal sub-colonies forming in locations

where the public congregates or where endangered species such as western snowy

plovers breed, may require management intervention. Similarly, disturbance of harbor

seals at specific locations may not affect population numbers but may affect where seals,

particularly females and pups, are distributed and thereby influence pup survival.
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8) The protocols mention using timing of pupping (seasonal parturition dates?) to monitor

climate change, but I don’t think there is any indication that timing in HASE, or

especially NESL, is responsive to climate. If there is compelling data on this topic (e.g.

relationships between pupping dates and temperature, or something climatological), it

should be included. The other issue here would be age structure. If there were changes in

timing over the past decades, one would need to determine if this was due to changes in

climate or changes in population age structure. In pinnipeds, it has been shown that older

females generally breed earlier within each season. These populations have effectively

grown from zero (in the mid-late 1970s/1980s to present), so changes in age structure

would be the most parsimonious explanation for a trend in timing if one was found.

Frankly, I was a bit surprised to see this emphasis on timing. It could be good, but if the

park wants to emphasize this parameter, it is imperative that some background analyses

are conducted first.

Peer review of an earlier draft of the protocol by Dr. David Ainley in 2004 emphasized

the importance of phenology. Phenology was added as a parameter to be measured at

Dr. Ainley’s request. The frequency and timing of both harbor seal and northern elephant

seal surveys already capture important phenological events, such as the date of the first

pup or maximum molt count, so adding phenology did not equate to an increase in field

effort.

The scientific literature clearly documents that shifts in the phenology of many plant and

animal species over the last decades is related to climate change (Visser and Both 2005).

In regards to marine mammals, studies from the Arctic region are most relevant, having

documented climate change impacts on abundance, distribution, migrations, and

phenology of both pinnipeds and cetaceans (Laidre et al. 2008; Moore 2008). In regards

to harbor seals and northern elephant seals, our biggest concern is that climate change

shifts in the abundance and timing of prey availability will affect breeding and, in the

case of elephant seals, migration (Edwards and Richardson 2004).

Phenology was highlighted as monitoring question rather than a specific, measurable

monitoring objective. Although our data set may not be robust enough to link changes in

phenology to climate change, our data set will add to a much larger data set that may be

analyzed in cooperation with other agencies and universities.

9) Steller’s Sea Lions (STSL) and California Sea Lion historically used these parks, and are

mentioned in the Protocols. There is good historical accounting of these species, but they

are generally not included in the plan. This is a bit strange as STSL is an endangered

species. Then again, until they return to PORE in greater numbers, how much monitoring

can be done?

California Sea Lions are still found at PORE and GOGA, while Steller’s Sea Lions still

occur only at PORE. Neither species, however, breeds in either park. PORE staff conduct

regular monitoring of all pinnipeds at the Point Reyes Headlands (see Section 2.6.2),

including these species, but that is not part of the formal I&M monitoring program.
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10) I’ll mention this again -- HASE are really the focal species as NPS has dedicated

resources to this study. I’m not sure that the focus on NESL can be sustained without

resources...as a volunteer program can only go so far...but it is necessary as this is the

species that will cause more management issues with its continuing population expansion

to new areas and probable interactions with the public. Somehow this funding deficiency

should be addressed in the protocols.

Because it is our hope that the NESL monitoring program will be funded in the future

either by PORE or through the I&M program, we have kept NESL in the monitoring

plan. We have addressed reviewer comments by adding a power analysis and data

reporting and analysis sections for NESL to the protocol. The protocol will serve to fully

direct NESL monitoring efforts, whether it be a volunteer based program or fully funded.

Reviewer #2 (R2)

I made comments as I went along, using the ‘track changes’ feature in MSWord; some of these

comments refer to the four specific “Process” questions, but others are more minor and refer to

clarity etc. (PRC Note: the separately attached Word draft is labeled with a person’s name who

was not the reviewer).

Overall comments: Based on the background materials on the CD, this document has been

reviewed (by David Ainley and Jim Harvey?) and revised before, and I felt that this was

reflected in the very complete nature of the current version. The document reflects the authors’

extensive experience with monitoring and managing pinnipeds in the SFAN. The protocol

describes how data will be collected, clearly and (for the most part) in detail, which will ensure

compatibility of data across years etc. In addition, the protocol clearly describes how change will

be detected. I would recommend doing a power analysis for the elephant seal (and if possible, the

all species) protocols, in addition to the one already completed for the harbor seal protocol. I also

was curious about how condition/trend management objectives thresholds for population

declines (p. 14) were determined, as they seem high to me, especially in light of the report’s

statement that if these thresholds are surpassed, management action might be initiated, and that

action would in many cases simply be to initiate further research into the possible causes of the

declines. Are these threshold levels standard to pinniped management in the U.S.? Of course, this

may simply reflect my bias towards exercising caution in these types of situations.

Following guidance from the PRC, we have included a power analysis for northern

elephant seals. See Protocol Section 2.5.2 and Appendix B.

In regards to the thresholds identified in the condition/trend management objectives, the

threshold levels have been modified based on the power analyses for harbor seals and

northern elephant seals (Appendices A and B). If any of these thresholds are surpassed,

we feel strongly that, at the very least, research should be initiated to determine the
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cause, especially of a population decline. Management actions may then be taken if

warranted.

My comments related to the four specific review questions are summarized below:

1. Background and objectives:

1.1. Background and history: well presented overall, with information on legal protection

(and why that was instituted), current population status and trends, and ongoing

monitoring. Included examples of current management issues (e.g., disturbance by

visitors, El Nino influences on pup production, etc.). Focus was on northern elephant

seals, with less data on harbor seals and very little on the other species (csl, nfs, etc.)

Perhaps add more information on current distribution, with accompanying maps? (There

are haul-out site maps in Section 2, Sampling Design, but if a description of current

distribution is meant to be part of background etc., it would be clearer to include

distribution maps here).

Paragraphs and two maps were added to Section 1.1 describing the ranges of northern

elephant seals and Pacific harbor seals.

1.2. Rationale for selecting pinnipeds for monitoring: clearly and completely presented, I

thought – clear statement of NPS I&M Program overall goals, and nice, concise

numbered list of reasons why pinnipeds were specifically selected for monitoring. Fairly

detailed section of legal mandates for protection also included.

1.3. Measurable objectives: presented clearly as a numbered list of ‘specific monitoring

objectives’. All are measurable (e.g., population trends), although it may be quite

challenging to analyze the data on disturbance levels, changing effects of disturbance,

impacts etc. I had some questions about how threshold levels (e.g., for % population

declines) were determined, as this did not seem to be stated in this section of the report. I

did see objectives and questions in this section, but not testable hypotheses (at least not

clearly identified as such).

The threshold levels written into the protocol result from our power analyses of our

northern elephant seal and harbor seal data. Text was added to Section 1.5.3 to

emphasize that the thresholds reflect the change that our monitoring data is capable of

detecting and that the levels are sufficient from a management perspective.

The specific monitoring objectives were crafted based on guidance from the NPS

Inventory and Monitoring Program. In conjunction with the threshold levels, the

monitoring objectives may be approached as testable hypotheses for long-term analyses.

2. Sampling design chosen

2.1. Rationale for design and site selection/replication in space and time: while the methods

were very clearly described, there were some points where the rationale for selecting

these methods seemed a bit thin. For example, “sampling design theories were applied to

determine the frequency and timing of seasonal surveys” (p. 17) seems vague to me.
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Presumably the power analysis came into play here somewhere, but this is not

specifically referenced in this section?

Efforts have been made to explain more clearly the rationale behind our field methods.

The above noted sentence has been removed. We emphasize that because we can survey

all of the harbor seal and northern elephant seal breeding sites in a timely manner, no

statistical sampling techniques are required to monitor the pinniped populations. We

further note that based on our power analyses, the frequency and timing of our surveys

have the ability to detect meaningful trends over time.

2.2. Site selection: the “population” being sampled is not defined specifically, but

presumably is all seals (of a given species) within park boundaries. Also, I think a figure

(e.g., a map showing study area, primary and secondary sites distinguished) would have

been great to include here. The lack of a stratified design (beyond “primary” vs.

“secondary” haul-out sites) was explained earlier in the report.

We have modified 2.2 Study Area and Site Selection to better outline the differences

between what are considered primary and secondary sites. We have also clarified that

our monitoring efforts are focused on primary sites where it is possible to count all

individuals. Secondary sites are not monitored, but some ancillary data may be collected

at these sites by I&M staff or volunteers. It is not really practical to list or map the

number of secondary sites at PORE and GOGA. Secondary habitat is really any part of

the coastline that is not a primary site. Because the primary sites encompass the vast

majority of harbor seals and northern elephant seals during their respective breeding

and molting seasons, we feel justified in describing our counts as censuses of the

population. Because female northern elephant seals only give birth and mate in large

colonies without returning to the water for approximately one month, these counts, which

serve as the basis for our long-term trend analyses, can truly be described as censuses.

2.3. Sampling frequency and replication: clearly described for the most part (the “other

species” category is only described briefly and are only counted at one site – perhaps

because this is the only site they are regularly seen at? this wasn’t explained in this

section)

This section related to the frequency and timing of all pinniped species surveys has been

removed from the protocol.

2.4. number/location of sampling sites: very clearly and simply described (essentially, “we

count them all”), and included maps

2.5. Level of change that can be detected: based on a power analysis for harbor seal survey

methods (81% likelihood of detecting a 40% decline over 5 yrs); power analysis has not

been done for elephant seal or all species survey methods, and so these sections are less

robust. The assumption for the elephant seal surveys is that the current level of surveying

has been sufficient, but this is less convincing than the section incorporating a power

analysis. The authors note that a power analysis may be done in the future for northern

elephant seals and other spp; I would recommend that if possible, it be done prior to
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finalizing the monitoring protocol, or, that plans to do one in the near future be

incorporated into the methods.

A power analysis for northern elephant seals has been included in the protocol, thereby

justifying our field methods and guiding our ability to detect trends. The all species

monitoring program was removed from the protocol.

3. Appropriate methods for sampling design chosen

3.1. Data collection methods: are described in detail, with sample data sheets, site maps, etc.

included. Data methods are appropriate for monitoring purposes. I am often concerned

about observer variability and/or observer bias when volunteers are used, but it sounds

like volunteers are extensively trained (for one entire season) before being allowed to

collect data independently.

3.2. Post-collection processing: Not really applicable as no tissue samples etc. are regularly

collected. However, data entry, proofing, data and report archiving, etc. are described.

4. Data analysis techniques – as discussed earlier, a power analysis has been conducted for the

harbor seal monitoring program; I would recommend that (if at all possible given lack of

funding) it also be done for the elephant seal and all species monitoring programs.

A power analysis for northern elephant seals has been included in the protocol, thereby

justifying our field methods and guiding our ability to detect trends. The all species

monitoring program was removed from the protocol.

4.1. Metadata procedures: applicable data standards used (for GIS datalayers etc.) are noted,

and (when an official standard does not exist, such as is the case for natural resource

databases and spreadsheets), the protocol states that SFAN will “complete the NPS

Metadata Profile to the greatest extent possible to document the annual and master

pinniped back-end databases”. I assume that use of the NPS Metadata Profile will ensure

that data is collected consistently and is compatible (or at least usable) by other parks,

researchers, etc.

As noted in the metadata section, the NPS metadata profile is based on the FGDC

standard. More information regarding our metadata procedures are included in SOP 4

Data Management. We have updated the SOP and noted that the metadata is developed

in the standard XML format and can thus be imported into other metadata programs.

4.2. Database design: a relational database is used (MS Access), with an overview of the

database included in the main report body, and additional detail in the Data Management

SOP. It is difficult for me to assess this database without really “seeing it in action” (i.e.,

sitting down at a computer and having someone walk me through it), but it sounds

sufficient.

4.3. Data entry, verification and editing: quality control measures, etc., are described in an

overview in the main report body, with additional data provided in the Data

Management SOP. Data is entered within a week of collection (ideally, data would be

entered on the same day, based on my own experience, but this is not always feasible I
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suppose). The potential for error in the volunteer data collection is addressed, which is

good.

4.4. Routine data summary procedures and statistical analyses to detect change, and methods

for longer-term trend analysis: yearly reports are produced, containing data summaries

for the counts, disturbance data collection, etc, with trend analyses done every 5 to 10

years. Change for harbor seal population is monitored using published regression models

for monitoring population change. I have used a similar method for assessing change in

seal populations, and like it because it is very straightforward and easy for readers and

the general public to understand, unlike some of the more sophisticated time-series

analysis methods preferred by some authors. Impacts of disturbance on population size

and productivity will be analyzed using GLM’s, in a method based on an in-press

publication. Change for elephant seal numbers are assessed using direct counts, allowing

calculation of indices of population trends. Description of how productivity indices are

calculated is included. I did not see any mention of how “all species” data would be

analyzed?

The all pinniped species component of the protocol has been removed from the protocol.

Statistical methods are sound and have the benefit of being relatively “user-friendly”,

making them more likely to be used by managers in other coastal areas, for purposes of

comparison between pinniped populations.

Review Comments: Penny Latham, 1/05/2009

This was a very nicely done and well-edited protocol. (I don’t think I saw ANY typos at all!!) I’d

like to thank the authors and previous editors and reviewers for their contributions as this round

of review went very well. I’d also like to apologize for the delay. Although this protocol review

was sent to me in December 2008, the ensuing holiday prevented my reviewing the materials

until now. I agree with the other reviewers decisions and feel that most of the important issues

related to the protocol have been mentioned in those reviews; however, there are a few additional

points that I would like to make.

1. The majority of editorial problems arose due to pagination issues relative to the NRRS

Instructions to Authors (IA) guidance. (This has been updated as of 12/30/2008.) There

are three main problem areas: how to organize the SOPs, the Table of Contents, and the

instructions regarding the page that First Order Headings should be placed on.

Contributing to the confusion about how to number the sections of the protocols is

Question 1 in Section 2 of the Checklist that asks about TOCs for SOPs. The IA states

that the document pages must all be consecutively numbered and all sections of the

document (including Figures and Tables) need to be identified in the Table of Contents.

There seem to be two primary ways to deal with the organizational issue: Put everything

into one document and number all the pages, tables, and figures consecutively or separate

the SOPs and narrative into two volumes each with its own TOC. Unless the authors have

a good alternative to providing unique page numbers, figures and tables that works for
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the series, I would suggest considering one or the other of these approaches. However, all

pages after the title page (unless otherwise directed in the IA, e.g. blank pages and cover

pages) should have a number.

The protocol narrative, SOPs, and Appendices are now all organized into one document

with pages, tables, and figures consecutively numbered. There is a TOC at the beginning

of the protocol narrative and a separate TOC for each SOP.

On the back cover page, “Natural Resource Program Center” in the banner should be

removed. In a previous review that I did for the network, I asked authors to insert this

title because the template I was working from showed it there. However, I spoke with

Jason Bennett about it, and it should be removed. The templates and instructions on the

NRPM web site have been updated.

Fixed

All sections of the report should be identified with a page number in the Table of

Contents(s). So this portion of the TOC will need to be added. Please note that SOP 7 is

not currently listed in the TOC.

Fixed

2. All figures and tables should have numbered captions that can be included in a TOC.

There are several figures and tables that have “informal” captions that should be

formalized with a number.

Fixed

3. The synthesized review from Dr. Agee mentioned clarification regarding the target

species and monitoring objectives. I agree that this needs clarification. Apparently for

now the parks have arranged that I&M will be responsible for monitoring harbor seals

whereas PORE will monitor elephant seals as long as it is possible. Data management

will be accomplished by I&M for both of these monitoring efforts. In addition to this

there are “Other species” that are monitored. It’s not very clear from the discussion the

extent to which the park is monitoring elephant seals, but after discussion with the

Network Coordinator, it is clear that the park is currently fully implementing this protocol

as part of their contribution toward Vital Signs monitoring using volunteers (and has for

many years). This should be clearer in the narrative.

Section 1.5.4 has been modified and now more clearly indicates what monitoring is

funded by the I&M program versus supported by the parks. With the addition of the

power analysis for the northern elephant seal data, we have retained methods for

monitoring this species in the protocol. Sections and the SOP related to “All Species

Monitoring” have been removed.
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4. On pg. 5, in the first paragraph under the figure, you state that the elephant seal

population grew by almost 9% from 2005 to 2006 and reference Table 1. Perhaps I

misinterpreted the table but population growth from the table seems to be about 18%

(2100/1771). Did you mean from 2006 to 2007? Also the next sentence refers to the total

population figures for 2005 and 2006. These are not the same figures as those in the table.

I think you mean 2006 and 2007. Please check these figures.

Data from Table 1 was reported in error. We have adjusted the first part of the

paragraph and compared the 2005 population estimate with 2007, indicating a 29%

increase. The paragraph now references the correct values and percent increase.

5. On pg. 9, there is a paragraph about the ESA to support choice of pinnipeds for

monitoring; however, the only pinniped that is listed is the Steller Sea Lion which is not

an official part of this protocol. You might expand on this paragraph to add more

explanation or de-emphasize this aspect of justification for monitoring.

The paragraph is primarily about the Marine Mammal Protection Act, which does apply

to our selected monitoring program. References to the Endangered Species Act are made

in regards to the selection of pinnipeds in general as an important resource to monitor,

not specifically in regards to harbor seal or northern elephant seal monitoring. Steller

Sea Lions are counted incidentally during our surveys, and that data is maintained within

our database. Language regarding the ESA was not modified within the protocol.

6. On pg. 11, you mention linkages between fish assemblages and pinniped monitoring and

list several important streams. Do these streams occur in the same watersheds where you

are monitoring pinnipeds?

Three of the streams monitored for salmonids by the SFAN I&M program flow into

estuaries monitored for harbor seals. A sentence noting this was added to the protocol.

7. Along with Reviewer 2, I also wondered about the difference between primary sites,

secondary sites, and their relationship to sampling descriptions that referred to “all”. It

was often difficult to tell when you were referring to a census or sampling all the sites

whether you meant just the “primary” sites or whether that included the “secondary” sites

as well. If the secondary sites are not being monitored with any consistency, it will be

hard to make the case that you are censusing the population (i.e. counting it all). It would

be helpful if you could include a small table that showed “n” for primary and secondary

sites and described the frequency with which you sample each. Reviewer 2 also

suggested a map showing these 2 strata.

We have modified 2.2 Study Area and Site Selection to better outline the differences

between what are considered primary and secondary sites. We have also clarified that

our monitoring efforts are focused on primary sites. Secondary sites are not monitored,

but some ancillary data may be collected at these sites by I&M staff or volunteers. It is

not really practical to list or map the number of secondary sites at PORE and GOGA.

Secondary habitat is really any part of the coastline that is not a primary site. Because
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the primary sites encompass the vast majority of harbor seals and northern elephant

seals during their respective breeding and molting seasons, we feel justified in describing

our counts as censuses of the population. Because female northern elephant seals only

give birth and mate in large colonies without returning to the water for approximately

one month, these counts, which serve as the basis for our long-term trend analyses, can

truly be described as censuses.

8. The description of field methods on pgs. 31 (Harbor Seals) and 32 (Northern Elephant

Seals) are not comparable in structure or style making it hard to compare the

methodology between the two species. Pg. 31 has two additional sections on tagging HS

that do not occur for NES. If you are not tagging NES it would be good to state that. Also

the section on population counts for HS does not give any information about what is

counted as does the corresponding paragraph on pg. 32. If the method is the same state it

for Harbor Seals (the primary species for this protocol) and then state how it differs or is

the same for NES. I would take a similar approach for each of the paragraphs on methods

adding other information as needed.

The comment above is incorrect. There are additional sections on tagging and resighting

for northern elephant seals, not for harbor seals. However, we added in these sections for

harbor seals just to clarify that this is not a part of the monitoring program although we

do collaborate in these regards with outside researchers. Our method for population

counts of harbor seals was clarified. The other methods sections were reviewed for

consistency.

9. In Table 4, the periodicity for synthetic reports is 5-10 years; however, throughout the

discussion of analysis and reporting in other sections and SOPs of the protocol, you

generally state that such an analysis will occur every 5 years. I point this out in case this

is something that you meant to change but didn’t.

Corrected Table 4 to indicate that synthesis reports will occur every 5 years.

10. Lit Cited: Other reviews have provided several comments. Also look for consistent use of

initials as citations mix use of initials and complete first names. Manuscripts that still are

being worked on are usually cited as (In prep).

Fixed

11. In the TOC for SOP 2 there is a bookmarking error for one of the sections on pg. 4 of the

SOP.

Fixed.

12. In SOP 7, subsequent appendix captions reference northern spotted owls instead of

pinnipeds.

Fixed.

225

SOP 6. Safety Procedures

Version 1.4

Revision History Log

Previous

Version #

Revision

Date

Author Changes Made Reasons for Change New Version

#

Nov. 2007 Dawn Adams Created To meet new formatting

and content guidelines.

1.0

1.0 June 2008 Dawn Adams,

Marcus Koenen

Layout, added

emergency #s

Edited for peer review 1.1

1.1 September

2009

D. Press, M.

Koenen

Formatting To meet NRPM

standards.

1.2

1.2 November

2009

K. Freeman, D.

Press

Formatting

requirements.

1.3

1.3 December

2009

D. Press Reformatted

headings and

borders of JHA

appendix.

Comments from Penny

Latham.

1.4
226

Contents

Page

1.0 Weather and Field Attire ...................................................................................................227

2.0 Field Hazards ....................................................................................................................227

Appendix SOP 6A. Job Hazard Analysis (JHA) for Pinniped Monitoring Activities................228
227

This SOP provides safety information related to monitoring pinnipeds at Golden Gate National

Recreation Area (GOGA) and Point Reyes National Seashore (PORE).

Also see SFAN Field Safety SOP maintained on the GOGA Marin Headlands server

(Inpgogamahe1\Divisions\Network I&M\Shared\Standard Operating Procedures\SFAN Field

SOPs\Standard Operating Procedures) for information on:

x Emergency Procedures

x Emergency Contacts for PORE and GOGA

x Vehicle Safety

x Air Quality Guidelines

x Slippery Substrates

x Mandatory Safety Equipment

x Recommended Personal Gear

1.0 Weather and Field Attire

Summer conditions are often mild (between 60 - 80°F), but when conducting fieldwork along the

coastal environment, it is important to dress appropriately for a range of weather conditions.

Because of the possibility of encountering poison oak and general uneven terrain encountered

off-trail, field personnel should wear long pants and high topped hiking boots. Leg gaiters are

also recommended to reduce the exposure to poison oak and the risk of tick bites during surveys.

Since surveys can last longer than anticipated, field personnel are encouraged to take extra food

and drinking water into the field.

2.0 Field Hazards

Biting or stinging invertebrates (wasps, spiders, ticks) may be encountered. The bites or stings

from these animals can be painful, but usually not fatal. If bitten or stung and painful swelling or

an allergic reaction occurs, seek medical attention immediately. Check your clothing and

exposed skins frequently when in the field for ticks and upon returning from the field, do a more

thorough body search for ticks.

Poison oak is found throughout the owl habitat in the study area. Before doing any fieldwork

personnel should become familiar with the dangers associated with exposure to this native plant.

If exposure occurs wash thoroughly with soap and rinse with plenty of water upon returning

from the field and then apply Tecnu® ointment (provided at headquarters). If a strong reaction

occurs, seek medical attention and alert your supervisor as soon as possible.

Appendix SOP 6 A is the Job Hazard Analysis (JHA) done for the pinniped monitoring program.

The JHA analyzes the duties, tasks, and potential hazards associated with the program, and

addresses the hazards through safe work behaviors and procedures.
228

Appendix SOP 6A. Job Hazard Analysis (JHA) for Pinniped Monitoring Activities.

POINT REYES NATIONAL SEASHORE Job Title: Seal Population, Tagging Date: June 12, 2006

Job Safety Analysis and Resight Surveys page 1 of 3

Analysis by: Heather Jensen, Dawn Adams, Jeannine Manna

Division: SCIENCE Title of person (who does this job): Reviewed by: Sarah Allen

Wildlife technician, Volunteer Approved by:

Location: Point Reyes National Seashore

Supervisor: Dave Press

Personal Protective Equipment: Thick pants, sturdy boots

Training and/or certifications Permits

A. SEQUENCE OF BASIC JOB STEPS B. POTENTIAL JOB HAZARDS C. SAFE BEHAVIORS- SAFE WORK PROCEDURES

REQUIRED TO COMPLETE THE JOB/PROJECT

Identify steps and sequence of work

activities

Task: Identify hazards in each basic

step. Site: Identify site hazards that

could affect workers

Determine specific controls and safe behaviors for each hazard.

Office Work- Computer use for email and

data entry

Muscle and eye strain, repetitive

stress injury

Proper posture and use of ergonomic furniture

Take breaks every hour

Travel to Field Locations in Vehicle Driving hazards such as accident Use defensive driving techniques

Expect oncoming traffic on one-lane roads in park

Be alert for foggy conditions

Watch for cow, deer, elk and other wildlife, and adjust speeds to

safely operate around areas of high use

Obey traffic laws and wear seatbelt at all times

Do not drive when fatigued, be familiar with route or prepare for

unknown route

Do not talk on radio or cell phone while driving
229

A. SEQUENCE OF BASIC JOB STEPS B. POTENTIAL JOB HAZARDS C. SAFE BEHAVIORS- SAFE WORK PROCEDURES

REQUIRED TO COMPLETE THE JOB/PROJECT

Travel to Field Locations in Vehicle (cont.) Driving hazards such as accident

(cont.)

Do not put hot drinks on your lap

Be familiar with the vehicle and its operation

Check gauges, tires, wipers, fluids and replace when necessary

Check vehicle has spare tires, jumper cable and jack with all

parts.

Seal capture, handling or tagging Seal bites while restraining After capture, control seal's head and flippers at all times.

Keep head at a safe distance from team while handling

Being charged by seals when tagging

or moving within the colony

Communicate location of seals clearly with your field partner,

and have one person watching seals at all times

Do not tag female seals; tag male seals only when they are

asleep.

Exposure to disease or blood borne

pathogens when handling dead seals

Wear protective gear (gloves and mask) when handling dead

seals to reduce disease exposure.

Hiking to work areas on trails, routes or off

trail navigation

Getting lost or confused as a group,

or losing a crew member

Have map and compass and other navigational aids and know

how to use them.

Travel together when off-trail

Make sure all members of the team are aware of location, and

can find route out if they are separated.

When trail hiking, plan stops at trail junctions to regroup.

Arrange meeting places and times -all crewmembers must wear

a watch.

Have travel and activity plan for each day and make sure it is

understood by all crewmembers

Stay in communication via radio or cell phone or stay in sight

Carry radio and spare batteries

If lost or disorientated, stay calm, look and listen for the ocean

and other landmarks. Assess location by consulting map and

landmarks, and proceed to nearest road or trail.
230

A. SEQUENCE OF BASIC JOB STEPS B. POTENTIAL JOB HAZARDS C. SAFE BEHAVIORS- SAFE WORK PROCEDURES

REQUIRED TO COMPLETE THE JOB/PROJECT

Hiking to work areas on trails, routes or off

trail navigation (cont.)

Getting lost or confused as a group,

or losing a crew member (cont.)

Do not panic- Have a mental plan for what to do if lost

If injured, stay put and radio or call dispatch.

Problem when working alone (falling,

lost)

Leave a travel/survey plan with a co-worker or responsible party

who will notify proper authorities in the event of a disappearance.

Carry a light source and extra batteries.

Loose footing When traveling in areas with steep or unstable terrain, stagger

your positions so that you are not immediately below someone,

yell "rock" if you dislodge one.

Lightning storms In the event of a lightening storm, turn your radio off, if near a

vehicle, get entirely inside. If in the out of doors try to do the

following: separate the group, get off ridge tops and away from

trees, get as low as possible and if possible lie on conductive

material.

Wind storms If it is windy enough to blow small twigs and branches out of the

trees, try to get out of the woods or find an area away from

hazard trees

Exposure to cold, wet conditions Wear proper equipment- and bring extra layers.

Recognize the signs of hypothermia in yourself and others

Carry and eat high-calorie foods, stay well-hydrated

Exposure to heat and sun Have hat, sunscreen and sunglasses

Overexertion and dehydration Recognize the signs of dehydration

Take frequent rest stops (15 min per every 2 hours) and stay

hydrated

Injuries due to hiking (aches, sprains

and blisters)

Pay attention to footing- plan ahead for the route to avoid steep,

unstable terrain

Use appropriate footwear, boots and socks.

Prevent blisters and have blister treatments (moleskin, tape etc)

accessible.
231

A. SEQUENCE OF BASIC JOB STEPS B. POTENTIAL JOB HAZARDS C. SAFE BEHAVIORS- SAFE WORK PROCEDURES

REQUIRED TO COMPLETE THE JOB/PROJECT

Hiking to work areas on trails, routes or off

trail navigation (cont.)

Injuries due to falling (lacerations,

broken bones, head injuries)

Pay particular attention to traveling on steep slopes, unstable

terrain, through dense vegetation, and in foggy conditions.

Practice fall- arrest techniques (roll on to stomach, dig elbow,

feet and knees in).

Have first aid kit, stabilize injured person, treat for shock and

know how to initiate rescue via radio

Injuries due to carrying a heavy pack Reduce pack weights when possible

Pay attention to how you put your pack on (avoid twisting

motions- get help or place pack on surface or against tree)

Make sure your pack is properly fitted and balanced

Bring hiking poles to use to stabilize yourself in unstable or steep

terrain.

Hiking to work areas on beaches and

across streams

Exposure to high tides on beach,

routes cut off

Check tides before going out and plan travel accordingly.

If caught on beach on a rising tide, move as high up the cliff as

possible, but in an area that you can be seen from above.

Use alternate land routes if possible for one leg of the trip.

Be careful on slippery logs, intertidal areas covered in algae, and

watch footing on either side of stream or channel crossings.

Adjust pace and footing to allow you sure footing as you move

through the tidal zone. Don't allow incoming waves to rush you.

Working in the outdoors Exposure to allergy causing plants

and insects

Alert crew members to possible problems with allergens. Be alert

for toxic plants and alert to common bee and wasp nesting

habitat and activity-especially the person in front.

Carry benedryl, epi-pen or other anti-histamine if you have

known allergic reactions.
232

A. SEQUENCE OF BASIC JOB STEPS B. POTENTIAL JOB HAZARDS C. SAFE BEHAVIORS- SAFE WORK PROCEDURES

REQUIRED TO COMPLETE THE JOB/PROJECT

 Working in the outdoors (cont.) Exposure to toxic plants Avoid poison oak when possible. Wear long sleeved shirts, long

pants, and hiking boots. Wash skin exposed to poison oak with

Technu or other appropriate cleaner and change clothes if

necessary at end of day/survey.

Do not eat any fungi or plant unless you are 100% sure it is

edible.

Exposure to ticks Wear proper attire (long sleeved shirts and long pants) and do

frequent tick checks. If bitten by black legged tick, properly

remove tick, save tick, send tick in for lab analysis, and monitor

general health condition.

Exposure to Giardia, E. coli and other

pathogens

Do not drink any water unless it has been filtered, boiled or

treated in some fashion

Do not create more contaminated areas- urinate away from

streams and water, dig a cathole for solid waste and bury toilet

paper.

Wash hands when possible and carry hand cleaner

Improper nutrition due to

inappropriate food choices

Bring a variety of healthy, nutritious food that will give you good

energy during travel and work. Do not rely on sugar snacks.

Loss of food to bears, ravens,

raccoons, small animals

Prevent animals from getting into your food by not leaving you

backpack open or accessible to animals.

Cougar attack If approached by cougar make yourself large and noisy, wave

arms, yell, bang pots, grab a stick. Back away from cougars but

do not turn and run, ever. If attacked, fight back

Strange or aggressive human

interactions

Terminate contact with visitor and leave the area, contact

dispatch
233

A. SEQUENCE OF BASIC JOB STEPS B. POTENTIAL JOB HAZARDS C. SAFE BEHAVIORS- SAFE WORK PROCEDURES

REQUIRED TO COMPLETE THE JOB/PROJECT

Working around seals on the beach Injuries from seals Alert dispatch to your presence on the beach (check in/out).

Work in pairs, with one person as a safety spotter.

Watch the surf zone for new seals arriving on the beach.

Identify escape routes away from the seals and danger.

Maintain safe distances away from the seals when not tagging.

Disease transmission Do not eat after handling seals. Wash hands with hand sanitizer

initially and follow up with soap and water when you return from

the field.

Injuries from falling rocks and debris Work in pairs, look above you periodically for deer, people, etc.,

that could cause a debris slide.

235

Appendix A: Power Analysis for the NPS San Francisco Bay

Area Network Harbor Seal (Phoca vitulina) Monitoring

Program.

Ben Becker

Pacific Coast Science and Learning Center

Point Reyes National Seashore

ben_becker@nps.gov

Introduction

The National Park Service’s (NPS) San Francisco Area Network (SFAN) Inventory and

Monitoring (I&M) program is interested in estimating the statistical power (probability of

detecting a trend, given one exists) of the harbor seal (Phoca vitulina) monitoring program at

Point Reyes and Golden Gate NRA. To date, no formal power analysis has been done. Here, I

use deterministic methods (software Trends; Gerrodette 1993; Taylor et al. 2007) and Monte

Carlo simulations using the Software Monitor v7.0 (Gibbs 1995) to estimate the likelihood that

the existing monitoring program will detect a 25% or 50% decline at individual colonies, and the

number of years it would take to detect a 10% annual compounded decline for the six major

colonies as a group, excluding Duxbury Reef and Point Bonita. These analyses should be

considered for guiding purposes only.

Methods

Maximum counts for adults and pups from surveys during the pupping season were compiled

from 2000 – 2008 for 8 colonies from north to south: Tomales Bay, Tomales Point, Point Reyes

Headlands, Drakes Estero, Double Point, Duxbury Reef, Bolinas Lagoon, and Point Bonita.

Because Duxbury Reef and Point Bonita are mainly molting sites with few pups, I used molting

season maximum count data for this analysis.

The primary objectives were to use legacy data to (1) assess number of years needed to detect a

25% or 50% decline at any one colony, and (2) to assess power to detect declines among the six

primary pupping sites. To assess the importance of temporal autocorrelation, autocorrelation

plots of each time series were produced. I then performed linear regressions (with normally

distributed errors) on maximum adult and pup counts (separately) during each pupping season

from 2000 – 2008 at each colony. The standard error of the regression estimates and mean counts

during the time series (Table 1) were used to develop a modified (detrended) CV for power

analysis (Hatch 2003). I then used the power analysis software Trends (Gerrodette 1987) to

assess power to detect trends at any given subsite. The Monte Carlo simulation software Monitor

v7.0 (Gibbs 1995) was used to assess power to detect changes over the entire SFAN population

during the pupping season, not including Duxbury Reef and Point Bonita (which are mainly

molting sites). The Trends software is not designed to assess multiple sites at once, while the

Monitor software can model multiple plots. Individual colony power analyses used the following

assumptions: 1-tailed tests, linear population trends through time, a relaxed Į = 0.20, CV

constant with abundance, and equal sampling intervals. The combined six colony power

estimates were estimated using Monitor v7.0 and each colony was weighted by its relative mean
236

abundance during the 2000 – 2008 study period. The alpha was reduced to 0.10 for this analysis

due to larger sample size.

Results

Time series of adult maximum counts are shown in Figure 1. Autocorrelation plots for maximum

counts of adults at each of the eight colonies did not suggest that there was any temporal

autocorrelation, as all values at lags 1-8 were far below significant, and always less than |0.4| (ns)

at lag 1 (Figure 2). The coefficient of variation for pupping season adults (here considered as the

standard error of the regression estimate / mean count during the study period) ranged from 0.10

(Tomales Bay adults) to 0.27 (Tomales Point adults) (Table 1).

All of the six pupping sites had an 80% chance of detecting a 50% decline in adults at any one

colony within 2-5 years, not including the base year (Table 1, Fig. 3). Detecting an overall 25%

decline in adults would always take at least 14 years, not including base year. 50% declines pups

at each of the six pupping sites could be detected in 2-7 years, and 25% declines for pups would

always take at least 14 years, except for at Bolinas Lagoon, which would only take 4 years.

Power was generally higher for both adults and pups for the six major SFAN pupping sites

pooled (excluding Duxbury Reef and Point Bonita). Current monitoring effort had a 90% chance

of detecting a 27% decline in overall population counts over 3 years (Table 2, Fig. 4). For pups,

an 88% chance of detecting a 36% decline would be realized after 4 years. Thus, after only three

years of monitoring (not including the baseline year) the current program is very likely to detect

~25% declines in both adults and pups.

Discussion

Statistical power to detect 50% declines at individual colonies for both adults and pups is quite

strong, with 2-5 years for adults, and 2-7 years for pups, not including the base year. However,

25% declines will be much more difficult to detect at these sites. It is encouraging that pooled

power at the six main pupping sites is quite good and would likely detect large declines in a

matter of a few years.

It is important to acknowledge the pitfalls of power analysis estimates. In this case, the

calculations make several assumptions that may prove to be untrue and could cause over or

under estimates of power. If temporal autocorrelation within a site was present, then the

estimates presented here are too optimistic. While there was no apparent autocorrelation in this

nine year time series, this is a small sample size and correlation could have simply not been

detected. Additional considerations are that CVs may well vary with population size as it does in

many animal populations; however, the residual plots for the regressions did not show any

patterns, suggesting that variance-mean relationships are stable within sites and with this dataset.

A plot of standard mean counts versus standard errors among sites does show increasing

variation – mean relationship, but this is to be expected and does not imply anything about

within site processes. It simply indicates that colonies with more seals have larger standard

deviations (which was modeled), not that standard errors change when a colony changes in size.

Other issues in power analyses that may affect power estimates include erroneous use of simple

coefficients of variation from a single year, which generally under estimates true variance (Hatch

2003). Here, I used the standard error of the regression estimate, which incorporates both within
237

year and between year variation, as well as removing any trend from the variance estimate.

Therefore, this should also not be an issue with this dataset.

Acknowledgements

This report benefited from conversations with Sarah Allen, David Press, Dale Roberts, Heather

Jensen, Dawn Adams, Bill Merkle, and Marcus Koenen. David Press and Dale Roberts provided

harbor seal count data for analyses. Sarah Allen and David Press reviewed previous drafts of this

report and their comments were incorporated.

Literature Cited

Gerrodette, T. 1987. A power analysis for detecting trends. Ecology 68: 1364-1372.

Gerrodette, T. 1993. Program Trends.

Gibbs, J.P. Monitor. 1995. MONITOR version 7.0 (web version) 07 June 2001 based on version

6.2, 15 April 1995. Accessed at: http://www.mbr-pwrc.usgs.gov/software/monitor.html

Hatch, S.A. 2003. Statistical power for detecting trends with applications to seabird monitoring.

Biological Conservation 111:317-329.

Taylor, B.L., M. Martinez, T. Gerrodette, J Barlow, and Y. N. Hrovat. 2007. Lessons from

Monitoring Trends in Abundance of Marine Mammals. Marine Mammal Science 23: 157–

175.
238
239
240
241
242
243

Appendix B. Power Analysis for the NPS San Francisco Bay

Area Network Northern Elephant Seal (Mirounga

angustirostris) Monitoring Program

Ben Becker

Pacific Coast Science and Learning Center

Point Reyes National Seashore

ben_becker@nps.gov

Introduction

The National Park Service’s (NPS) San Francisco Area Network (SFAN) Inventory and

Monitoring (I&M) program is interested in estimating the statistical power (probability of

detecting a trend, given one exists) of the northern elephant seal monitoring program at Point

Reyes National Seashore. To date, no formal power analysis has been done. Here, I use

deterministic methods (software Trends; Gerrodette 1993; Taylor et al. 2007) and Monte Carlo

simulations using the Software Monitor v7.0 (Gibbs 1995) to estimate the likelihood that the

existing monitoring program will detect a 25 or 50% decline at individual colonies, and the

number of years it would take to detect a 10% annual compounded decline or increase for total

maximum count. These analyses should be considered for guiding purposes only since many

assumptions may be violated by the actual data.

Methods

Maximum counts for adult cows and pups+weaners from surveys during the breeding season

were compiled from 1998 – 2009 for Point Reyes Headlands, South Beach, and North Drakes

Beach, as well as the maximum count day for all colonies. Cow adults were used as a proxy for

total breeding population size because northern elephant seal males, particularly sub-adults, are

highly mobile during the breeding season, which can result in them being double-counted. The

total number of breeding females is estimated using the maximum count of adult females during

peak pupping adjusted to include the adult female counts 33 days prior to and 33 days after the

peak count for each colony site. This adjustment takes into account females that depart early and

those that have not yet arrived at the time of the peak count. The maximum count of pups plus

weaners for each colony provides an estimate of actual pup production.

The primary objectives were to use legacy data to (1) assess number of years needed to detect a

25% or 50% decline at any one colony, and (2) to assess power to detect increases or declines

among the 6 primary pupping sites when pooled. To assess the importance of temporal

autocorrelation, autocorrelation plots of each time series were produced. I then performed linear

regressions (with normally distributed errors) on maximum cow and pup counts (separately)

during each pupping season from 1998 – 2009 at each colony. The standard error of the

regression estimates and mean counts during the time series (Table 1) were used to develop a

modified (detrended) CV for power analysis (Hatch 2003). I then used the power analysis

software Trends (Gerrodette 1987) to assess power to detect trends at the three major colonies.

The Monte Carlo simulation software Monitor v7.0 (Gibbs 1997) was used to assess power to

detect changes over the entire SFAN population during the pupping season. The Trends software

is not designed to assess multiple sites at once, while the Monitor software can model multiple
244

plots. Individual colony power analyses used the following assumptions: 1-tailed tests, linear

population trends through time, a relaxed Į = 0.20, CV constant with abundance, and equal

sampling intervals. The combined six colony power estimates were estimated using Monitor v7.0

but rather than using each colony separately, analysis was performed on the maximum daily

count of all colonies.

Results

Both cows and pups+weaners tended to increase at most colonies, except Point Reyes

Headlands, which has shown some leveling in recent years (Figs. 1 and 2).

The coefficient of variation for cows (here considered as the standard error of the regression

estimate / mean count during the study period) ranged from 0.13 for the total population of cows

up to 0.37 at South Beach (Table 1). Pups had a similar range from 0.18 to 0.42. The standard

error of the regressions increased linearly with the mean. Temporal autocorrelation at lag = 1 was

significant for two of the colonies, as well as all colonies combined (Fig. 3); nonetheless, the

power analysis did not incorporate autocorrelation and some pitfalls of this are discussed below.

For cows, Point Reyes Headlands had an 80% chance of detecting a 50% decline in only 2 years,

as well as the population as a whole. However, North Drakes Beach and South Beach would take

8-9 years to detect a 50% decline. Detecting an overall 25% decline in adults would always take

at least 7 years for the population pooled (at alpha = 0.2 and 80% certainty). 50% declines in

pups pooled could be detected in 2 years, and 25% declines for pups would take at least 12 years

to detect. Figure 4 shows the power curves.

Using Monitor for all sites combined, monitoring effort had an 86% chance of detecting a 36%

decline in cows over 4 years (Table 2). For pups, an 83% chance of detecting a 41% decline

would be realized after 5 years. Increases were easier to detect, generally having 0.1 - 0.2 higher

power. Thus, after only 4-5 years of monitoring (not including the baseline year) the current

program is very likely to detect 36-41% declines or increases in both adult cows and pups (Fig.

5).

Comparison of adjusted cows versus pups+weaners indicate 80 pups for every 100 females on

average for the total population from 1998 – 2009 (Fig 6). However, the individual colonies vary

greatly with PRH having on average only 76 pups for every 100 females, and both SB and NDB

having 98-99 pup+weaners for every 100 females (Fig. 6). The higher number of pups+weaners

to cows at DSB represents dispersal of pups+weaners from the adjacent PRH due to

overcrowding and storm-related events.

Discussion

It is important to acknowledge the pitfalls of power analysis estimates. In this case, the

calculations make several assumptions that may prove to be untrue and could cause over or

underestimates of power. The apparent temporal autocorrelation at two of the sites and the

population as a whole may have inflated the predicted ability to detect trends, thus, the estimates

at North Drakes Beach, South Beach, and the total population may be slightly optimistic. When

these trends are actually tested, analysts should be careful to use Poisson (or similar count based)

regression with autoregressive errors to account for this autocorrelation. Additional
245

considerations are that CVs may well vary with population size as it does in many animal

populations, however, the residual plots for the regressions did not show any patterns of

increasing variance (although there was some heteroscedasticity due to the increasing population

with time), suggesting that variance-mean relationships are possibly stable within sites and this

dataset. A plot of standard mean counts vs. standard errors among sites does show increasing

variation – mean relationship, but this is to be expected and does not imply anything about

within site processes, it simply indicates that colonies with more seals, have larger standard

deviations (which was modeled), not that standard errors change when a colony changes in size.

Other issues in power analyses that may affect power estimates include erroneous use of simple

coefficients of variation from a single year, which generally underestimate true variance (Hatch

2003). Here, I used the standard error of the regression estimate, which incorporates both within

year and between year variation, as well as removing any trend from the variance estimate.

Therefore, this should also not be an issue with this dataset.

The pup+weaner:cow ratios and their variation through time (Fig. 6) may serve as a foundation

to understanding those colonies that are better suited to pupping, as well as local movements of

weaners and cows. The overall 0.80 cow:pup+weaner ratio is considerably lower than for Año

Nuevo and SE Farallon Island rookeries (Huber 1987; Le Boeuf and Reiter 1988; Huber et al.

1991), where an estimated 97.5% and 93.2% of the females in residence give birth, respectively.

Finally, a new version of Monitor (Version 10.0) is in development (as of August 2009) and is

expected to model temporal autocorrelation as well as autocorrelation among plots (colonies). I

recommend reperforming these analyses with the updated software since there may be an

autocorrelation issue for these eseal time series data (Fig. 3) that could overestimate power.

In summary, the monitoring program appears to have good power to detect population wide

declines of >36% over 4 years. However, the significant interannual autocorrelation observed

(likely due to the increasing population), may slightly overestimate power in this analysis.

Acknowledgements

This report benefitted from conversations with Sarah Allen, David Press, Dale Roberts, Heather

Jensen, Dawn Adams, Bill Merkle, and Marcus Koenen. David Press and Dale Roberts provided

elephant seal count data for analyses. Sarah Allen and David Press reviewed previous drafts of

this report and their comments were incorporated.

Literature Cited

Gerrodette, T. 1987. A power analysis for detecting trends. Ecology 68: 1364-1372.

Gerrodette, T. 1993. Program Trends.

Gibbs, J.P. Monitor. 1995. MONITOR version 7.0 (web version) 07 June 2001 based on version

6.2 15 April 1995. Accessed at: http://www.mbr-pwrc.usgs.gov/software/monitor.html

Hatch, S.A. 2003. Statistical power for detecting trends with applications to seabird monitoring.

Biological Conservation 111:317-329.
246

Huber, H.R. 1987. Natality and weaning success in relation to age of first reproduction in

northern elephant seals. Canadian Journal of Zoology 65:13111316.

Huber, H.R., A.C. Rovetta, L.A. Fry, and S. Johnston. 1991. Age-specific natality of northern

elephant seals at the South Farallon Islands, California. Journal of Mammalogy 72:525534.

Le Boeuf, B.J., and J. Reiter. 1988. Lifetime reproductive success in northern elephant seals.

Pages 344362 in T. H. CluttonBrock, editor. Reproductive Success: Studies of Individual

Variation in Contrasting Breeding Systems. University of Chicago Press, Chicago.

Taylor, B.L., M. Martinez, T. Gerrodette, J Barlow, and Y. N. Hrovat. 2007. Lessons from

Monitoring Trends in Abundance of Marine Mammals. Marine Mammal Science 23: 157–

175.
247
248
249
250
251
252
253

255

Appendix C. Program Products

This appendix is a sampling of publications and other products produced or supported through

data collected by long-term pinniped monitoring at Golden Gate National Recreation Area and

Point Reyes National Seashore.

Peer-reviewed Publications

Adams D., H. Jensen, H. Nevins, K. Truchinski, D. Roberts and S Allen. 2007. Northern

Elephant Seal Monitoring 2005-2007 Report, Point Reyes National Seashore. Natural

Resource Technical Report NPS/SFAN/NRTR–2008/085. National Park Service, Fort

Collins, Colorado.

Allen, S. G., S. C. Peaslee and H. R. Huber. 1989. Colonization by northern elephant seals of the

Point Reyes Peninsula, California. Marine Mammal Science. 5:298-302.

Allen, S.G., H.R. Huber, C.A. Ribic, and D. G. Ainley. 1989. Population dynamics of harbor

seals in the Gulf of the Farallones, California. Calif. Fish and Game, 75:224-232.

Allen, S.G. 1999. Mirounga massing at Point Reyes National Seashore. Park Science 19:30-31.

Allen, S.G. 2004. Seals and sea lions: indicators of marine ecosystem condition at Point Reyes.

Natural Resource Year in Review 2003. pg 42-43.

Anderson, S.D., B.H. Becker, and S.G. Allen. 2008. Observations of white sharks,

Carcharodon carcharias, at Point Reyes National Seashore: 1982–2004. California Fish and

Game 94(1):33-43.

Becker, B.H., D.T. Press, and S.G. Allen. 2009. Modeling the effects of El Nino, density

dependence, and disturbance on harbor seal (Phoca vitulina) counts in Drakes Estero,

California:1997-2007. Marine Mammal Science 25(1): 1–18.

Flynn, E., D. Press, S. Codde, D. Roberts, and S. Allen. 2009. Pacific harbor seal (Phoca vitulina

richardsi) monitoring at Point Reyes National Seashore and Golden Gate National

Recreation Area: 2008 annual report. Natural Resource Technical Report

NPS/SFAN/NRTR–2008/267. National Park Service, Fort Collins, Colorado.

Goldestein, T., F. Gulland, B. Aldridge, J. Harvey, T. Rowles, D. Lambourn, S. Jeffries, L.

Measures, P. Yochem, B. Stewart, R. Small, D. King, J. Stott, J. Mazet. 2003. Antibodies to

Phocine herpesvirus-1 are common in North American harbor seals. J. Wildlife Diseases.

39:487-494.

Goldstein, T., J.A. Mazet, F.M.D.Gulland, T. Rowles, J. T. Harvey, S. Allen, D. King, B.

Aldridge, J. Stott. 2004. The transmission of Phocine herpesvirus-1 in rehabilitated and freeranging harbor seals (Phoca vitulina) in California. Veterinary Microbiology. 103:131-141.
256

Grigg E. K., Allen S.G., Green D.E., Markowitz H. 2004. Harbor seal, Phoca vitulina richardii,

population trends in the San Francisco Bay Estuary, 1970-2002. California Fish and Game

90(2):51-70.

Grigg, E.K., A.P. Klimley, S.G. Allen, D.E. Green, D.E. Elliott-Fisk, and H. Markowitz. 2009.

Spatial and seasonal relationships between Pacific harbor seals (Phoca vitulina richardii) and

their prey, at multiple scales. Fish. Bull. 107:359-372.

Gulland, F. M. D., Lowenstine, L. J., Lapointe, J. M., Spraker, T., King, D. P., 1997. Herpesvirus

infection in stranded Pacific harbor seals of coastal California. J. Wildl. Dis. 33, 450-458.

Moore, E., S. Lyday, J. Roletto, K. Litle, J.K. Parrish, H. Nevins, J. Harvey, J. Mortenson, D.

Greig, M. Piassa, A. Hermance, D. Lee, D. Adam, S. Allen, and S. Kell. 2009.

Entanglements of marine mammals and seabirds in central California and the north-west

coast of the United States 2001-2005. Marine Pollution Bulletin 58:1045-1051.

Neale J.C.C., Gulland F.M.D., Schmelzer K.R., Harvey J.T., Berg E.A., Allen S.G., Greig D.J.,

Grigg E.K., and Tjeerdema R.S. 2005. Contaminant loads and hematological correlates in the

harbor seal (Phoca vitulina) of San Francisco Bay, California. J. Toxicol. Environ. Health,

Part A, 68: 617-633.

Stewart, B. S., B. J. Le Boeuf, P. K. Yochem, H. R. Huber, R. L. DeLong, R. J. Jameson, W.

Sydeman, and S. G. Allen. 1994. History and present status of the northern elephant seal

population. In: B. J. Le Boeuf and R. M. Laws (eds.) Elephant Seals. Univ. Calif. Press, Los

Angeles, 414 pp.

Sydeman, W.J. and S.G. Allen. 1999. Pinniped population dynamics in central California:

Correlations with sea surface temperature and upwelling indices. Marine Mammal Science

15(2): 446-461.

Truchinski K., E. Flynn, D. Press, D. Roberts, and S. Allen. 2008. Pacific harbor seal (Phoca

vitulina richardii) monitoring at Point Reyes National Seashore and Golden Gate National

Recreation Area: 2007 annual report. Natural Resource Technical Report

NPS/SFAN/NRTR–2008/118. National Park Service, Fort Collins, Colorado.

Graduate Theses

Allen, S.G. 1988. The movement and activity patterns of harbor seals in Drakes Estero,

California. M.S. Thesis, Univ. of California, Berkeley, 70 pp.

Goldstein, Tracy. 2003. Epidemiology and pathogenesis of Phocine herpesvirus-1 infections in

Pacific harbor seals. Ph. D. Thesis. University of California, Davis.

Grigg, Emma. 2008. University of California, Davis. Habitat analyses of harbor seals in the San

Francisco Bay Area. Ph. D. Thesis. University of California, Davis.
257

Oates, Stori. (in prep). The dispersal of juvenile harbor seals from site of birth. M.S. Thesis. San

Jose State University, Moss Landing Marine Lab.

Neale, Jennifer (in prep). Immune function of harbor seals and contaminant loads. Ph. D. Thesis.

University of California, Davis.

Pettee, Jessica. 1999. Female Northern Elephant Seal Reproductive Success at Point Reyes

National Seashore and Micro-habitat Features. M.S. Thesis, San Francisco State University.

Unpublished Reports

Ainley, D. G., H. R. Huber, and S. G. Allen. 1979. Marine Mammal Management Plan for Point

Reyes National Seashore, California. Report to PRNS.

Allen, S. G. and H. R. Huber. 1983. Pinniped assessment in the Point Reyes/Farallon Islands

National Marine Sanctuary, 1982-83. Final Rpt. to U. S. Dept. of Commerce, Sanctuary

Programs Office.

Allen, S. G. and H. R. Huber. 1984. Pinniped assessment in the Point Reyes/Farallon Islands

National Marine Sanctuary, 1983-84. Final Rpt. to U. S. Dept. of Commerce, Sanctuary

Programs Office. 71 pp.

Allen, S. G. and H. R. Huber. 1984. Human/pinniped interactions in the Point Reyes/Farallon

Islands National Marine Sanctuary. Final Rpt. to U. S. Dept. of Commerce, Sanctuary

Programs Office. 27 pp.

Allen, S. G., D. G. Ainley, G. W. Page, and C. A. Ribic. 1985. The effect of disturbance on

harbor seal haul out patterns at Bolinas Lagoon, California, 1978-1979. U. S. Fishery Bull.

82:493-500.

Allen, S. G., S. Peaslee, and H. R. Huber. 1986. A colony of northern elephant seals on Point

Reyes Peninsula, California. Final Rpt. to the U. S. Dept. of Commerce, Sanctuary Programs

Office.

Allen, S. G., D. G. Ainley, L. Fancher, and D. Shuford. 1986. Movement and activity patterns of

harbor seals (Phoca vitulina) from the Drakes Estero population, California, 1985-86. Final

Rpt. to the U. S. Dept. of Commerce, Sanctuary Programs Office. 133 pp.

Allen, S. G. and S. Peaslee. 1987. Northern elephant seals at Point Reyes, California, during the

breeding season, 1986-1987. Final Rpt. U. S. Dept. of Commerce, Sanctuary Programs

Office. 12 pp.

Allen, S. G., J. F. Penniman and D. G. Ainley. 1987. Movements and activity patterns of harbor

seals at Drakes Estero population, California, 1986-87. Final Rpt. to the U. S. Dept. of

Commerce, Sanctuary Programs Office. 42 pp.

Allen, S. G. 1988. Northern elephant seals at Point Reyes, California, 1987-88. Final Rpt. to the

U. S. Dept. of Interior, Point Reyes National Seashore. 14 pp.
258

Allen, S. G. 1989. Monitoring of northern elephant seals on the Point Reyes Peninsula,

California, 1989. Final Rpt. to the U. S. Dept. of Interior, Point Reyes National Seashore. 14

pp.

Allen, S. G. 1991. Harbor seal habitat restoration in San Francisco Bay. N.T.I.S. No. PB91-

212332. 44 pp.

Allen, S., and M. King. 1992. Tomales Bay harbor seals: a colony at risk. Proceedings from the

Third Biennial State of Tomales Bay Conference, October 1992. pp. 33-37.

Allen, S.G. 1995. Northern elephant seal management plan for Point Reyes National Seashore.

Rept. to N.P.S. 35 pp.

Allen, S., S. Waber, W. Holter and D. Press. 2004. Long-term monitoring of harbor seals at Point

Reyes, California: five year annual report 1997-2001. National Park Service Technical

Report. 66 pp.

Barlow, J., P. Boveng, M. S. Lowry, B. S. Stewart, B. J. Le Boeuf, W. J. Sydeman, R. J.

Jameson, S. G. Allen, and C.W. Oliver. 1993. Status of the northern elephant seal population

along the U.S. west coast in 1992. Admin. Rept. LJ-93-01. Southwest Fisheries Science

Center, National Marine Fisheries Service, P.O. Box 271, La Jolla, CA. 32 pp.

Barlow, J., P. Boveng, M. Lowry, B. Stewart, B. Le Boeuf, Wm. Sydeman, R. Jameson, S.

Allen, and C. Oliver. 1992. Status of the northern elephant seal population along the U. S.

west coast in 1992. (NMFS stock status report).

Boveng, P. 1988. Status of the northern elephant seal population on the U.S. West Coast. Admin.

Rep. LJ-88-05 Southwest Fisheries Science Center, National Marine Fisheries Service, P.O.

Box 271, La Jolla, CA. 35pp.

Boveng, P. 1988. Status of the Pacific harbor seal population on the U.S. west coast. Admin.

Rep. LJ-88-06. Southwest Fisheries Science Center, National Marine Fisheries Service, P.O.

Box 271, La Jolla, CA 92038. 43 pp.

Chan, G.L. 1979. Reconnaissance survey of Double Point, Point Reyes Headland, and Bird

Rock. Report to California Department of Fish and Game and the State Water Resources

Control Board No. 79-15, 80-01, and 80-02. 51 pp.

Green, D.E., Grigg, E., Allen, S., and Markowitz, H. (2006) Monitoring the potential impact of

the seismic retrofit construction activities at the Richmond-San Rafael Bridge on harbor seals

(Phoca vitulina): May 1, 1998 – December 31, 2004. Final Report, IHA 11/19/03-11/18/04.

100pp.

Manna, J., D. Roberts, D. Press, and S. Allen. 2006. San Francisco Bay Area Network Harbor

Seal Monitoring 2006 Annual Report. Natural Resource Report NPS/PWR/SFAN/NRTR –
259

2007/005. San Francisco Bay Area Network. Golden Gate National Recreation Area. Fort

Cronkhite, Sausalito, California.

Morgan, L., K. Hanni, L. Gage, D. Smith, and S. Allen. 1993. Biological parameters as release

criteria the fate of rehabilitated harbor seal orphans (Phoca vitulina richardsi). In: D. Ludwig

(ed.) National Wildlife Rehabilitators Association Proceedings. Vol II.

Nevins, H.M. 2004. Monitoring northern elephant seals at Point Reyes National Seashore, 5-year

report, 1997/98-2001/02. Technical Report to the National Park Service. (in preparation)

Page, G. W. and S. G. Allen. 1985. Affected Mammals - Part 3. in: The impacts of the T/V

Puerto Rican oil spill on marine birds and mammal populations in the Gulf of the Farallones,

6-19 November, 1984. A special scientific report produced by the Point Reyes Bird

Observatory. 70 pp.

Risebrough, R. W., D. Alcorn, S. G. Allen, V. C. Alderlini, L. Booren, R. L. DeLong, L. E.

Fancher, R. E. Jones, S. M. McGinnis and T. T. Schmidt. 1978. Population biology of harbor

seals in San Francisco Bay. N.T.I.S. No. PB-81-107963.

Vanderhoof, M. and S. Allen. 2005. Harbor seal monitoring at Point Reyes National Seashore

and Golden Gate NRA. Annual Report to the National Park Service, Inventory and

Monitoring Program. 19pp.

Interpretive Products

Bettenhausen, B. 2009. Elephant Seals: Our window to the oceans. Pacific Coast Science and

Learning Center, CA. Short Documentary.

National Park Service. 2007. Harbor Seal Monitoring at Point Reyes National Seashore and

Golden Gate National Recreation Area. Research Project Summary. Pacific Coast Science

and Learning Center, CA.

National Park Service. 2007. Keeping Track of Elephant Seals at Point Reyes National Seashore.

Parks for Science. Pacific Coast Science and Learning Center, CA. Spring 2007. Issue 5.

National Park Service. 2006. Harbor Seals and Northern Elephant Seals: Indicators of Marine

Ecosystem Conditions. Research Project Summary. Pacific Coast Science and Learning

Center, CA.

National Park Service. 2005. Harbor Seal Monitoring Update. Coastal Science Review. Pacific

Coast Science and Learning Center, CA. Fall 2007. Issue 3.

National Park Service. 2004. Statewide Population Assessment of Harbor Seals. Coastal Science

Review. Pacific Coast Science and Learning Center, CA. Summer 2004. Issue 2.

National Park Service. 2001. Discovering Northern Elephant Seals at Point Reyes National

Seashore: A field guide for middle school science teachers. Point Reyes National Seashore,

CA.

The Department of the Interior protects and manages the nation’s natural resources and cultural heritage; provides scientific and

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