NOAA Technical Memorandum NMFS-NWFSC-84

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

A Spatially Explicit

Ecosystem Model

of the California Current’s

Food Web and Oceanography

October 2007
NOAA Technical Memorandum

NMFS-NWFSC Series

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Reference throughout this document to trade names does 

not imply endorsement by the National Marine Fisheries 

Service, NOAA.

This document should be referenced as follows:

Brand, E.J., I.C. Kaplan. C.J. Harvey, P.S. Levin, E.A. 

Fulton, A.J. Hermann, and J.C. Field. 2007. A spatially 

explicit ecosystem model of the California Current’s food 

web and oceanography. U.S. Dept. Commer., NOAA Tech. 

Memo. NMFS-NWFSC-84, 145 p.
NOAA Technical Memorandum NMFS-NWFSC-84

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

A Spatially Explicit

Ecosystem Model

of the California Current’s

Food Web and Oceanography

E.J. Brand, I.C. Kaplan, C.J. Harvey, P.S. Levin,

E.A. Fulton,

1

 A.J. Hermann,

2

 and J.C. Field3

Northwest Fisheries Science Center

Fishery Resource Analysis and Monitoring Division

2725 Montlake Boulevard East

Seattle, Washington 98112

Commonwealth Scientific and Industrial Research Organization

Marine and Atmospheric Research

GPO Box 1538

Hobart, Tasmania 7001

Australia

NOAA Pacific Marine Environmental Laboratory

7600 Sand Point Way Northeast

Seattle, Washington 98115

Southwest Fisheries Science Center

Fisheries Ecology Division

110 Shaffer Road

Santa Cruz, California 95060

October 2007

1

2

3
Most NOAA Technical Memorandums

NMFS-NWFSC are available online at the 

Northwest Fisheries Science Center

web site (http://www.nwfsc.noaa.gov)

Copies are also available from:

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phone orders (1-800-553-6847)

e-mail orders (orders@ntis.fedworld.gov)

ii
Table of Contents 

List of Figures...............................................................................................................................................v 

List of Tables ..............................................................................................................................................vii 

Executive Summary .....................................................................................................................................ix 

Acknowledgments........................................................................................................................................xi 

Acronyms and Abbreviations ....................................................................................................................xiii 

Introduction...................................................................................................................................................1 

Northern California Current Ecosystem...................................................................................................1 

NCCE Species..........................................................................................................................................2 

Food Web Modeling.................................................................................................................................4 

Methods ........................................................................................................................................................6 

Model Scenario and Application ..............................................................................................................6 

Model Structure ........................................................................................................................................6 

Primary Production ..............................................................................................................................8

Invertebrates.......................................................................................................................................18 

Vertebrates .........................................................................................................................................18 

Nutrients.............................................................................................................................................19 

Process Assumptions: Predation and Recruitment.............................................................................20 

Oceanography.....................................................................................................................................20 

Data Sources...........................................................................................................................................23 

Calibration ..............................................................................................................................................25 

Results.........................................................................................................................................................27 

Discussion...................................................................................................................................................49 

References...................................................................................................................................................53 

Appendix A: California Current Model Documentation ............................................................................67 

Benthic Habitat and Sediment Type.......................................................................................................67 

Nutrients, Salinity, and Dissolved Oxygen ............................................................................................67 

Overview of Biological Parameters........................................................................................................68 

Growth and Clearance Rates..............................................................................................................68 

Beverton Holt Recruitment Parameters..............................................................................................69 

iii
Migration............................................................................................................................................70 

Phytoplankton (PS, PL)......................................................................................................................70 

Zooplankton (ZL, ZM, ZS, ZG, PWN) ..............................................................................................71 

Cephalopods (CEP, BMS)..................................................................................................................71 

Benthic Invertebrates (BC, BML, BFF, BMD, BG) ..........................................................................71 

Small Planktivorous Fish (FPS) .........................................................................................................72 

Large Planktivorous Fish (FPL).........................................................................................................73 

Shallow Piscivorous Fish (FDE)........................................................................................................73 

Deep Vertical Migrators (FBP)..........................................................................................................73 

Deep Demersal Fish (FDD)................................................................................................................74 

Rockfish (FDB, FDC, FDO, SHR, FDS) ...........................................................................................74 

Flatfish (FDF).....................................................................................................................................76 

Hake (FMM) ......................................................................................................................................76 

Sablefish (FMN).................................................................................................................................77 

Large Piscivorous Flatfish (FVD)......................................................................................................77 

Large Demersal Predators (FVS) .......................................................................................................77 

Salmon (FVB) ....................................................................................................................................78 

Albacore (FVT)..................................................................................................................................78 

Skates and Rays (SSK).......................................................................................................................78 

Small Demersal Sharks (SHB)...........................................................................................................79 

Demersal Sharks (SHD).....................................................................................................................79 

Pelagic Sharks (SHP) .........................................................................................................................79 

Migrating Birds (FVO).......................................................................................................................79 

Surface-Feeding Birds (SB) ...............................................................................................................80 

Diving Birds (SP)...............................................................................................................................80 

Pinnipeds (PIN)..................................................................................................................................81 

Transient Orcas (REP)........................................................................................................................82 

Baleen Whales (WHB).......................................................................................................................82 

Toothed Whales (WHT).....................................................................................................................83 

Sea Otters (WDG) ..............................................................................................................................83 

Appendix B: Predator-Prey Parameters......................................................................................................85 

iv
List of Figures 

Figure 1. Schematic of Atlantis modules for oceanography, ecology, and fishing......................................5

Figure 2. Map of the Northern California Current model area. ...................................................................7

Figure 3. Map of Region 1, Washington, defined by bathymetric depth layers.. ........................................9

Figure 4. Seasonal salinity .........................................................................................................................22

Figure 5. Seasonal temperature variation...................................................................................................23

Figure 6. Seasonal vector velocity .............................................................................................................24

Figure 7. Spatial distribution of chlorophyll a. ..........................................................................................27

Figure 8. Spatial distribution of deep benthic filter feeders.......................................................................28

Figure 9. Spatial distribution of small flatfish ...........................................................................................29

Figure 10. Abundance of rockfish, skates, and rays over time, spatially aggregated ................................30

Figure 11. Abundance of groundfish groups over time, spatially aggregated ...........................................31

Figure 12. Abundance of pelagic groups over time, spatially aggregated .................................................32

Figure 13. Abundance of shark and seabird groups over time, spatially aggregated.................................33

Figure 14. Abundance of marine mammal groups over time, spatially aggregated...................................34

Figure 15. Abundance of nutrients and carrion over time, spatially aggregated .......................................36

Figure 16. Abundance of filter feeders, kelp, and seagrass groups over time, spatially aggregated.. .......37

Figure 17. Abundance of invertebrate groups over time, spatially aggregated..........................................38

Figure 18. Abundance of plankton groups over time, spatially aggregated...............................................39

Figure 19. Abundance of benthic invertebrate groups over time, spatially aggregated.............................40

Figure 20. Unfished biomass predicted by Alantis versus single species assessments..............................42

Figure 21. Seasonal distribution of hake....................................................................................................43

Figure 22. Change in reserve and structural nitrogen for rockfish and skates...........................................44

Figure 23. Change in reserve and structural nitrogen for other groundfish ...............................................45

Figure 24. Change in reserve and structural nitrogen for pelagic groups..................................................46

Figure 25. Change in reserve and structural nitrogen for shark and bird groups.......................................47

Figure 26. Change in reserve and structural nitrogen for marine mammals..............................................48

Figure 27. Unfished biomass predicted by Atlantis for groups lacking single species assessments .........50

v
vi
List of Tables 

Table 1. Regional division of model area. ..................................................................................................8

Table 2. List of major species by functional group and respective proportional biomass.........................10

Table 3. Life history parameters for vertebrates........................................................................................12

Table 4. Invertebrate and primary producer functional groups and key parameters..................................15

Table 5. Migration data..............................................................................................................................21

Table B-1. Consumption parameters in the calibrated model for predation on groups including birds 

and fish........................................................................................................................................................86

Table B-2. Consumption parameters in the calibrated model for additional prey including fish and 

sharks. .........................................................................................................................................................91

Table B-3. Consumption parameters in the calibrated model for seabird and mammal prey....................96

Table B-4. Consumption parameters in the calibrated model of benthic prey...........................................99

Table B-5. Consumption parameters in the calibrated model for prey including plankton, shrimp, 

and squid. ..................................................................................................................................................104

Table B-6. Consumption parameters in the calibrated model for prey including macroalgae, 

seagrass, bacteria, meiobenthos, detritus, and carrion ..............................................................................109

Table B-7. Ratio of calibrated consumption parameters/initial consumption parameters for birds 

and fish......................................................................................................................................................115

Table B-8. Ratio of calibrated consumption parameters/initial consumption parameters for fish and 

sharks.. ......................................................................................................................................................120

Table B-9. Ratio of final values/initial values for consumption parameters after calibration versus 

before calibration for mammals and seabirds.. .........................................................................................125

Table B-10. Ratio of final values/initial values for consumption parameters of benthos prey groups.. ..129

Table B-11. Ratio of final values/initial values for consumption parameters after calibration versus 

before calibration for plankton, cephalopods, and shrimp prey groups....................................................134

Table B-12. Ratio of final values/initial values for consumption parameters of macroalgae, seagrass, 

bacteria, detritus, and carrion....................................................................................................................138

vii
viii
Executive Summary 

Fisheries managers along the U.S. West Coast must increasingly balance trade-offs 

between competing species and competing fisheries. They also must build management plans 

that respond to the dynamic oceanography and productivity of the region. New management 

tools, such as spatial closures or climate-triggered fishing policies, could help address some of 

these issues, but a modeling framework is needed against which to test such potential policies. 

To address this need, an ecosystem model was constructed of the Northern California Current 

Ecosystem, which extends from the U.S.-Canada border to Point Conception, California, and out 

to the 1,200 m isobath. 

Presented here are the coupled biological-oceanographic model and documented 

assumptions, parameterization, and data sources. Later versions will include the fisheries and 

will be used to evaluate management strategies. The model structure, Atlantis, includes the 

trophic dynamics of 54 functional groups in the food web, using nitrogen as a common currency 

between groups. Functional groups include habitat-forming species such as kelp, corals and 

sponges, as well as phytoplankton, detritus, and consumers such as fish and zooplankton. 

The model is divided into 62 three-dimensional spatial zones, each with up to 7 depth 

layers. This allows us to explicitly test hypotheses regarding migrations, movement behavior, 

and spatial management options such as marine protected areas. The model is forced with 

hydrodynamic flows, salinity, and temperature outputs from a high-resolution Regional Ocean 

Modeling System, allowing us to test the impacts that climate-driven changes in upwelling or 

coastal currents have on nutrients and primary productivity. 

ix
x
Acknowledgments 

Many individuals provided data and advice that helped construct the model. Curt 

Whitmire, Northwest Fisheries Science Center (NWFSC), provided habitat data from the 

Essential Fish Habitat Environmental Impact Statement database. Maria Juan Jorda, Oregon 

State University (OSU), made CTD data available. Neil Banas, University of Washington, and 

Pat Wheeler and Burke Hales, OSU, provided advice on oceanography and the spatial grid that 

was used. The NWFSC Fishery Resource Analysis and Monitoring Division survey team, led by 

Aimee Keller, collected data on groundfish abundance and distribution. Beth Horness provided 

summarized data for Atlantis. Bill Peterson and Julie Keister, NWFSC-Newport, provided 

insight into some of the zooplankton data, and Bill Sydeman, Point Reyes Bird Observatory, 

discussed some of the parameters and groupings for sea birds. Dawn Noren, NWFSC, provided 

advice and parameters for marine mammals. Nick Tolimieri, NWFSC, and Sarah Gaichas, 

Alaska Fisheries Science Center, provided helpful reviews of the manuscript. 

xi
xii
Acronyms and Abbreviations 

CalCOFI California Cooperative Oceanic Fisheries Investigations 

COADS Comprehensive Ocean-Atmosphere Data Set 

CSIRO Commonwealth Scientific and Industrial Research Organization (Australia) 

EFH EIS Essential Fish Habitat Environmental Impact Statement 

ERSEM European Regional Seas Ecosystem Model 

IGBEM Integrated Generic Bay Ecosystem Model 

MSE management strategy evaluation 

NCCE Northern California Current Ecosystem 

NCEP National Center for Environmental Prediction 

NEP Northeast Pacific 

NPac North Pacific 

NRC National Research Council 

PDO Pacific Decadal Oscillation 

PFMC Pacific Fishery Management Council 

PRBO Point Reyes Bird Observatory 

RCA rockfish conservation area 

ROMS Regional Ocean Modeling System 

xiii
xiv
Introduction 

The marine area off the coast of Washington, Oregon, and northern California is 

characterized by an eastern boundary current system flowing over a narrow continental shelf, 

linking cooler subarctic waters to the north and warmer subtropical water to the south. These 

currents interact with distinctive oceanographic and geomorphic features of the North American 

continent to create the complex and dynamic Northern California Current Ecosystem (NCCE). 

The pronounced latitudinal oceanographic variation of this system directly impacts the physical 

and chemical variables which drive primary production and affect the growth, survival, and 

spatial distributions of fauna ranging from zooplankton to large predatory fishes, sea birds, and 

marine mammals (Croll et al. 1998, Francis 2003). 

Populations of species such as Pacific hake (Merluccius productus), which migrate 

through the system en masse, and rockfish (Sebastes spp.), which are long-lived, relatively 

nonmigratory residents, respond dramatically to the climatic and oceanographic variability of 

this system (Field and Francis 2002). Fishing has depleted many species like bocaccio rockfish 

(S. paucispinis), and their sporadic recruitment linked to climate has led to a slow and partial 

recovery (Parker et al. 2000, Field et al. 2001, Ruckelshaus et al. 2002). 

Management faces the challenge of relating changes in the biology to these physical 

factors and to fishing and other human activities, and incorporating them into management 

strategies (Parker et al. 2000, Pikitch et al. 2004). Examples include species rebuilding plans 

created by the Pacific Fishery Management Council (PFMC) and marine protected areas, such as 

rockfish conservation areas that have been implemented in recent years to limit targeted and 

incidental rockfish harvest. Here we offer a simulation tool that includes realistic levels of 

complexity in the ecosystem, as a way to more fully explore management policy options and to 

facilitate decision making. 

Northern California Current Ecosystem 

Three key characteristics of the NCCE underlie its dynamics and its likely response to 

management actions: 1) the spatial pattern of the biology and physics, 2) large annual, 

interannual, and interdecadal variability in physical forcing such as currents and upwelling, and 

3) the wide variety of life histories of species that live in this patchy and fluctuating 

environment. The biology and physics of the NCCE are driven by three major currents, the 

California Current, the Davidson Current, and the California Undercurrent, which shift in 

strength and distance from shore throughout the year in response to climatic forcing. 

The chief current, the California Current, runs widely along the surface pushing cold, 

nutrient-rich water from the tip of Vancouver Island southward down to Baja California, 

typically offshore in the fall and winter and inshore during the spring and summer. The 

California Undercurrent and Davidson Current both run north, bringing warmer, saltier, hypoxic 

waters from the equator. The subsurface California Undercurrent runs off the shelf break in the 
summer and fall, while the Davidson Current runs more nearshore at the surface in the winter 

and spring (Hickey 1979, Landry and Hickey 1989, Field 2004). These currents drive ecosystem 

variability, directly impacting the seasonal and annual dynamics of the nutrients and organisms 

(GLOBEC 1994, Hickey 1998). 

The interface of the California Current system and the unique geomorphology and 

physical oceanography of the U.S. Pacific coastline results in relatively static and latitudinally 

defined shifts in temperatures and species biomass along the coast throughout the year (Hickey 

1979, Chelton et al. 1982, GLOBEC 1994). For example, Cape Flattery, Cape Blanco, Cape 

Mendocino, and Point Conception influence nearshore cyclonic and anticyclonic eddies and 

meandering jets, which propagate localized mixing between offshore and shelf water (Batteen 

1997, Barth et al. 2000, Field 2004). 

Concentrated areas of upwelling are created by the latitudinal variation in continental 

shelf width and large geographic features like Astoria Canyon and Monterey Bay. Heavier 

northern flows of fresh water input introduce latitudinally varied levels of nutrients into the 

system year-round. Habitat-forming marine flora such as kelp and seagrass are limited by these 

conditions and live scattered along the coast. The headlands and resulting eddies and jets 

enhance the strong winter storms and spring and summer upwelling that influence the 

spatiotemporal variation in primary productivity and zooplankton biomass of the NCCE 

(GLOBEC 1994, Lynn et al. 2003). 

The NCCE is sensitive to seasonal current changes as well as large scale climate shifts 

that significantly alter these typical seasonal patterns. Interannual shifts from El Niño–Southern 

Oscillation upset these patterns by bringing stronger currents of warmer and less productive 

water farther north, thus decreasing the influence of the southward California Current (Landry 

and Hickey 1989). 

While El Niño patterns alter the climate of the ecosystem for several years, the longerscale regime shift known as the Pacific Decadal Oscillation (PDO) can influence the NCCE for 

decades. The last definitive major regime shift occurred in 1977, bringing warmer water and 

leading to community shifts and major changes in the biomass of pelagic fish and crustaceans 

(Field and Francis 2002, McGowan et al. 2003). Climatic studies of the past century indicate the 

1977 regime shift may be part of a multidecadal warm-cool regime shift pattern (Trenberth 1990, 

MacCall 1996, McGowan et al. 2003). There is evidence of a recent PDO shift in 1998 to cooler 

waters, but that is in dispute at this time (Bond et al. 2003, Peterson and Schwing 2003, Goericke 

et al. 2004, Hsieh et al. 2005). 

NCCE Species 

Species in the NCCE have developed specific strategies to maximize their success in this 

dynamic environment (EPAP 1999, Field and Francis 2002). For example, rockfish have 

developed a long-living, late-maturing, live-bearing strategy that takes advantage of periodic 

recruitment opportunities related to annual climatic variability (Love et al. 2002). 

Metapopulations of anadromous salmon— for example, coho (Oncorhynchus kisutch) and 

Chinook salmon (O. tshawytscha)—are another prime example (Groot and Margolis 1991), 

allowing the species to cope with spatially and temporally variable freshwater and ocean 

2
conditions. The low-frequency variability of pelagic forage fish such as anchovy (Engraulis 

mordax), sardine (Sardinops sagax), and mackerel (Scomber japonicus), as well as crustacean 

species like Dungeness crab (Cancer magister) and pandalid shrimp (Pandalus spp.), appears to 

be a strategy related to both biological interactions and climate regime shifts of the system 

(GLOBEC 1994, MacCall 1996). Other species such as Pacific hake, sardines, albacore 

(Thunnus alalunga), sooty shearwaters (Puffinus griseus), and a variety of mammals typically 

migrate south through the system in the fall into warmer waters to reproduce and travel north in 

the spring to colder waters to feed. This influx in predation significantly impacts prey biomass 

and ecosystem dynamics (Chelton et al. 1982, Carretta et al. 2002, Field and Francis 2002). It is 

crucial for sustainable fishery management plans to consider these tailored life history strategies 

and their ecosystem-level implications. 

Traditional single species stock assessments do not address the climate forcing that 

underlies the system, the different spatial responses to climate forcing and to fishing pressure, 

and the interactions between the species adapted to this ecosystem. There is increasing evidence 

that neglecting such aspects will hinder fishery management and the understanding of fish 

population dynamics. For instance, predation on depleted rockfish stocks by predators such as 

lingcod (Ophiodon elongatus) or Pacific hake can slow their recovery rates (Mangel and Levin 

2005, Harvey et al. in press). Ignoring this trophic interaction could cause management plans to 

miss recovery targets. 

Climate patterns strongly influence the recruitment and population dynamics of bocaccio 

rockfish (Tolimieri and Levin 2005, Zabel et al. in prep.), sablefish (Anoplopoma fimbria); 

(Schirripa and Colbert 2005), sardines (Jacobson and MacCall 1995) and other species. Spatial 

overlap of abundant migratory predators (notably Pacific hake) with their prey varies annually 

(Bailey et al. 1982) and could lead to large variations in predation mortality on prey species. 

Similarly, the spatial overlap of bottom trawling and living substrate determines the impact of 

fishing on benthic habitat (NRC 2002) and this fluctuates with changes in fishing behavior and 

regulations. Although the PFMC and the states of Washington, Oregon, and California have 

management policies in place for individual species or management groups, there is no holistic, 

integrative model that incorporates interactions between species, management plans, and 

management jurisdictions. 

Management agencies and councils have several new policy tools that address some of 

these interactions between fisheries and the ecosystems within which they are embedded. One 

example of this is that the PFMC recently proposed a ban on krill (Euphausiidae spp.) 

harvesting, as a way to safeguard forage resources for current target species. State and federal 

management agencies have also implemented spatial closures and marine reserves (Airame et al. 

2003) to reduce fishing mortality and to preserve benthic habitat and biodiversity. Currently, 

PFMC is in the process of closing all West Coast waters greater than 700 fathoms (>1,280 m, 

approximately 75% of the U.S. West Coast exclusive economic zone) to bottom trawling. 

The outcome of such closures involves movement of adults, dispersal of larvae and 

recruits (Tuck and Possingham 2000), and predation within closed areas on target species 

(Martell et al. 2005). Additional new policy tools available to managers include the buyback of 

trawl permits and the use of specialized trawl gear that reduces rockfish bycatch. A modeling 

3
framework is needed to evaluate the effectiveness of such policies in the northern California 

Current. 

Food Web Modeling 

To begin to include ecology and management issues that traditional single species stock 

assessments neglect, Field (2004) and Field et al. (2006) developed a food web model of the 

NCCE, using the Ecopath with Ecosim software (Christensen and Walters 2004). The model 

starts with a mass balance accounting of production and mortality for 62 biomass pools (species 

or functional groups). In forward simulations, the model projects the biomass dynamics of these 

pools in response to predation, fishing, and other mortality. 

Field’s model has been used to identify climate drivers in the system ( Field et al. 2006), 

to weight the importance of such drivers against the direct impact of fishing (Field 2004), to 

illustrate trade-offs between fleets (Little et al. in prep.), and to identify key trophic interactions 

within the food web (e.g., between hake and crustaceans). Moreover, Field (2004) identified key 

data gaps and also derived the first estimate of coast-wide abundance of some species, estimated 

from the energetic demands and diets of their predators. However, there is a need to go beyond 

the Ecopath with Ecosim approach to include spatial processes, more realistic nutrient and 

climate forcing, and finer age structure. Here we used Field’s work as the foundation of our 

spatially explicit model, building on the lessons learned from his model and on his 

parameterization. 

Atlantis, a modeling approach developed by scientists (Fulton 2004, Fulton et al. 2004) 

with the Australian Commonwealth Scientific and Industrial Research Organization (CSIRO), 

achieves the crucial goal of integrating physical, chemical, ecological, and fisheries dynamics in 

a three-dimensional, spatially explicit domain (Fulton et al. 2003). In Atlantis, marine ecosystem 

dynamics are represented by spatially explicit submodels that simulate hydrographic processes 

(current-, light- and temperature-driven fluxes of water and nutrients), biogeochemical factors 

driving primary production, food web relations among functional groups, crude habitat 

interactions, and fishing fleet behavior (Figure 1). 

Fulton developed Atlantis from a series of models that explored optimal ecosystem model 

complexity (Fulton and Smith 2002, Fulton 2004, Fulton et al. 2004). A precursor to Atlantis, 

the Integrated Generic Bay Ecosystem Model (IGBEM) (Fulton et al. 2004), was a combination 

of the biological modules of the European Regional Seas Ecosystem Model (ERSEM) (Baretta 

and Baretta-Bekker 1997) and the physical processes and spatial layout of the Port Phillip Bay 

Integrated Model (Murray and Parslow 1997). Efforts to simplify the physiological processes in 

IGBEM resulted in Bay Model 2 (BM2), a more parsimonious framework that still effectively 

captures system dynamics (Fulton 2001, 2004). Atlantis is a modified version of BM2, 

established to improve upon ecosystem based fishery management tools (Fulton et al. 2003). 

There are 11 applications of Atlantis at this time. Two of the most well developed models are by 

Fulton et al. and focus on Port Phillip Bay, Australia (Fulton et al. 2003) and the Southeast 

Australian regional ecosystem (Fulton et al. 2005). Models for nine other systems within 

Australia and the United States, including the NCCE, are in development. 

4
Fisheries 

submodel 

Ecology 

submodel 

Hydrographic 

submodel 

Figure 1. Schematic of Atlantis modules for oceanography, ecology, and fishing. This paper discusses 

the ecology and hydrographic submodels. 

Here we present the first version of a spatially explicit ecosystem model for the NCCE, 

using the Atlantis framework. This version of the model includes the biology and oceanography 

of the system, with no fishing or other anthropogenic effects. In this technical memorandum, we 

document the model structure, parameterization, and assumptions. Future modeling and 

manuscripts will focus on including fisheries, fitting to historical time series of abundance, and 

evaluating management strategy. Ultimately, the model is intended as a strategic management 

tool that will allow the identification of trade-offs between and among species, fleets, and 

management goals, and to identify direct and indirect effects of management policies. As with 

any complex simulation model, its use is not intended for making short-term tactical decisions 

(e.g., annual decisions in fishing mortality rates). However, the Atlantis framework is an ideal 

operating model to be used in management strategy evaluation (MSE), in which management 

policies and assessment methods are tested against simulations that represent a real ecosystem 

and its complexities (Kirkwood 1997, Sainsbury et al. 2000, Hilborn et al. 2002). 

In this framework, the NCCE Atlantis model is useful in that it reproduces qualitative 

behavior of the system and exhibits a range of dynamic responses similar to that observed in the 

ecosystem. The ecosystem model can serve as a filter to identify which policies (e.g., marine 

protected areas placement and monitoring) and methods (e.g., stock assessment techniques) are 

promising and which are flawed or likely to be ineffective. 

5
Methods 

The Atlantis model reaches from Cape Flattery, Washington, to Point Conception, 

California, the region defined as the NCCE (Figure 2). This area totals 144,887 km2and is 

approximately 1.25 by 105 km3 in volume. To allow explicit representation of migrations, 

movement behavior, and spatial management such as marine protected areas, the model area is 

divided into eight coastal regions, each with six depth zones defined by bathymetric contours 

(Table 1 and Appendix A). Coastal regions and depth zones were defined based on 

biogeography, management boundaries, and data availability considerations. These 48 boxes are 

flanked by 14 nondynamic boundary boxes on the seaward, northern, and southern edges. The 

model also divides the water column into depth layers, ranging from one depth layer for 

nearshore boxes to seven depth layers for the offshore boundary boxes (Figure 3). Atlantis 

defines habitat uniformly by box. Proportions of sediment type (hard or soft) and kelp and 

seagrass coverage per box are delineated from data generated by the West Coast groundfish 

Essential Fish Habitat Environmental Impact Statement (EFH EIS) (Appendix A). 

Model Scenario and Application 

The results presented here are from a 42-year period without fishing. The initial 

conditions for the biological model include abundance and weight-at-age of each vertebrate 

group in each area, and biomass per area for all other groups. These initial conditions are based 

on data from approximately 1995–2005. We used this as a starting point, allowing the model 

without fishing to “spin up” to a quasi-equilibrium unfished state. Growth and abundance of 

most groups stabilized within the 42 years. 

We used this unfished scenario to compare the Atlantis predictions of unfished 

abundance to the unfished abundance (B0) predicted by single species stock assessments. On the 

U.S. West Coast, unfished biomass (B0) is a management reference point. Walters et al. (2005) 

found systematic differences between reference points (maximum sustainable yield) estimated 

under single species versus multispecies assumptions. Here we tested whether similar 

differences are predicted by single species models versus Atlantis. We calculated the abundance 

at the end of the unfished Atlantis model run relative to the abundance at initial (fished) 

conditions. This was compared to stock assessments, primarily PFMC assessments from 2003. 

Model Structure 

The Atlantis model is fully described in Fulton (2001) and Fulton et al. (2004). Here we 

give a brief description of the generic model structure and specific attributes of the model for the 

California Current. 

6
Figure 2. Map of the northern California Current model area, with northern boundary at the U.S.-Canada 

border, the southern at Point Conception, California, the eastern at the shoreline, and the western 

at the 2,400 m isobath. Each of the eight regions contains seven spatial boxes, defined by 

isobaths. The northernmost and southernmost boxes, and the offshore boxes defined by the 

1,200-2,400 m isobath, are not dynamic and handle boundary conditions only. 

7
8

Table 1. Regional division of model area. 

Region Area (km2

) 

Total area 144,888.61 

Cape Flattery to Columbia River 18,278.03 

Columbia River to Cape Blanco 27,167.86 

Cape Blanco to Cape Mendocino 13,484.69 

Cape Mendocino to Eureka 2,008.22 

Eureka to Santa Cruz 16,513.70 

Santa Cruz to Monterey 1,533.15 

Monterey to Morro Bay 5,545.68 

Morro Bay to Point Conception 9,028.18 

Total boundary box area 51,329.11 

The ecological module of the California Current model simulates the dynamics of 54 

functional groups in the food web (Tables 2, 3, and 4), using nitrogen as a common currency 

between groups. Silica is also handled dynamically, as is oxygen, though in a very rudimentary 

fashion. Functional groups include habitat forming species such as kelp, corals and sponges, as 

well as additional benthic invertebrates, vertebrates, phytoplankton, zooplankton, refractory and 

labile detritus, and carrion. 

Primary Production 

Primary producer abundance is modeled as an aggregated biomass pool in each spatial 

box. The model tracks nitrogen abundance (mg N/m3) per box. Biomass growth is limited by 

nutrient, light, and space availability. Biomass is lost to predation, lysis, and linear and quadratic 

mortality. Linear mortality represents additional density independent mortality not explicitly 

modeled. Quadratic mortality represents density dependent mortality (for instance, self shading). 

Rate of change for standard water column (w) primary producer (PX) is: 

∑ =

= − − − −

i predatorgroups

PXw lys PX lin quad PXw i

w G M M M P

dt

d PX , ,

( ) (1) 

G PX = μPX ⋅δ irr ⋅δ N ⋅δ space ⋅ PX (2) 

where GPX stands for the growth of PX, Mlys,PX is the loss of PX due to lysis, Mlin and Mquad are 

loss due to linear and quadratic mortality, PPX,I are the losses of PX due to predation, μPX is the 

maximum growth rate, and δirr is light limitation, δN is nutrient limitation , and δspace is space 

limitation. Table 4 contains values for μ, Mlin and Mquad for our model; Mlys was set to 0. 
BB = 1,201–2,400 m 

6 = 551–1,200 m 

5 = 201–550 m 

4 = 151–200 m 

3 = 101–150 m 

2 = 51–100 m 

Depth Division

1 = 0–50 m 

Figure 3. Map of Region 1, Washington, defined by bathymetric depth layers. The map displays the 

isobaths that divide the seven boxes (from 50 to 2,400 m) within each region. Each box has up to 

seven depth layers. 

9
Table 2. List of major species by functional group and respective proportional biomass. Relative 

abundances of miscellaneous nearshore fish (FDE) are not known; life history parameters similar 

to the white croaker (Genyonemus lineatus) were assumed. 

Code Group Species Scientific name Proportion 

Lampfish Myctophidae 0.34 

Pacific viperfish Chauliodus macouni 0.22 

Lanternfish Myctophidae 0.17 

FBP Deep vertical migrators 

Longfin dragonfish Tactostoma macropus 0.15 

Shortbelly Sebastes jordani 0.43 

Stripetail Sebastes saxicola 0.39 

FDB Shallow small rockfish 

Greenstriped Sebastes elongatus 0.12 

Longspine thornyhead Sebastolobus altivelis 0.59 

Sharpchin Sebastes zacentrus 0.19 

Splitnose Sebastes diploproa 0.18 

FDC Deep small rockfish 

Aurora Sebastes aurora 0.03 

Pacific grenadier Coryphaenoides acrolepis 0.41 

Giant grenadier Albatrossia pectoralis 0.31 

Grenadier Macrouridae 0.08 

FDD Deep miscellaneous fish 

Bigfin eelpout Lycodes cortezianus 0.05 

White croaker Genyonemus lineatus NA* 

Sculpin Cottidae NA 

FDE Miscellaneous nearshore 

demersal 

Midshipman Porichthys notatus NA 

Dover sole Microstomus pacificus 0.72 

Rex sole Glyptocephalus zachirus 0.13 

FDF Small flatfish 

Pacific sanddab Citharichthys sordidus 0.08 

FDO Deep large rockfish Shortspine thornyhead Sebastolobus alascanus 0.72 

Darkblotched Sebastes crameri 0.23 

SHR Shallow large rockfish Redstriped Sebastes proriger 0.88 

Yelloweye Sebastes ruberrimus 0.05 

Chilipepper Sebastes goodei 0.53 

Widow Sebastes entomelas 0.18 

Pacific ocean perch Sebastes alutus 0.14 

FDS Midwater rockfish 

Yellowtail Sebastes flavidus 0.10 

FMM Hake Pacific hake Merluccius productus 0.97 

FMN Sablefish Sablefish Anoplopoma fimbria 1.00 

FPL Large planktivores Jack mackerel Trachurus symmetricus 0.92 

Pacific mackerel Scomber japonicus 0.08 

Anchovies Engraulis mordax 0.59 

Sardines Sardinops sagax 0.39 

FPS Small planktivores 

Herring Clupea pallasii pallasii 0.02 

FVB Salmon Chinook Oncorhynchus tshawytscha 0.95 

Coho Oncorhynchus kisutch 0.05 

Arrowtooth flounder Atheresthes stomias 0.71 

Pacific halibut Hippoglossus stenolepis 0.15 

FVD Large flatfish 

Petrale sole Eopsetta jordani 0.14 

FVS Large demersal predators Lingcod Ophiodon elongatus 1.00 

FVT Large pelagic predators Albacore Thunnus alalunga 1.00 

10
11

Table 2 continued. List of major species by functional group and respective proportional biomass. 

Relative abundances of miscellaneous nearshore fish (FDE) are not known; life history 

parameters similar to the white croaker (Genyonemus lineatus) were assumed. 

Code Group Species Scientific name Proportion 

Dogfish Squalus acanthias 0.73 

Spotted ratfish Hydrolagus colliei 0.17 

Brown catshark Apristurus brunneus 0.07 

SHB Small demersal sharks 

Pacific angel Squatina californica 0.06 

SHD Large demersal sharks Sleeper Somniosus pacificus 0.97 

Sixgill Hexanchus griseus 0.03 

SHP Misc. pelagic sharks Soupfin Galeorhinus galeus 0.88 

Longnose skate Raja rhina 0.63 

Bering skate Bathyraja interrupta 0.13 

Skate Rajidae 0.11 

SSK Skates and rays 

Roughtail skate Bathyraja trachura 0.07 

FVO Migrating birds Sooty shearwaters Puffinus griseus 0.90 

Common murre Uria aalge 0.59 

Rhinoceros auklet Cerorhinca monocerata 0.19 

SP Diving seabirds 

Cormorants, shags Phalacrocoracidae 0.16 

Gulls Larus glaucescens 0.81 

Brown pelican Pelecanus occidentalis 0.09 

SB Surface seabirds 

Storm petrels Oceanites spp. 0.05 

WDG Sea otters Sea otter Enhydra lutris 1.00 

Northern fur seals Callorhinus ursinus 0.25 

Northern elephant seals Mirounga angustirostris 0.42 

California sea lions Zalophus californianus 0.35 

PIN Pinnipeds 

Harbor seals Phoca vitulina 0.20 

Sperm Physeter macrocephalus 0.67 

Cuvier’s beaked Ziphius cavirostris 0.17 

Baird’s beaked Berardius bairdii 0.07 

Beaked Mesoplodon spp. 0.05 

WHT Toothed whales 

Resident, offshore orca Orcinus orca 0.03 

Gray Eschrichtius robustus 0.62 

Fin Balaenoptera physalus 0.18 

WHB Baleen whales 

Blue Balaenoptera musculus 0.15 

REP Transient orcas Transient orca Orcinus orca 1.00 

* NA = Not available. 
Table 3. Life history parameters for vertebrates. Most life history parameters are from FishBase (Froese and Pauly 2005). 

parameters for each functional group are the average of life history parameters for each species in the functional grrelative abundance. NMFS triennial trawl surveys for 1998-2003 were used to estimate relative abundance of mos

K are from the von Bertalanffy length-age relationship. Parameters a and b are from the length-weight relationship 

the life history parameters to predict size at age; from this we were able to calculate growth per day for each age cl

and consumption per day for each age class (C in Equation 10). See the appendix for more details on calculation o

Holt parameters. Mlin and Mquad are linear and quadratic mortality terms in Equation 7; values of Mlin and Mqua

postcalibration. 

Group Code Linf K Mortality

Age 

mature 

Initial 

biomass 

(mt) a b Steepness 

Bev-Holt 

alpha 

Bev-Holt 

beta 

Max 

age 

Adult 

Mlin 

(linea

mort.

Deep vertical migrators FBP 24.8 0.35 0.45 2.00 3.09E+05 0.00 3.00 0.50 1.89E+10 7.91E+11 10.00 0 Shallow small rockfish FDB 27.5 0.15 0.18 5.00 4.82E+04 0.01 3.13 0.50 1.65E+09 2.47E+11 40.00 0 Deep small rockfish FDC 30.6 0.10 0.14 13.00 3.38E+05 0.01 3.26 0.50 1.80E+09 4.66E+11 60.00 0 Deep misc. fish FDD 82.0 0.06 0.08 25.00 1.79E+05 0.02 3.21 0.50 8.87E+06 1.12E+11 70.00 0 Misc. nearshore demersal FDE 60.0 0.04 0.77 2.00 7.06E+04 0.01 3.03 0.50 1.27E+10 4.85E+13 20.00 0 Small flatfish FDF 71.1 0.12 0.22 8.00 7.45E+05 0.01 3.16 0.90 1.79E+08 7.24E+10 60.00 0 Deep large rockfish FDO 62.3 0.07 0.06 12.00 1.24E+05 0.01 3.25 0.80 6.08E+08 2.22E+10 90.00 0 Shallow large rockfish SHR 55.0 0.09 0.11 11.00 6.20E+04 0.03 2.79 0.50 8.25E+08 2.72E+08 70.00 0 Midwater rockfish FDS 47.0 0.13 0.19 12.00 4.08E+05 0.04 2.81 0.50 4.02E+07 4.28E+11 80.00 0 Hake FMM 86.0 0.13 0.23 3.00 2.70E+06 0.02 2.74 0.90 5.28E+09 1.54E+12 10.00 0 Sablefish FMN 78.0 0.20 0.07 4.00 1.18E+05 0.01 3.19 0.90 1.52E+08 4.81E+10 60.00 0 

12
Table 3 continued. Life history parameters for vertebrates. Most life history parameters are from FishBase (Froese and Pa

parameters for each functional group are the average of life history parameters for each species in the functional grrelative abundance. NMFS triennial trawl surveys for 1998-2003 were used to estimate relative abundance of mos

K are from the von Bertalanffy length-age relationship. Parameters a and b are from the length-weight relationship the life history parameters to predict size at age; from this we were able to calculate growth per day for each age cland consumption per day for each age class (C in Equation 10). See the appendix for more details on calculation o

Holt parameters. Mlin and Mquad are linear and quadratic mortality terms in Equation 7; values of Mlin and Mqua

postcalibration. 

Group Code Linf K Mortality

Age 

mature 

Initial 

biomass 

(mt) a b Steepness 

Bev-Holt 

alpha 

Bev-Holt 

beta 

Max 

age 

Adult 

Mlin 

(linea

mort.

Large planktivores FPL 60.3 0.09 0.13 1.00 9.81E+05 0.00 3.36 0.80 9.78E+09 8.81E+12 30.00 0 Small planktivores FPS 22.2 0.30 0.83 2.00 3.74E+06 0.01 2.97 0.80 2.26E+11 1.20E+12 10.00 0 Salmon FVB 153.3 0.15 0.20 4.00 3.75E+04 0.01 3.00 0.50 3.63E+06 1.58E+11 10.00 0 Large flatfish FVD 92.9 0.13 0.20 7.00 1.19E+05 0.01 3.14 0.50 2.44E+07 1.46E+11 20.00 9.00E-0Large demersal predators FVS 130.2 0.10 0.18 5.00 2.28E+04 0.00 3.40 0.90 2.31E+07 8.76E+06 20.00 1.50E-1Large pelagic predators FVT 140.0 0.23 0.30 5.00 1.31E+03 0.05 2.79 0.80 4.61E+04 6.99E+08 10.00 9.00E-1

Small demersal sharks SHB 96.5 0.14 0.16 29.00 1.18E+05 0.01 3.03 0.50 3.55E+07 8.52E+10 50.00 0 

Large demersal sharks SHD 200.0 0.15 0.05 16.00 9.36E+02 0.01 3.34 0.50 7.63E+03 1.16E+09 50.00 0 

Misc. pelagic sharks SHP 200.0 0.13 0.23 9.00 3.74E+03 0.01 2.94 0.50 5.44E+05 8.89E+09 30.00 0 Skates and rays SSK 107.2 0.17 0.20 8.00 5.40E+04 0.01 3.03 0.50 8.80E+06 7.20E+10 20.00 0 

13
Table 3 continued. Life history parameters for vertebrates. Most life history parameters are from FishBase (Froese and Pa

parameters for each functional group are the average of life history parameters for each species in the functional grrelative abundance. NMFS triennial trawl surveys for 1998-2003 were used to estimate relative abundance of mos

K are from the von Bertalanffy length-age relationship. Parameters a and b are from the length-weight relationship the life history parameters to predict size at age; from this we were able to calculate growth per day for each age cland consumption per day for each age class (C in Equation 10). See the appendix for more details on calculation o

Holt parameters. Mlin and Mquad are linear and quadratic mortality terms in Equation 7; values of Mlin and Mqua

postcalibration. 

Group Code Linf K Mortality

Age 

mature 

Initial 

biomass 

(mt) a b Steepness 

Bev-Holt 

alpha 

Bev-Holt 

beta 

Max 

age 

Adult 

Mlin 

(linea

mort.

Shearwaters FVO 103.0 0.51 0.07 6.00 2.42E+03 0.00 3.00 0.33 6.24E+06 4.51E+10 30.00 0 Diving seabirds SP 85.0 0.63 0.14 4.00 2.87E+03 0.00 3.00 0.33 6.64E+05 4.92E+09 20.00 0 Surface seabirds SB 140.0 0.46 0.14 4.00 3.90E+02 0.00 3.00 0.33 1.53E+05 4.86E+08 30.00 0 Pinnipeds PIN 218.0 0.66 0.25 5.00 6.54E+04 0.00 3.63 0.33 5.60E+05 8.14E+11 20.00 0 Toothed whales WHT 1313.0 0.21 0.05 10.00 2.60E+04 0.17 2.53 0.33 4.91E+02 1.89E+11 70.00 0 Baleen whales WHB 1667.0 0.16 0.05 8.00 9.79E+05 0.55 2.44 0.33 9.03E+03 8.36E+12 90.00 0 Transient orcas REP 850.0 0.28 0.01 13.00 1.84E+02 0.17 2.44 0.33 2.33E+01 1.23E+09 50.00 2.00E-0Otters WDG 120.0 0.92 0.13 3.0 8.25E+01 0.02 3.00 0.33 5.37E+03 1.23E+09 20.00 0 

14
Table 4. Invertebrate and primary producer functional groups and key parameters. Parameter C is the ingestion rate (mg N

Equation 10. The ‘maximum growth rate’ parameter (mg N/day/m^3) corresponds to μ from Equation 2 (for primafrom Equation 10 (for invertebrates). ML and Mquad are linear and quadratic mortality from Equation 3. C or g in the calibrated value was less than or equal to 0.1 x initial value. C or g values in gray boxes indicate that the calibr

than or equal to 10x the initial value. Initial values for C and g for ZG, ZL, ZM, ZS, BFF, BD, BG, BML, BMD, afrom Field’s (2004) production/biomass and consumption/biomass ratios. Initial values for other groups simply faexpected for Atlantis models of other systems (e.g. Fulton 2001). 

Code Group Species 

C, postcalibration C, pre- calibration g, post- calibration g, pre- calibration M

m

BC Carnivorous 

infauna 

Polychaetes, nematodes, burrowing crustacea, peanut worms, flatworms 

0.3104 31.047 0.07 2.70384 

BD Deposit feeders Amphipods, isopods, small crustacea, snails, 

ghost shrimp, sea cucumber, worms, sea mouse, sea slug, barnacles, solenogaster, hermit crabs 

0.248 2.477474 0.6 0.3120166 

BFD Deep benthic filter 

feeders 

Anemones, deep corals, lampshells, reticulate sea anemone, rough purple sea anemone, swimming sea anemone, gigantic sea anemone, corals, sponges 

0.00395 0.00395 0.000344 0.000344 

BFS Shallow benthic 

filter feeders 

Barnacles, seafan, soft corals, Gorgonian corals, black coral, green colonial tunicate, sea pens, sea whips, sea potato, vase sponge, mussels, scallops 

0.0474 0.0474 0.04128 0.004128 

BFF Other benthic filter 

feeders 

Geoducks, barnacles, razor clams, littleneck, Manila clams, miscellaneous bivalves, Vancouver scallop, glass scallop, green urchin, red urchin 

2.0 2.369605 0.4 0.2063656 

BG Benthic 

herbivorous grazers 

Snails, abalone, nudibranches, sand dollars, make solarelle, Dorid nudibranches, limpets, heart sea urchin, spot prawns, pandalid shrimp 

0.12 0.282876 0.012 0.0345023 

PWN Prawns Crangon and mysid shrimp 0.13032 0.0013032 0.5068 0.0001166 

ZM Zooplankton Meroplankton 0.8 0.3105 1.8 0.0100575 

BMD Deep macrozoobenthos Sea stars, moonsnail, whelk, leather sea star, bat star, sunflower sea star, common mud 

star, crinoids, brittle sea star, basketstar 

0.7938 0.7937948 0.0326 0.0726238 

15
Table 4 continued. Invertebrate and primary producer functional groups and key parameters. Parameter C is the ingestion 

from Equation 10. The ‘maximum growth rate’ parameter (mg N/day/m^3) corresponds to μ from Equation 2 (for 

g from Equation 10 (for invertebrates). ML and Mquad are linear and quadratic mortality from Equation 3. C or g 

that the calibrated value was less than or equal to 0.1 x initial value. C or g values in gray boxes indicate that the cgreater than or equal to 10x the initial value. Initial values for C and g for ZG, ZL, ZM, ZS, BFF, BD, BG, BML, 

converted from Field’s (2004) production/biomass and consumption/biomass ratios. Initial values for other groups 

range expected for Atlantis models of other systems (e.g. Fulton 2001). 

Code Group Species 

C, postcalibration C, pre- calibration g, post- calibration g, pre- calibration M

m

BMS Shallow macrozoobenthos Giant, bigeye, yellowring, and smoothskin octopi, and flapjack devilfish 0.67 0.6698 0.1 0.10234 BML Mega-zoobenthos Dungeness crab, tanner crab, spiny lobster, 

pinchbug crab, red rock crab, graceful rock crab, spider crab, grooved tanner crab, Bairdi, scarlet king crab, California king crab 

0.0571 0.057102 0.174908 0.0074908 

BO Meiobenthos Flagellates, cilliates, nematodes 0.079 0.079 0.00688 0.00688 CEP Cephalopods Market squid, japetella, gonatus, 

chiroteuthis, abraliopsis, robust clubhook, rhomboid squid, sandpaper squid, vampire 

squid 

0.02 0.0005122 0.02 0.00008 

ZG Gelatinous 

zooplankton 

Salps, jellyfish, ctenophores, comb jellies 0.15 0.0030844 0.015 0.0002376 

ZL Large zooplankton Euphausiids, chaetognaths, pelagic shrimp, 

pelagic polychaetes, crimson pasiphaeid 

0.767 0.767 0.45 0.035636 

ZM Mesozooplankton Copepods, cladocera 0.8 NA 1.8 NA ZS Microzooplankton Ciliates, dinoflagellates, nanoflagellates, 

gymnodinoids, protozoa 

2.083 2.0838 0.5 0.067497 

PL Large 

phytoplankton 

Diatoms NA NA 0.7 NA 

PS Small 

phytoplankton 

Picophytoplankton NA NA 1 NA 

SG Seagrass NA NA 0.18 NA MA Macroalgae Kelp NA NA 0.25 NA BB Benthic bacteria NA NA 2 250 

16
17

Table 4 continued. Invertebrate and primary producer functional groups and key parameters. Parameter C is the ingestion 

from Equation 10. The ‘maximum growth rate’ parameter (mg N/day/m^3) corresponds to μ from Equation 2 (for 

g from Equation 10 (for invertebrates). ML and Mquad are linear and quadratic mortality from Equation 3. C or g 

that the calibrated value was less than or equal to 0.1 x initial value. C or g values in gray boxes indicate that the cgreater than or equal to 10x the initial value. Initial values for C and g for ZG, ZL, ZM, ZS, BFF, BD, BG, BML, 

converted from Field’s (2004) production/biomass and consumption/biomass ratios. Initial values for other groups 

range expected for Atlantis models of other systems (e.g. Fulton 2001). 

Code Group Species 

C, postcalibration C, pre- calibration g, post- calibration g, pre- calibration M

m

PB Pelagic bacteria NA NA 0.5 50 BO Meiobenthos 0.079 NA 0.00688 NA DC Carrion NA NA NA NA DL Labile detritus NA NA NA NA DR Refractory detritus NA NA NA NA 
Invertebrates 

Invertebrates are also modeled simply as aggregated biomass pools in each spatial box. 

The model tracks abundance (mg N/m3) per box, based on growth, predation, and linear and 

quadratic mortality. Quadratic mortality in this case represents density dependent effects 

(predation, disease) that are not explicitly modeled; the ultimate effect is to impose a reasonable 

carrying capacity. In general we attempted to set linear and quadratic mortality to zero when 

possible (Table 4). We have attempted to explicitly include all significant ecological 

components. Thus there was limited need to call upon these extra mortality terms, which 

represent ecological components not treated explicitly. 

Rate of change for a standard invertebrate consumer (CX) is: 

CX

i predatorgroups

CX linCX MMG quadCX iCX FP

dt

CXd −−−= ∑ − =

,

)( (3)

( ) space 2o

j DL DR

j, CXCX j

prey

i living

GCX ε CX Pi,CX P ε ⋅δ ⋅δ

⎟

⎟

⎟

⎠

⎞

⎜

⎜

⎜

⎝

⎛

⋅= ∑ + ∑ ⋅ = = ,

,

 (4)

where GCX is growth, MlinCX and MquadCX are linear and quadratic mortality, Pi,j is predation by 

group j and group i, and FCX is fishing on this group (this is set to zero for the unfished scenario 

here). εCX is the growth efficiency of CX when feeding on live prey, εCX,j the efficiency when 

feeding on detritus (DL treated separately to DR), δspace is space limitation, and δO2 is oxygen 

limitation. Table 4 contains values for Mlin, Mquad for our model. 

Vertebrates 

Vertebrates can have multiple age classes (in this case 10). These classes need not be a 

single year long, but represent different phases in the life cycle, so that for some groups it may be 

one year while for other, long-lived groups it could represent a decade or more. This is the most 

computationally efficient way of representing vertebrates with drastically different longevities 

within a common model framework. The life span of each vertebrate is detailed in Table 3, and 

the duration of each of the 10 age classes is 10% of this. 

For each age class and each spatial cell, the model tracks the number of individuals and 

their average structural weight (bones and hard parts, in mg N) and reserve weight (soft tissue, in 

mg N). Growth and abundance are functions of recruitment, predation, consumption, and linear 

and quadratic mortality. We tracked abundance, biomass, weight-at-age, and condition (reserve 

weight/structural weight) of each group through time, in each box and for the entire model 

domain. We evaluated model performance based upon how closely model-predicted values for 

these quantities matched expected values, with expected values from von Bertalanffy growth 

parameters (for weight at age), stock assessments (for unfished abundance), or from an expected 

ratio of 2.65:1 for reserve weight:structural weight (Fulton 2001). 

18
The rate of change for a vertebrate group (FX) is 

( )

FX si

si G

dt

FXd

,

, = (5)

( )

FX ri

ri G

dt

FXd

,

, = (6)

FXi

j predatorgroups

FXIMM FXEMM ilin iquad jFX

di TT MM FP

dt

FXd

i i −−−−= ∑ − =

, , , , ,

, )(

 (7)

where the subscript i represents age group i (there is one equation for each age class included), s 

stands for structural weight, r for reserve weight, and d for density. The T terms represent the 

movement of fish in to (TIMM,Fxi) and out of (TEM,Fxi) the cell. In addition there are short-term 

spawning and recruitment events which affect the various FX pools. Other notation is as 

described above. The growth for each fish group is calculated by equations of the same form as 

(4), but per age group of each fish. The result is then apportioned to structural and reserve 

weight, favoring replenishment of reserves when the animal is underweight. Life history 

parameters and values for Mlin and Mquad are contained in Table 2. 

Nutrients 

Water column nitrogen (ammonia and nitrate) concentrations are governed by uptake by 

autotrophs, excretion by consumers, nitrification, and denitrification. 

Rates of change for ammonia (NH) and nitrate (NO) in the water column are: 

( ) NIT PAB NET w

bacteria i pelagic

i

i FX

i

i CX , BF

NH MB NH MA NH PFB i

i PX

NH i

w P P P P E E E S R 

dt 

d NH 

w

w w w w

w

w

= − ∑ , − , − , − , + ∑ + ∑ + ∑ − , + ,

= = = =

 (8) 

( ) NO MB NO MA NIT PAB

i PX

NO i

w P P P S

dt

NOd

ww w

w

w −= ∑ , − , − , + ,

= (9) 

where PN,XX is the uptake of NH or NO by the autotrophs (either generic, microphytobenthos 

MB, or macroalgae MA), ECX is the production of NH by the consumer CX, SNIT,XB is the 

amount of NH converted to NO during nitrification by the bacteria XB, and RNET is the amount 

of NH produced by denitrification. 

Full descriptions of the dynamics of other forms of nitrogen, silica, bacteria, detritus, and 

sediment chemistry, as well as parameterizations specific for dinoflagellates and macrophytes, 

are contained in Fulton (2004). 

19
Process Assumptions: Predation and Recruitment 

Growth of vertebrates is based on von Bertalanffy growth parameters, but varies with 

consumption. A Holling type II functional response was chosen for predation, as previous work 

by Fulton et al. (2004) suggests this is simple to parameterize, yet is as effective as other 

representations given the nature of questions to be asked of strategic models. Alternative feeding 

functional responses exist within Atlantis and future sensitivity analyses could consider their use 

when evaluating potential model structural sensitivity. Implementation of the Holling type II 

functional response is 

⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛

⋅⋅+⋅⋅+⋅⋅+⋅⋅+

⋅ ⋅ ⋅ =

∑ ∑ ∑ ∑ = = = =

r

y

jyy

r

j

d

x

jxx

d

j

f

h

jhh

f

j

l

k

jkk

l

j

j

j

jjiji

ij

aBEaBEaBEaBE

g

C

CBaB

P

1

,

1

,

1

,

1

, 1

 (10) 

where Pij is the consumption of prey i by predator j, BB

i is the biomass of prey i and Bj

B is the 

biomass of predator j, aij is the availability of prey i to predator j, Cj is the maximum ingestion 

rate of predator j, gj is the maximum growth rate of predator j, El

j is the efficiency of predator j 

on live food (the l superscript), Ef

j is the efficiency of predator j on seagrass, macroalgae, or 

phytoplankton, Ed

j is the efficiency of predator j on labile detritus, and Erj is the efficiency of 

predator j on refractory detritus. The sums in the denominator are simply the sums of each of the 

available food biomasses (one for live food, one for seagrass, and one each for labile and 

refractory detritus). Values for C and g are contained in Tables 3 and 4. Values for prey 

availability parameters (variable a in Equation 10) are detailed in Appendix B. 

Recruitment is based on Beverton-Holt parameters, though Atlantis offers many 

alternative options which could be explored in the future. Details of parameterization of the 

Beverton-Holt relationship are in Appendix A and Table 3. 

For the movement of ecological groups, we allowed density dependent movement of 

nekton, sea birds, and marine mammals between boxes, as well as advection of plankton. The 

equations that govern density dependent movement are described in Fulton et al. (2004), but 

overall movement serves to transfer abundance towards neighboring cells with higher potential 

growth rates. For several functional groups (e.g., Pacific hake, albacore, marine mammals and 

birds) we also forced the model with seasonal migrations (Table 5). The differential equations 

for the system dynamics are solved using a simple adaptive forward difference method, with an 

overall time step of 12 hours. 

Oceanography 

The model is forced with circulation, salinity, and temperature outputs from a Regional 

Ocean Modeling System (ROMS; Figures 4, 5, and 6), allowing us to test the impacts that 

climate-driven changes in upwelling or coastal currents have on nutrients and primary 

productivity. ROMS is a state-of-the-art, free surface, hydrostatic primitive equation ocean 

circulation model developed at Rutgers University and the University of California Los Angeles. 

ROMS is a terrain-following, finite difference (Arakawa C-grid) model. It features a unified 

20
Table 5. Migration data. 

Parameter 

Leave 

date 

Return 

date 

Migration 

window 

Juvenile 

biomass 

increasea

Adult biomass 

increasea

Proportion 

migrating 

FPSb 288 166 30 19.252020 0.1744309 1.00 

FVTc 244 196 30 7.088320 0.1744300 1.00 

FVOd 305 46 30 0.496500 0.0104250 1.00 

FVBe 244 152 60 1.290550 0.3918480 0.25 

FMMf 305 91 30 2.831966 0.1068130 1.00 

PINg 349 213 30 0.591039 0.0352610 0.40 

WHBh 349 335 30 0.152940 0.0012680 0.65 

WHBh 349 46 30 0.152949 0.0012680 0.65 

WHTi 305 135 30 0.320200 0.0064980 0.30 a

 Proportional increase of biomass per individual while outside model domain. 

b

 Hart 1943, Hargreaves et al. 1994. 

c

 Love 1996. 

d

 Briggs and Chu 1986. 

e

 Groot and Margolis 1991. 

f

 Bailey et al. 1992. 

g

 Carretta et al. 2005. 

h

 Stern 2002. 

i Carretta et al. 2003. 

treatment of surface and bottom boundary layers, based on the Large et al. (1994) and Styles and 

Glenn (2000) algorithms, and an integrated set of procedures for data assimilation. Numerical 

details can be found in Haidvogel et al. (2000), Moore et al. (2004) and Shchepetkin and 

McWilliams (2005), and on the ROMS Web site (http://www.myroms.org). 

For the work reported here, we used an existing suite of basin and regional scale 

circulation models based on ROMS, linked via one-way coupling. The nested model domains 

are a basin scale model encompassing the North Pacific Basin (NPac) at 20–40 km resolution 

(Curchitser et al. in press), and a regional model at approximately 10 km resolution spanning the 

Northeast Pacific (NEP) (Hermann et al. in prep.). The NEP domain covers the area from the 

Baja Peninsula to the Bering Sea and from the coast out to 2,000 km offshore. One-way nesting 

of the models has been implemented using a hybrid of nudging and radiation approaches, as 

described in Marchesiello et al. (2001). 

In our implementation, the NEP model receives its initial and lateral boundary conditions 

from prestored NPac model output. The NPac model was forced with coarse-scale COADS 

(Comprehensive Ocean-Atmosphere Data Set) winds and heat fluxes; the NEP model was forced 

with winds and heat fluxes from a regional atmospheric model (MM5), implemented at 15–45 

km resolution (Bond et al. in prep.). The NEP model was also forced with freshwater runoff 

time series at the coast, as described in Hermann et al. (in prep.). Surface fluxes of heat and 

momentum are calculated from the National Center for Environmental Prediction using bulk 

21
LAS 6.4.0/Ferret 5.81– – NOAA/PMEL 

Depth (m): 10 

Time: 03–JAN–2002 12 Data set: nep_c 

16.4 

16 

15.6 

15.2 

14.8 

14.4 

14 

13.6 

13.2 

12.8 

12.4 

12 

11.6 

11.2 

10.8 

10.4 

10 

9.6 

9.2 

8.8 

8.4 

8 

 127°W 125°W 123°W 121°W 119°W 

 127.0°W 125.0°W 123.0° 121.0°W 119.0°W

 127°W 125°W 123°W 121°W 119°W 

46°N 

42°N 

38°N 

34°N 

46°N 

42°N 

38°N 

34°N 

Temperature (deg C) Temperature (deg C) 

7 

7.4 

7.8 

8.2 

8.6 

9 

9.4 

9.8 

10.2 

10.6 

11 

11.4 

11.8 

12.2 

12.6 

13 

13.4 

13.8 

14.2 

14.6 

LAS 6.4.0/Ferret 5.81– – NOAA/PMEL 

Depth (m): 10 

Time: 02–APR–2001 12 Data set: nep_c 

Figure 4. Seasonal salinity. These maps show seasonal shift in salinity from January to April in the 

California Current. This output was used to force the Atlantis model. 

formulae, which include the instantaneous model sea surface temperature (SST). No tides are 

included in these simulations. 

NEP hindcasts were generated for the period 1996–2003, and results stored as 3-day 

averages. These were interpolated onto the Atlantis model geometry, using the latitudelongitude coordinates of each box (or polygon). Velocities normal to each vertical face of the 

box, along with the mean salinity and temperature along each face, were then calculated from the 

stored NEP hindcast. These were interpolated in time onto 12 hourly values. We looped the 8-

year oceanographic time series six times to span the 42-year run. 

We forced the biology in Atlantis with the temperature and velocity fields from ROMS. 

We also imported the ROMS salinity fields, but salinity does not currently affect the biological 

model. Temperatures influence the respiration rates of each biological group, and each group 

also has a defined thermal tolerance and a narrower thermal range for spawning. Current 

velocities across each box face advect nutrients and plankton groups. This has a direct effect on 

nutrient (NH and NO) availability to primary producers, following Equation 2 above. Advected 

22
LAS 6.4.0/Ferret 5.81– – NOAA/PMEL 

Depth (m): 10 

Time: 03–JAN–2002 12 Data set: nep_c 

LAS 6.4.0/Ferret 5.81– – NOAA/PMEL 

Depth (m): 10 

Time: 02–APR–2001 12 Data set: nep_c 

16.4 

16 

15.6 

15.2 

14.8 

14.4 

14 

13.6 

13.2 

12.8 

12.4 

12 

11.6 

11.2 

10.8 

10.4 

10 

9.6 

9.2 

8.8 

8.4 

8 

46°N 

42°N 

38°N 

34°N 

 127°W 125°W 123°W 121°W 119°W 

Temperature (deg C) 

 127°W 125°W 123°W 121°W 119°W 

Temperature (deg C) 

34°N 

38°N 

42°N 

46°N 

7 

7.4 

7.8 

8.2 

8.6 

9 

9.4 

9.8 

10.2 

10.6 

11 

11.4 

11.8 

12.2 

12.6 

13 

13.4 

13.8 

14.2 

14.6 

Figure 5. These maps show seasonal change in temperature from January and April in the California 

Current. This output was used to force the Atlantis model. 

plankton groups include large and small phytoplankton and large, gelatinous, meso, and 

microzooplankton. 

Data Sources 

Model parameters are necessarily derived from a wide variety of sources, which are 

detailed in Appendix A. Briefly, fish life history parameters were primarily drawn from Love 

(1996), Love et al. (2002), Cailliet et al. (2000), or FishBase (Froese and Pauly 2005). Marine 

mammal life history parameters came from many sources, notably Carretta et al. (2005) and 

Perrin et al. (2002). Seabird life history parameters were drawn largely from Schreiber and 

Burger (2002) and Russell (1999). Species-level parameters were weighted by the relative 

biomass of those species to form life history parameters for the functional group (Tables 2 and 

3). Species within each functional group have similar life histories, diets, and distributions. 

Invertebrate functional groups were fairly coarse, in some cases resolving phyla into one or two 

functional groups (Table 4). Fish, mammal, and bird functional groups generally contain 3–12 

species.

23
46°N 

42°N 

38°N 

34°N 34°N 

 127°W 125°W 123°W 121°W 119°W 127°W 125°W 123°W 121°W 119°W 

East–velocity North–velocity 

→ 0.199

East–velocity North–velocity 

→ 0.171

38°N 

46°N 

42°N 

LAS 6.4.0/Ferret 5.81– – NOAA/PMEL 

Depth (m): 10 

Time: 02–APR–2001 12:00 Data set: nep_c 

LAS 6.4.0/Ferret 5.81– – NOAA/PMEL 

Depth (m): 10 

Time: 03–JAN–2002 12:00 Data set: nep_c 

Figure 6. Seasonal vector velocity. These maps show seasonal change in vector velocity from January to 

April in the California Current. This output was used to force the Atlantis model. 

Anticipating future model applications for fisheries management, we attempted to make 

finfish functional groups incorporate less than five species caught by similar gears. Modeling all 

species individually is impossible due to limitations in the current code implementation. 

However, in some cases we devoted a functional group to just one or a few species because of 

their importance to West Coast fisheries, (e.g., hake, sablefish), or due to their conservation 

importance (orcas). 

Estimates of fish abundance rely on published stock assessments (primarily from 2003), 

or on two NMFS trawl surveys: the 1998–2002 NWFSC slope survey (Builder Ramsey et al. 

2002, Keller et al. 2005, 2006a, 2006b) and the 2003 NWFSC “extended” shelf slope survey. 

Data for these surveys were extracted from the NWFSC’s West Coast Groundfish Survey 

Database on 28 December 2004. We adjusted survey catch by catchabilities recommended in 

Millar and Methot (2002) and Rogers et al. (1996). In cases where neither stock assessments nor 

reliable trawl survey data were available, we used estimates from Field (2004). Field’s estimates 

for these data-poor species involve top-down balancing of an Ecopath model, essentially 

estimating abundance of a functional group based upon the amount necessary to sustain its 

predators. Estimates of marine mammal abundance were taken from published stock 

24
assessments (Angliss and Lodge 2004, Carretta et al. 2005). Seabird abundances were derived 

from Parrish and Logerwell (2001). 

Atlantis allows two types of migration: small in-domain seasonal migrations and 

extensive out-of-domain yearly migrations. Seasonal migrations prescribe the proportion of each 

group’s biomass in each spatial box during each quarter of the year. Yearly migrations describe 

the dates each species enters and leaves the model area, and the boxes through which they enter 

or exit. Functional groups including Pacific hake, albacore, small pelagic fish, most sea birds, 

salmon, and marine mammals demonstrate annual migrations in the model (Table 5). Yearly 

migrations also require parameters that represent the physical changes species experience outside 

of the area and these parameters are described in more detail in Appendix A. 

Unlike models such as Ecosim (Christensen et al. 2000) or Multispecies Virtual 

Population Analysis (Sparre 1991), Atlantis does not directly incorporate information on 

observed diets. Instead we simply specify estimates of availability of prey to each predator 

(interaction parameter a, see tables in Appendix B), and then the proportion of each prey item in 

the diet is treated as an emergent property that dynamically responds to changes in predator and 

prey abundance. In the current parameterization, these availability parameters are converted to a 

Holling type II functional response, with gape limitation such that predators can only consume 

prey below a size threshold. For instance, for fish this was 40% of the predator size, and for 

birds 25%. Future work could involve calibrating the model to observed time series of diets 

from trawl surveys or other work. 

Calibration 

Model calibration currently involves trial and error, with the aim of finding parameter 

combinations that 1) allow all or most species to persist in the unfished scenario 2) predict 

unfished abundances within 50% to 200% of the unfished abundances estimated from stock 

assessments or monitoring (when available), and 3) predict vertebrate size-at-age within 50% to 

150% of the size-at-age reported in the literature (when available). We calibrated the model 

manually, due to long model run times that prevent us from searching the parameter space with 

automated procedures. 

For vertebrates, model calibration generally involved first modifying consumption rates, 

growth rates, and diet interactions (parameters C, g, and a in Equation 10 and Table 3) until 

predicted size-at-age matched expectations from the literature. We then compared predictions of 

population abundance to expectations from monitoring and stock assessments. In cases where 

predicted abundance was outside 50% to 200% of our expectation, we modified the strength of 

diet interactions (parameter a in Equation 10) and linear and quadratic mortality (parameters Mlin

and Mquad in Equation 7). We generally did not alter the starting values for abundance or weight. 

The sources for our starting estimates of consumption, growth, and diets are detailed in 

Appendix A. Since much of our diet data was based on small sample sizes from limited 

geographic range, we treated these data as qualitative, simply beginning the calibration with diet 

interactions (variable a) that Fulton (2001) suggests roughly correspond with expected 

interaction strengths. 

25
Calibration of invertebrates and primary producers involved modifying consumption 

rates, growth rates, and diet interactions (parameters C, g, and a in Equation 10, and μ in 

Equation 2) until predicted biomass was near our expectations from monitoring and stock 

assessments. If necessary we also invoked linear and quadratic mortality (parameters Mlin and 

Mquad in Equations 1 and 3). Table 4 illustrates how our parameters for invertebrate growth and 

consumption changed during calibration. In general, we increased consumption and growth 

rates, particularly for shrimp (PWN), squid (CEP) and zooplankton (ZL and ZM). 

For primary producers, model calibration involved adjusting linear and quadratic 

mortalities (parameters Mlin and Mquad in Equation 1), growth rate (μ in Equation 2 ), and the 

strength of grazing (parameter a in Equation 10). 

The diet interaction parameters (variable a) are a useful example of the calibration 

process, and generally required the most adjustment, both to achieve reasonable size-at-age and 

for reasonable population abundances. Tables B-1 through B-6 (Appendix B) show the final 

calibrated values for all diet interaction parameters, and Tables B-7 through B-12 show these 

calibrated values relative to our initial estimates. In general, we found that we needed lower 

values of variable a than other Atlantis models (e.g., Fulton 2004). This shift to lower 

consumption parameters is evidenced by the number of shaded cells in Tables B-7 through B-12. 

Overall, two patterns emerge from Tables B-7 through B-12: light gray columns indicating prey 

groups that initially experienced excessive predation, which we decreased during calibration; and 

dark gray rows indicating predators that were starving, for which we increased diet interactions 

(variable a) with prey. There were relatively few cases where predators grew excessively due to 

excessive predation, or where we chose to invoke additional predation to limit the abundance of 

a prey group. 

26
Results 

With no fishing, the model was able to recreate expected growth, abundance, and 

seasonal patterns for most functional groups (Figures 7 through 14). 

Cell 

Figure 7. Spatial distribution of chlorophyll a in the surface layer (mg N/m3, 0-50m) at the end of a 42-

year run. Each of the 62 spatial areas is colored proportional to chlorophyll a abundance; the 

region displayed is the same as in Figure 2 (Point Conception to the Canadian border). The 

bottom panel illustrates the abundance over time in one cell, the southernmost model area 

between the 200 and 550 m isobaths. Chlorophyll a integrates the abundance of 

picophytoplankton and diatoms. The annual oscillations are due to seasonal trends in light and 

nutrient availability. 

27
Cell 

Figure 8. Spatial distribution of deep benthic filter feeders (BFD, in mg N/m2) at the end of a 42-year 

run. The bottom panel illustrates the abundance over time in one cell, a region off Oregon 

between the 150 and 200 m isobaths. 

28
Cell 

Figure 9. Spatial distribution of small flatfish, (FDF, mg N/m3) at the end of a 42-year run. The bottom 

panel illustrates the abundance over time in one cell, a region off Oregon between the 150 and 

200 m isobaths. The annual oscillation is due to seasonal patterns of recruitment and growth. 

29
Midwater rockfish Shallow small rockfish 

Deep small rockfish 

Year Year

Deep large rockfish

Year Year

Shallow large rockfish Skates and rays

Year Year

Figure 10. Abundance over the 42-year run for rockfish, skates, and rays spatially aggregated. The six 

groups plotted in metric tons show the total abundance in the model region. Groups plotted in mg 

N/m3 show the average concentration in the model region. Abundances illustrate the seasonal 

effects of recruitment and growth. 

30
Large flatfish Large demersal fish

Hake Sablefish

Small flatfish Deep miscellaneous fish

Year

Yea Year r

Year Year

Year Year

Figure 11. Abundance of groundfish over the 42-year run for six groundfish groups. Groups plotted in 

metric tons show the total abundance in the model region. Groups plotted in mg N/m3 show the 

average concentration in the model region. Abundances illustrate the seasonal effects of 

recruitment and growth. Migratory groups (hake) show additional variability because abundance 

outside the model region is excluded. 

31
Small planktivores Large planktivores

Tuna Salmon

Deep vertical migrators Misc. nearshore demersal 

Year Year

Year Year

Year Year

Figure 12. Abundance of six pelagic groups over the 42-year run. Groups plotted in metric tons show the 

total abundance in the model region. Groups plotted in mg N/m3

 show the average concentration 

in the model region. Abundances illustrate the seasonal effects of recruitment and growth. 

Migratory groups (small planktivores, tuna, salmon) show additional variability because 

abundance outside the model region is excluded. 

32
Small demersal sharks Large demersal sharks 

Pelagic sharks Migrating birds

Surface seabirds Diving seabirds

Year Year

Year Year

Year Year

Figure 13. Abundance over the 42-year run for shark and seabird groups, spatially aggregated. The six 

groups plotted in metric tons show the total abundance in the model region. Groups plotted in mg 

N/m3 show the average concentration in the model region. Vertebrate abundances illustrate the 

seasonal effects of recruitment and growth. Migratory groups (migrating birds) show additional 

variability because abundance outside the model region is excluded. 

33
Pinnipeds Baleen whales

Year Year

Toothed whales Transient orcas

Year Year

Otters 

Year

Figure 14. Abundance over the 42-year run for five marine mammal groups. Groups plotted in metric 

tons show the total abundance in the model region. Groups plotted in mg N/m3

 show the average 

concentration in the model region. Abundances illustrate the seasonal effects of recruitment and 

growth. Migratory groups (pinnipeds, baleen whales, and toothed whales) show additional 

variability because abundance outside the model region is excluded. 

34
Abundance of large and small phytoplankton (Figures 7 and 15) fluctuated seasonally as 

expected, based on light intensity and nutrient availability driven by advection from the ROMS 

current fields. Seasonal mean phytoplankton abundance increased fourfold from our initial 

estimates, which were based on field observations from winter or early spring. This increase 

may in part be due to unrealistic levels of NH3

+

and NO3

-

 accumulation that probably released 

phytoplankton from nutrient limitation. Despite the fact that we looped the eight-year 

oceanographic time series, phytoplankton does not show a strong eight-year periodicity. 

Seagrass declined in abundance (Figure 16) due to light limitation, but adjusting the depth of 

seagrass upwards from the middepth of inshore boxes (25m) should address this issue. 

Invertebrates lack age structure and therefore generally had smooth population dynamics 

(Figures 8, 17, 18, and 19). Zooplankton groups showed strong seasonal effects due to a strong 

trophic link with primary production. Most zooplankton groups also increased in abundance 

from our initial estimate, tracking the increase in primary producers. Of the zooplankton groups, 

relative abundance of microzooplankton increased the most, possibly because they experience 

little predation by vertebrate groups that increased during this unfished scenario. Benthos 

exhibited smoother dynamics that were less affected by seasonal variation in primary 

productivity. Deposit feeders (amphipods) and other filter feeders (barnacles [Cirripedia spp.] 

and bivalves [Bivalvia spp.]) went extinct due to excessive predation (probably excessive values 

of a in Equation 10). Similarly shrimp and shallow macrobenthos (octopus [Octopoda spp.]) 

declined to low levels of abundance as populations of their predators, such as finfish, increased. 

Vertebrates showed strong seasonal changes in total biomass, due to annual recruitment, 

growth, and migration (Figures 9 and 10 through 14). Most vertebrate groups reached 

equilibrium levels of abundance by the end of the 42-year model run, with the notable exception 

of midwater rockfish, which experienced an increase in predation after year 25. The dominant 

trend was an increase in biomass from the initial conditions (≈1995–2005 abundance) due in part 

to the lack of fishing mortality. This was especially true for the rockfish, flatfish, and marine 

mammal groups, which are currently depleted. Recovery of depleted large rockfish was rapid 

(<10 years) relative to expectations (e.g., Parker et al. 2000), perhaps due to excessively high 

recruitment parameters (Figure 10). High recruitment in shallow small rockfish resulted in large 

intraannual fluctuations in total biomass of those groups. 

Trophic effects were evident for some fish species, particularly forage species. Small 

planktivores (e.g., anchovies), deep vertical migrators (e.g., Myctophidae), and miscellaneous 

nearshore demersal fish (e.g., white croaker) declined in abundance, with fluctuations in this 

declining trend due to the abundance of their predators (Figure 12). Midwater rockfish (Figure 

10) increased in abundance but then declined as predation mortality increased. Small deep 

rockfish (longspine thornyhead, Figures 10 and 11) declined in part due to an increase in 

abundance of their predator sablefish (Figure 11). Large demersal fish (lingcod, Figure 11) 

showed an increasing trend like most species recovering from depletion, but with a sharp 

increase in abundance at year 20 due to a drop in predation mortality. 

35
NH3 NO3

Chlorophyll a Carrion

Year Year

Year Year

Figure 15. Abundance over the 42-year run for nutrients and carrion. Groups plotted in metric tons show 

the total abundance in the model region. Groups plotted in mg N/m3 show the average 

concentration in the model region. 

36
Kelp Seagrass

Shallow filter feeders Deep filter feeders

Other filter feeders 

Year Year

Year Year

Year

Figure 16. Abundance over the 42-year run for filter feeders, kelp and seagrass groups. Groups plotted in 

metric tons show the total abundance in the model region. The five groups plotted in mg N/m3 

show the average concentration in the model region. 

37
Cephalopods Shrimp juvenile

Shrimp adult Pelagic bacteria

Sedimentary bacteria Deposit feeders

Year Year

Year Year

Year Year

Figure 17. Abundance over the 42-year run for six invertebrate groups. Groups plotted in metric tons 

show the total abundance in the model region. Groups plotted in mg N/m3 show the average 

concentration in the model region. 

38
Diatom Picophytoplankton

Gelatinous zooplankton 

Year Year

Carnivorous zooplankton

Zooplankton Microzooplankton

Year Year

Year Year

Figure 18. Abundance over the 42-year run for six plankton groups. Groups plotted in metric tons show 

the total abundance in the model region. Groups plotted in mg N/m3 show the average 

concentration in the model region. 

39
Megazoobenthos Benthic carnivores

Shallow macrobenthos 

Year Year

Deep macrobenthos

Year Year

Figure 19. Abundance over the 42-year run for four benthic invertebrate groups. Groups plotted in 

metric tons show the total abundance in the model region. Groups plotted in mg N/m3 show the 

average concentration in the model region. 

40
We compared predictions of unfished biomass (B0) at the end of the 42-year simulation to 

estimates of unfished biomass available from stock assessments (Figure 20). We note that the 

this “B0” value from assessments represents equilibrium biomass before fishing began, while the 

value from Atlantis is equilibrium abundance after a release from fishing; nonetheless, we would 

expect the two to be comparable. The models are also similar in that they currently assume fairly 

constant ocean condition through time. However, in 10 of 14 cases Atlantis predicts lower 

unfished biomass than single species models. In one case (transient orcas), the difference in 

abundance was four times, but typically the difference was 50% to 100%. These differences 

between Atlantis and single species models persisted, even though as part of the calibration 

process we attempted to bring Atlantis to the same equilibrium levels of abundance as predicted 

by single species assessments. 

As noted above, this Atlantis model run includes an increase in the densities of primary 

producers to levels approximately four times higher than expected. If primary producer 

abundance were lower, Atlantis estimates of unfished vertebrate abundance would likely be 

lower, strengthening this trend of lower unfished abundance in Atlantis than in single species 

models. 

In this unfished scenario, we expected seasonal abundance trends to clearly reflect the 

migrations specified in the input parameters. As expected, the model exhibited forced seasonal 

movement within the California Current as well as more extensive migrations that we imposed 

on migratory groups (Figure 10). For instance, hake exited the model in winter months, and 

returned in the spring (Figure 21). Salmon and albacore showed the correct seasonal pattern, but 

each showed periods of very low biomass for approximately 10 years. 

Weight-at-age is dynamic within Atlantis, and is a useful check of whether parameters for 

consumption, growth, and reproductive costs are within a reasonable range. Weight-at-age has 

two components: reserve weight (muscle and fat) and structural weight (bones and hard parts). 

In Atlantis, reductions in reserve weight represent starvation due to insufficient maximum 

consumption rates, low prey abundance, low prey availability, or gape limitation. Structural 

weight will also decline if groups starve and fail to grow, but it is less sensitive to starvation than 

reserve weight. In this unfished scenario, weight-at-age of most groups stabilized over the 42 

year run. No group suffered mortality directly due to starvation, but many groups exhibited 

lower than expected weights (Figures 22 through 26). This means through the course of the 42-

year simulation, weight-at-age declined relative to our initial values, which derived from field 

studies. Rockfish and flatfish (Figures 22 and 23) generally only grew to about half the expected 

weights. Planktivores, tuna, deep vertical migrators, large demersal predators, and baleen whales 

all showed unreasonably low growth. Further calibration of diet, growth, and consumptions 

parameters may resolve this.

41
0

2

4

6

8

10

12

Small planktivores

Small flatfish

Large demersal predators

Salmon

Hake

Sablefish

Midwater rockfish

Shallow large rockfish

Deep large rockfish

Pinnipeds

Transient orcas

Baleen whales

Toothed whales

Otters

Biomass / current biomass

Figure 20. Unfished biomass relative to current biomass from Atlantis versus published assessments. 

Current biomass was used as the initial condition for Atlantis, and data sources are detailed in 

Appendix A. Black bars are the biomass predicted by Atlantis after 42 years without fishing. 

Gray bars are based on estimates of Bo (virgin biomass) from the following assessments: small 

planktivores, Conser et al. 2003; small flatfish, Sampson and Wood 2001; large demersal 

predators, Cope et al. 2003, Jagielo et al. 2004; salmon, see FVB, Appendix A; hake, Helser et al. 

2003; sablefish, Schirripa 2002; midwater rockfish, Hamel et al. 2003; shallow large rockfish, 

Ralston and Dick 2003 and Wallace et al. 2002; deep large rockfish, Piner and Methot 2001; 

pinnipeds, transient orcas, baleen whales, and toothed whales, Springer et al. 2003; otters, U.S. 

Fish and Wildlife Service 2003. 

42
 

Figure 21. Seasonal distribution of hake biomass distribution displayed in winter, summer, and fall (top 

to bottom panels).

43
Megazoobenthos 

rockfish 

Small shallow

rockfish 

Small deep

rockfish 

Large deep 

rockfish 

Large shallow

rockfish Skates and rays N, relative to initial N N, relative to initial N N, relative to initial N 

Age class Age class 

Age class Age class 

N, relative to initial N N, relative to initial N N, relative to initial N N, relative to initial N 

Age class Age class 

Figure 22. Change in reserve and structural nitrogen for rockfish and skates. Structural nitrogen (black 

bars) and reserve nitrogen (gray bars) for five rockfish groups and skates and rays, at the end of 

the 42-year unfished scenario relative to the initial values. Initial values derive from expected 

weight-at-age observed in field studies (from FishBase, see Table 3). Structural nitrogen 

represents bones and hard parts, and reserve nitrogen represents muscle and fat. All vertebrates 

contain 10 age classes. A decline in reserve nitrogen below a ratio of 0.8 is symptomatic of 

starvation, while ratios greater than 1.2 generally indicate excessive consumption. 

44
N, relative to initial N 

Hake out of model 

region 

Large flatfish Large demersal fish 

Sablefish 

Small flatfish Deep misc. fish N, relative to initial N N, relative to initial N N, relative to initial N 

Age class 

Age class Age class 

N, relative to initial N 

Age class Age class 

Figure 23. Change in reserve and structural nitrogen for other groundfish. Structural nitrogen (black 

bars) and reserve nitrogen (gray bars) for six groundfish groups, at the end of the 42-year 

unfished scenario relative to the initial values. Initial values derive from expected weight-at-age 

observed in field studies (from FishBase, see Table 3). Structural nitrogen represents bones and 

hard parts, and reserve nitrogen represents muscle and fat. All vertebrates contain 10 age classes. 

A decline in reserve nitrogen below a ratio of 0.8 is symptomatic of starvation, while ratios 

greater than 1.2 generally indicate excessive consumption. Hake were outside of the model, 

having migrated south of the model region, at the time point shown here. 

45
N, relative to initial N 

Small planktivores Large planktivores N, relative to initial N 

Salmon 

Misc. nearshore 

demersal 

Tuna 

Deep vert. migrators 

N, relative to initial N N, relative to initial N 

Age class Age class 

Age class Age class 

N, relative to initial N N, relative to initial N 

Age class Age class 

Figure 24. Change in reserve and structural nitrogen for pelagic groups. Structural nitrogen (black bars) 

and reserve nitrogen (gray bars) for pelagic groups, at the end of the 42-year unfished scenario 

relative to the initial values. Initial values derive from expected weight-at-age observed in field 

studies (from FishBase, see Table 3). Structural nitrogen represents bones and hard parts, and 

reserve nitrogen represents muscle and fat. All vertebrates contain 10 age classes. A decline in 

reserve nitrogen below a ratio of 0.8 is symptomatic of starvation, while ratios greater than 1.2 

generally indicate excessive consumption. 

46
Figure 25. Structural nitrogen (black bars) and reserve nitrogen (gray bars) for shark and bird 

groups at the end of the 42-year unfished scenario relative to the initial values. Initial values 

derive from expected weight-at-age observed in field studies (from FishBase, see Table 3). 

Structural nitrogen represents bones and hard parts, and reserve nitrogen represents muscle and 

fat. All vertebrates contain 10 age classes. A decline in reserve nitrogen below a ratio of 0.8 is 

symptomatic of starvation, while ratios greater than 1.2 generally indicate excessive consumption. N, relative to initial N 

Large demersal 

shark 

Small demersal 

shark 

Misc. pelagic 

N, relative to initial N N, relative to initial N 

Age class Age class 

Migrating seabirds 

shark 

N, relative to initial N 

Age class Age class 

N, relative to initial N N, relative to initial N 

Surface 

seabirds 

Diving seabirds 

Age class Age class 

47
Pinnipeds 

N, relative to initial N 

N, relative to initial N 

Baleen 

Whales 

Toothed whales Transient orcas 

Age class Age class 

Age class 

N, relative to initial N 

Age class 

N, relative to initial N N, relative to initial N 

Otters 

Age class 

Figure 26. Structural nitrogen (black bars) and reserve nitrogen (gray bars) for marine mammal groups at 

the end of the 42-year unfished scenario relative to the initial values. Initial values derive from 

expected weight-at-age observed in field studies (from FishBase, see Table 3). Structural 

nitrogen represents bones and hard parts, and reserve nitrogen represents muscle and fat. All 

vertebrates contain 10 age classes. A decline in reserve nitrogen below a ratio of 0.8 is 

symptomatic of starvation, while ratios greater than 1.2 generally indicate excessive consumption. 

48
Discussion 

The full promise of this Atlantis model lies in its use for MSE, but parameterizing the 

ecology shown here forced a rethinking of many assumptions about the California Current 

ecosystem. For instance, large amounts of unexplained linear mortality on the large rockfish 

groups had to be invoked in order to keep their biomass near reasonable levels, until we realized 

that historically a large fraction of northern fur seals breed in Alaska waters but overwinter and 

feed in the California Current. Their diet in Oregon and Washington includes rockfish as a 

major prey item (Ream et al. 2005). Including these migratory fur seals in our model, with 

rockfish in their diets, allowed us to reduce the linear mortality term for large rockfish. 

A second example of this type of learning through parameterization occurred as we tuned 

predator-prey availability parameters. Overall we found that the model came closest to matching 

expected unfished biomasses (Figure 27) when we used fairly low availability parameters. 

Substituting higher availability parameters from the southeast Australia Atlantis model led to 

extinction of many species. This could simply be a model parameterization artifact or a real 

difference regarding bottom habitat and refuges from predation. We also found that many of our 

initial vertebrate consumption rates were much too low, leading to insufficient growth (i.e., 

weight-at-age below estimates from field and laboratory aging analyses). This was addressed by 

switching from using consumption to biomass estimates from Ecopath models, to consumption 

rates predicted by von Bertalanffy growth rates and an assumed assimilation efficiency. 

Finally, similar to other Atlantis modelers, we have struggled to parameterize the model 

in a way that keeps shrimp abundance above a small fraction of current abundance. We believe 

this lends some evidence to support the hypothesis of predator control of shrimp populations 

(Worm and Myers 2003). Here in our unfished scenario, hake, which are a major shrimp 

predator, increase in abundance by four times. We view model building with Atlantis as a useful 

way to generate hypotheses about how the ecosystem functions, and to synthesize data that allow 

us to look for evidence regarding existing hypotheses. 

The results from the final parameterization of the unfished scenario shown here are 

generally consistent with the biological interactions predicted by Field (2004) and Field et al. 

(2006), who fit a spatially-aggregated Ecosim model to data from the California Current. Both 

models demonstrate that fishing mortality is the major driver of most finfish populations, with 

strong recovery in the unfished Atlantis model, comparable to the strong declines due to 

depletion in the Ecosim model with fishing. In both models, trophic interactions are a secondary 

effect after fishing, but are generally stronger for forage species. Both models saw strong effects 

of predation by hake on shrimp and by sablefish on small deep rockfish (thornyhead). In part the 

similarity between models is expected, because here we relied on many parameter estimates from 

the Ecosim model. However, the commonalities between the two models suggest that these 

results are at least not artifacts of structural assumptions in the models. Comparative analyses 

across models and across ecosystems are a promising area of future research. 

49
0

2

4

6

8

10

Large planktivores

Tuna

Deep vert. migrators

Deep misc. fish

Misc. nearshore fish

Large flatfish

Deep small rockfish

Small shallow rockfish

Small demersal sharks

Large demersal sharks

Pelagic sharks

Skates and rays

Surface feeding birds

Diving bird

Unfished / current biomass 

s

Figure 27. Biomass predicted by Atlantis after 40 years of no fishing, relative to current (≈2006) 

biomass. Current biomass was used as the initial condition for the start of the 42-year simulation. 

These species or functional groups are not assessed, so Atlantis estimates of unfished abundance 

are not compared to estimates of the assessments. 

Unlike the Field et al. (2006) Ecosim model, the Atlantis model so far seems less 

sensitive to interannual fluctuations in climate. Field et al. (2006) found that forcing their model 

with top-down or bottom-up climate forcing improved model fits to data. The Atlantis model 

showed seasonal patterns of productivity, but no obvious interannual fluctuations. Including a 

longer time series of oceanographic forcing into Atlantis, including data prior to 1996, may 

capture some of the PDO climate signal that appears important in the Ecosim model. We expect 

this signal will be most easily detected in zooplankton, since in the unfished scenario they show 

the strongest response to seasonal changes in phytoplankton. 

Ongoing work with the California Current Atlantis model will focus first on including 

historical fisheries catches, then on including fisheries fleet dynamics calibrated to match 

historical catches. Previous work with multispecies simulation models suggests model behavior 

must be constrained by calibrating the models so that population dynamics match trends in 

abundance observed in surveys or predicted by assessments (Cox et al. 2002). 

Further calibration will strengthen comparisons such as that shown here between 

predictions of unfished biomass in Atlantis vs. single species models. Walters et al. (2005) 

showed that a series of ecosystem models predicted lower maximum sustainable yield than 

single species models. Fishing at rates predicted by single species models to give maximum 

yield would lead to overfishing in the ecosystem model. We hope to be able to use the 

California Current Atlantis model to make robust conclusions about reference points such as B0

and maximum sustainable yield. Here we showed that for 10 of 14 functional groups, Atlantis 

50
predicted less of a recovery of depleted stocks than did single species models. We expect that 

this pattern will hold true as we further develop this comparison, since the ecosystem model 

imposes realistic carrying capacities due to food limitation and predation that are not explicitly 

included in single species assessments. 

The California Current Atlantis model is intended as a strategic MSE tool to identify 

tradeoffs between species, fleets, and management goals, and to identify effects of management 

policies. It is not intended for tactical management, for instance, setting annual quotas for target 

stocks. Instead we will use this Atlantis model to evaluate how management strategies, such as 

new ways of conducting stock assessments or limiting fishing effort, perform when faced with a 

realistic ecosystem that includes trophic effects and climate. Although the Atlantis model only 

qualitatively matches the ecosystem dynamics of the real world, like the real world it contains 

more ecological complexity than assessment or management models, and does not follow the 

same underlying equations. We can expect that management strategies that fail when applied in 

Atlantis will also fail in the real world. 

Our work with this biological and oceanographic model has revealed several limitations 

in the model framework (Atlantis), the data, and our results to date. A few prominent limitations 

to the Atlantis framework include: 1) a lack of an “accounting” step before the model begins the 

dynamic simulation, so that the model must be run for minutes to hours before users identify 

gross misparameterizations that lead to extinction or excessive population growth; 2) the use of 

predator/prey interaction parameters only, rather than explicit input of diet data; 3) growth that 

can deviate radically from expected von Bertalanffy age-weight relationships, if consumption 

parameters are incorrect; and 4) the time-intensive process of parameter input and model 

calibration. Future programming efforts will address these issues. Data limitations include a 

lack of full spatiotemporal data for almost all functional groups; a lack of reliable biomass 

estimates for some groups, particularly invertebrates and benthos; and a lack of reliable diet data 

for many functional groups. Other difficulties with data are listed in Appendix A. 

Key problems with the output include: 1) poor growth of planktivores, large demersal 

predators, tuna, deep vertical migrators, and baleen whales; 2) excessive recruitment leading to 

extremely rapid recovery of depleted groups such as large deep rockfish, and excessive intraannual variation in the abundance of other groups such as small rockfish; 3) extinction of sea 

grass, shallow filter feeders, and deposit feeders; 4) accumulation of NH3

+

 and NO3

-

; and 5) 

periods of very low abundance for salmon and tuna, two of the migratory species. We will 

attempt to resolve these behaviors as we further develop the California Current Model and 

calibrate it to historical data.

Despite the need for further calibration and the addition of fisheries information, we 

believe that the California Current model will be a useful tool for MSE for U.S. West Coast 

fisheries. The model synthesizes biotic and abiotic information from a variety of sources, and in 

the near future we will integrate this into the full MSE framework available in Atlantis. In this 

framework we can test harvest decisions, assessment techniques, and the utility of new and 

ongoing ocean monitoring programs. A similar model for southeast Australia has been used for 

more than five years, first to identify ecological indicators for fishery management, and now as a 

policy screening tool in the current restructuring of Australia’s southern federally managed 

fisheries. An additional advantage of the Atlantis modeling approach is that it can easily be 

51
modified to nest fine-scale models within a coarser coast-wide model. We anticipate using this 

approach in central California to consider local ecological processes and management topics. 

Finally, on the level of basic ecological research, we have found that model outputs serve as 

hypotheses about the responses of species to changes in climate and management, and we expect 

that this will stimulate field research and collaboration. 

52
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Appendix A: California Current 

Model Documentation 

Benthic Habitat and Sediment Type 

Habitat type and sediment classification are represented in Atlantis by proportional 

coverage within each spatial box. Sediment is classified as either soft or hard, and biogenic 

habitat as kelp, seagrass, or neither. This information is used in conjunction with functional 

group preference to regulate species movement within the model domain. 

We derived habitat and sediment coverage from the groundfish Essential Fish Habitat 

Environmental Impact Statement (EFH EIS) data (NMFS 2004). These data are a compilation of 

survey data taken by several state, federal, and private organizations in Washington, Oregon, and 

California at different periods of time, and provide the most comprehensive habitat list available. 

We used Arcview GIS software (ESRI, Redlands, California) to calculate the coverage of each 

habitat and sediment type within each box. 

Studies relating spatial coverage to biomass density enabled the conversion of the EFH 

EIS spatial coverage of kelp and seagrass data into biomass estimates, required by Atlantis. The 

estimates of biomass per unit area from beds of giant kelp (Macrocystis integrifolia) and bull 

kelp (Nereocystis leutkeana) from central California to Vancouver Island are summarized in 

Coon et al. (1981), Barns and Kalvass (1993), Sutherland et al. (1995), and Fox et al. (1999). 

Biomass density of seagrass was based on measurements of eel grass (Zostera marina) by 

Ruesink et al. (2006) in Willapa Bay, Washington. Biomasses of kelp and seagrass were 

converted to mg N per unit area using nitrogen content measurements. 

Nutrients, Salinity, and Dissolved Oxygen 

The ROMS model and Atlantis generate dynamic nutrient, salinity, and dissolved oxygen 

concentrations, but we also collected field observations of these quantities as initial conditions 

and for calibration purposes. Initial nutrient concentrations (dissolved inorganic nitrogen and 

silicate), salinity, and dissolved oxygen were largely derived from measurements at multiple 

depths collected on GLOBEC sampling cruises between 1997 and 2004 (Wetz et al. 2004); 

California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises from 2000 to 2004 

(CalCOFI 2007); and cruises and mooring buoys in Monterey Bay, California (Bruland et al. 

2001). 

These efforts covered the region from the southerly boundary to lat 44°65′N, and in 

waters from coastal areas to our model boundary boxes. For regions outside of the area 

described above, we used data from Whitney and Freeland (1999), Hickey and Banas (2003), 

and the Line P long-term data collected off the British Columbia coast (Robert 2007). We 

focused on values from winter or early spring sampling periods because Atlantis takes initial 

67
concentrations of nutrients and other solutes, assumed to occur on January 1 of the model year, 

then calculates subsequent fluxes of materials based on physical forcing, biological uptake, and 

recycling. 

Iron data were considerably scarcer than data for other nutrients. Most dissolved iron 

data were taken from Chase et al. (2002), with additional data derived from Johnson et al. 

(1997), and Bruland et al. (2001). Sediment iron concentrations were assumed from Johnson et 

al. (1997). 

We assumed that nutrient input from terrestrial sources, via river outflows, was 

negligible. This assumption may be faulty, particularly in coastal and shelf regions near major 

human population centers or in the northern portion of the model domain where river inputs are 

highest. For example, San Francisco Bay is a source of nitrate and silicate to coastal waters 

under some climate conditions (Wilkerson et al. 2002). The Columbia River is likely a major 

source of dissolved silicate, particulate organic carbon and particulate organic nitrogen (Hill and 

Wheeler 2002). Terrestrial sources of iron are also important, particularly in upwelling regions 

where iron is often a limiting nutrient (Bruland et al. 2001). Thus the assumption of negligible 

nutrient input from rivers may need to be amended during the tuning phase of model 

development. 

Initial solute concentrations at depth were averaged or interpolated from empirical values 

in the same manner as described for chlorophyll a (see Phytoplankton subsection below). 

Overview of Biological Parameters 

Our parameter estimates closely follow those in Field (2004) for the 1990s California 

Current, with some additional references, particularly where our functional groups differed from 

his. Where possible we provide a comparison below between our parameter estimates and 

Field’s (2004). Most of the differences and additional citations are necessitated by the capacity 

for representing spatial distributions within Atlantis, which was not possible in Field’s 2004 

Ecosim model. Life history and rate parameters are found in Table 3 for vertebrates, and in 

Table 4 for invertebrates. 

Growth and Clearance Rates 

Atlantis requires input of daily estimates of growth and clearance (consumption rates per 

individual) for each age class of all vertebrate groups. Growth rates were calculated from the 

von Bertalanffy growth curves (Table 3) for an archetypical species in each functional group; the 

archetypical species’ parameters are the averages of the parameters for each species, weighted by 

their relative abundance (Table 2). Clearance rates were slightly more complicated. Where our 

functional groups overlapped with those of Field (2004), we attempted to convert his Ecopath 

Q/B (i.e., annual consumption/standing stock biomass) parameters to Atlantis clearance rates. 

However, we found that in most cases these Q/Bs led to lower growth than that expected from 

the von Bertalanffy and length-weight parameters. 

Instead of using Ecopath Q/Bs, we calculated Atlantis clearance rates for juveniles by 

assuming a 10% conversion efficiency between consumption and growth (and no other metabolic 

68
costs). Clearance rates of adult age classes equal those of the oldest juveniles, scaled by the ratio 

of size of the adult to the size of the oldest juvenile, raised to the three-fourths power. This 

captures the basic intuition that: 1) juveniles are converting most energy (or N) intake into 

growth, following some conversion efficiency, and 2) adult consumption rates 

(mg/day/individual) should generally be slightly higher than for juveniles, even though most of 

this energy is converted to reproduction, not growth. Respiration and consumption are generally 

related to biomass by the three-fourths power (Schmidt-Nielsen 1997). The resulting clearance 

rates generally yield better growth than converting Ecopath Q/Bs, likely due to the lack of age 

structure in the Field (2004) model. 

Beverton Holt Recruitment Parameters 

We used the standard form of the Beverton Holt recruitment model: 

R= α × S / (β + S) 

where α represents the maximum number of recruits produced (number of individuals), and β

represents the spawning stock biomass at which recruitment is one-half maximum (measured in 

mg N). Recruitment R is the product of alpha times stock size S divided by the sum of beta plus 

stock size S. Here we use the ecological definition of recruits: fish that are approximately 60–

180 days old and have settled out of the plankton and begun feeding. Atlantis does not explicitly 

model larvae or larval dispersal. Recruits are distributed evenly in all areas where juveniles can 

exist. 

For most fish groups, estimates of unfished recruitment (α) were available for at least one 

species in the functional group. This was scaled up to an entire functional group using the 

proportion of each species in the 1998–2002 NMFS NWFSC slope survey (Builder Ramsey et 

al. 2002, Keller et al. 2005, Keller et al. 2006a, 2006b) and the 2003 NWFSC extended shelfslope survey. This implies that we assume equal levels of depletion within a functional group. 

To derive β, we first calculated unfished spawner biomass in a way similar to unfished 

recruitment, scaling up from the level of an assessed species to the functional group. β was then 

equal to a proportion of this spawner biomass, where the proportion was calculated from stock 

recruit steepness (see Hilborn et al. 2003 for the conversion from steepness to β). 

Steepness ranges from 0.2 to 1.0, where low values indicate a gradual increase in recruit 

abundance as spawning stock biomass increases (for instance, a constant 100 recruits per female 

spawner), and high values represent constant or “flat” recruitment across a very large range of 

spawning stock biomass. When possible, we used the values for steepness either estimated or 

assumed in stock assessment. When stock assessments assumed no stock-recruitment 

relationship, we used steepness of 0.9, that is, a flat relationship between spawners and recruits. 

When no assessments were available, we assumed steepness of 0.5 for groundfish, and 0.8 for 

pelagic fish, which frequently show a fairly flat stock recruit relationship. The use of fixed stock 

recruit parameters imposes a fairly strict density dependence on the model; in the future we may 

consider alternative stock-recruit relationships that rely less on uncertain estimates of steepness 

and unfished biomass and recruitment. Table 3 contains values for steepness, α, and β for all 

vertebrates. 

69
For mammals and birds, we calculated α as the maximum number of offspring per adult, 

multiplied by an estimate of virgin adult abundance. We assumed mild compensation, 

equivalent to a steepness of 0.33, suggesting that at one-third historical abundance, mammals and 

birds could produce one-half of the maximum amount of offspring. Data on maximum number 

of offspring per adult were taken from Perrin et al. (2002) for mammals and Schreiber and 

Burger (2002) for birds. Estimates of historical levels of abundance are derived from the U.S. 

Fish and Wildlife Service (2003) and Springer et al. (2003) for marine mammals and Veit et al. 

(1996) and Oedekoven et al. (2001) for birds. We calculated β by scaling abundance to 

historical abundance, then multiplying by one-third. This implies that at one-third their historical 

biomass, mammals or birds could produce one-half their historical level of recruitment. 

Migration 

Atlantis identifies two types of migration: smaller seasonal migrations within the model 

domain and more extensive yearly migrations that take groups outside of the model boundary. 

Most groups display seasonal migration that shifts their biomass within the model area. Seasonal 

migration is quantified by allocating the total biomass of a group within each box by season, 

depending on that group’s behavior. 

Nine functional groups in the NCCE perform extensive migrations that take them outside 

of the model domain for part of every year. These groups are small planktivores, salmon, tuna, 

hake, migratory birds, pinnipeds, baleen whales, toothed whales, and dolphins. Out of this list, 

pinnipeds, salmon and baleen whales undergo two yearly migrations. Parameters for these 

extensive migrations for both juvenile and adult behavior are in Table 5. 

Phytoplankton (PS, PL) 

Biomass estimates for diatoms (PL) and microphytoplankton (PS) were largely derived 

from chlorophyll a concentrations measured throughout the model area at multiple depths on 

GLOBEC sampling cruises between 1997 and 2004 (Wetz et al. 2004), CalCOFI cruises from 

2000 to 2004 (CalCOFI 2007), and cruises and mooring buoys in Monterey Bay. These efforts 

covered the region from the southerly boundary to lat 44°65′N, and in waters from coastal areas 

to our model boundary boxes. For regions outside of the area described above, we used Ocean 

Transect P data from Boyd and Harrison (1999). We focused on chlorophyll levels from winter 

or early spring sampling periods because Atlantis takes an initial phytoplankton biomass, 

assumed to occur on January 1 of the model year, and then calculates subsequent production and 

biomass based on factors such as ambient light, availability of nutrients, and grazer pressure. 

Ambient light is forced using a repeating 1 year time series, while nutrients and grazing pressure 

is dynamic within Atlantis. 

Chlorophyll values were first averaged over the depth strata (0–50 m, 51–100 m, etc.) 

from which they were collected. They were then converted to standing stock phytoplankton 

estimates (in units of mg N m-3). We further assumed 75% of the phytoplankton biomass was 

diatoms and 25% was picoplankton, as is thought to be characteristic of productive upwelling 

regions (e.g., Bruland et al. 2001 and references therein). Because coverage with empirical 

values only accounted for roughly 25% of all possible polygons and layers in our model area, we 

were forced to make considerable coarse-scale interpolations across regions and depths. 

70
Generally, if a volume of water did not have a chlorophyll estimate, averages were taken of the 

nearest neighbor estimates to the north and south at the same depth stratum. 

Zooplankton (ZL, ZM, ZS, ZG, PWN) 

Zooplankton groups include large carnivorous zooplankton (euphausiids, ZL), 

mesozooplankton (copepods, ZM), microzooplankton (ZS), gelatinous zooplankton (ZG), and 

crangon and mysid shrimp(PWN) (Table 4). For all zooplankton groups in our model, relative 

abundance varies with distance from shore, following surveys 5–165 km off Brookings, Oregon 

(Laurs 1967). Estimates of absolute abundance of large carnivorous zooplankton (euphausiids) 

and shrimp, and how these varied with depth, are derived from sampling along the Newport line 

off Oregon from 1960 to 1968 (Pearcy 1970, Pearcy 1972). We averaged day and night values 

for use in the model. 

Estimates of absolute abundance of gelatinous zooplankton and mesozooplankton 

between 0 and 200 m depth are also from Pearcy (1972). As a starting point, we assume that 

gelatinous zooplankton and mesozooplankton were not present beneath this depth. Densities of 

mesozooplankton along the Newport transect range from 1.92 to 18 mg C/m3 (Peterson and 

Miller 1977, Peterson et al. 2002, Peterson and Keister 2003). We chose 1.92 mg C/m3

, or 0.33 

mg N/m3 as our starting estimate for mesozooplankton, and 0.02 mg N/m3 as our starting 

estimate for gelatinous zooplankton. 

Initial abundance estimates of zooplankton do not vary latitudinally, since the vast 

majority of zooplankton data available were from Oregon, the central portion of our model area.

For all zooplankton groups, mg C/m3 was converted to mg N/m3 following Table 11 in 

Parsons et al. (1984). We could not find estimates of microzooplankton abundance off the U.S. 

West Coast, so we used ZS values from Fulton (2001). 

Cephalopods (CEP, BMS) 

The cephalopods in our system are split into two functional groups: Octopi (BMS) and all 

other cephalopod species (CEP). Despite the lack of data on both of these subgroups, we felt it 

necessary to split the cephalopod family by general life history parameters in order to more 

appropriately represent their respective behaviors and roles within the ecosystem. 

The “all other cephalopod” functional group is generally represented by market squid 

(Loligo opalescens), the most common and heavily harvested squid off the Pacific Coast. We 

used an estimate of 1.954 mt/km2

 from Field (2004). We assumed that 75% of the biomass of 

this semelparous species was in the juvenile group, and 25% in the adult group, equal to 0.0264 

mg N/m3

 and 0.0088 mg N/m3 respectively. Field’s estimates are from top-down balancing of 

his 1990s Ecopath model and include octopus, which we model as a separate group. 

Benthic Invertebrates (BC, BML, BFF, BMD, BG) 

Benthic infauna and epifauna in the model are grouped into carnivorous infauna such as 

polychaetes (BC), megazoobenthos such as crustaceans (BML), other benthic filter feeders such 

as mollusks (BFF), deep macro-zoobenthos such as echinoderms but excluding sea urchins 

71
(BMD), and benthic grazers (BG, primarily sea urchins). Due to limited data, initial biomass 

density estimates in the model vary with depth but not with latitude. 

Starting biomass assigned to these model groups between depths of 0–200 m are from the 

work of Lie (1969). Lie (1969) sampled off the coast of Washington in the summer of 1967 in 

three regions: 13–65 m depth, 104–329 m, and 50–155 m. 

Biomass estimates for these benthic groups between 200 and 2,400 m are from Carey 

(1972). Carey sampled benthic infauna and macroepifauna from 1962 to 1965 along the 

Newport transect line, in depths from 30 to 200 m. We made the crude assumption that 

abundance beyond 200 m was similar to Carey’s estimates at 200 m.

Both Lie (1969) and Carey (1972) report echinoderm biomass without differentiating 

between sea urchins and other types of echinoderms. To parse their estimates of echinoderm 

abundance into these two groups, we used estimates of relative abundance from Alton’s (1972) 

sampling in northern Oregon near the mouth of the Columbia River. Alton found that urchin 

abundance, as a proportion of total echinoderm abundance, increased from 10% at 100–150 m 

depth to 90% at 200–250 m, and then declined to zero as depth increased to 750–850 m. 

Our megazoobenthos group primarily consists of Dungeness crabs (Cancer magister) and 

tanner crabs (Chionoecetes bairdi). Abundance of these two groups follows Field (2004). His 

estimate of 41,000 metric tons (mt) of Dungeness crab is based on landings, assuming that 75% 

of adult males are caught, a 50:50 sex ratio, and an equal biomass of juveniles and adults. 

Adding Field’s top-down Ecopath estimate of 0.79 mt/km2 of tanner crabs yields a total of 0.12 

mg DW/m2

. 

Clearance (ingestion) rates and maximum growth rates are from Field (2004), assuming 

that maximum clearance rate is 1.2*Q/B (average consumption per biomass) in Ecopath. Table 4 

lists the final clearance and growth parameters after calibration. 

Biomass estimates for octopus (BMS), shallow benthic filter feeders (BFS), and 

anemones (BFD) are not currently available, and we used reference values from the S.E. 

Australia Atlantis model as a starting point for these groups. 

Small Planktivorous Fish (FPS) 

The small planktivorous fish group consists primarily of sardines (Sardinops sagax), 

anchovy (Engraulis mordax), saury (Cololabis saira), and herring (Clupea harengus). We used 

an estimate of 1,000,090 mt of sardines for the entire U.S. West Coast, from Conser et al. (2003). 

Richardson (1981) estimated Oregon anchovy abundance ranged from 100,000 mt to 

1 million mt in 1975–1976, and Stauffer and Charter (1982) estimated California anchovy 

populations to be 1.5 million mt in 1979. We assumed an abundance of 2.5 million mt of 

anchovy for our model region. Smith et al. (1970) estimated that saury abundance was 0.37 

mt/km2 off California, and 0.27mt/km2 off Oregon. We used 0.31 mt/km2 as an approximation 

for the entire coast. The California Fish and Game Commission (2004) estimated the biomass of 

the San Francisco Bay spawning stock of herring to be 45,000 mt, which we used as our estimate 

of herring abundance since we lacked additional information on herring. Shad (Alosa 

72
sapidissima), eulachon (Thaleichthys pacificus), some herring stocks, and a few other important 

forage fish are not included in these estimates, and we therefore chose estimates of biomass on 

the high end of the ranges reported for sardines and anchovies. 

Our total estimate of 3.84 million mt of small planktivores is an average of 41 mt/km2, 

higher than Field’s estimate of 27 mt/km2

 (26 tons/km2 of “forage fish” and 1 ton of 

sardines/km2). Life history parameters were taken from Gunderson (1997), Butler et al. (1993), 

Hargreaves et al. (1994), Love (1996), and FishBase (Froese and Pauly 2005). Diet was derived 

from Love (1996). Beverton Holt parameters are based upon the assumption that stock and 

recruitment are currently at unfished levels, and steepness is 0.8 (Table 3). A northern stock of 

anchovies, which comprise roughly 60% of this functional group, gather offshore of the 

Columbia River in the summer to spawn, and this is reflected in the seasonal migration 

parameters. 

Large Planktivorous Fish (FPL) 

This group consists primarily of jack mackerel (Trachurus symmetricus) and also Pacific 

mackerel (Scomber japonicus). We used a biomass estimate of 81,000 mt of Pacific mackerel 

from a 2003 stock assessment (Hill and Crone 2004). MacCall and Stauffer (1983) estimated 

640,000 to 1.3 million mt of jack mackerel in the Cal COFI sampling area; we used 900,000 mt 

as a starting point for the biomass of this species, yielding a sum of 171,000 mt for both species. 

Life history and diet parameters are based on jack mackerel from MacCall and Stauffer (1983), 

Love (1996), and FishBase (Froese and Pauly 2005). Beverton Holt parameters are based upon 

our assumption that stock and recruitment are currently at unfished levels, and steepness is 0.8 

(Table 3). While this group does not exhibit extensive migrations, older adults do shift 

northwards in the summer, and this is reflected in our seasonal distribution parameters. 

Shallow Piscivorous Fish (FDE) 

The shallow piscivorous fish group is dominated by croaker (Genyonemus lineatus) and 

sculpin (Cottidae). Life history parameters are weighted by species’ relative abundance in the 

NMFS trawl survey and are from FishBase (Froese and Pauly 2005). Our biomass estimate of 

60,181 mt was derived from Field’s benthic fish estimate (259,420 mt) minus the biomass of our 

deep miscellaneous fish group (179,207 mt) and estimated ratfish (Hydrolagus colliei) 

population (20,032 mt). This group does not exhibit proportional seasonal migrations in the 

model since it only lives within the nearshore boxes (0–50 m isobath). Beverton Holt parameters 

assume a steepness of 0.5 (Table 3), and that stock and recruitment are at historical levels. 

Deep Vertical Migrators (FBP) 

This group includes lanternfish and lampfish (Myctophidae), Pacific viperfish 

(Chauliodus macouni), and other mesopelagic species that exhibit diel vertical migrations from 

the deep slope to the midwater and near surface. We estimated biomass from several relevant 

studies (Pearcy and Laurs 1966, Beamish et al. 1999, Savinykh 1999, Field 2004). 

Life history parameters, including von Bertalanffy growth parameters, length-weight 

conversions, natural mortality, age at maturity, maximum age, and diet were taken from 

73
FishBase (Froese and Pauly 2005). We assumed that the 1998–2003 NMFS trawl surveys 

accurately sampled the community composition, and weighted the functional group’s life history 

parameters accordingly. The resulting functional-group parameters are therefore based mainly 

on those of myctophids, longfin dragonfish (Tactostoma macropus), and Pacific viperfish. 

Beverton Holt parameters assume a steepness of 0.5 (Table 3), and that current levels of stock 

and recruitment are equal to historical levels. This functional group is not known to exhibit 

seasonal migrations.

Deep Demersal Fish (FDD) 

This group includes hagfish, eelpouts, grenadiers, and other similar fish, but is dominated 

by Pacific grenadier (Coryphaenoides acrolepis) and giant grenadier (Albatrossia pectoralis). 

Biomass estimates are from the 1998–2003 NMFS trawl survey data. However, camera sled 

surveys suggest the trawl surveys severely undersample hagfish, so the hagfish component of the 

deep demersal group was adjusted based on the observed ratio of hagfish to eelpouts reported by 

Wakefield (Wakefield 1991). This functional group’s life history parameters are weighted based 

on relative biomass of the species within the group. Life history parameters including diet, 

maximum age and length, movement, and habitat preferences were derived from Merrett and 

Haedrich (1997). Other parameters, including von Bertalanffy growth parameters, length-weight 

conversions and natural mortality, were taken from FishBase (Froese and Pauly 2005). Beverton 

Holt parameters assume a steepness of 0.5 (Table 3), and that current levels of stock and 

recruitment are equal to historical levels. Spatial distribution of this group is based on the NMFS 

trawl survey data and does not vary seasonally. 

Rockfish (FDB, FDC, FDO, SHR, FDS) 

Rockfish populations were divided into five groups by size and depth location: small 

shallow, large shallow, small deep, large deep, and midwater. Most of these species are not 

assessed, and therefore assessments can not be used to estimate biomass per functional group. 

Our estimates of rockfish biomass generally rely on 1998–2003 NMFS triennial trawl survey 

data corrected for differences in catchability. Where assessments were available, we compare 

their species level predictions to our estimates of biomass for the functional group. To date, we 

have incorporated assessment data from 2003; in the future we will incorporate additional 

information from the 2005 round of groundfish assessments. 

The small deep rockfish group includes longspine thornyheads (Sebastolobus altivelis), 

sharpchin (Sebastes zacentrus), splitnose (S. diploproa), and aurora rockfish (S. aurora). 

Biomass estimates of small deep rockfish were estimated from trawl survey data, assuming 

catchability (Q) of 0.65. This is the average of catchabilities estimated by Rogers et al. (1996) 

for splitnose and sharpchin rockfish. Life history parameters and diet are from Love et al. 

(2002), FishBase (Froese and Pauly 2005), and Cailliet et al. (2000) and were weighted by the 

relative biomass of each species in the group. Our biomass estimate of 338,000 mt is higher than 

the approximate 255,000 mt predicted by extrapolating Field’s (2004) biomasses to our model 

region. This comparison assumes that our deep small rockfish group would incorporate 20% of 

Field’s juvenile rockfish group, 50% of his juvenile thornyhead group, 100% of his longspine 

thornyhead group, and 50% of his slope rockfish group. No assessments are available for deep 

74
small rockfish. Beverton Holt parameters assume a steepness of 0.5 (Table 3), and that current 

levels of stock and recruitment are equal to half the unfished level.

The large deep rockfish group includes shortspine thornyhead (Sebastolobus alascanus) 

and darkblotched rockfish (Sebastes crameri). Biomass of large deep rockfish was estimated 

from NMFS 1998–2003 trawl survey data, assuming catchability (Q) of 0.50. This is a general 

estimate of catchability suggested by Rogers et al. (1996). Our biomass estimate is therefore 

124,000 mt. In comparison, extrapolating Field’s estimate of 1.678 mt/km2 to our model area 

gives 159,000 mt. This comparison assumes that our deep large rockfish group includes 20% of 

Field’s juvenile rockfish, 50% of juvenile thornyhead, 100% of shortspine thornyhead, and 50% 

of slope rockfish. Of the species in this functional group, only shortspine thornyhead and 

darkblotched rockfish have been assessed; with 30,000–62,000 mt of shortspine thornyhead 

(Piner and Methot 2001), and 7,300 mt of age 1+ darkblotched (Piner and Methot 2001, Rogers 

2003). These estimates are low relative to the 124,000 mt, considering the fact that these two 

species account for 95% of the biomass of deep large rockfish caught by the 1998–2003 NMFS 

trawl survey. 

Life history parameters for this group were weighted by the relative biomass of each 

species in the group, and come from Love et al. (2002), FishBase (Froese and Pauly 2005), 

Cailliet et al (2000), and Wilkins et al. (1998). Beverton Holt parameters are based on scaling up 

from the unfished stock and recruitment estimates for shortspine thornyhead, which make up 

72% of this group’s biomass in the 1998–2003 NMFS trawl survey data. We assume a steepness 

of 0.8 (Table 3), intermediate between the assessment values of 0.5 for darkblotched rockfish 

(Piner and Methot 2001), and no density dependence assumed in the shortspine thornyhead 

assessment (Rogers 2003). 

We estimated midwater rockfish biomass to be 408,000 mt, using the NMFS trawl survey 

data and assuming a catchability of 0.18 (Millar and Methot 2002). This is higher than the 

325,000 mt estimated by summing the biomasses of canary (S. pinniger), bocaccio (S. 

paucispinis), yellowtail (S. flavidus), and Pacific ocean perch (S. alutus) in Field (2004) and 

extrapolating to our model area. Assessments are available for bocaccio, 2,914 mt (MacCall 

2003), canary rockfish, 6,500 mt (Methot and Piner 2001), widow rockfish (S. entomelas),

62,000 mt (Williams et al. 2000), yellowtail rockfish, 63,388 mt (Lai et al. 2003), and Pacific 

ocean perch, 23,073 mt (Hamel et al. 2003). These assessed species account for 59% of 

midwater rockfish biomass in the 1998–2003 NMFS trawl survey. 

The functional group’s life history parameters are based on the parameters of the assessed 

stocks, and are weighted by their relative abundance. Life history parameters are from Pacific 

Fishery Management Council (PFMC) Groundfish Fisheries Assessment (1999), Hamel et al. 

(2003), MacCall (2003), Wilkins et al. (1998), and Methot and Piner (2001). Beverton Holt 

parameters are based on scaling up from the unfished stock and recruitment of Pacific ocean 

perch (16% of this functional group’s biomass in the NMFS trawl survey data), and a steepness 

of 0.5 (Table 3). This is intermediate between bocaccio assessments (MacCall 2003) which 

assume no stock-recruit relationship, canary rockfish steepness of 0.289 (Methot and Piner 

2001), and Pacific ocean perch steepness of 0.32 (Hamel et al. 2003). 

75
Biomass of small nearshore rockfish such as stripetail (S. saxicola), shortbelly (S. 

jordani), and greenstriped (S. elongatus) was estimated to be 48,000 mt based on the 1998–2003 

NMFS trawl survey, assuming a catchability of 0.5 (Rogers et al. 1996). Life history parameters 

are from Love et al. (2002), PFMC Groundfish Fisheries Assessment (1999), FishBase (Froese 

and Pauly 2005) and Cailliet et al. (2000), and are weighted by biomass in the trawl survey. 

Beverton Holt parameters assume a steepness of 0.5 (Table 3) and that current stock and biomass 

are at 50% of historical levels. 

The large nearshore rockfish group includes redstriped (S. proriger), yelloweye (S. 

ruberrimus), and black rockfish (S. melanops), among others. Biomass was estimated to be 

62,000 mt from the 1998–2003 NMFS trawl survey, assuming catchability of 0.2 (based on 

catchability for yelloweye, (Rogers et al. 1996). Ralston and Dick (2003) estimated 11,200 mt of 

age 2+ black rockfish, and Wallace et al. (2002) estimated there to be 255 mt of yelloweye 

rockfish. Both functional groups of shallow rockfish total 108,000 mt, compared to 100,000 mt 

if we extrapolate black rockfish plus shelf rockfish from Field (2004) to our model area. 

Life history parameters derive from Cailliet et al (2000), the black rockfish assessment 

(Ralston and Dick 2003), the cowcod (S. levis) assessment (Butler et al. 2003), PFMC 

Groundfish Fisheries Assessment (1999), Barker (1979), Gowan (1983), Rosenthal et al. (1982), 

and Workman et al. (1998). Beverton Holt parameters are based on scaling up the unfished stock 

and biomass estimated for yelloweye rockfish, and a steepness of 0.5 (Table 3). This is 

intermediate between a steepness of 0.429 for yelloweye rockfish (Rogers et al. 1996) and 0.65 

for black rockfish (Ralston and Dick 2003). 

Rockfish do not have forced seasonal migrations in the model. Their spatial distribution 

is based on the 1998–2003 NMFS trawl survey. 

Flatfish (FDF) 

Biomasses of flatfish such as English sole (Parophrys vetulus), rex sole (Glyptocephalus 

zachirus), and Dover sole (Microstomus pacificus) were estimated from 1998 to 2003 NMFS 

trawl survey data, assuming catchability (Q) of 0.50. This is intermediate between a catchability 

of 0.79 found for Dover sole (Sampson and Wood 2001) and 0.35 for English sole (Field 2004). 

The resulting biomass of 745,000 mt is close to Field’s estimate of 721,000 mt, and the 

differences are likely caused by using slightly different years of NMFS trawl survey data. 

Sampson and Wood (2001) estimated age 5+ Dover sole biomass to be 115,000 mt. Life history 

parameters and diet are from Cailliet et al. (2000), Love (1996), and FishBase (Froese and Pauly 

2005). The values were weighted by the relative biomass of each species in the NMFS trawl 

survey. Beverton Holt parameters are based on scaling up unfished stock and recruitment of 

Dover sole, which are 72% of the functional group’s biomass, based on NMFS trawl data. We 

assume a steepness of 0.9 because Sampson and Wood (2001) assume no density dependence. 

The functional group does not have forced seasonal migrations in the model. 

Hake (FMM) 

The Pacific hake (Merluccius productus) group also includes tomcod (Microgadus 

proximus), Pacific cod (Gadus macrocephalus), and walleye pollock (Theragra chalcogramma), 

76
but the functional group is parameterized as Pacific hake because of their numerical dominance 

and importance to the fishery. Biomass estimates of 2.7 million mt are from the Helser et al. 

(2003) stock assessment. 

Life history parameters are from Helser et al. (2003) and Bailey et al. (1982). Beverton 

Holt parameters are based on estimates of unfished stock and recruitment from the assessment. 

We used a steepness of 0.9 because Helser et al. (2003) assume no density dependence (Table 3). 

Seasonal migration patterns were also derived from Bailey et al. (1982). Hake migrations are 

prescribed so that they are south of the system during the winter, come in close to shore in the 

spring, spread out over the shelf/slope break during the summer, and move away towards the 

outer shelf in the fall. 

Sablefish (FMN) 

Sablefish (Anoplopoma fimbria) biomass estimates of 118,000 mt are from Schirripa 

(2002). Length-weight parameters are from Sigler et al. (2003), lifespan is from Love (1996), 

natural mortality is from Hilborn et al. (2001), and von Bertalanffy parameters are from FishBase 

(Froese and Pauly 2005). Sablefish do not migrate seasonally (Love 1996). As a starting point, 

we distributed them in all boxes between 150 and 1,200 m depth. Beverton Holt parameters are 

based on estimates of unfished stock and recruitment from the assessment. We used a steepness 

of 0.9 because Schirripa (2002) assumes no density dependence (Table 3). 

Large Piscivorous Flatfish (FVD) 

This group includes California halibut (Paralichthys californicus), Pacific halibut 

(Hippoglossus stenolepis), arrowtooth flounder (Atheresthes stomias), and petrale sole (Eopsetta 

jordani). From Field (2004) we estimated that there were 1.24 mt/km2 of arrowtooth, petrale, 

and California halibut. This was estimated by adding 50% of the juvenile flatfish abundance to 

the arrowtooth, halibut and petrale sole biomass estimates. We added an additional 3,600 mt of 

Pacific halibut following the assessment for IPHC area 2A (Clark and Hare 2004). Life history 

parameters and diets are from Cailliet et al (2000), Love (1996), and FishBase (Froese and Pauly 

2005). Stock recruit parameters are not available for arrowtooth, the dominant component of this 

group. We therefore assume a steepness of 0.5 (Table 3), and current stock and recruitment at 

historical levels. We do not force seasonal migrations for this species, but their spatial 

distribution was taken from 1998–2003 NMFS trawl survey data.

Large Demersal Predators (FVS) 

Large demersal predators are parameterized primarily as lingcod (Ophiodon elongatus) 

and cabezon (Scorpaenichthys marmoratus). This group’s biomass is estimated as two times the 

female lingcod biomass (11,000 mt) reported in Jagielo et al. (2004), plus 830 mt of cabezon 

(Cope et al. 2003). Life history parameters and diet for lingcod are used for this group, derived 

from Love (1996) and Jagielo et al. (2004). We base Beverton Holt parameters on scaling up 

estimates of historical stock and recruitment for lingcod to the entire functional group. We 

assume a steepness of 0.9 because the assessment assumes no density dependence (Table 3). 

Lingcod and cabezon spatial distributions were derived from the 1998–2003 NMFS trawl survey 

data.

77
Salmon (FVB) 

Due to the varied and complex life histories of the salmonid species in the California 

Current system, we were unable to fully represent their unique dynamics. As a compromise, we 

focused our attention on two of the most prevalent species, Chinook salmon (Oncorhynchus 

tshawytscha) and coho salmon (O. kisutch). To estimate the biomass of our salmon group, we 

replicated Field’s (2004) methodology by taking the total coastal commercial and recreational 

trolling catch of Chinook and coho in 2004 (Weitkamp et al. 1995, Myers et al. 1998, PFMC 

2005) of 1,148,800 individual salmon. This figure, multiplied by an average weight of a mature 

Chinook (0.0081 mt, Groot and Margolis 1991), gave us a total in metric tons of fish caught on 

coast. We did not differentiate between wild and hatchery fish. Following Field (2004), we 

assume this number represented 50% of the salmon in the system (i.e., 50% escapement) and 

further that 50% of the total population that swims through our system may be present in the 

system. This brought us to a total biomass of 37,221 mt. This figure, averaged over the area of 

our system, equals 0.4 mt/km2. This average closely matches Field’s (2004) estimate of 0.418 

mt/km2

. We patterned salmon migration off fall run Chinook salmon, due to their prevalence in 

the system. Beverton Holt stock recruit parameters assume a steepness of 0.5 and that the stock 

is at 25% of historical levels (Table 3). Migration follows Myers et al. (1998) and Healey 

(1983), and the remainder of the salmon life history parameters were derived from Groot and 

Margolis (1991). 

Albacore (FVT) 

Albacore tuna (Thunnus alalunga) biomass estimates are from Field (2004), who 

estimated 0.014 tons/km2 as an annual average, assuming albacore only spent summer months 

(one-fourth of the year) within the California Current. We multiplied his estimate by four, since 

we can explicitly represent the migration of albacore into our region during summer. Life 

history parameters are from FishBase (Froese and Pauly 2005), except for natural mortality, 

which was taken from PFMC (2003). Diets are from Love (1996). Beverton Holt parameters 

assume that stock size and recruitment are at half of unfished levels, and a steepness of 0.8 

(Table 3).

Skates and Rays (SSK) 

Skate and ray biomass is estimated from the 1998–2003 NMFS trawl survey. In the 

absence of stock assessments for skates and rays in our system, we assume a catchability of 1. 

The life history parameters are weighted by relative biomass in the trawl, which is dominated by 

Bering skate (Bathyraja interrupta), roughtail skate (B. trachura), and longnose skate (Raja 

rhina). Life history parameters are from Zeiner and Wolf (1993), Cailliet et al. (2000), Love 

(1996), and FishBase (Froese and Pauly 2005). Our estimate of 54,000 mt is higher than Field’s 

prediction of 39,000 mt (0.04 mt/km2

 times 93,559 km2 in our model area). We based Beverton 

Holt parameters on an assumption that stock size and recruitment are at two-thirds unfished 

levels, and that steepness is 0.5 (Table 3).

78
Small Demersal Sharks (SHB) 

The small demersal shark group is primarily spiny dogfish (Squalus acanthias) and 

spotted ratfish (Hydrolagus colliei). Small demersal shark biomass was taken directly from the 

1998–2003 NMFS trawl survey, and the assumed catchability was 1.0. Life history parameters 

were weighted by species biomass, which is dominated by dogfish. Our estimate of 118,000 mt 

is slightly higher than the 94,000 mt (1 ton/km2 times 93,559 km2) estimated by Field (2004); 

however, Field (2004) also noted during some years in the 1990s, slope surveys suggested 

abundances of > 2 tons/km2. Life history parameters are from Love (1996), Cailliet et al (2000), 

and FishBase (Froese and Pauly 2005). Not enough is known about dogfish migration patterns 

to effectively represent them in this model (Love 1996). Beverton Holt parameters assume that 

stock size and recruitment are at unfished levels, and a steepness of 0.5 (Table 3). 

Demersal Sharks (SHD) 

Biomass estimates of demersal sharks—sixgill (Hexanchus griseus), sevengill 

(Notorynchus cepedianus), and sleeper sharks (Somniosus pacificus)—are not available from the 

literature. We assumed that one-fifth of Field’s (2004) mass-balance estimate of shark biomass 

was demersal shark. Life history parameters are from FishBase (Froese and Pauly 2005) and are 

those of sevengill sharks, since life history parameters were not available for the other species. 

Beverton Holt parameters assume that stock size and recruitment are at unfished levels, and a 

steepness of 0.5 (Table 3).

Pelagic Sharks (SHP) 

Biomass estimates of pelagic sharks (primarily soupfin, Galeorhinus galeus, and 

thresher, Alopias vulpinus) are not available. We assumed that four-fifths of Field’s (2004) 

mass-balance estimate of shark biomass was pelagic shark. Life history parameters are those of 

thresher and soupfin sharks (thresher shark length parameters were not used because of the 

extremely long tail), taken from PFMC (2003), Love (1996), and FishBase (Froese and Pauly 

2005). Beverton Holt parameters assume stock size and recruitment are at one-fourth unfished 

levels, and a steepness of 0.5 (Table 3). The model does not assume consistent seasonal 

migrations in our region.

Migrating Birds (FVO) 

The primary component of the migratory bird group is the sooty shearwater (Puffinus 

griseus), which makes up roughly 90% of the biomass of seabirds that make large (>1,000 km) 

aerial migrations into and out of the California Current ecosystem. Lesser components are the 

black-footed albatross (Phoebastria nigripes), Laysan albatross (P. immutabilis), northern fulmar 

(Fulmaris glacialis), and black-legged kittiwake (Rissa tridactyla). Population estimates for 

these species come from seasonal at sea and nesting colony counts in the 1970s and 1980s, as 

compiled by Parrish and Logerwell (2001). Population sizes were then converted to biomass 

estimates using average weight data compiled by Schreiber and Burger (2002), and a P/B ratio of 

0.1 was derived from Field (2004). All general life history parameters (age at maturity, 

maximum age, clutch size, natural mortality rate; see Table 3) were taken from Schreiber and 

Burger (2002), and were weighted according to the abundance of the constituent species. 

79
Shearwaters feed in a different manner than many other seabirds. They surface feed and 

can perform pursuit dives averaging 39 m and sometimes approaching 70 m (Weimerskirch and 

Sagar 1996). Thus their diets are considerably more diverse than the surface feeding or diving 

bird trophospecies. Beverton Holt parameters assume a steepness of 0.34, and that the 

populations have been reduced to 10% of their historical level (Veit et al. 1996). 

The migratory pattern for shearwaters is to enter the model region on approximately 

February 15 of each year, generally coming in from the south or west into the offshore regions of 

the California Current. They typically remain around shelf break regions of the system and 

forage until November 1, when they will return to their southern hemisphere breeding and 

nesting habitats (Briggs and Chu 1986). Importantly, shearwaters do not necessarily come to the 

northeast Pacific during their northerly migration; in recent years, the bulk of the shearwater 

biomass has migrated to the northwest Pacific, possibly in relation to oceanic productivity 

declines in the California Current (Spear and Ainley 1999). Thus the population estimates of 

Parrish and Logerwell (2001) might best be viewed as maximum values, and sizable decreases 

may occur that owe to changes in migration behavior (e.g., northerly migrations to the western 

Pacific rather than to the California Current) rather than massive population die-offs (Spear and 

Ainley 1999). 

Surface-Feeding Birds (SB) 

The surface feeding bird group is comprised of gulls (Larus spp.), phalaropes 

(Phalaropus spp.), storm petrels (particularly Leach’s storm petrel [Oceanodroma leucorhoa] 

and the fork-tailed storm petrel [O. furcata]), brown pelicans (Pelecanus occidentalis), and 

Caspian terns (Sterna caspia). More than 80% of this group by biomass are gulls. Biomass 

estimates come from seasonal at sea and nesting colony counts in the 1970s and 1980s, compiled 

by Parrish and Logerwell (2001), and average weight data, compiled by Schreiber and Burger 

(2002). All general life history parameters (age at maturity, maximum age, clutch size, natural 

mortality rate) were taken from Schreiber and Burger (2002), and were weighted according to 

the abundance of the constituent species (Table 3). Beverton Holt parameters assume a 

steepness of 0.34 and that the populations are currently at historical levels. Most of this 

trophospecies feeds in coastal and shelf waters, although some gulls and most of the storm 

petrels make use of slope waters. With the exception of pelicans, which move south in cooler 

months, this group is considered nonmigratory; therefore, the functional group as a whole does 

not migrate in the model. 

Diving Birds (SP) 

Diving birds are a diverse group that includes common murres (Uria aalge), rhinoceros 

auklets (Cerorhinca monocerata), Cassin’s auklets (Ptychoramphus aleuticus), tufted puffins 

(Fratercula cirrhata), pigeon guillemots (Cepphus columba), Brandt’s cormorants 

(Phalacrocorax penicillatus), double-crested cormorants (P. auritus), ancient murrelets 

(Synthliboramphus antiquum), and marbled murrelets (Brachyramphus marmoratus). Common 

murres make up about 60% of this group by biomass, with auklets (≈20%) and cormorants (16%) 

contributing sizable portions as well. Biomass estimates come from seasonal at sea and nesting 

colony counts in the 1970s and 1980s, compiled by Parrish and Logerwell (2001) and by Perry 

and McKinnell (2005), and average weight data, compiled by Schreiber and Burger (2002). All 

80
general life history parameters (age at maturity, maximum age, clutch size, natural mortality rate) 

were taken from Schreiber and Burger (2002), and were weighted according to the abundance of 

the constituent species (Table 3). Beverton Holt parameters assume a steepness of 0.34 and that 

the populations are currently at historical levels. 

This trophospecies is typically found in coastal waters and over the shelf. We assume 

they are essentially nonmigratory, although this is unclear because of difficulties in seasonal 

censuses of these birds, many of which dig nesting burrows in breeding seasons and then 

disperse at sea for other parts of the year (Parrish and Logerwell 2001). The difficulties in 

enumerating these species are highlighted by differences in species counts by Parrish and 

Logerwell (2001) and Perry and McKinnell (2005); we have generally followed the counts of 

Parrish and Logerwell because they are more thoroughly documented, but have included PICES 

counts for species not counted by Parrish and Logerwell (pigeon guillemots, Cassin’s auklets, 

and murrelets).

Pinnipeds (PIN) 

The pinniped group includes northern elephant seals (Mirounga angustirostris), harbor 

seals (Phoca vitulina), California sea lions (Zalophus californianus), Steller sea lions 

(Eumetopias jubatus), and northern fur seals (Callorhinus ursinus). Population sizes are based 

on counts from recent NOAA stock assessments (Angliss and Lodge 2004, Carretta and Forney 

2004) and supporting studies (Jeffries et al. 2003, Lowry and Carretta 2003, Ream et al. 2005). 

Population biomasses were assumed using average individual body masses (Trites and Pauly 

1998) and were also weighted by P/B ratios from Field (2004). 

Body masses were weighted by sex because adult pinnipeds are sexually dimorphic 

(males larger than females, Trites and Pauly 1998) and sex ratios are often heavily skewed 

toward females (Perrin and Thewissen 2002). Pinniped diets and many life history parameters 

were drawn mainly from Perrin and Thewissen (2002), with additional information on longevity, 

maximum length and length-weight relationships from Trites and Pauly (1998), and growth rates 

of Steller sea lions from Winship et al. (2001) (Table 3). Beverton Holt parameters assume the 

populations are at 10% of historical levels (Springer et al. 2003), and a steepness of 0.34, which 

implies that at one-third historical levels the stock could produce one-half the historical 

maximum number of pups. 

A major component of the pinniped trophospecies is the northern elephant seal, owing to 

its relatively large estimated population size (>100,000) and very large individual biomass 

(male/female weighted average = 344 kg). The seasonal migration of the functional group is 

therefore based primarily on elephant seal movements. Male northern elephant seals undergo 

two migrations each year between the model domain and the North Pacific, whereas females 

migrate no further north than roughly lat 45°N (Carretta et al. 2005). The northerly migrations 

are for feeding. Elephant seals pup on offshore islands in the model domain during the winter 

months, then move north to feed. They return to the model domain to molt in the spring and 

summer and then return to the feeding grounds in the late summer and fall. 

Additionally, the vast majority of the northern fur seal biomass in the model area consists 

of females and immature males that emigrate from Alaska waters and overwinter over shelf 

81
waters of the NCCE from approximately February through mid-May; they then migrate north to 

Alaska waters for the summer months (Ream et al. 2005). The other major components of the 

pinniped biomass, California sea lions and harbor seals, do not migrate seasonally. 

Transient Orcas (REP) 

Transient orcas (Orcinus orca) are those killer whales that feed primarily on marine 

mammals, occasionally supplementing their diets with seabirds, fish, and invertebrates. The 

population estimate of approximately 120 animals is based on counts from recent NOAA marine 

mammal stock assessments (Black et al. 1997, Angliss and Lodge 2004, Carretta et al. 2005). 

Population biomass was assumed using growth rates (Noren unpubl. data) and length-weight 

relationships from Trites and Pauly (1998). Other life history data included natural mortality 

rates from Heppell et al. (1999) and longevity and maximum size data from Trites and Pauly 

(1998). Transient orca diet information came from Ford et al. (1998), Perrin and Thewissen 

(2002), and unpublished anecdotal reports. Beverton Holt parameters assume the population is 

at one-third of historical levels (Springer et al. 2003), and a steepness of 0.34. We devoted a full 

functional group to this small population because they are of critical conservation concern.

Baleen Whales (WHB) 

Baleen whales include gray whales (Eschrichtius robustus), humpback whales 

(Megaptera novaeangliae), blue whales (Balaenoptera musculus), fin whales (B. physalus), sei 

whales (B. borealis), and minke whales (B. acutorostrata). Population sizes are based on counts 

from recent NOAA marine mammal stock assessments (Angliss and Lodge 2004, Carretta et al. 

2005) and supporting literature (Hobbs and Rush 1999, Barlow and Taylor 2001, Barlow 2003). 

Population biomasses were assumed using average individual body masses (Trites and Pauly 

1998). Natural mortality rate estimates were available for humpback whales (Mizroch et al. 

2004) and sei whales (Perrin and Thewissen 2002); von Bertalanffy k estimates were available 

for gray whales (Rice and Wolman 1971), fin whales (Sampson 1990), and minke whales (Olsen 

and Sunde 2002); and longevity information and length-weight relationships came from Trites 

and Pauly (1998). Baleen whale diet information was derived mainly from Perrin and Thewissen 

(2002), with additional data in Dunham and Duffus (2002) and Tershy (1992) (Table 3). 

Beverton Holt parameters assume that the populations are at one-seventh of historical levels 

(Springer et al. 2003), and a steepness of 0.34. 

Because of their relatively large population (more than 26,000, Hobbs and Rush 1999, 

Angliss and Lodge 2004), gray whales represent more than 61% of the baleen whale biomass 

pool. This is important because gray whales have diets distinct from the rest of this functional 

group. Whereas other baleen whales filter feed on pelagic invertebrates and small fishes, gray 

whales prefer to feed on benthic invertebrates, which they scoop from the sediments (Dunham 

and Duffus 2002). Gray whales also undergo very different migrations than the other baleen 

whales. They calve south in Mexican coastal waters (south of the model domain) in winter and 

then migrate up the coast in the late winter through spring, ultimately bound for feeding grounds 

in the Bering and Chukchi seas. In the fall, they migrate south again, through the model domain 

and back to their calving grounds (Carretta et al. 2005). 

82
The other baleen whales also exhibit seasonal migrations. Humpback whales winter off 

Central America before moving as far north as British Columbia in the summer and fall; blue and 

fin whales typically occur no further north than California and Oregon during the summer 

months and are out of the model domain in cooler months; and minke whales occur throughout 

the model domain at all times of the year (Angliss and Lodge 2004, Carretta et al. 2005). We 

based this functional group’s seasonal movement parameters on gray whales, since they account 

for the majority of the biomass. 

Toothed Whales (WHT) 

Toothed whales are comprised of larger-bodied toothed whales (except for transient 

orcas, which have distinct diets). The toothed whales include both the coastal resident and 

offshore populations of orcas (n ≈ 80 and 400, respectively), sperm whales (Physeter 

macrocephalus), pygmy sperm whales (Kogia breviceps), Cuvier’s beaked whale (Ziphius 

cavirostris), Baird’s beaked whale (Berardius bairdii), and mesoplodont beaked whales 

(Mesoplodon spp.). Population sizes are based on counts from recent NOAA marine mammal 

stock assessments (Carretta et al. 2005) and supporting literature (Barlow 1997, Black et al. 

1997, Barlow 2003). Population biomasses were assumed using average individual body masses 

(Trites and Pauly 1998) and were also weighted by P/B ratios because sperm whales are much 

larger than the other whales in this group. However, Field (2004) did not report a P/B value for 

sperm whales or larger beaked whales, so we assigned sperm whales the same P/B value Field 

assigned to orcas (0.02) and the remaining large toothed whales the same P/B value that Field 

assigned to dolphins and porpoises (0.07). 

Growth rate and mortality rate estimates for sperm whales came from Evans and Hindell 

(2004); growth rates for orcas came from Noren (unpubl. data); natural mortality rates for orcas 

were derived from Heppell et al. (1999); and length-weight relationships, longevity, and 

maximum size for many species came from Trites and Pauly (1998) (Table 3). Diets for large 

toothed whales were taken from Perrin and Thewissen (2002). Beverton Holt parameters assume 

the populations are at one-fifth of historical levels (Springer 2003), and a steepness of 0.34. 

Sperm whales are relatively large and abundant, and thus comprise the bulk of this 

functional group. This is important because sperm whales have a distinct diet from other whales 

in this group, utilizing large cephalopods to a greater extent (Perrin and Thewissen 2002). 

Sperm whales, along with the offshore orcas, are in deeper waters of the model region in all 

seasons (Carretta et al. 2005). Little is known about the distributions of the beaked whales and 

pygmy sperm whale, which comprise roughly 29% of this trophospecies. They are believed to 

occur in offshore areas in the summer and migrate out of the model domain in the remaining 

months (Carretta et al. 2005). 

Sea Otters (WDG) 

There are two sea otter (Enhydra lutris) population centers in the model region, one in central 

and northern California waters and one in Washington and British Columbia waters. The 

California population accounts for about 85% of the roughly 2,750 individuals in the U.S. 

portion of the study region, according to the last stock assessment conducted in 1995 (see 

Appendix 5 of Carretta et al. 2005), but more than 1,500 are believed to live off of Vancouver 

83
Island (Watson et al. 1997). Individual sea otter biomass for the model region was difficult to 

find in the literature, so we assumed the same length-to-weight relationship as observed in 

pinnipeds (Trites and Pauly 1998) and assigned a von Bertalanffy k similar to that of harbor 

porpoises, which grow to roughly the same length in the same number of years. An estimate of 

sea otter natural mortality (as an Ecopath P/B parameter) was given in Okey and Pauly (1999). 

Sea otter diets were summarized in Van Blaricom and Estes (1988) and Perrin and Thewissen 

(2002). Beverton Holt parameters assume the population is at 13% of historical levels (USFWS 

2003) and a steepness of 0.34. Sea otters are nonmigratory. 

84
85

Appendix B: Predator-Prey Parameters 

This appendix, consisting of tables B-1 through B-12, details the values for the predatorprey (variable a) parameters, as represented in Equation 10. This parameter specifies the 

availability of each prey to each predator. The proportion of each prey item in the diet is then 

treated as an emergent property that dynamically responds to changes in predator and prey 

abundance. In the current parameterization, these availability parameters are converted to a 

Hollings type II functional response, with gape limitations such that predators can only consume 

prey below a size threshold. Tables B-1 through B-6 contain the values for the predator-prey 

(variable a) parameter in the calibrated model, and Tables B-7 through B-12 show their relative 

change from the original uncalibrated values. 
Table B-1. Consumption parameters (variable a in Equation 10) in the calibrated model for predation on groups including 

(all other groups). A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM Fj  j FPL Large planktivores 0.05 0.1 0 0.3 0.1 0.1 0 0.01 0a  j FPL Large planktivores 0 0.1 0 0 0 0 0 0 0 j  a FPL Large planktivores 0.01 0.1 0 0.05 0.01 0.01 0 0.1 0a  a FPL Large planktivores 0 0.1 0 0 0 0 0 0 0 j  j FPS Small planktivores 0.1 0.00002 0 0.3 0.05 0.1 0 0.1 0a  j FPS Small planktivores 0 0 0 0 0 0 0 0 0 j  a FPS Small planktivores 0.00003 0.00003 0 0.1 0.00002 0.1 0 0.0001 0a  a FPS Small planktivores 0 0 0 0 0 0 0 0 0 j  j FVD Large flatfish 0 0 0 0.0002 0 0 0 0.002 0a  j FVD Large flatfish 0 0 0 0 0 0 0 0 0 j  a FVD Large flatfish 0.0001 0.0005 0 0.0002 0.0001 0 0 0.002 0a  a FVD Large flatfish 0.0005 0.0005 0 0 0 0 0 0 0j  j FVS Large demersal predators 0.01 0.01 0 0.05 0 0 0 0.1 0a  j FVS Large demersal predators 0 0.01 0 0 0 0 0 0 0 

j  a FVS Large demersal predators 0.0002 0.001 0 0.05 0.001 0 0 0.1 

860

a  a FVS Large demersal predators 0.0005 0.001 0 0 0 0 0 0.1 0 

j  j FVT Large pelagic predators 0.1 0.1 0 0 0.1 0.1 0 0.2 0 a  j FVT Large pelagic predators 0.1 0.1 0 0 0 0.05 0 0.2 0 j  a FVT Large pelagic predators 0.1 0.1 0 0 0.1 0.1 0 0.2 0 a  a FVT Large pelagic predators 0.1 0.1 0 0 0 0.1 0 0.1 0 j  j FVO Shearwaters 0.0001 0.001 0 0 0.0001 0.05 0 0.01 0 a  j FVO Shearwaters 0 0.001 0 0 0 0 0 0 0 j  a FVO Shearwaters 0.0001 0.005 0 0 0.0001 0.05 0 0.01 0 a  a FVO Shearwaters 0 0.005 0 0 0 0 0 0 0 j  j FVB Salmon 0.001 0.01 0 0 0.002 0.1 0 0.01 0 a  j FVB Salmon 0 0.01 0 0 0 0 0 0 0 j  a FVB Salmon 0 0.1 0 0 0 0 0 0 0 a  a FVB Salmon 0 0.1 0 0 0 0 0 0 0 j  j FMM Hake 0.0001 0.0001 0 0.3 0.000003 0.001 0 0.0001 0a  j FMM Hake 0 0.00001 0 0 0 0 0 0 0 

j  a FMM Hake 0.0001 0.0001 0 0.001 0.000003 0.001 0 0.0001 0
Table B-1 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for predation on groups 

and fish (all other groups). A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM a  a FMM Hake 0 0.00001 0 0 0 0 0 0 j  j FMN Sablefish 0.0001 0.001 0 0.005 0 0 0 0.01 a  j FMN Sablefish 0 0.001 0 0 0 0 0 0 j  a FMN Sablefish 0.0001 0.001 0 0.005 0 0 0 0.01 a  a FMN Sablefish 0.0003 0.001 0 0 0 0 0 0.005 j  j FBP Deep vertical migrators 0.1 0.001 0 0 0 0.2 0 0.1 a  j FBP Deep vertical migrators 0 0 0 0 0 0 0 0 j  a FBP Deep vertical migrators 0.1 0.002 0 0 0.002 0.15 0 0.001 a  a FBP Deep vertical migrators 0 0.002 0 0 0 0 0 0 j  j FDD Deep miscellaneous fish 0 0 0 0 0 0 0 0.005 a  j FDD Deep miscellaneous fish 0 0 0 0 0 0 0 0 j  a FDD Deep miscellaneous fish 0 0 0 0.001 0 0 0 0.005 a  a FDD Deep miscellaneous fish 0 0 0 0 0 0 0 0 j  j FDS Midwater rockfish 0.00001 0.001 0 0.001 0.001 0 0 0.001 a  j FDS Midwater rockfish 0 0.001 0 0 0 0 0 0 j  a FDS Midwater rockfish 0.00001 0.0001 0 0.001 0.00001 0 0 0.0001 a  a FDS Midwater rockfish 0.00001 0.0001 0 0 0 0 0 0.0001 j  j FDB Small shallow rockfish 0.001 0.001 0 0 0 0 0 0.01 a  j FDB Small shallow rockfish 0 0.001 0 0 0 0 0 0 j  a FDB Small shallow rockfish 0.001 0.001 0 0.01 0.001 0 0 0.01 a  a FDB Small shallow rockfish 0 0.001 0 0 0 0 0 0 j  j FDC Deep small rockfish 0 0.001 0 0 0 0 0 0.01 a  j FDC Deep small rockfish 0 0.001 0 0 0 0 0 0 j  a FDC Deep small rockfish 0.0005 0.001 0 0 0 0 0 0.01 a  a FDC Deep small rockfish 0 0 0 0 0 0 0 0 j  j FDO Deep large rockfish 0 0.001 0 0 0 0 0 0.01 a  j FDO Deep large rockfish 0 0.001 0 0 0 0 0 0 j  a FDO Deep large rockfish 0.0005 0.001 0 0.01 0 0.02 0 0.01 a  a FDO Deep large rockfish 0 0 0 0 0 0 0 0.01 j  j FDE Miscellaneous nearshore 0 0 0 0.3 0 0 0 0.1 a  j FDE Miscellaneous nearshore 0 0 0 0 0 0 0 0 j  a FDE Miscellaneous nearshore 0.0003 0.001 0 0.001 0.001 0 0 0.01 

87
Table B-1 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for predation on groups 

and fish (all other groups). A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM Fa  a FDE Miscellaneous nearshore 0 0 0 0 0 0 0 0 j  j FDF Small flatfish 0 0.001 0 0.01 0.0001 0 0 0.01 a  j FDF Small flatfish 0 0 0 0 0 0 0 0 j  a FDF Small flatfish 0 0.001 0 0.01 0.0001 0 0 0.01 a  a FDF Small flatfish 0 0.001 0 0 0 0 0 0 j  j SHD Large demersal sharks 0 0 0 0.5 0 0 0 0.1 a  j SHD Large demersal sharks 0 0 0 0.01 0 0 0 0.2 j  a SHD Large demersal sharks 0 0 0 0.2 0 0 0 0.1 a  a SHD Large demersal sharks 0 0 0 0.01 0 0 0 0.2 j  j SHP Misc. pelagic sharks 0.001 0.001 0 0.0001 0.002 0.02 0 0.01 a  j SHP Misc. pelagic sharks 0.1 0.01 0 0.001 0 0.2 0 0.001 j  a SHP Misc. pelagic sharks 0.0005 0.001 0 0.0001 0.002 0.02 0 0.01 a  a SHP Misc. pelagic sharks 0.02 0.01 0 0.001 0.00005 0.2 0 0.001 

j  j SHB Small demersal sharks 0 0.01 0 0.01 0 0.05 0 0.01 a  j SHB Small demersal sharks 0 0.01 0 0 0 0.1 0 0 j  a SHB Small demersal sharks 0 0.01 0 0.01 0 0.05 0 0.01 a  a SHB Small demersal sharks 0 0.01 0 0 0 0.1 0 0 j  j SHR Shallow large rockfish 0.005 0.01 0 0.01 0.001 0 0 0.01 a  j SHR Shallow large rockfish 0 0.01 0 0 0 0 0 0 j  a SHR Shallow large rockfish 0.005 0.01 0 0.01 0.001 0 0 0.01 a  a SHR Shallow large rockfish 0 0.01 0 0 0 0 0 0 j  j SSK Skates and rays 0 0 0 0.01 0 0 0 0.01 a  j SSK Skates and rays 0 0 0 0 0 0 0 0 j  a SSK Skates and rays 0 0 0 0.01 0 0 0 0.01 a  a SSK Skates and rays 0 0 0 0 0 0 0 0 j  j SB Surface seabirds 0.1 0.1 0 0 0.05 0.1 0 0.1 a  j SB Surface seabirds 0 0.1 0 0 0 0 0 0 j  a SB Surface seabirds 0.1 0.1 0 0 0.05 0.1 0 0.1 a  a SB Surface seabirds 0 0.01 0 0 0 0 0 0 j  j SP Diving seabirds 0.03 0.1 0 0 0.05 0.1 0 0.1 

a  j SP Diving seabirds 0 0.01 0 0 0 0 0 0 

88
Table B-1 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for predation on groups 

and fish (all other groups). A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM Fj  a SP Diving seabirds 0.03 0.1 0 0 0.05 0.1 0 0.1 0 a  a SP Diving seabirds 0 0.01 0 0 0 0 0 0 0 j  j REP Transient orcas 0 0 0 0 0 0 0 0 0 a  j REP Transient orcas 0 0 0 0 0 0 0 0 0 j  a REP Transient orcas 0 0 0 0 0 0 0 0 0 a  a REP Transient orcas 0 0 0 0 0 0 0 0 0 j  j PIN Pinnipeds 0.005 0.0005 0 0.0001 0.0005 0.005 0 0.005 0a  j PIN Pinnipeds 0.01 0.01 0 0.001 0.00002 0 0 0.001 0j  a PIN Pinnipeds 0.005 0.0005 0 0.0001 0.0005 0.005 0 0.005 0a  a PIN Pinnipeds 0.01 0.01 0 0.001 0.00002 0.05 0 0.003 0j  j WHB Baleen whales 0 0 0 0 0 0 0 0 0 a  j WHB Baleen whales 0 0 0 0 0 0 0 0 0 j  a WHB Baleen whales 0 0 0 0 0 0 0 0 0 a  a WHB Baleen whales 0 0 0 0 0 0 0 0 0 j  j WHT Toothed whales 0.0005 0.001 0 0.001 0.0001 0.002 0 0.01 0a  j WHT Toothed whales 0.001 0.001 0 0.001 0.00002 0.02 0 0.01 0

j  a WHT Toothed whales 0.001 0.01 0 0.001 0.0001 0.002 0 0.01 0a  a WHT Toothed whales 0.001 0.001 0 0.001 0.00002 0.02 0 0.01 0

j  j WDG Otters 0 0 0 0 0 0 0 0 0 a  j WDG Otters 0 0 0 0 0 0 0 0 0 j  a WDG Otters 0 0 0 0 0 0 0 0 0 a  a WDG Otters 0 0 0 0 0 0 0 0 0 

ZG Gelatinous zooplankton 0.0001 0.0001 0 0 0.00001 0.02 0 0.0001 0 ZL Large zooplankton 0 0 0 0 0 0 0 0 0 ZM Mesozooplankton 0 0 0 0 0 0 0 0 0 ZS Microzooplankton 0 0 0 0 0 0 0 0 0 BD Deposit feeders 0 0 0 0 0 0 0 0 0 BO Meiobenthos 0 0 0 0 0 0 0 0 0 

BC Carnivorous infauna 0 0 0 0 0 0 0 0 0 

BFS Shallow benthic filter 

f d

0 0 0 0 0 0 0 0 0 

BFF Other benthic filter feeders 0 0 0 0 0 0 0 0 0 BFD Deep benthic filter feeders 0 0 0 0 0 0 0 0 0 

89
Table B-1 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for predation on groups 

and fish (all other groups). A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM F

BMS Shallow macro-zoobenthos 0 0 0 0.1 0 0 0 0 0 BML Mega-zoobenthos 0 0 0 0.002 0 0 0 0.0001 0

BMD Deep macro-zoobenthos 0 0 0 0 0 0 0 0 0 

BG Benthic grazers 0 0 0 0 0 0 0 0 0 CEP Cephalopods 0.001 0.005 0 0.01 0.005 0.1 0 0.01 0PWN Shrimp 0 0 0 0 0 0 0 0 0 PWN Shrimp 0 0 0 0 0 0 0 0 0 

* In the stages column, j  j signifies juvenile predation on juveniles, a  j signifies adult predation on juveniles, j  a signifies juvenile predation on 

adult predation on adults. 

90
Table B-2. Consumption parameters (variable a in Equation 10) in the calibrated model for additional prey including fish a

are listed by column. A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD j  j FPL Large planktivores 0.1 0.1 0.05 0 0 0 0 0 a  j FPL Large planktivores 0 0 0 0 0 0 0 0 j  a FPL Large planktivores 0.03 0.05 0.01 0 0 0 0 0 a  a FPL Large planktivores 0.015 0 0 0 0 0 0 0 j  j FPS Small planktivores 0.0001 0.05 0.05 0 0 0 0 0 a  j FPS Small planktivores 0 0 0 0 0 0 0 0 j  a FPS Small planktivores 0.00005 0.1 0.0001 0 0 0 0 0 a  a FPS Small planktivores 0 0 0 0 0 0 0 0 j  j FVD Large flatfish 0.00015 0.0002 0.0006 0.001 0.0005 0.2 0 0 a  j FVD Large flatfish 0.001 0 0.0002 0.001 0 0.3 0 0 j  a FVD Large flatfish 0.00015 0.0002 0.00006 0.001 0.0001 0.01 0.0001 0 a  a FVD Large flatfish 0.001 0 0.0002 0.001 0 0.3 0.1 0 j  j FVS Large demersal predators 0.1 0.05 0.05 0.01 0.1 0.1 0 0 a  j FVS Large demersal predators 0.1 0 0.05 0.1 0 0.3 0 0 j  a FVS Large demersal predators 0.1 0.01 0.01 0.01 0.005 0.1 0.00005 0 a  a FVS Large demersal predators 0.1 0 0.01 0.01 0 0.1 0.01 0 j  j FVT Large pelagic predators 0.005 0.01 0.001 0 0 0 0 0 a  j FVT Large pelagic predators 0.1 0 0.1 0 0 0 0 0 j  a FVT Large pelagic predators 0.1 0.1 0.1 0 0 0 0 0 a  a FVT Large pelagic predators 0.3 0 0.1 0 0 0 0 0 j  j FVO Shearwaters 0 0.01 0.001 0 0 0 0 0 a  j FVO Shearwaters 0 0 0 0 0 0 0 0 j  a FVO Shearwaters 0 0.1 0.001 0 0 0 0 0 a  a FVO Shearwaters 0 0 0 0 0 0 0 0 j  j FVB Salmon 0.1 0.01 0.005 0 0 0 0 0 a  j FVB Salmon 0.15 0 0 0 0 0 0 0 j  a FVB Salmon 0.1 0 0 0 0 0 0 0 a  a FVB Salmon 0.15 0 0 0 0 0 0 0 j  j FMM Hake 0.002 0.01 0.00005 0.001 0.1 0.1 0 0 

91
Table B-2 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for additional prey inclu

Prey groups are listed by column. A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD a  j FMM Hake 0.002 0 0.05 0.01 0 0.3 0 0 j  a FMM Hake 0.001 0.0001 0.00005 0.0001 0.001 0.003 0 0 a  a FMM Hake 0.002 0 0 0.0001 0 0.3 0 0 j  j FMN Sablefish 0 0.002 0.001 0.015 0.0002 0.1 0 0 a  j FMN Sablefish 0.01 0 0.003 0.003 0 0.3 0 0 j  a FMN Sablefish 0 0.002 0.001 0.015 0.0002 0.005 0.00003 0 a  a FMN Sablefish 0.01 0.002 0 0.003 0.00001 0.005 0.0005 0 

j  j FBP Deep vertical migrators 0 0 0 0 0 0 0 0 a  j FBP Deep vertical migrators 0 0 0 0 0 0 0 0 j  a FBP Deep vertical migrators 0 0.01 0.05 0.1 0.1 0.1 0 0 a  a FBP Deep vertical migrators 0 0 0 0 0 0 0 0 j  j FDD Deep miscellaneous fish 0 0 0 0.01 0.00001 0.01 0 0 a  j FDD Deep miscellaneous fish 0 0 0 0.001 0 0.06 0 0 j  a FDD Deep miscellaneous fish 

920 0.001 0 0.01 0.00001 0.06 0.000005 0 

a  a FDD Deep miscellaneous fish 0 0 0 0.001 0 0.06 0.0001 0 j  j FDS Midwater rockfish 0.001 0.01 0.001 0.01 0.001 0.1 0 0 a  j FDS Midwater rockfish 0.01 0 0.001 0.001 0 0.3 0 0 j  a FDS Midwater rockfish 0.001 0.0002 0.0001 0.01 0.001 0.1 0 0 a  a FDS Midwater rockfish 0.01 0.5 0.0001 0.001 0 0.3 0 0 j  j FDB Small shallow rockfish 0.1 0.1 0.01 0 0 0.1 0 0 a  j FDB Small shallow rockfish 0.15 0 0 0 0 0.3 0 0 j  a FDB Small shallow rockfish 0.1 0.1 0.01 0 0 0.1 0 0 a  a FDB Small shallow rockfish 0.15 0 0 0 0 0.3 0 0 j  j FDC Deep small rockfish 0 0.1 0 0.02 0.3 0.1 0 0 a  j FDC Deep small rockfish 0 0 0 0 0 0.3 0 0 j  a FDC Deep small rockfish 0 0 0 0.02 0.1 0.1 0 0 a  a FDC Deep small rockfish 0 0 0 0 0 0.3 0 0 j  j FDO Deep large rockfish 0 0.1 0 0.02 0.1 0.1 0 0 
Table B-2 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for additional prey inclu

Prey groups are listed by column. A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD a  j FDO Deep large rockfish 0 0 0 0.1 0 0.3 0 0 j  a FDO Deep large rockfish 0.04 0.002 0.005 0.02 0.001 0 0.0003 0 a  a FDO Deep large rockfish 0 0.002 0 0.001 0 0.3 0.1 0 j  j FDE Misc. nearshore 0.05 0.01 0.05 0 0 0.1 0 0 a  j FDE Misc. nearshore 0 0 0 0 0 0 0 0 j  a FDE Misc. nearshore 0.0002 0.01 0.001 0 0 0.1 0 0 a  a FDE Misc. nearshore 0.001 0 0.05 0 0 0.3 0 0 j  j FDF Small flatfish 0.01 0.01 0.001 0.01 0.001 0.1 0 0 a  j FDF Small flatfish 0.1 0 0 0 0 0 0 0 j  a FDF Small flatfish 0.1 0.001 0.001 0.01 0.001 0.001 0 0 a  a FDF Small flatfish 0.01 0 0 0 0 0 0 0 j  j SHD Large demersal sharks 0.1 0 0 0 0 0.2 0.01 0.05 a  j SHD Large demersal sharks 0.01 0 0 0 0 0.2 0.1 0 j  a SHD Large demersal sharks 0.1 0 0 0 0 0.2 0.01 0.05 a  a SHD Large demersal sharks 0.01 0 0 0 0 0.2 0.1 0 j  j SHP Misc. pelagic sharks 0.0001 0.0002 0.00005 0.005 0.005 0 0.01 0.05 a  j SHP Misc. pelagic sharks 0.001 0.001 0.001 0.005 0.001 0 0.1 0.05 j  a SHP Misc. pelagic sharks 0.05 0.0002 0.00005 0.005 0.005 0 0.01 0.1 a  a SHP Misc. pelagic sharks 0.0005 0.001 0.001 0.005 0.002 0 0.1 0.1 j  j SHB Small demersal sharks 0.02 0.02 0.0005 0.02 0.01 0.1 0.003 0 a  j SHB Small demersal sharks 0.07 0 0 0 0 0.3 0 0 j  a SHB Small demersal sharks 0.05 0.01 0.003 0.02 0.01 0.001 0.003 0 

a  a SHB Small demersal sharks 0.01 0 0 0 0 0.1 0.05 0 j  j SHR Shallow large rockfish 0.01 0.01 0.003 0.01 0.1 0.1 0 0 a  j SHR Shallow large rockfish 0.01 0 0.05 0 0 0.1 0 0 j  a SHR Shallow large rockfish 0.01 0.01 0.005 0.01 0.01 0.1 0 0 a  a SHR Shallow large rockfish 0.04 0 0.005 0 0 0.1 0 0 j  j SSK Skates and rays 0.01 0.01 0.001 0.02 0.01 0.1 0 0 a  j SSK Skates and rays 0.02 0 0 0 0 0.1 0 0 

j  a SSK Skates and rays 0.03 0.01 0.001 0.02 0.02 0.01 0 0 

93
Table B-2 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for additional prey inclu

Prey groups are listed by column. A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD a  a SSK Skates and rays 0.02 0 0 0 0 0.1 0 0 j  j SB Surface seabirds 0 0.01 0.02 0 0 0 0 0 a  j SB Surface seabirds 0 0 0 0 0 0 0 0 j  a SB Surface seabirds 0 0.01 0.02 0 0 0 0 0 a  a SB Surface seabirds 0 0 0 0 0 0 0 0 j  j SP Diving seabirds 0.1 0.01 0.005 0.02 0.1 0 0 0 a  j SP Diving seabirds 0.3 0 0 0 0 0 0 0 j  a SP Diving seabirds 0.1 0.01 0.005 0.02 0.1 0 0 0 a  a SP Diving seabirds 0.3 0 0 0 0 0 0 0 j  j REP Transient orcas 0 0 0 0 0 0 0 0 a  j REP Transient orcas 0 0 0 0 0 0 0 0 j  a REP Transient orcas 0 0 0 0 0 0 0 0 a  a REP Transient orcas 0 0 0 0 0 0 0 0 j  j PIN Pinnipeds 0.1 0.0005 0.0001 0.005 0.003 0.01 0.001 0 a  j PIN Pinnipeds 0.0005 0.001 0.001 0.005 0.001 0.01 0.01 0 j  a PIN Pinnipeds 0.1 0.0005 0.0001 0.005 0.003 0.01 0.001 0 a  a PIN Pinnipeds 0.0005 0.001 0.0001 0.005 0.001 0.06 0.01 0 j  j WHB Baleen whales 0 0 0 0 0 0 0 0 a  j WHB Baleen whales 0 0 0 0 0 0 0 0 j  a WHB Baleen whales 0 0 0 0 0 0 0 0 a  a WHB Baleen whales 0 0 0 0 0 0 0 0 j  j WHT Toothed whales 0.055 0.0005 0.0001 0.001 0.001 0.001 0.001 0.1 a  j WHT Toothed whales 0.001 0.001 0.0001 0.001 0.001 0.006 0.001 0.1 

j  a WHT Toothed whales 0.055 0.0005 0.0001 0.001 0.003 0.001 0.001 0.1 a  a WHT Toothed whales 0.001 0.001 0.0003 0.001 0.001 0.006 0.001 0.1 

j  j WDG Otters 0.055 0 0.05 0 0 0.5 0 0 a  j WDG Otters 0.1 0 0.05 0 0 0.6 0 0 j  a WDG Otters 0.055 0 0.05 0 0 0.5 0 0 a  a WDG Otters 0.1 0 0.05 0 0 0.6 0 0 

ZG Gelatinous zooplankton 0.00001 0.01 0.00001 0.0001 0.0005 0 0 0 

94
95

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD 

ZL Large zooplankton 0 0 0 0 0 0 0 0 ZM Mesozooplankton 0 0 0 0 0 0 0 0 ZS Microzooplankton 0 0 0 0 0 0 0 0 BD Deposit feeders 0 0 0 0 0 0 0 0 BO Meiobenthos 0 0 0 0 0 0 0 0 

BC Carnivorous infauna 0 0 0 0 0 0 0 0 

BFS Shall. Benthic filter feeders 0 0 0 0 0 0 0 0 BFF Other benthic filter feeders 0 0 0 0 0 0 0 0 BFD Deep benthic filter feeders 0 0 0 0 0 0 0 0 

BMS Shall. macro-zoobenthos 0.02 0.01 0.005 0.01 0.1 0.1 0.01 0 

BML Mega-zoobenthos 0.0001 0.0001 0.00005 0.0001 0.0001 0.0001 0 0 BMD Deep macro-zoobenthos 0 0 0 0 0 0 0 0 

BG Benthic grazers 0 0 0 0 0 0 0 0 

CEP Cephalopods 0.001 0.01 0.0005 0.001 0.1 0 0 0 

PWN Shrimp 0 0 0 0 0 0 0 0 PWN Shrimp 0 0 0 0 0 0 0 0 

* In the stages column, j  j signifies juvenile predation on juveniles, a  j signifies adult predation on juveniles, j  a signifies juvenile predation on 

adult predation on adults. 

Table B-2 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for additional prey inclu

Prey groups are listed by column. A value of 0 indicates cases where that predator does not eat that prey. 
Table B-3. Consumption parameters (variable a in Equation 10) in the calibrated model for seabird and 

mammal prey. A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group SB SP PIN REP WHB WHT WDG 

j  j FPL Large planktivores 0 0 0 0 0 0 0 

a  j FPL Large planktivores 0 0 0 0 0 0 0 

j  a FPL Large planktivores 0 0 0 0 0 0 0 

a  a FPL Large planktivores 0 0 0 0 0 0 0 

j  j FPS Small planktivores 0 0 0 0 0 0 0 

a  j FPS Small planktivores 0 0 0 0 0 0 0 

j  a FPS Small planktivores 0 0 0 0 0 0 0 

a  a FPS Small planktivores 0 0 0 0 0 0 0 

j  j FVD Large flatfish 0 0 0 0 0 0 0 

a  j FVD Large flatfish 0 0 0 0 0 0 0 

j  a FVD Large flatfish 0 0 0 0 0 0 0 

a  a FVD Large flatfish 0 0 0 0 0 0 0 

j  j FVS Large demersal predators 0 0 0 0 0 0 0 

a  j FVS Large demersal predators 0 0 0 0 0 0 0 

j  a FVS Large demersal predators 0 0 0 0 0 0 0 

a  a FVS Large demersal predators 0 0 0 0 0 0 0 

j  j FVT Large pelagic predators 0 0 0 0 0 0 0 

a  j FVT Large pelagic predators 0 0 0 0 0 0 0 

j  a FVT Large pelagic predators 0 0 0 0 0 0 0 

a  a FVT Large pelagic predators 0 0 0 0 0 0 0 

j  j FVO Shearwaters 0 0 0 0 0 0 0 

a  j FVO Shearwaters 0 0 0 0 0 0 0 

j  a FVO Shearwaters 0 0 0 0 0 0 0 

a  a FVO Shearwaters 0 0 0 0 0 0 0 

j  j FVB Salmon 0 0 0 0 0 0 0 

a  j FVB Salmon 0 0 0 0 0 0 0 

j  a FVB Salmon 0 0 0 0 0 0 0 

a  a FVB Salmon 0 0 0 0 0 0 0 

j  j FMM Hake 0 0 0 0 0 0 0 

a  j FMM Hake 0 0 0 0 0 0 0 

j  a FMM Hake 0 0 0 0 0 0 0 

a  a FMM Hake 0 0 0 0 0 0 0 

j  j FMN Sablefish 0 0 0 0 0 0 0 

a  j FMN Sablefish 0 0 0 0 0 0 0 

j  a FMN Sablefish 0 0 0 0 0 0 0 

a  a FMN Sablefish 0 0 0 0 0 0 0 

j  j FBP Deep vertical migrators 0 0 0 0 0 0 0 

a  j FBP Deep vertical migrators 0 0 0 0 0 0 0 

j  a FBP Deep vertical migrators 0 0 0 0 0 0 0 

a  a FBP Deep vertical migrators 0 0 0 0 0 0 0 

j  j FDD Deep miscellaneous fish 0 0 0 0 0 0 0 

a  j FDD Deep miscellaneous fish 0 0 0 0 0 0 0 

j  a FDD Deep miscellaneous fish 0 0 0 0 0 0 0 

a  a FDD Deep miscellaneous fish 0 0 0 0 0 0 0 

j  j FDS Midwater rockfish 0 0 0 0 0 0 0 

a  j FDS Midwater rockfish 0 0 0 0 0 0 0 

96
Table B-3 continued. Consumption parameters (variable a in Equation 10) in the calibrated model 

for seabird and mammal prey. A value of 0 indicates cases where that predator does not eat 

that prey. 

Predator Prey group 

Stages* Code Group SB SP PIN REP WHB WHT WDG 

j  a FDS Midwater rockfish 0 0 0 0 0 0 0 

a  a FDS Midwater rockfish 0 0 0 0 0 0 0 

j  j FDB Small shallow rockfish 0 0 0 0 0 0 0 

a  j FDB Small shallow rockfish 0 0 0 0 0 0 0 

j  a FDB Small shallow rockfish 0 0 0 0 0 0 0 

a  a FDB Small shallow rockfish 0 0 0 0 0 0 0 

j  j FDC Deep small rockfish 0 0 0 0 0 0 0 

a  j FDC Deep small rockfish 0 0 0 0 0 0 0 

j  a FDC Deep small rockfish 0 0 0 0 0 0 0 

a  a FDC Deep small rockfish 0 0 0 0 0 0 0 

j  j FDO Deep large rockfish 0 0 0 0 0 0 0 

a  j FDO Deep large rockfish 0 0 0 0 0 0 0 

j  a FDO Deep large rockfish 0.3 0.3 0.1 0 0 0 0.1 

a  a FDO Deep large rockfish 0 0 0 0 0 0 0 

j  j FDE Miscellaneous nearshore 0 0 0 0 0 0 0 

a  j FDE Miscellaneous nearshore 0 0 0 0 0 0 0 

j  a FDE Miscellaneous nearshore 0 0 0 0 0 0 0 

a  a FDE Miscellaneous nearshore 0 0 0 0 0 0 0 

j  j FDF Small flatfish 0 0 0 0 0 0 0 

a  j FDF Small flatfish 0 0 0 0 0 0 0 

j  a FDF Small flatfish 0 0 0 0 0 0 0 

a  a FDF Small flatfish 0 0 0 0 0 0 0 

j  j SHD Large demersal sharks 0 0 0 0 0 0 0 

a  j SHD Large demersal sharks 0 0 0 0 0 0 0 

j  a SHD Large demersal sharks 0 0 0 0 0 0 0 

a  a SHD Large demersal sharks 0 0 0 0 0 0 0 

j  j SHP Misc. pelagic sharks 0.1 0.3 0.3 0 0 0 0.4 

a  j SHP Misc. pelagic sharks 0.5 0.5 0.3 0 0 0 0.4 

j  a SHP Misc. pelagic sharks 0.1 0.3 0.25 0.1 0 0.1 0.4 

a  a SHP Misc. pelagic sharks 0.4 0.5 0.3 0.1 0.2 0.1 0.4 

j  j SHB Small demersal sharks 0 0 0 0 0 0 0 

a  j SHB Small demersal sharks 0 0 0 0 0 0 0 

j  a SHB Small demersal sharks 0 0 0 0 0 0 0 

a  a SHB Small demersal sharks 0 0 0 0 0 0 0 

j  j SHR Shallow large rockfish 0 0 0 0 0 0 0 

a  j SHR Shallow large rockfish 0 0 0 0 0 0 0 

j  a SHR Shallow large rockfish 0 0 0 0 0 0 0 

a  a SHR Shallow large rockfish 0 0 0 0 0 0 0 

j  j SSK Skates and rays 0 0 0 0 0 0 0 

a  j SSK Skates and rays 0 0 0 0 0 0 0 

j  a SSK Skates and rays 0 0 0 0 0 0 0 

a  a SSK Skates and rays 0 0 0 0 0 0 0 

j  j SB Surface seabirds 0 0 0 0 0 0 0 

a  j SB Surface seabirds 0 0 0 0 0 0 0 

j  a SB Surface seabirds 0 0 0 0 0 0 0 

a  a SB Surface seabirds 0 0 0 0 0 0 0 

j  j SP Diving seabirds 0 0 0 0 0 0 0 

a  j SP Diving seabirds 0 0 0 0 0 0 0 

97
98

Table B-3 continued. Consumption parameters (variable a in Equation 10) in the calibrated model 

for seabird and mammal prey. A value of 0 indicates cases where that predator does not eat 

that prey. 

 Predator Prey group 

Stages* Code Group SB SP PIN REP WHB WHT WDG 

j  a SP Diving seabirds 0 0 0 0 0 0 0 

a  a SP Diving seabirds 0 0 0 0 0 0 0 

j  j REP Transient orcas 0.1 0.3 0.3 0 0.002 0.1 0.6 

a  j REP Transient orcas 0.4 0.5 0.3 0 0.2 0.1 0.6 

j  a REP Transient orcas 0.1 0.3 0.3 0 0.002 0.1 0.6 

a  a REP Transient orcas 0.4 0.5 0.3 0 0.2 0.1 0.6 

j  j PIN Pinnipeds 0 0 0 0 0 0 0 

a  j PIN Pinnipeds 0 0 0 0 0 0 0 

j  a PIN Pinnipeds 0 0 0 0 0 0 0 

a  a PIN Pinnipeds 0 0 0 0 0 0 0 

j  j WHB Baleen whales 0 0 0 0 0 0 0 

a  j WHB Baleen whales 0 0 0 0 0 0 0 

j  a WHB Baleen whales 0 0 0 0 0 0 0 

a  a WHB Baleen whales 0 0 0 0 0 0 0 

j  j WHT Toothed whales 0 0 0 0 0 0 0 

a  j WHT Toothed whales 0 0 0 0 0 0 0 

j  a WHT Toothed whales 0 0 0 0 0 0 0 

a  a WHT Toothed whales 0 0 0 0 0 0 0 

j  j WDG Otters 0 0 0 0 0 0 0 

a  j WDG Otters 0 0 0 0 0 0 0 

j  a WDG Otters 0 0 0 0 0 0 0 

a  a WDG Otters 0 0 0 0 0 0 0 

ZG Gelatinous zooplankton 0 0 0 0 0 0 0 

ZL Large zooplankton 0 0 0 0 0 0 0 

ZM Mesozooplankton 0 0 0 0 0 0 0 

ZS Microzooplankton 0 0 0 0 0 0 0 

BD Deposit feeders 0 0 0 0 0 0 0 

BO Meiobenthos 0 0 0 0 0 0 0 

BC Carnivorous infauna 0 0 0 0 0 0 0 

BFS Shallow benthic filter feeders 0 0 0 0 0 0 0 

BFF Other benthic filter feeders 0 0 0 0 0 0 0 

BFD Deep benthic filter feeders 0 0 0 0 0 0 0 

BMS Shallow macro-zoobenthos 0 0 0 0 0 0 0 

BML Mega-zoobenthos 0 0 0 0 0 0 0 

BMD Deep macro-zoobenthos 0 0 0 0 0 0 0 

BG Benthic grazers 0 0 0 0 0 0 0 

CEP Cephalopods 0 0 0 0 0 0 0 

PWN Shrimp 0 0 0 0 0 0 0 

PWN Shrimp 0 0 0 0 0 0 0 

* In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies 

juvenile predation on adults, and aa signifies adult predation on adults. 
Table B-4. Consumption parameters (variable a in Equation 10) of benthic prey in the calibrated model. A value of 0 indi

predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi j  j FPL Large planktivores 0 0 0 0 0 0 0 0.01 a  j FPL Large planktivores 0 0 0 0 0 0 0 0.01 j  a FPL Large planktivores 0 0 0 0 0 0 0.1 0.01 a  a FPL Large planktivores 0 0 0 0 0 0 0.1 0.01 j  j FPS Small planktivores 0 0 0 0 0 0 0 0.1 a  j FPS Small planktivores 0 0 0 0 0 0 0 0.1 j  a FPS Small planktivores 0 0 0 0 0 0 0 0.1 a  a FPS Small planktivores 0 0 0 0 0 0 0 0.1 j  j FVD Large flatfish 0 0.02 0.1 0 0.1 0.05 0.1 0.1 a  j FVD Large flatfish 0 0.02 0.1 0 0.1 0.05 0.1 0.1 

j  a FVD Large flatfish 0 0.02 0.1 0 0.1 0.05 0.1 0.1 a  a FVD Large flatfish 0 0.02 0.1 0 0.1 0.05 0.1 0.1 

j  j FVS Large demersal predators 0 0.1 0.1 0 0.1 0.05 0.1 0.1 a  j FVS Large demersal predators 0 0.1 0.1 0 0.1 0.05 0.1 0.1 

j  a FVS Large demersal predators 0 0.1 0.1 0 0.1 0.05 0.1 0.1 a  a FVS Large demersal predators 0 0.1 0.1 0 0.1 0.05 0.1 0.1 

j  j FVT Large pelagic predators 0 0 0 0 0 0 0 0.01 a  j FVT Large pelagic predators 0 0 0 0 0 0 0 0.01 j  a FVT Large pelagic predators 0 0 0 0 0 0 0 0.01 a  a FVT Large pelagic predators 0 0 0 0 0 0 0 0.01 j  j FVO Shearwaters 0 0 0 0 0 0 0 0 a  j FVO Shearwaters 0 0 0 0 0 0 0 0 j  a FVO Shearwaters 0 0 0 0 0 0 0 0 a  a FVO Shearwaters 0 0 0 0 0 0 0 0 j  j FVB Salmon 0 0 0 0 0 0 0 0.1 a  j FVB Salmon 0 0 0 0 0 0 0 0.1 j  a FVB Salmon 0 0 0 0 0 0 0 0 a  a FVB Salmon 0 0 0 0 0 0 0 0 j  j FMM Hake 0 0 0 0 0 0.05 0.1 0.1 a  j FMM Hake 0 0 0 0 0 0.05 0.1 0.1 j  a FMM Hake 0 0 0 0 0 0.05 0.1 0.1 

99
Table B-4 continued. Consumption parameters (variable a in Equation 10) of benthic prey in the calibrated model. A valu

where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi a  a FMM Hake 0 0 0 0 0 0.05 0.1 0.1 j  j FMN Sablefish 0 0.02 0.15 0.01 0.05 0.05 0.1 0.1 a  j FMN Sablefish 0 0.02 0.15 0.01 0.05 0.05 0.1 0.1 j  a FMN Sablefish 0 0.02 0.15 0.01 0.05 0.05 0.1 0.1 a  a FMN Sablefish 0 0.02 0.15 0.01 0.05 0.05 0.1 0.1 j  j FBP Deep vertical migrators 0 0 0 0 0 0 0 0.01 a  j FBP Deep vertical migrators 0 0 0 0 0 0 0 0.01 j  a FBP Deep vertical migrators 0 0 0 0 0 0 0 0.01 a  a FBP Deep vertical migrators 0 0 0 0 0 0 0 0.01 j  j FDD Deep miscellaneous fish 0 0.01 0.15 0.01 0.05 0.05 0.1 0.1 

a  j FDD Deep miscellaneous fish 0 0.01 0.15 0.01 0.05 0.05 0.1 0.1 j  a FDD Deep miscellaneous fish 0 0.01 0.15 0.01 0.05 0.05 0.1 0.1 

a  a FDD Deep miscellaneous fish 0 0.01 0.15 0.01 0.05 0.05 0.1 0.1 j  j FDS Midwater rockfish 0 0.01 0 0 0 0.05 0.1 0.1 a  j FDS Midwater rockfish 0 0.01 0 0 0 0.05 0.1 0.1 j  a FDS Midwater rockfish 0 0.01 0 0 0 0.05 0.1 0.1 a  a FDS Midwater rockfish 0 0.01 0 0 0 0.05 0.1 0.1 j  j FDB Small shallow rockfish 0 0.1 0 0 0.1 0.4 0.1 0.1 a  j FDB Small shallow rockfish 0 0.1 0 0 0.1 0.4 0.1 0.1 

j  a FDB Small shallow rockfish 0 0.1 0 0 0.1 0.4 0.1 0.1 a  a FDB Small shallow rockfish 0 0.1 0 0 0.1 0.4 0.1 0.1 

j  j FDC Deep small rockfish 0 0.1 0.05 0 0 0.4 0.1 0.1 a  j FDC Deep small rockfish 0 0.1 0.05 0 0 0.4 0.1 0.1 

j  a FDC Deep small rockfish 0 0.1 0.05 0 0 0.4 0.1 0.1 a  a FDC Deep small rockfish 0 0.1 0.05 0 0 0.4 0.1 0.1 

j  j FDO Deep large rockfish 0 0.02 0.05 0 0 0.05 0.1 0.1 a  j FDO Deep large rockfish 0 0.02 0.05 0 0 0.05 0.1 0.1 

j  a FDO Deep large rockfish 0 0 0 0 0 0.05 0.1 0 

a  a FDO Deep large rockfish 0 0.02 0.05 0 0 0.05 0.1 0.1 

j  j FDE Miscellaneous nearshore 0 0.005 0 0 0.08 0.02 0.1 0.05 a  j FDE Miscellaneous nearshore 0 0.005 0 0 0.08 0.02 0.1 0.05 

100
Table B-4 continued. Consumption parameters (variable a in Equation 10) of benthic prey in the calibrated model. A valu

where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi j  a FDE Miscellaneous nearshore 0 0.005 0 0 0.08 0.02 0.1 0.05 a  a FDE Miscellaneous nearshore 0 0.005 0 0 0.08 0.02 0.1 0.05 j  j FDF Small flatfish 0 0.03 0.05 0.01 0.1 0.02 0.1 0.1 a  j FDF Small flatfish 0 0.03 0.05 0.01 0.1 0.02 0.1 0.1 

j  a FDF Small flatfish 0 0.03 0.05 0.01 0.1 0.02 0.1 0.1 a  a FDF Small flatfish 0 0.03 0.05 0.01 0.1 0.02 0.1 0.1 

j  j SHD Large demersal sharks 0 0.02 0.15 0.1 0.1 0.02 0.1 0.1 a  j SHD Large demersal sharks 0 0.02 0.15 0.1 0.1 0.02 0.1 0.1 j  a SHD Large demersal sharks 0 0.02 0.15 0.1 0.1 0.02 0.1 0.1 a  a SHD Large demersal sharks 0 0.02 0.15 0.1 0.1 0.02 0.1 0.1 j  j SHP Miscellaneous pelagic sharks 0 0 0 0 0 0.1 0.1 0 a  j SHP Miscellaneous pelagic sharks 0 0 0 0 0 0.1 0.1 0 j  a SHP Miscellaneous pelagic sharks 0 0 0 0 0 0.1 0.1 0 a  a SHP Miscellaneous pelagic sharks 0 0 0 0 0 0.1 0.1 0 j  j SHB Small demersal sharks 0 0.1 0.1 0.05 0 0.1 0.1 0.1 a  j SHB Small demersal sharks 0 0.1 0.1 0.05 0 0.1 0.1 0.1 j  a SHB Small demersal sharks 0 0.1 0.1 0.05 0 0.1 0.1 0.1 a  a SHB Small demersal sharks 0 0.1 0.1 0.05 0 0.1 0.1 0.1 j  j SHR Shallow large rockfish 0 0.005 0 0 0 0.02 0.1 0.05 a  j SHR Shallow large rockfish 0 0.005 0 0 0 0.02 0.1 0.05 j  a SHR Shallow large rockfish 0 0.005 0 0 0 0.02 0.1 0.05 a  a SHR Shallow large rockfish 0 0.005 0 0 0 0.02 0.1 0.05 j  j SSK Skates and rays 0 0.1 0.1 0.05 0.1 0.2 0.1 0.1 a  j SSK Skates and rays 0 0.1 0.1 0.05 0.1 0.2 0.1 0.1 

j  a SSK Skates and rays 0 0.1 0.1 0.05 0.1 0.2 0.1 0.1 a  a SSK Skates and rays 0 0.1 0.1 0.05 0.1 0.2 0.1 0.1 

j  j SB Surface seabirds 0 0.1 0 0 0 0 0 0 a  j SB Surface seabirds 0 0.1 0 0 0 0 0 0 j  a SB Surface seabirds 0 0.1 0 0 0 0 0 0 

a  a SB Surface seabirds 0 0.1 0 0 0 0 0 0 j  j SP Diving seabirds 0 0.005 0 0 0 0.02 0 0.05 

101
Table B-4 continued. Consumption parameters (variable a in Equation 10) of benthic prey in the calibrated model. A valu

where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi a  j SP Diving seabirds 0 0.005 0 0 0 0.02 0 0.05 j  a SP Diving seabirds 0 0.005 0 0 0 0.02 0 0.05 a  a SP Diving seabirds 0 0.005 0 0 0 0.02 0 0.05 j  j REP Transient orcas 0 0 0 0 0 0 0 0 a  j REP Transient orcas 0 0 0 0 0 0 0 0 j  a REP Transient orcas 0 0 0 0 0 0 0 0 a  a REP Transient orcas 0 0 0 0 0 0 0 0 j  j PIN Pinnipeds 0 0.05 0 0 0.1 0.1 0.1 0 a  j PIN Pinnipeds 0 0.5 0 0 0.1 0.1 0.1 0 j  a PIN Pinnipeds 0 0.05 0 0 0.1 0.1 0.1 0 a  a PIN Pinnipeds 0 0.5 0 0 0.1 0.1 0.1 0 j  j WHB Baleen whales 0 0.1 0.1 0 0.1 0.1 0.1 0.1 a  j WHB Baleen whales 0 0.1 0.1 0 0.1 0.1 0.1 0.1 

j  a WHB Baleen whales 0 0.1 0.1 0 0.1 0.1 0.1 0.1 a  a WHB Baleen whales 0 0.1 0.1 0 0.1 0.1 0.1 0.1 

j  j WHT Toothed whales 0 0.001 0.1 0 0 0.002 0.1 0 a  j WHT Toothed whales 0 0.001 0.1 0 0 0.002 0.1 0 j  a WHT Toothed whales 0 0.001 0.1 0 0 0.002 0.1 0 a  a WHT Toothed whales 0 0.001 0.1 0 0 0.002 0.1 0 j  j WDG Otters 0 0.1 0 0.5 0.1 0.2 0.1 0.1 a  j WDG Otters 0 0.1 0 0.5 0.1 0.2 0.1 0.1 j  a WDG Otters 0 0.1 0 0.5 0.1 0.2 0.1 0.1 a  a WDG Otters 0 0.1 0 0.5 0.1 0.2 0.1 0.1 

ZG Gelatinous zooplankton 0 0 0 0 0 0 0 0.01 

ZL Large zooplankton 0 0 0 0 0 0 0 0.01 

ZM Mesozooplankton 0 0 0 0 0 0 0 0 ZS Microzooplankton 0 0 0 0 0 0 0 0 

BD Deposit feeders 0 0 0 0 0 0 0 0.1 BO Meiobenthos 0 0 0 0 0 0 0 0 

BC Carnivorous infauna 0 0 0 0 0 0 0 0.01 

BFS Shallow benthic filter feeders 0 0 0 0 0 0 0 0 

102
Table B-4 continued. Consumption parameters (variable a in Equation 10) of benthic prey in the calibrated model. A valu

where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi 

BFF Other benthic filter feeders 0 0 0 0 0 0 0 0 BFD Deep benthic filter feeders 0 0 0 0 0 0.001 0 0.01 BMS Shallow macro-zoobenthos 0 0.001 0 0 0.001 0.003 0.1 0.05 BML Mega-zoobenthos 0 3E-05 0 0.000 0 0.0001 0 0.01 BMD Deep macro-zoobenthos 0 0.0002 0 0.001 0.001 0.001 0 0.01 BG Benthic grazers 0 0 0 0 0 0 0 0 CEP Cephalopods 0 0 0 0 0 0 0 0.01 PWN Shrimp 0 0 0 0 0 0 0 0.01 PWN Shrimp 0 0 0 0 0 0 0 0.01 

a In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies juvenile predation on adu

predation on adults. 

b BFS = shallow benthic filter feeders. c BFF = other benthic filter feeders. d BFD = deep benthic filter feeders. e BG = benthic grazers. 

103f BMD = deep macro-zoobenthos. 

g BML = mega-zoobenthos. h BMS = shallow macro-zoobenthos. i BD = deposit feeders. j BC = carnivorous infauna. 
Table B-5. Consumption parameters (variable a in Equation 10) in the calibrated model for prey including plankton, shrim

of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPhj  j FPL Large planktivores 0.1 0.2 0.01 0.0000 0 0.00001 0 a  j FPL Large planktivores 0.1 0.2 0.01 0.0000 0 0.00001 0 

j  a FPL Large planktivores 0.0001 0.01 0.03 0 0 0.00001 0 a  a FPL Large planktivores 0.0001 0.01 0.03 0 0 0.00001 0 

j  j FPS Small planktivores 0.00004 0.0002 0.0002 0.0000 0 0.0001 0 a  j FPS Small planktivores 0.00004 0.0002 0.0002 0.0000 0 0.0001 0 j  a FPS Small planktivores 0.0002 0.0002 0.0002 0 0 0.0001 0 a  a FPS Small planktivores 0.00004 0.0002 0.0002 0 0 0.0001 0 j  j FVD Large flatfish 0 0.01 0 0 0.005 0.01 0.03 a  j FVD Large flatfish 0 0.01 0 0 0.005 0.01 0.03 j  a FVD Large flatfish 0 0.01 0 0 0.005 0.01 0.03 a  a FVD Large flatfish 0 0.01 0 0 0.005 0.01 0.03 j  j FVS Large demersal predators 0 0.05 0.005 0 0.008 0.01 0.05 a  j FVS Large demersal predators 0 0.05 0.005 0 0.008 0.01 0.05 

j  a FVS Large demersal predators 0 0.01 0 0 0.008 0.01 0.05 a  a FVS Large demersal predators 0 0.01 

104

0 0 0.008 0.01 0.05 

j  j FVT Large pelagic predators 0.0005 0.01 0.05 0 0 0.2 0.2 a  j FVT Large pelagic predators 0.0005 0.075 0.05 0 0 0.1 0.1 

j  a FVT Large pelagic predators 0.0005 0.075 0 0 0 0.1 0.1 a  a FVT Large pelagic predators 0.0005 0.075 0 0 0 0.1 0.1 j  j FVO Shearwaters 0.001 0.001 0 0 0 0.001 0 a  j FVO Shearwaters 0.001 0.001 0 0 0 0.001 0 j  a FVO Shearwaters 0.001 0.001 0 0 0 0.001 0 a  a FVO Shearwaters 0.001 0.001 0 0 0 0.001 0 j  j FVB Salmon 0.003 0.01 0.01 0 0 0.01 0.01 a  j FVB Salmon 0.004 0.01 0.01 0 0 0.01 0.01 j  a FVB Salmon 0 0 0 0 0 0 0 a  a FVB Salmon 0 0 0 0 0 0 0 j  j FMM Hake 0.000003 0.00001 0.00001 0 0.00001 0.00001 0.001 a  j FMM Hake 0.000003 0.00001 0.00001 0 0.00001 0.00001 0.001 

j  a FMM Hake 0.000003 0.00001 0 0 0.00001 0.00001 0.001 

a  a FMM Hake 0.000003 0.00001 0 0 0.00001 0.00001 0.001 
Table B-5 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for prey including plank

A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPhj  j FMN Sablefish 0.0003 0.0001 0.001 0 0.001 0.001 0.01 a  j FMN Sablefish 0.0003 0.0001 0.001 0 0.001 0.001 0.01 j  a FMN Sablefish 0.0003 0.0001 0 0 0.001 0.001 0.01 a  a FMN Sablefish 0.0005 0.0001 0 0 0.001 0.001 0.01 j  j FBP Deep vertical migrators 0.0005 0.001 0.0005 0.002 0 0.001 0 a  j FBP Deep vertical migrators 0.0005 0.001 0.0005 0.002 0 0.001 0 j  a FBP Deep vertical migrators 0.0005 0.001 0.0005 0 0 0.001 0 a  a FBP Deep vertical migrators 0.0005 0.001 0.0005 0 0 0.001 0 j  j FDD Deep misc. fish 0 0.01 0 0 0.007 0.01 0 a  j FDD Deep misc. fish 0 0.01 0 0 0.007 0.01 0 j  a FDD Deep misc. fish 0 0.01 0 0 0.007 0.01 0 a  a FDD Deep misc. fish 0 0.01 0 0 0.007 0.01 0 j  j FDS Midwater rockfish 0.00001 0.00001 0.0001 0 0.00001 0.00001 0.005 a  j FDS Midwater rockfish 0.00001 0.00001 0.0001 0 0.00001 0.00001 0.005 j  a FDS Midwater rockfish 0.00001 0.00001 0 0 0.00001 0.00001 0.005 a  a FDS Midwater rockfish 0.00001 0.00001 0 0 0.00001 0.00001 0.005 j  j FDB Small shallow rockfish 0.001 0.001 0.001 0 0.001 0.001 0 a  j FDB Small shallow rockfish 0.001 0.001 0.001 0 0.001 0.001 0 j  a FDB Small shallow rockfish 0.001 0.001 0.001 0 0.001 0.001 0 a  a FDB Small shallow rockfish 0.001 0.001 0.001 0 0.001 0.001 0 j  j FDC Deep small rockfish 0.0005 0.001 0.001 0 0.001 0.001 0 a  j FDC Deep small rockfish 0.0005 0.001 0.001 0 0.001 0.001 0 j  a FDC Deep small rockfish 0.0005 0.001 0.001 0 0.001 0.001 0 a  a FDC Deep small rockfish 0.0005 0.001 0.001 0 0.001 0.001 0 j  j FDO Deep large rockfish 0.0001 0.001 0.001 0 0.001 0.001 0.001 a  j FDO Deep large rockfish 0.0003 0.001 0.001 0 0.001 0.001 0.001 

j  a FDO Deep large rockfish 0 0 0 0 0 0.001 0.001 a  a FDO Deep large rockfish 0.0005 0.001 0 0 0.001 0.001 0.001 j  j FDE Misc. nearshore 0.0005 0.1 0.05 0 0.01 0.1 0 a  j FDE Misc. nearshore 0.0005 0.1 0.05 0 0.01 0.1 0 j  a FDE Misc. nearshore 0.0005 0.1 0.05 0 0.01 0.1 0 

105
Table B-5 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for prey including plank

A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPha  a FDE Misc. nearshore 0.0005 0.1 0.05 0 0.01 0.1 0 j  j FDF Small flatfish 0.0001 0.001 0 0 0.001 0.001 0 a  j FDF Small flatfish 0.0001 0.001 0 0 0.001 0.001 0 j  a FDF Small flatfish 0.0001 0.001 0 0 0.001 0.001 0 a  a FDF Small flatfish 0.0001 0.001 0 0 0.001 0.001 0 j  j SHD Large demersal sharks 0 0 0 0 0.1 0.1 0.1 a  j SHD Large demersal sharks 0 0 0 0 0.1 0.1 0.1 j  a SHD Large demersal sharks 0 0 0 0 0.1 0.1 0.1 a  a SHD Large demersal sharks 0 0 0 0 0.1 0.1 0.1 j  j SHP Misc. pelagic sharks 0 0 0 0 0 0.1 0.1 a  j SHP Misc. pelagic sharks 0 0 0 0 0 0.1 0.1 j  a SHP Misc. pelagic sharks 0 0 0 0 0 0.1 0.1 a  a SHP Misc. pelagic sharks 0 0 0 0 0 0.1 0.1 j  j SHB Small demersal sharks 0.001 0.01 0 0 0.005 0.01 0 a  j SHB Small demersal sharks 0.001 0.01 0 0 0.005 0.01 0 

j  a SHB Small demersal sharks 0.001 0.01 0 0 0.005 0.01 0 a  a SHB Small demersal sharks 0.001 0.01 0 0 0.005 0.01 0 

j  j SHR Shallow large rockfish 0.0005 0.01 0.001 0 0.005 0.01 0.05 a  j SHR Shallow large rockfish 0.0005 0.01 0.001 0 0.005 0.01 0.05 j  a SHR Shallow large rockfish 0.0005 0.01 0 0 0.005 0.01 0.05 a  a SHR Shallow large rockfish 0.0005 0.01 0 0 0.005 0.01 0.05 

j  j SSK Skates and rays 0 0 0 0 0.01 0 0 a  j SSK Skates and rays 0 0 0 0 0.01 0 0 j  a SSK Skates and rays 0 0 0 0 0.01 0 0 a  a SSK Skates and rays 0 0 0 0 0.01 0 0 j  j SB Surface seabirds 0.05 0.1 0 0 0 0.1 0 a j SB Surface seabirds 0.05 0.1 0 0 0 0.1 0 j  a SB Surface seabirds 0.05 0.1 0 0 0 0.1 0 a  a SB Surface seabirds 0.05 0.1 0 0 0 0.1 0 j  j SP Diving seabirds 0.0005 0.1 0.01 0 0.1 0.1 0 a  j SP Diving seabirds 0.0005 0.1 0.01 0 0.1 0.1 0 

106
Table B-5 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for prey including plank

A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPhj  a SP Diving seabirds 0.0005 0.1 0.01 0 0.1 0.1 0 a  a SP Diving seabirds 0.0005 0.1 0.01 0 0.1 0.1 0 j  j REP Transient orcas 0 0 0 0 0 0 0 a  j REP Transient orcas 0 0 0 0 0 0 0 j  a REP Transient orcas 0 0 0 0 0 0 0 a  a REP Transient orcas 0 0 0 0 0 0 0 j  j PIN Pinnipeds 0 0.01 0 0 0.01 0.01 0.01 a  j PIN Pinnipeds 0 0.01 0 0 0.01 0.01 0.01 j  a PIN Pinnipeds 0 0.01 0 0 0.01 0.01 0.01 a  a PIN Pinnipeds 0 0.01 0 0 0.01 0.01 0.01 j  j WHB Baleen whales 0.000005 0.1 0.00002 0 0.00001 0.0001 0 a  j WHB Baleen whales 0.000005 0.1 0.00002 0 0.00001 0.0001 0 j  a WHB Baleen whales 0.000005 0.01 0.00002 0 0.00001 0.0001 0 a  a WHB Baleen whales 0.000005 0.01 0.00002 0 0.00001 0.0001 0 j  j WHT Toothed whales 0 0.001 0 0 0 0.001 0.015 a  j WHT Toothed whales 0 0.001 0 0 0 0.001 0.015 j  a WHT Toothed whales 0 0.001 0 0 0 0.001 0.015 a  a WHT Toothed whales 0 0.001 0 0 0 0.001 0.015 j  j WDG Otters 0 0.1 0 0 0.1 0.1 0.1 a  j WDG Otters 0 0.1 0 0 0.1 0.1 0.1 j  a WDG Otters 0 0.1 0 0 0.1 0.1 0.1 a  a WDG Otters 0 0.1 0 0 0.1 0.1 0.1 

ZG Gelatatinous zooplankton 0.00005 0.0008 0.001 0.0002 0 0.01 0 ZL Large zooplankton 0.0002 0.0008 0.001 0.0002 0 0 0 ZM Mesozooplankton 0 0 0.00008 0.0001 0 0 0 

ZS Microzooplankton 0 0 0 0.0002 0 0 0 

BD Deposit feeders 0 0 0.001 0.0002 0 0 0 BO Meiobenthos 0 0 0 0.00001 0 0 0 BC Carnivorous infauna 0 0 0 0 0 0 0 BFS Shall. benthic filter feeders 0 0 0.001 0.002 0 0 0 

BFF Other benthic filter feeders 0 0 0.008 0.0001 0 0 0 

107
Table B-5 continued. Consumption parameters (variable a in Equation 10) in the calibrated model for prey including plank

A value of 0 indicates cases where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPh

BFD Deep benthic filter feeders 0 0.001 0.001 0.002 0.01 0 0 BMS Shallow macro-zoobenthos 0 0 0 0 0.001 0.001 0 BML Mega-zoobenthos 0 0 0.001 0 0.001 0 0 BMD Deep macro-zoobenthos 0 0 0 0 0.01 0 0 BG Benthic grazers 0 0 0 0 0 0 0 CEP Cephalopods 0.001 0.001 0.005 0 0 0.01 0 PWN Shrimp 0 0 0 0 0.00001 0 0 PWN Shrimp 0 0 0 0 0.00001 0 0 

a In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies juvenile predation on adu

predation on adults. 

b ZG = gelatinous zooplankton. c ZL = large zooplankton. d ZM = mesozooplankton. e ZS = microzooplankton. f PWN = shrimp. 

108g PWNjuv = juvenile shrimp. 

h CEP = cephalopods. 
Table B-6. Parameters in the calibrated model for consumption (variable a in Equation 10) of macroalgae, seagrass, bacter

detritus, and carrion. A value of 0 indicates cases where that predator does not eat that prey. 

Prey group 

Predator 

Macro algae 

Sea grass

Pelagic bacteria 

Sed. bacteria 

Meiobenthos Labile detritus Refr. detritus Carrion 

Labile detritus in sed. 

Refract. detritus in sed. 

Stages* Code Group MA SG PB BB BO DL DR DC DLsed DRsed j  j FPL Lg. planktivores 0 0 0.1 0 0 0.0001 0 0 0 0 a  j FPL Lg. planktivores 0 0 0.1 0 0 0.0001 0 0 0 0 j  a FPL Lg. planktivores 0 0 0.1 0 0 0.0001 0 0 0 0 a  a FPL Lg. planktivores 0 0 0.1 0 0 0.0001 0 0 0 0 j  j FPS Sm. Planktivores 0 0 0.1 0 0 0.0001 0 0 0 0 a  j FPS Sm. Planktivores 0 0 0.1 0 0 0.0001 0 0 0 0 j  a FPS Sm. Planktivores 0 0 0.1 0 0 0.0001 0 0 0 0 a  a FPS Sm. Planktivores 0 0 0.1 0 0 0.0001 0 0 0 0 j  j FVD Lg. flatfish 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 a  j FVD Large flatfish 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 

j  a FVD Large flatfish 0 0 0 0 0 0 0 0.01 0 0 a  a FVD Large flatfish 0 0 0 0 0 0 0 0.01 0 0 j  j FVS Large demersal 

predators 

0 0 0.1 0.01 0.01 0.01 0 0.01 0.01 0 

a  j FVS Large demersal 

predators 

0 0 0.1 0.01 0.01 0.01 0 0.01 0.01 0 

j  a FVS Large demersal 

predators 

0 0 0 0 0 0 0 0.01 0 0 

a  a FVS Large demersal 

predators 

0 0 0 0 0 0 0 0.01 0 0 

j  j FVT Lg. pelagic pred. 0 0 0.01 0 0 0.01 0 0 0 0 a  j FVT Lg. pelagic pred. 0 0 0.01 0 0 0.01 0 0 0 0 j  a FVT Lg. pelagic pred. 0 0 0 0 0 0 0 0 0 0 a  a FVT Lg. pelagic pred. 0 0 0 0 0 0 0 0 0 0 j  j FVO Shearwaters 0 0 0 0 0 0 0 0.01 0 0 a  j FVO Shearwaters 0 0 0 0 0 0 0 0.01 0 0 j  a FVO Shearwaters 0 0 0 0 0 0 0 0.01 0 0 a  a FVO Shearwaters 0 0 0 0 0 0 0 0.01 0 0 j  j FVB Salmon 0 0 0.1 0 0 0.01 0 0 0 0 a  j FVB Salmon 0 0 0.1 0 0 0.01 0 0 0 0 

109
Table B-6 continued. Parameters in the calibrated model for consumption (variable a in Equation 10) of macroalgae, seagr

meiobenthos, detritus, and carrion. A value of 0 indicates cases where that predator does not eat that prey. 

Prey group 

Predator 

Macro algae 

Sea grass

Pelagic bacteria 

Sed. bacteria 

Meiobenthos Labile detritus Refr. detritus Carrion 

Labile detritus in sed. 

Refract. detritus sed. 

Stages* Code Group MA SG PB BB BO DL DR DC DLsed DRsed j  a FVB Salmon 0 0 0 0 0 0 0 0 0 0 a  a FVB Salmon 0 0 0 0 0 0 0 0 0 0 j  j FMM Hake 0 0 0 0 0.01 0.0001 0 0 0 0 a  j FMM Hake 0 0 0 0 0.01 0.0001 0 0 0 0 j  a FMM Hake 0 0 0 0 0 0.0001 0 0 0 0 a  a FMM Hake 0 0 0 0 0 0.0001 0 0 0 0 j  j FMN Sablefish 0 0 0 0 0.01 0.0001 0 0.01 0.01 0 a  j FMN Sablefish 0 0 0 0 0.01 0.0001 0 0.01 0.01 0 j  a FMN Sablefish 0 0 0 0 0 0.0001 0 0.01 0 0 a  a FMN Sablefish 0 0 0 0 0 0.0001 0 0.01 0 0 j  j FBP Deep vertical 

Migrators 

0 0 0.1 0 0 0.0001 0.01 0.01 0 0 

a  j FBP Deep vertical 

Migrators 

0 0 0.1 0 0 0.0001 0.01 0.01 0 0 

j  a FBP Deep vertical 

Migrators 

0 0 0.1 0 0 0.0001 0.01 0.01 0 0 

a  a FBP Deep vertical 

Migrators 

0 0 0.1 0 0 0.0001 0.01 0.01 0 0 

j  j FDD Deep misc. fish 0 0 0 0.01 0.01 0.01 0.01 0.01 0.01 0 a  j FDD Deep misc. fish 0 0 0 0.01 0.01 0.01 0.01 0.01 0.01 0 j  a FDD Deep misc. fish 0 0 0 0.01 0.01 0.01 0.01 0.01 0.01 0 a  a FDD Deep misc. fish 0 0 0 0.01 0.01 0.01 0.01 0.01 0.01 0 j  j FDS Midwater rockfish 0 0 0.1 0 0 0.0001 0 0.01 0.01 0 a  j FDS Midwater rockfish 0 0 0.1 0 0 0.0001 0 0.01 0.01 0 j  a FDS Midwater rockfish 0 0 0 0 0 0 0 0.01 0 0 a  a FDS Midwater rockfish 0 0 0 0 0 0 0 0.01 0 0 j  j FDB Small shallow 

rockfish 

0 0 0.01 0.01 0.01 0.0001 0 0.01 0.01 0 

110
Table B-6 continued. Parameters in the calibrated model for consumption (variable a in Equation 10) of macroalgae, seagr

meiobenthos, detritus, and carrion. A value of 0 indicates cases where that predator does not eat that prey. 

Prey group 

Predator 

Macro algae 

Sea grass

Pelagic bacteria 

Sed. bacteria 

Meiobenthos Labile detritus Refr. detritus Carrion 

Labile detritus in sed. 

Refract. detritus in sed. 

Stages* Code Group MA SG PB BB BO DL DR DC DLsed DRsed a  j FDB Small shallow 

rockfish 

0 0 0.1 0.01 0.01 0.0001 0 0.01 0.01 0 

j  a FDB Small shallow 

rockfish 

0 0 0.1 0.01 0.01 0.0001 0 0.01 0.01 0 

a  a FDB Small shallow 

rockfish 

0 0 0.1 0.01 0.01 0.0001 0 0.01 0.01 0 

j  j FDC Deep small 

Rockfish 

0 0 0.01 0.01 0.01 0.0001 0 0.01 0.01 0 

a  j FDC Deep small 

Rockfish 

0 0 0.01 0.01 0.01 0.0001 0 0.01 0.01 0 

j  a FDC Deep small 

Rockfish 

0 0 0.01 0.01 0.01 0.0001 0 0.01 0.01 0 

a  a FDC Deep small 

Rockfish 

0 0 0.01 0.01 0.01 0.0001 0 0.01 0.01 0 

j  j FDO Deep lg. rockfish 0 

111 0 0.01 0.01 0.01 0.0001 0 0.01 0.01 0 

a  j FDO Deep lg. rockfish 0 0 0.01 0.01 0.01 0.0001 0 0.01 0.01 0 

j  a FDO Deep lg. rockfish 0 0 0 0 0 0 0 0.01 0 0 a  a FDO Deep lg. rockfish 0 0 0 0 0 0 0 0.01 0 0 j  j FDE Misc. nearshore 0 0 0 0.01 0.01 0.01 0.01 0.01 0.01 0 a  j FDE Misc. nearshore 0 0 0 0.01 0.01 0.01 0.01 0.01 0.01 0 

j  a FDE Misc. nearshore 0 0 0 0.01 0.01 0.01 0.01 0.01 0.01 0 a  a FDE Misc. nearshore 0 0 0 0.01 0.01 0.01 0.01 0.01 0.01 0 

j  j FDF Small flatfish 0 0 0 0.01 0.01 0.0001 0 0.01 0.01 0 a  j FDF Small flatfish 0 0 0 0.01 0.01 0.0001 0 0.01 0.01 0 

j  a FDF Small flatfish 0 0 0 0.01 0.01 0.0001 0 0.01 0.01 0 a  a FDF Small flatfish 0 0 0 0.01 0.01 0.0001 0 0.01 0.01 0 

j  j SHD Lg. dem. sharks 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 a  j SHD Lg. dem. sharks 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 j  a SHD Lg. dem. sharks 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 a  a SHD Lg. dem. sharks 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 j  j SHP Misc. pelagic 

sharks 

0 0 0 0 0 0 0 0.01 0 0 
Table B-6 continued. Parameters in the calibrated model for consumption (variable a in Equation 10) of macroalgae, seagr

meiobenthos, detritus, and carrion. A value of 0 indicates cases where that predator does not eat that prey. 

Prey group 

Predator 

Macro algae 

Sea grass

Pelagic bacteria 

Sed. bacteria 

Meiobenthos Labile detritus Refr. detritus Carrion 

Labile detritus in sed. 

Refract. detritus in sed. 

Stages* Code Group MA SG PB BB BO DL DR DC DLsed DRsed a  j SHP Misc. pelagic 

sharks 

0 0 0 0 0 0 0 0.01 0 0 

j  a SHP Misc. pelagic 

sharks 

0 0 0 0 0 0 0 0.01 0 0 

a  a SHP Misc. pelagic 

sharks 

0 0 0 0 0 0 0 0.01 0 0 

j  j SHB Small demersal 

sharks 

0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 

a  j SHB Small demersal 

sharks 

0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 

j  a SHB Small demersal 

sharks 

0 0 0 0 0 0 0 0.01 0.01 0 

a  a SHB Small demersal 

sharks 

0 0 0 0 0 0 0 0.01 0.01 0 

j  j SHR Shallow large 

Rockfish 

0 0 0.1 0.01 0 0.01 0 0.01 0.01 0 

a  j SHR Shallow large 

Rockfish 

0 0 0.1 0.01 0 0.01 0 0.01 0.01 0 

j  a SHR Shallow large 

Rockfish 

0 0 0 0 0 0 0 0.01 0 0 

a  a SHR Shallow large 

Rockfish 

0 0 0 0 0 0 0 0.01 0 0 

j  j SSK Skates and rays 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 a  j SSK Skates and rays 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 j  a SSK Skates and rays 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 a  a SSK Skates and rays 0 0 0 0.01 0.01 0.01 0 0.01 0.01 0 j  j SB Surface seabirds 0 0 0 0 0 0 0 0.01 0 0 a  j SB Surface seabirds 0 0 0 0 0.01 0 0 0.01 0 0 j  a SB Surface seabirds 0 0 0 0 0 0 0 0.01 0 0 a  a SB Surface seabirds 0 0 0 0 0 0 0 0.01 0 0 j  j SP Diving seabirds 0 0.001 0 0.01 0.01 0 0 0.01 0.01 0 a  j SP Diving seabirds 0 0.001 0 0.01 0.01 0 0 0.01 0.01 0 

112
Table B-6 continued. Parameters in the calibrated model for consumption (variable a in Equation 10) of macroalgae, seagr

meiobenthos, detritus, and carrion. A value of 0 indicates cases where that predator does not eat that prey. 

Prey group 

Predator 

Macro algae 

Sea grass

Pelagic bacteria 

Sed. bacteria 

Meiobenthos Labile detritus Refr. detritus Carrion 

Labile detritus in sed. 

Refract. detritus in sed. 

Stages* Code Group MA SG PB BB BO DL DR DC DLsed DRsed j  a SP Diving seabirds 0 0.001 0 0.01 0.01 0 0 0.01 0.01 0 a  a SP Diving seabirds 0 0.001 0 0.01 0.01 0 0 0.01 0.01 0 j  j REP Transient orcas 0 0 0 0 0 0 0 0.01 0 0 a  j REP Transient orcas 0 0 0 0 0 0 0 0.01 0 0 j  a REP Transient orcas 0 0 0 0 0 0 0 0.01 0 0 a  a REP Transient orcas 0 0 0 0 0 0 0 0.01 0 0 j  j PIN Pinnipeds 0 0 0 0 0 0 0 0.01 0 0 a  j PIN Pinnipeds 0 0 0 0 0 0 0 0.01 0 0 j  a PIN Pinnipeds 0 0 0 0 0 0 0 0.01 0 0 a  a PIN Pinnipeds 0 0 0 0 0 0 0 0.01 0 0 j  j WHB Baleen whales 0 0 0 0 0.01 0.0001 0 0 0.01 0 a  j WHB Baleen whales 0 0 0 0 0.01 0.0001 0 0 0.01 0 j  a WHB Baleen whales 0 0 0 0 0.01 0.0001 0 0 0.01 0 a  a WHB Baleen whales 0 0 0 0 0.01 0.0001 0 0 0.01 0 j  j WHT Toothed whales 0 0 0 0 0 0 0 0.01 0 0 a  j WHT Toothed whales 0 0 0 0 0 0 0 0.01 0 0 j  a WHT Toothed whales 0 0 0 0 0 0 0 0.01 0 0 a  a WHT Toothed whales 0 0 0 0 0 0 0 0.01 0 0 j  j WDG Otters 0 0 0 0 0 0 0 0.01 0 0 a  j WDG Otters 0 0 0 0 0 0 0 0.01 0 0 j  a WDG Otters 0 0 0 0 0 0 0 0.01 0 0 a  a WDG Otters 0 0 0 0 0 0 0 0.01 0 0 

ZG Gelatinous 

zooplankton 

0 0 0.001 0 0 0.0001 0.01 0 0 0 

ZL Lg. 

zooplankton 

0 0 0.001 0 0 0.0001 0 0 0 0 

ZM Mesozooplankton 0 0 0.001 0 0 0.0001 0.01 0 0 0 ZS Microzooplankton 0 0 0.001 0 0 0.0001 0.01 0 0 0 

BD Deposit feeders .05 0 0.001 0.01 0.01 0.01 0.01 0.01 0.01 0.01 

113
Table B-6 continued. Parameters in the calibrated model for consumption (variable a in Equation 10) of macroalgae, seagr

meiobenthos, detritus, and carrion. A value of 0 indicates cases where that predator does not eat that prey. 

Prey group 

Predator 

Macro algae 

Sea grass

Pelagic bacteria 

Sed. bacteria 

Meiobenthos Labile detritus Refr. detritus Carrion 

Labile detritus in sed. 

Refract. detritus in sed. 

Stages* Code Group MA SG PB BB BO DL DR DC DLsed DRsed 

BO Meiobenthos 0 0 0.001 0.01 0.01 0.01 0.01 0.01 0.01 0.01 

BC Carnivorous 

infauna 

0 0 0 0.01 0.01 0.0001 0.001 0.01 0.01 0.01 

BFS Shallow benthic 

filter feeders 

0 0 0.001 0.01 0.01 0.0001 0.01 0 0.01 0.01 

BFF Other benthic 

filter feeders 

0 0 0.001 0.01 0.01 0.0001 0.01 0 0.01 0.01 

BFD Deep benthic filter 

feeders 

0 0 0.001 0.01 0.01 0 0.01 0.01 0.01 0.01 

BMS Shallow macrozoobenthos 0 0 0 0.01 0.01 0.0001 0.01 0.01 0.01 0.01 

BML Mega-zoobenthos 0 0 0.001 0.01 0.01 0.0001 0.01 0.01 0.01 0.01 

BMD Deep macrozoobenthos 0 0 0 0.01 0.01 0 0 0.01 0.01 0.01 BG Benthic grazers 0.5 0.1 0 0.01 0 0 0 0 0.01 0.01 CEP Cephalopods 0 0 0 0 0 0.01 0 0.01 0 0 PWN Shrimp 0 0 0.01 0.01 0.01 0.001 0.01 0.01 0.01 0.01 PWN Shrimp 0 0 0.01 0.01 0.01 0.001 0.01 0.01 0.01 0.01 

114

* In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies juvenile predation on ad

predation on adults. 
Table B-7. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare parameter

versus before calibration. Prey groups are primarily birds (FVO) and fish. A ratio of 1 indicates that we did not ch

parameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, and ratios less thlight gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM j  j FPL Large planktivores 1 1,000 0 1 2,000 0.6667 1 a  j FPL Large planktivores 100 

j  a FPL Large planktivores 1,000 1,000 0 100 200 0.6667 100 a  a FPL Large planktivores 10,000 j  j FPS Small planktivores 1 0.02 0 1 1 0.6667 1 a  j FPS Small planktivores j  a FPS Small planktivores 0.03 0.3 0 0.333 0.02 0.6667 0.01 a  a FPS Small planktivores j  j FVD Large flatfish 0 0.004 0.015 a  j VD fish F Large flat j  a FVD Large flatfish 1 0.5 0 0.004 1 0.015 a  a FVD Large flatfish 1 0.5 j  j FVS Large demersal predators 100 10 0 0.5 10 a  j FVS Large demersal predators 10 

115

j  a FVS Large demersal predators 1 1 0 0.5 1 10 a  a FVS Large demersal predators 1 1 0.25 j  j FVT Large pelagic predators 200 1 100 2 1 a  j FVT Large pelagic predators 50 10 1 1 j  a FVT Large pelagic predators 200 2 100 2 1 a  a FVT Large pelagic predators 50 10 1 2 j  j FVO Shearwaters 1 0.1 1 0.1667 1 a  j VO ters F Shearwa 1 j  a FVO Shearwaters 1 0.1 1 0.1667 0.1 a  a VO ters F Shearwa 1 j  j FVB Salmon 1 1 0.02 0.6667 1 a  j VB mon 1 

a VB mon

a VB mon

F Sal 

j  F Sal a  F Sal 
Table B-7 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare 

calibration versus before calibration. Prey groups are primarily birds (FVO) and fish. A ratio of 1 indicates that wconsumption parameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, an

equal to 0.1 are light gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM j  j FMM Hake 0.2 0.01 0 1 0.003 0.0033 0.002 a  j M ake F M H 1 j  a FMM Hake 0.1 0.01 0 0.01 0.003 0.0033 0.002 

a  a M ake F M H 1 j  j FMN Sablefish 1 0.1 0 0.05 1 a  j FMN Sablefish 0.1 j  a FMN Sablefish 1 0.1 0 0.05 1 a  a FMN Sablefish 1 1 0.013 j  j FBP Deep vertical migrators 1 1 1.3333 1 a  j FBP Deep vertical migra torsj  a FBP Deep vertical migrators 1 2 0.4 1 0.1 a  a FBP Deep vertical migrators 10 j  j FDD Deep miscellaneous fish 0 0.5 a 

116

j DD F Deep miscellaneous fish 

j  a FDD Deep miscellaneous fish 0 0.01 0.5 a  a DD F Deep miscellaneous fish j  j FDS Midwater rockfish 1 10 0.01 100 0.01 a  j FDS Midwater rockfish 10 j  a FDS Midwater rockfish 1 1 0 0.01 1 0.01 a  a FDS Midwater rockfish 1 1 3E-04 j  j FDB Small shallow rockfish 1 0.1 1 a  j FDB Small shallow rockfish 1 j  a FDB Small shallow rockfish 1 0.1 0.025 1 1 a  a DB F Small shallow rock fish 1 j  j FDC Deep small rockfish 1 0 0.1 a  j DC fish F Deep small rock 1 j  a FDC Deep small rockfish 1 1 0 0.1 a  a FDC Deep small rockfish 
Table B-7 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare 

calibration versus before calibration. Prey groups are primarily birds (FVO) and fish. A ratio of 1 indicates that wconsumption parameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, an

equal to 0.1 are light gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM j  j FDO Deep large rockfish 1 0 1 a  j DO fish F Deep large rock 1 j  a FDO Deep large rockfish 1 0.2 0.1 0.0667 1 

a  a FDO Deep large rockfish 0.025 j  j FDE Miscellaneous nearshore 0 1 1 a  j FDE Miscellaneous nearshore j  a FDE Miscellaneous nearshore 0.06 0.01 0 0.002 0.1 0.1 a  a FDE Miscellaneous nearshore j  j FDF Small flatfish 1 0 0.1 0.5 0.1 a  j FDF fish Small flat j  a FDF Small flatfish 1 0 0.1 1 0.1 a 

117a FDF fish Small flat 1 

j  j SHD Large demersal sharks 0 1 1 a  j SHD Large demersal sharks 0.025 0.5 j  a SHD Large demersal sharks 0 1 1 a  a SHD Large demersal sharks 0.025 0.5 j  j SHP Miscellaneous pelagic sharks 0.1 0.01 0.0002 0.1 0.04 0.2 0.2 a  j SHP Miscellaneous pelagic sharks 1 0.2 0.001 0.4 1 0.002 j  a SHP Miscellaneous pelagic sharks 0.05 0.01 0.0002 0.1 0.04 0.2 0.2 a  a SHP Miscellaneous pelagic sharks 1 1 0.001 0.5 0.4 1 0.002 j  j SHB Small demersal sharks 1 0 0.02 0.1667 0.1 a  j SHB Small demersal sharks 1 0.3333 j  a SHB Small demersal sharks 1 0 0.02 0.1667 0.1 a  a SHB Small demersal sharks 1 0.3333 j  j SHR Shallow large rockfish 1 1 0 0.2 0.1 0.1 a  j HR S Shallow large rock fish 1 j  a SHR Shallow large rockfish 1 1 0 0.2 0.1 0.1 a  a HR S Shallow large rock fish 1 
Table B-7 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare 

calibration versus before calibration. Prey groups are primarily birds (FVO) and fish. A ratio of 1 indicates that wconsumption parameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, an

equal to 0.1 are light gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM j  j SSK Skates, rays 0 0.025 0.1 a  j SSK rays Skates, j  a SSK Skates, rays 0 0.025 0.1 

a  a SSK rays 

j REP rcas 0.2

j REP rcas 1

Skates, 

j  j SB Surface seabirds 1 1 1 0.3333 1 a  j SB Surface seabirds 1 j  a SB Surface seabirds 1 1 1 0.3333 1 a  a SB Surface seabirds 1 j  j SP Diving seabirds 1 1 1 0.3333 1 a  j SP Diving seabirds 1 j  a SP Diving seabirds 1 1 1 0.3333 1 a  a SP Diving seabirds j  Transient o a  Transient o j  a REP Transient orcas 0.2 a  a REP Transient orcas 1 j  j PIN Pinnipeds 0.5 0.01 0 0.0003 0.05 0.0167 0.1 a  j PIN Pinnipeds 0.0333 1 0 0.001 0.004 0.002 j  a PIN Pinnipeds 0.5 0.01 0 0.0003 0.05 0.0167 0.1 a  a PIN Pinnipeds 0.0333 1 0 0.001 0.004 0.25 0.006 j 

118

j H ales

j H ales

a H ales

a H ales

W B Baleen wh 

a  W B Baleen wh j  W B Baleen wh a  W B Baleen wh j  j WHT Toothed whales 1 0.2 0 0.2 0.02 0.0067 0.2 a  j WHT Toothed whales 0.3333 1 0 0.1 0.02 0.0667 0.033 j  a WHT Toothed whales 0.3333 1 0 0.2 0.02 0.0067 0.2 a  a WHT Toothed whales 0.3333 0.2 0 0.1 0.02 0.0667 0.033 
Table B-7 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare 

calibration versus before calibration. Prey groups are primarily birds (FVO) and fish. A ratio of 1 indicates that wconsumption parameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, an

equal to 0.1 are light gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FPL FPS FVD FVS FVB FVT FVO FMM j  j WDG Otters 0a  j D ters W G Ot j  a WDG Otters 0

a  a D ters W G Ot 

ZG Gelatinous zooplankton 1 0.1 0.1 0.2 0.1 

ZLBD rsBO thosBC unaBFF rs

Large zooplan kton

ZM Mesozooplankton 

ZS Microzooplankton 

Deposit fee deMeioben 

Carnivorous infa 

BFS Shallow benthic filter feeders 

Other benthic filter fee de

BFD Deep benthic filter feeders 

BMS Shallow macro-zoobenthos 0 1 BML Mega-zoobenthos 0 1 1 

BMD B

Deep macro-zoobenthos 

zers

119

G

WW imp

Benthic gra 

CEP Cephalopods 

rimp

1 1 1 1 1 1 

P N Sh P N Shr 

* In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies juvenile predation on ad

predation on adults. 
Table B-8. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare parameter

versus before calibration. Prey groups here include fish and sharks. A ratio of 1 indicates that we did not change c

from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, and ratios less than or equal Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD j  j FPL Large planktivores 1,000 1 1 a  j FPL Large planktivores j  a FPL Large planktivores 300 50 100 

a  a FPL Large planktivores 0.3 j  j FPS Small planktivores 0.002 0.5 5 

a  j FPS Small planktivores j  a FPS Small planktivores 0.001 1 0.2 a  a FPS Small planktivores j  j FVD Large flatfish 0.005 0.2 1.2 0.02 10 1 a  j FVD Large flatfish 0.0333 0.4 1 1 j  a FVD Large flatfish 0.005 0.004 0.12 0.01 1 0.05 1 a  a FVD Large flatfish 0.0333 0.4 1 1 1 j  j FVS Large demersal predators 3.3333 1 50 0.1 1 

a  j FVS Large demersal predators 3.3333 5 1 1 j  a FVS Large demersal predators 3.3333 0.2 10 0.1 1 0.2 1 a  a FVS Large demersal predators 3.3333 1 10 0.167 1 

j  j FVT Large pelagic predators 1 1 1 a  j FVT Large pelagic predators 10 20 

j  a FVT Large pelagic predators 1 10 100 

120

a  a FVT Large pelagic predators 3 20 j  j FVO Shearwaters 1 1 a  j FVO Shearwaters j  a FVO Shearwaters 1 1 a  a FVO Shearwaters j  j FVB Salmon 3.3333 0.2 1 a  j FVB Salmon 5 j  a FVB Salmon 1 a  a FVB Salmon 1.5 
Table B-8 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare 

calibration versus before calibration. Prey groups here include fish and sharks. A ratio of 1 indicates that we did nparameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, and ratios less thlight gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD j  j FMM Hake 2 0.05 0.05 0.01 0.5 1 a  j FMM Hake 2 1 1 1 j  a FMM Hake 1 0.002 0.05 0.002 1 0.015 

a  a FMM Hake 2 1 j  j FMN Sablefish 0.04 1 1.5 1 1 

a  j FMN Sablefish 1 0.6 3 1 j  a FMN Sablefish 0.04 1 0.3 1 0.025 1 

a  a FMN Sablefish 1 0.02 3 1 0.025 1 j  j FBP Deep vertical migrators a  j FBP Deep vertical migrators j  a FBP Deep vertical migrators 0.1 1 1 1 1 

a  a FBP Deep vertical migrators j  j FDD Deep miscellaneous fish 0.2 1 0.05 

a  j FDD Deep miscellaneous fish 1 0.3 j  a FDD Deep miscellaneous fish 0.01 0.2 1 0.3 1 a  a FDD Deep miscellaneous fish 1 0.3 1 j  j FDS Midwater rockfish 0.2 0.1 10 0.2 10 1 

a  j FDS Midwater rockfish 2 1 1 1 j  a FDS Midwater rockfish 0.2 0.004 1 0.2 1 1 

a  a FDS Midwater rockfish 2 1 0.1 1 1 

j  j FDB Small shallow rockfish 2 1 0.5 1 a  j FDB Small shallow rockfish 3 1 j  a FDB Small shallow rockfish 2 1 0.5 1 a  a FDB Small shallow rockfish 3 1 j  j FDC Deep small rockfish 1 0.4 1 1 a  j FDC Deep small rockfish 1 j  a FDC Deep small rockfish 0.4 1 1 a  a FDC Deep small rockfish 1 

121
Table B-8 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare 

calibration versus before calibration. Prey groups here include fish and sharks. A ratio of 1 indicates that we did nparameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, and ratios less thlight gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD j  j FDO Deep large rockfish 1 0.4 1 1 a  j FDO Deep large rockfish 1 1 j  a FDO Deep large rockfish 1.3333 0.02 0.5 0.4 0.2 1 

a  a FDO Deep large rockfish 0.02 1 1 1 j  j FDE Miscellaneous nearshore 1 0.1 1 1 a  j FDE Miscellaneous nearshore j  a FDE Miscellaneous nearshore 0.004 0.1 0.1 1 

a  a FDE Miscellaneous nearshore 0.02 1 1 j  j FDF Small flatfish 1 0.1 0.1 0.2 0.5 1 a  j FDF Small flatfish 10 

j  a FDF Small flatfish 1 0.1 0.1 0.2 0.2 0.002 

a  a FDF Small flatfish 2 j  j SHD Large demersal sharks 1 1 1 1 a  j SHD Large demersal sharks 1 1 1 j  a SHD Large demersal sharks 1 1 1 1 a  a SHD Large demersal sharks 1 1 1 j  j SHP Miscellaneous pelagic sharks 0.002 0.02 0.005 0.1 0.5 1 1 a  j SHP Miscellaneous pelagic sharks 0.005 0.002 0.1 0.5 1 1 1 j  a SHP Miscellaneous pelagic sharks 1 0.02 0.005 0.1 0.5 1 1 

a  a SHP Miscellaneous pelagic sharks 0.005 0.002 0.1 0.5 0.2 1 1 

j  j SHB Small demersal sharks 0.4 2 0.05 0.4 1 1 1 

a  j SHB Small demersal sharks 1.4 1 j  a SHB Small demersal sharks 1 1 0.3 0.4 1 0.002 1 a  a SHB Small demersal sharks 0.2 0.333 1 j  j SHR Shallow large rockfish 0.2 0.1 0.6 1 1 1 

a  j SHR Shallow large rockfish 0.2 1 0.333 j  a SHR Shallow large rockfish 0.2 1 1 1 0.1 1 

a  a SHR Shallow large rockfish 0.8 1 0.333 

122
Table B-8 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare 

calibration versus before calibration. Prey groups here include fish and sharks. A ratio of 1 indicates that we did nparameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, and ratios less thlight gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD j  j SSK Skates, rays 0.2 1 0.1 0.4 1 1 a  j SSK Skates, rays 0.4 0.333 j  a SSK Skates, rays 1 1 0.1 0.2 1 0.017 

a  a SSK Skates, rays 0.4 0.25 j  j SB Surface seabirds 0.1 0.4 a  j SB Surface seabirds j  a SB Surface seabirds 0.1 0.4 a  a SB Surface seabirds j  j SP Diving seabirds 1 0.1 1 1 1 a  j SP Diving seabirds 1.5 j  a SP Diving seabirds 1 0.1 1 1 1 a  a SP Diving seabirds 3 

123

j  j REP Transient orcas a  j REP Transient orcas j  a REP Transient orcas a  a REP Transient orcas j  j PIN Pinnipeds 1 0.01 0.01 0.1 0.6 0.025 1 

a  j PIN Pinnipeds 0.005 0.0016 0.1 1 0.5 0.017 0.1 j  a PIN Pinnipeds 1 0.01 0.01 0.1 0.6 0.025 1 a  a PIN Pinnipeds 0.005 0.0016 0.01 1 0.5 0.1 0.02 j  j WHB Baleen whales a  j WHB Baleen whales j  a WHB Baleen whales a  a WHB Baleen whales j  j WHT Toothed whales 1 0.0167 0.05 0.3333 0.05 0.01 0.3333 1 a  j WHT Toothed whales 0.3333 0.02 0.05 1 0.5 0.06 0.2 1 j  a WHT Toothed whales 1 0.0167 0.05 0.3333 0.15 0.01 0.3333 1 a  a WHT Toothed whales 0.3333 0.02 0.15 1 0.5 0.06 0.2 1 
124

Table B-8 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare 

calibration versus before calibration. Prey groups here include fish and sharks. A ratio of 1 indicates that we did nparameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, and ratios less thlight gray. Blank cells indicate cases where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group FDE FDS FDB FDC FDO FDF SHB SHD j  j WDG Otters 1 1 1 a  j WDG Otters 1 1 1 j  a WDG Otters 1 1 1 a  a WDG Otters 1 1 1 

ZG Gelatinous zooplankton 0.1 0.1 0.1 1 0.5 

ZL Large zooplankton 

ZM Mesozooplankton 

ZS Microzooplankton BD Deposit feeders BO Meiobenthos 

BC Carnivorous infauna 

BFS Shallow benthic filter feeders BFF Other benthic filter feeders 

BFD Deep benthic filter feeders 

BMS Shallow macro-zoobenthos 2 0.1 1 2 1 1 1 BML Mega-zoobenthos 1 1 1 1 1 1 BMD Deep macro-zoobenthos BG Benthic grazers 

CEP Cephalopods 1 0.1 1 1 1 

PWN Shrimp PWN Shrimp 

* In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies juvenile predation on ad

predation on adults. 
Table B-9. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to 

compare parameterization after calibration versus before calibration. Prey groups include 

mammals and seabirds. A ratio of 1 indicates we did not change consumption parameters from 

their initial values. Ratios less than or equal to 0.1 are light gray. Blank cells indicate cases 

where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group SB SP PIN REP WHB WHT WDG 

j  j FPL Large planktivores 

a  j FPL Large planktivores 

j  a FPL Large planktivores 

a  a FPL Large planktivores 

j  j FPS Small planktivores 

a  j FPS Small planktivores 

j  a FPS Small planktivores 

a  a FPS Small planktivores 

j  j FVD Large flatfish 

a  j FVD Large flatfish 

j  a FVD Large flatfish 

a  a FVD Large flatfish 

j  j FVS Large demersal predators 

a  j FVS Large demersal predators 

j  a FVS Large demersal predators 

a  a FVS Large demersal predators 

j  j FVT Large pelagic predators 

a  j FVT Large pelagic predators 

j  a FVT Large pelagic predators 

a  a FVT Large pelagic predators 

j  j FVO Shearwaters 

a  j FVO Shearwaters 

j  a FVO Shearwaters 

a  a FVO Shearwaters 

j  j FVB Salmon 

a  j FVB Salmon 

j  a FVB Salmon 

a  a FVB Salmon 

j  j FMM Hake 

a  j FMM Hake 

j  a FMM Hake 

a  a FMM Hake 

j  j FMN Sablefish 

a  j FMN Sablefish 

j  a FMN Sablefish 

a  a FMN Sablefish 

j  j FBP Deep vertical migrators 

a  j FBP Deep vertical migrators 

j  a FBP Deep vertical migrators 

a  a FBP Deep vertical migrators 

125
Table B-9 continued. Ratio of final values/initial values for consumption parameter (variable a in 

Equation 10) to compare parameterization after calibration versus before calibration. Prey groups 

include mammals and seabirds. A ratio of 1 indicates we did not change consumption parameters 

from their initial values. Ratios less than or equal to 0.1 are light gray. Blank cells indicate cases 

where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group SB SP PIN REP WHB WHT WDG 

j  j FDD Deep miscellaneous fish 

a  j FDD Deep miscellaneous fish 

j  a FDD Deep miscellaneous fish 

a  a FDD Deep miscellaneous fish 

j  j FDS Midwater rockfish 

a  j FDS Midwater rockfish 

j  a FDS Midwater rockfish 

a  a FDS Midwater rockfish 

j  j FDB Small shallow rockfish 

a  j FDB Small shallow rockfish 

j  a FDB Small shallow rockfish 

a  a FDB Small shallow rockfish 

j  j FDC Deep small rockfish 

a  j FDC Deep small rockfish 

j  a FDC Deep small rockfish 

a  a FDC Deep small rockfish 

j  j FDO Deep large rockfish 

a  j FDO Deep large rockfish 

j  a FDO Deep large rockfish 1.00 1.00 1.00 1.00 

a  a FDO Deep large rockfish 

j  j FDE Miscellaneous nearshore 

a  j FDE Miscellaneous nearshore 

j  a FDE Miscellaneous nearshore 

a  a FDE Miscellaneous nearshore 

j  j FDF Small flatfish 

a  j FDF Small flatfish 

j  a FDF Small flatfish 

a  a FDF Small flatfish 

j  j SHD Large demersal sharks 

a  j SHD Large demersal sharks 

j  a SHD Large demersal sharks 

a  a SHD Large demersal sharks 

j  j SHP Miscellaneous pelagic sharks 0.33 0.43 1.00 1.00 

a  j SHP Miscellaneous pelagic sharks 1.00 1.00 1.00 1.00 

j  a SHP Miscellaneous pelagic sharks 0.25 0.43 1.25 1.00 1.00 1.00 

a  a SHP Miscellaneous pelagic sharks 1.00 1.00 1.00 1.00 1.00 1.00 1.00 

j  j SHB Small demersal sharks 

a  j SHB Small demersal sharks 

j  a SHB Small demersal sharks 

a  a SHB Small demersal sharks 

126
Table B-9 continued. Ratio of final values/initial values for consumption parameter (variable a in 

Equation 10) to compare parameterization after calibration versus before calibration. Prey groups 

include mammals and seabirds. A ratio of 1 indicates we did not change consumption parameters 

from their initial values. Ratios less than or equal to 0.1 are light gray. Blank cells indicate cases 

where that predator does not eat that prey. 

Predator Prey group 

Stages* Code Group SB SP PIN REP WHB WHT WDG 

j  j SHR Shallow large rockfish 

a  j SHR Shallow large rockfish 

j  a SHR Shallow large rockfish 

a  a SHR Shallow large rockfish 

j  j SSK Skates, rays 

a  j SSK Skates, rays 

j  a SSK Skates, rays 

a  a SSK Skates, rays 

j  j SB Surface seabirds 

a  j SB Surface seabirds 

j  a SB Surface seabirds 

a  a SB Surface seabirds 

j  j REP Transient orcas 0.25 0.43 1.50 0.01 10.0 1.00 

a  j REP Transient orcas 1.00 1.00 1.50 1.00 1.00 1.00 

j  a REP Transient orcas 0.25 0.43 1.50 0.01 1.00 1.00 

a  a REP Transient orcas 1.00 1.00 1.50 1.00 1.00 1.00 

j  j PIN Pinnipeds 

a  j PIN Pinnipeds 

j  a PIN Pinnipeds 

a  a PIN Pinnipeds 

j  j WHB Baleen whales 

a  j WHB Baleen whales 

j  a WHB Baleen whales 

a  a WHB Baleen whales 

j  j WHT Toothed whales 

a  j WHT Toothed whales 

j  a WHT Toothed whales 

a  a WHT Toothed whales 

j  j WDG Otters 

a  j WDG Otters 

j  a WDG Otters 

a  a WDG Otters 

ZG Gelatinous zooplankton 

ZL Large zooplankton 

ZM Mesozooplankton 

ZS Microzooplankton 

BD Deposit feeders 

BO Meiobenthos 

BC Carnivorous infauna 

BFS Shallow benthic filter feeders 

127
128

Table B-9 continued. Ratio of final values/initial values for consumption parameter (variable a in 

Equation 10) to compare parameterization after calibration versus before calibration. Prey groups 

include mammals and seabirds. A ratio of 1 indicates we did not change consumption parameters 

from their initial values. Ratios less than or equal to 0.1 are light gray. Blank cells indicate cases 

where that predator does not eat that prey. 

 Predator Prey group 

Stages* Code Group SB SP PIN REP WHB WHT WDG 

BFF Other benthic filter feeders 

BFD Deep benthic filter feeders 

BMS Shallow macro-zoobenthos 

BML Mega-zoobenthos 

BMD Deep macro-zoobenthos 

BG Benthic grazers 

CEP Cephalopods 

PWN Shrimp 

PWN Shrimp 

* In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies 

juvenile predation on adults, and aa signifies adult predation on adults. 
Table B-10. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare paramet

calibration versus before calibration. Prey groups shown are benthos, and most consumption parameters were left 

which corresponds to a ratio of 1. Blank cells indicate cases where that predator does not eat that prey. 

Predators Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi BCjj  j FPL Large planktivores 1 a  j FPL Large planktivores 1 j  a FPL Large planktivores 1 1 a  a FPL Large planktivores 1 1 j  j FPS Small planktivores 1 a  j FPS Small planktivores 1 j  a FPS Small planktivores 1 a  a FPS Small planktivores 1 j  j FVD Large flatfish 1 1 1 1 1 1 1 a  j FVD Large flatfish 1 1 1 1 1 1 1 j  a FVD Large flatfish 1 1 1 1 1 1 1 a  a FVD Large flatfish 1 1 1 1 1 1 1 j  j FVS Large demersal pred. 1 1 1 1 1 1 1 a  j FVS Large demersal pred. 1 1 1 1 1 1 1 j  a FVS Large demersal pred. 1 1 1 1 1 1 1 a  a FVS Large demersal pred. 1 1 1 1 1 1 1 j  j FVT Large pelagic predators 1 a  j FVT Large pelagic predators 1 j  a FVT Large pelagic predators 1 a  a FVT Large pelagic predators 1 j  j FVO Shearwaters a  j FVO Shearwaters j  a FVO Shearwaters a  a FVO Shearwaters j  j FVB Salmon 1 a  j FVB Salmon 1 j 

129

a VB mon

a VB mon

F Sal 

a  F Sal 
Table B-10 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Prey groups shown are benthos, and most consumption parameters were left 

which corresponds to a ratio of 1. Blank cells indicate cases where that predator does not eat that prey. 

Predators Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi BCjj  j FMM Hake 1 1 1 1 a  j FMM Hake 1 1 1 1 j  a FMM Hake 1 1 1 1 a  a FMM Hake 1 1 1 1 j  j FMN Sablefish 1 1 1 1 1 1 1 1 a  j FMN Sablefish 1 1 1 1 1 1 1 1 j  a FMN Sablefish 1 1 1 1 1 1 1 1 a  a FMN Sablefish 1 1 1 1 1 1 1 1 j  j FBP Deep vertical migrators 1 a  j FBP Deep vertical migrators 1 j  a FBP Deep vertical migrators 1 a  a FBP Deep vertical migrators 1 j  j FDD Deep miscellaneous fish 1 1 1 1 1 1 1 1 a  j FDD Deep miscellaneous fish 1 1 1 1 1 1 1 1 j  a FDD Deep miscellaneous fish 1 1 1 1 1 1 1 1 a  a FDD Deep miscellaneous fish 1 1 1 1 1 1 1 1 j  j FDS Midwater rockfish 1 1 1 1 1 a  j FDS Midwater rockfish 1 1 1 1 1 j  a FDS Midwater rockfish 1 1 1 1 1 a  a FDS Midwater rockfish 1 1 1 1 1 j  j FDB Small shallow rockfish 1 1 1 1 1 1 a  j FDB Small shallow rockfish 1 1 1 1 1 1 j  a FDB Small shallow rockfish 1 1 1 1 1 1 a  a FDB Small shallow rockfish 1 1 1 1 1 1 j  j FDC Deep small rockfish 1 1 1 1 1 1 a  j FDC Deep small rockfish 1 1 1 1 1 1 j  a FDC Deep small rockfish 1 1 1 1 1 1 a  a FDC Deep small rockfish 1 1 1 1 1 1 

130
Table B-10 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Prey groups shown are benthos, and most consumption parameters were left 

which corresponds to a ratio of 1. Blank cells indicate cases where that predator does not eat that prey. 

Predators Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi BCjj  j FDO Deep large rockfish 1 1 1 1 1 1 a  j FDO Deep large rockfish 1 1 1 1 1 1 j  a FDO Deep large rockfish 1 1 a  a FDO Deep large rockfish 1 1 1 1 1 1 j  j FDE Miscellaneous nearshore 1 1 1 1 1 1 a  j FDE Miscellaneous nearshore 1 1 1 1 1 1 j  a FDE Miscellaneous nearshore 1 1 1 1 1 1 a  a FDE Miscellaneous nearshore 1 1 1 1 1 1 j  j FDF Small flatfish 1 1 1 1 1 1 1 1 a  j FDF Small flatfish 1 1 1 1 1 1 1 1 j  a FDF Small flatfish 1 1 1 1 1 1 1 1 a  a FDF Small flatfish 1 1 1 1 1 1 1 1 j  j SHD Large demersal sharks 1 1 1 1 1 1 1 1 a  j SHD Large demersal sharks 1 1 1 1 1 1 1 1 j  a SHD Large demersal sharks 1 1 1 1 1 1 1 1 a  a SHD Large demersal sharks 1 1 1 1 1 1 1 1 j  j SHP Misc. pelagic sharks 1 1 a  j SHP Misc. pelagic sharks 1 1 j  a SHP Misc. pelagic sharks 1 1 a  a SHP Misc. pelagic sharks 1 1 j  j SHB Small demersal sharks 1 1 1 1 1 1 1 a  j SHB Small demersal sharks 1 1 1 1 1 1 1 j  a SHB Small demersal sharks 1 1 1 1 1 1 1 a  a SHB Small demersal sharks 1 1 1 1 1 1 1 j  j SHR Shallow large rockfish 1 1 1 1 1 a  j SHR Shallow large rockfish 1 1 1 1 1 j  a SHR Shallow large rockfish 1 1 1 1 1 a  a SHR Shallow large rockfish 1 1 1 1 1 

131
Table B-10 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Prey groups shown are benthos, and most consumption parameters were left 

which corresponds to a ratio of 1. Blank cells indicate cases where that predator does not eat that prey. 

Predators Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi BCjj  j SSK Skates, rays 1 1 1 1 1 1 1 1 a  j SSK Skates, rays 1 1 1 1 1 1 1 1 j  a SSK Skates, rays 1 1 1 1 1 1 1 1 a  a SSK Skates, rays 1 1 1 1 1 1 1 1 j  j SB Surface seabirds 1 a  j SB Surface seabirds 1 j  a SB Surface seabirds 1 a  a SB Surface seabirds 1 j  j SP Diving seabirds 1 1 1 1 a  j SP Diving seabirds 1 1 1 1 j  a SP Diving seabirds 1 1 1 1 a  a SP Diving seabirds 1 1 1 1 j  j REP Transient orcas a  j REP Transient orcas j  a REP Transient orcas a  a REP Transient orcas j  j PIN Pinnipeds 1 1 1 1 a  j PIN Pinnipeds 1 1 1 1 j  a PIN Pinnipeds 1 1 1 1 a  a PIN Pinnipeds 1 1 1 1 j  j WHB Baleen whales 2 1 1 1 1 1 1 a  j WHB Baleen whales 2 1 1 1 1 1 1 j  a WHB Baleen whales 2 1 1 1 1 1 1 a  a WHB Baleen whales 2 1 1 1 1 1 1 j  j WHT Toothed whales 1 1 1 1 a  j WHT Toothed whales 1 1 1 1 j  a WHT Toothed whales 1 1 1 1 a  a WHT Toothed whales 1 1 1 1 

132
133

Table B-10 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Prey groups shown are benthos, and most consumption parameters were left 

which corresponds to a ratio of 1. Blank cells indicate cases where that predator does not eat that prey. 

Predators Prey group 

Stagesa Code Group BFSb BFFc BFDd BGe BMDf BMLg BMSh BDi BCjj  j WDG Otters 1 1 1 1 1 1 1 a  j WDG Otters 1 1 1 1 1 1 1 j  a WDG Otters 1 1 1 1 1 1 1 a  a WDG Otters 1 1 1 1 1 1 1 

ZG Gelatinous zooplankton 1 

ZL Large zooplankton 1 

ZM Mesozooplankton 

ZS Microzooplankton BD Deposit feeders 1 BO Meiobenthos 

BC Carnivorous infauna 1 1 

BFS Shall. benthic filter feed. BFF Other benthic filter feed. BFD Deep benthic filter feed. 1 1 1 BMS Shall. macro-zoobenthos 1 1 1 1 1 1 BML Mega-zoobenthos 1 1 1 1 1 BMD Deep macro-zoobenthos 1 1 1 1 1 1 

BG Benthic grazers 

CEP Cephalopods 1 PWN Shrimp 1 1 PWN Shrimp 1 1 

a In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies juvenile predation on adu

predation on adults. 

b BFS = shallow benthic filter feeders. c BFF = other benthic filter feeders. d BFD = deep benthic filter feeders. e BG = benthic grazers. f BMD = deep macro-zoobenthos. g BML = mega-zoobenthos. h BMS = shallow macro-zoobenthos. i BD = deposit feeders. j BC = carnivorous infauna. 
Table B-11. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to 

compare parameterization after calibration versus before calibration. Prey groups here include 

plankton, cephalopods, and shrimp. A ratio of 1 indicates that we did not change consumption 

parameters from their initial values. Ratios equal to or greater than 10 are in dark gray and italics, 

and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that 

predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPh

j  j FPL Large planktivores 1.000 40 3.33333 0.00667 0.0001 

a  j FPL Large planktivores 1.000 40 3.33333 0.00667 0.0001 

j  a FPL Large planktivores 1 2 10 0.0001 

a  a FPL Large planktivores 1 2 10 0.0001 

j  j FPS Small planktivores 0.0008 0.002 0.002 0.002 0.001 

a  j FPS Small planktivores 0.0008 0.002 0.002 0.002 0.001 

j  a FPS Small planktivores 0.004 0.02 0.002 0.001 

a  a FPS Small planktivores 0.0008 0.002 0.002 0.001 

j  j FVD Large flatfish 0.1 0.05 0.1 0.3 

a  j FVD Large flatfish 0.1 0.05 0.1 0.3 

j  a FVD Large flatfish 0.1 0.05 0.1 0.3 

a  a FVD Large flatfish 0.1 0.05 0.1 0.3 

j  j FVS Large demersal pred. 0.5 0.05 0.08 0.1 0.5 

a  j FVS Large demersal pred. 0.5 0.05 0.08 0.1 0.5 

j  a FVS Large demersal pred. 0.1 0.08 0.1 0.5 

a  a FVS Large demersal pred. 0.1 0.08 0.1 0.5 

j  j FVT Large pelagic pred. 1 0.1 0.50251 1 1 

a  j FVT Large pelagic pred. 1 1 0.50251 1 1 

j  a FVT Large pelagic pred. 1 1 1 1 

a  a FVT Large pelagic pred. 1 1 1 1 

j  j FVO Shearwaters 0.2 0.1 0.1 

a  j FVO Shearwaters 2 0.01333 0.01 

j  a FVO Shearwaters 2 0.01333 0.01 

a  a FVO Shearwaters 2 0.01333 0.01 

j  j FVB Salmon 0.06 0.13333 0.1 0.1 0.1 

a  j FVB Salmon 0.08 0.1 0.1 0.1 0.1 

j  a FVB Salmon 

a  a FVB Salmon 

j  j FMM Hake 0.00006 0.00005 0.00005 0.0001 0.00005 0.1 

a  j FMM Hake 0.00006 0.0001 0.0001 0.0001 0.0001 0.01 

j  a FMM Hake 0.00006 0.0001 0.0001 0.0001 0.01 

a  a FMM Hake 0.00006 0.001 0.0001 0.0001 0.01 

j  j FMN Sablefish 0.006 0.001 0.01 0.01 0.01 0.1 

a  j FMN Sablefish 0.006 0.001 0.01 0.01 0.01 0.1 

j  a FMN Sablefish 0.006 0.001 0.01 0.01 0.1 

a  a FMN Sablefish 0.01 0.001 0.01 0.01 0.1 

j  j FBP Deep vert. migrators 1 0.1 0.1 0.2 0.01 

a  j FBP Deep vert. migrators 1 0.1 0.1 0.2 0.01 

j  a FBP Deep vert. migrators 1 0.1 0.05 0.01 

a  a FBP Deep vert. migrators 1 0.1 0.05 0.01 

134
Table B-11 continued. Ratio of final values/initial values for consumption parameter (variable a in 

Equation 10) to compare parameterization after calibration versus before calibration. Prey groups 

here include plankton, cephalopods, and shrimp. A ratio of 1 indicates that we did not change 

consumption parameters from their initial values. Ratios equal to or greater than 10 are in dark 

gray and italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases 

where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPh

j  j FDD Deep misc. fish 0.1 0.07 0.1 

a  j FDD Deep misc. fish 0.1 0.07 0.1 

j  a FDD Deep misc. fish 0.1 0.07 0.1 

a  a FDD Deep misc. fish 0.1 0.07 0.1 

j  j FDS Midwater rockfish 0.0002 0.0001 0.001 0.0001 0.0001 0.05 

a  j FDS Midwater rockfish 0.0002 0.0001 0.001 0.0001 0.0001 0.05 

j  a FDS Midwater rockfish 0.0002 0.0001 0.0001 0.0001 0.05 

a  a FDS Midwater rockfish 0.0002 0.0001 0.0001 0.0001 0.05 

j  j FDB Small shall. rockfish 0.02 0.01 0.01 0.01 0.01 

a  j FDB Small shall. rockfish 0.02 0.01 0.01 0.01 0.01 

j  a FDB Small shall. rockfish 0.02 0.01 0.01 0.01 0.01 

a  a FDB Small shall. rockfish 0.02 0.01 0.01 0.01 0.01 

j  j FDC Deep small rockfish 0.01 0.01 0.01 0.01 0.01 

a  j FDC Deep small rockfish 0.01 0.01 0.01 0.01 0.01 

j  a FDC Deep small rockfish 0.01 0.01 0.01 0.01 0.01 

a  a FDC Deep small rockfish 0.01 0.01 0.01 0.01 0.01 

j  j FDO Deep large rockfish 0.002 0.01 0.01 0.01 0.01 0.01 

a  j FDO Deep large rockfish 0.006 0.01 0.01 0.01 0.01 0.01 

j  a FDO Deep large rockfish 0.01 0.01 

a  a FDO Deep large rockfish 0.01 0.01 0.01 0.01 0.01 

j  j FDE Misc. nearshore 1 1 0.625 0.1 1 

a  j FDE Misc. nearshore 1 1 0.625 0.1 1 

j  a FDE Misc. nearshore 1 1 0.625 0.1 1 

a  a FDE Misc. nearshore 1 1 0.625 0.1 1 

j  j FDF Small flatfish 0.002 0.01 0.01 0.01 

a  j FDF Small flatfish 0.002 0.01 0.01 0.01 

j  a FDF Small flatfish 0.002 0.01 0.01 0.01 

a  a FDF Small flatfish 0.002 0.01 0.01 0.01 

j  j SHD Large demersal sharks 1 1 1 

a  j SHD Large demersal sharks 1 1 1 

j  a SHD Large demersal sharks 1 1 1 

a  a SHD Large demersal sharks 1 1 1 

j  j SHP Misc. pelagic sharks 1 1 

a  j SHP Misc. pelagic sharks 1 1 

j  a SHP Misc. pelagic sharks 1 1 

a  a SHP Misc. pelagic sharks 1 1 

j  j SHB Small demersal sharks 0.02 0.1 0.05 0.1 

a  j SHB Small demersal sharks 0.02 0.1 0.05 0.1 

j  a SHB Small demersal sharks 0.02 0.1 0.05 0.1 

a  a SHB Small demersal sharks 0.02 0.1 0.05 0.1 

135
Table B-11 continued. Ratio of final values/initial values for consumption parameter (variable a in 

Equation 10) to compare parameterization after calibration versus before calibration. Prey groups 

here include plankton, cephalopods, and shrimp. A ratio of 1 indicates that we did not change 

consumption parameters from their initial values. Ratios equal to or greater than 10 are in dark 

gray and italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases 

where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPh

j  j SHR Shallow large rockfish 1 0.1 0.0125 0.05 0.1 0.5 

a  j SHR Shallow large rockfish 1 0.1 0.0125 0.05 0.1 0.5 

j  a SHR Shallow large rockfish 1 0.1 0.05 0.1 0.5 

a  a SHR Shallow large rockfish 1 0.1 0.05 0.1 0.5 

j  j SSK Skates, rays 0.1 

a  j SSK Skates, rays 0.1 

j  a SSK Skates, rays 0.1 

a  a SSK Skates, rays 0.1 

j  j SB Surface seabirds 1 1 1 

a  j SB Surface seabirds 1 1 1 

j  a SB Surface seabirds 1 1 1 

a  a SB Surface seabirds 1 1 1 

j  j SP Diving seabirds 1 1 0.125 1 1 

a  j SP Diving seabirds 1 1 0.125 1 1 

j  a SP Diving seabirds 1 1 0.125 1 1 

a  a SP Diving seabirds 1 1 0.125 1 1 

j  j REP Transient orcas 

a  j REP Transient orcas 

j  a REP Transient orcas 

a  a REP Transient orcas 

j  j PIN Pinnipeds 0.1 0.1 0.1 0.1 

a  j PIN Pinnipeds 0.1 0.1 0.1 0.1 

j  a PIN Pinnipeds 0.1 0.1 0.1 0.1 

a  a PIN Pinnipeds 0.1 0.1 0.1 0.1 

j  j WHB Baleen whales 0.0001 1 0.0002 0.0001 0.001 

a  j WHB Baleen whales 0.0001 1 0.0002 0.0001 0.001 

j  a WHB Baleen whales 0.0001 0.1 0.0002 0.0001 0.001 

a  a WHB Baleen whales 0.0001 0.1 0.0002 0.0001 0.001 

j  j WHT Toothed whales 0.02 0.01 0.15 

a  j WHT Toothed whales 0.02 0.01 0.15 

j  a WHT Toothed whales 0.02 0.01 0.15 

a  a WHT Toothed whales 0.02 0.01 0.15 

j  j WDG Otters 1 1 1 1 

a  j WDG Otters 1 1 1 1 

j  a WDH Otters 1 1 1 1 

a  a WDG Otters 1 1 1 1 

ZG Gelatinous zooplank. 1 1 2 1 0.1 

ZL Large zooplankton 0.4 1 1.28205 1 

ZM Mesozooplankton 10 10 

ZS Microzooplankton 0.2 

136
137

Table B-11 continued. Ratio of final values/initial values for consumption parameter (variable a in 

Equation 10) to compare parameterization after calibration versus before calibration. Prey groups 

here include plankton, cephalopods, and shrimp. A ratio of 1 indicates that we did not change 

consumption parameters from their initial values. Ratios equal to or greater than 10 are in dark 

gray and italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases 

where that predator does not eat that prey. 

Predator Prey group 

Stagesa Code Group ZGb ZLc ZMd ZSe PWNf PWNjuvg CEPh

BD Deposit feeders 0.3 0.2 

BO Meiobenthos 1 

BC Carnivorous infauna 

BFS Shall. benthic 

filter feeders 

 0.11765 2 

 BFF Other benthic 

filter feeders 

 100 1 

 BFD Deep benthic 

filter feeders 

0.01 0.1 0.2 0.2 

 BMS Shallow macrozoobenthos  0.01 0.01 

BML Mega-zoobenthos 0.02 

 BMD Deep macrozoobenthos  0.2 

BG Benthic grazers 

CEP Cephalopods 1 0.2 1 0.1 

PWN Shrimp 0.0002 

PWN Shrimp 0.0002 

a

 In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies 

juvenile predation on adults, and aa signifies adult predation on adults. b ZG = gelatinous zooplankton. 

c

 ZL = large zooplankton. 

d

 ZM = mesozooplankton. 

e

 ZS = microzooplankton. 

f

 PWN = shrimp. 

g

 PWNjuv = juvenile shrimp. 

h CEP = cephalopods. 
Table B-12. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compare paramet

calibration versus before calibration. Consumed groups here include macroalgae, seagrass, bacteria, detritus, and cindicates that we did not change consumption parameters from their initial values. Ratios equal to or greater than 1italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that predator does not 

Prey group 

Predator 

Stagesa Code Group 

Macro algae MA 

Sea grassSG 

Pelagic bacteriaPB 

Sed. bacteriaBBb

MeiobenthosBO 

Labile detritusDL 

Refr. detritus DRc

Carrion DC 

Labile detritusin sed. DLsedd

Refr. detritus in sed. DRsede

Cin D

j  j FPL Large 

planktivores 

1.00 0.01 

a  j FPL Large 

planktivores 

1.00 0.01 

j  a FPL Large 

planktivores 

1.00 0.01 

a  a FPL Large 

planktivores 

1.00 0.01 

j  j FPS Small 

planktivores 

1.00 0.01 

a  j FPS Small 

planktivores 

1.00 0.01 

j  a FPS Small 

planktivores 

1.00 0.01 

a  a FPS Small 

planktivores 

1.00 0.01 

j  j FVD Lg. flatfish 1.00 1.00 1.00 1.00 1.00 1a  j FVD Lg. flatfish 1.00 1.00 1.00 1.00 1.00 1j  a FVD Lg. flatfish 1.00 a  a FVD Lg. flatfish 1.00 j  j FVS Lg. demersal 

predators 

1.00 1.00 1.00 1.00 1.00 1.00 1

a  j FVS Lg. demersal 

predators 

1.00 1.00 1.00 1.00 1.00 1.00 1

j  a FVS Lg. demersal 

predators 

1.00 

a  a FVS Lg. demersal 

predators 

1.00 

j  j FVT Lg. pelagic 

predators 

1.00 1.00 

a  j FVT Lg. pelagic 

predators 

1.00 1.00 

138
Table B-12 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Consumed groups here include macroalgae, seagrass, bacteria, detritus, and c

indicates that we did not change consumption parameters from their initial values. Ratios equal to or greater than 1italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that predator does not 

Prey group 

Predator 

Stagesa Code Group 

Macro algae MA 

Sea grassSG 

Pelagic bacteriaPB 

Sed. bacteriaBBb

MeiobenthosBO 

Labile detritusDL 

Refr. detritus DRc

Carrion DC 

Labile detritusin sed. DLsedd

Refr. detritus in sed. DRsede

Cin D

j  a FVT Lg. pelagic 

predators 

a  a FVT Lg. pelagic 

predators 

j  j FVO Shearwaters 1.00 a  j FVO Shearwaters 1.00 j  a FVO Shearwaters 1.00 a  a FVO Shearwaters 1.00 j  j FVB Salmon 1.00 1.00 a  j FVB Salmon 1.00 1.0 j 

139a V mon V mon F B Sal a  a F B Sal 

j  j FMM Hake 1.00 0.01 

a  j FMM Hake 1.00 0.01 j  a FMM Hake 0.01 a  a FMM Hake 0.01 j  j FMN Sablefish 1.00 0.01 1.00 1.00 1a  j FMN Sablefish 1.00 0.01 1.00 1.00 1j  a FMN Sablefish 0.01 1.00 a  a FMN Sablefish 0.01 1.00 j  j FBP Deep vert. 

migrators 

1.00 0.01 1.00 1.00 

a  j FBP Deep vert. 

migrators 

1.00 0.01 1.00 1.00 

j  a FBP Deep vert. 

migrators 

1.00 0.01 1.00 1.00 

a  a FBP Deep vert. 

migrators 

1.00 0.01 1.00 1.00 

j  j FDD Deep misc. 

fish 

1.00 1.00 1.00 1.00 1.00 1.00 1
Table B-12 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Consumed groups here include macroalgae, seagrass, bacteria, detritus, and c

indicates that we did not change consumption parameters from their initial values. Ratios equal to or greater than 1italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that predator does not 

Prey group 

Predator 

Stagesa Code Group 

Macro algae MA 

Sea grassSG 

Pelagic bacteriaPB 

Sed. bacteriaBBb

MeiobenthosBO 

Labile detritusDL 

Refr. detritus DRc

Carrion DC 

Labile detritusin sed. DLsedd

Refr. detritus in sed. DRsede

Cin D

a  j FDD Deep misc. 

fish 

1.00 1.00 1.00 1.00 1.00 1.00 1

j  a FDD Deep misc. 

fish 

1.00 1.00 1.00 1.00 1.00 1.00 1

a  a FDD Deep misc. 

fish 

1.00 1.00 1.00 1.00 1.00 1.00 1

j  j FDS Midwater 

rockfish 

1.00 0.01 1.00 1.00 1

a  j FDS Midwater 

rockfish 

1.00 0.01 1.00 1.00 1

j  a FDS Midwater 

rockfish 

1.00 

a  a FDS Midwater 

rockfish 

1.00 

j  j FDB Sm. Shallow 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

a  j FDB Sm. Shallow 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

j  a FDB Sm. Shallow 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

a  a FDB Sm. Shallow 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

j  j FDC Deep small 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

a  j FDC Deep small 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

j  a FDC Deep small 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

a  a FDC Deep small 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

140
Table B-12 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Consumed groups here include macroalgae, seagrass, bacteria, detritus, and c

indicates that we did not change consumption parameters from their initial values. Ratios equal to or greater than 1italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that predator does not 

Prey group 

Predator 

Stagesa Code Group 

Macro algae MA 

Sea grassSG 

Pelagic bacteriaPB 

Sed. bacteriaBBb

MeiobenthosBO 

Labile detritusDL 

Refr. detritus DRc

Carrion DC 

Labile detritusin sed. DLsedd

Refr. detritus in sed. DRsede

Cin D

j  j FDO Deep large 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

a  j FDO Deep large 

rockfish 

1.00 1.00 1.00 0.01 1.00 1.00 1

j  a FDO Deep large 

rockfish 

1.00 

a  a FDO Deep large 

rockfish 

1.00 

j  j FDE Misc. 

nearshore 

1.00 1.00 1.00 1.00 1.00 1.00 1

a  j FDE Misc. 

nearshore 

1.00 1.00 1.00 1.00 1.00 1.00 1

j  a FDE Misc. 

nearshore 

1.00 1.00 1.00 1.00 1.00 1.00 1

a  a FDE Misc. 

nearshore 

1.00 1.00 1.00 1.0 1.0 1.00 1

j  j FDF Small flatfish 1.00 1.00 0.01 1.00 1.00 1

a  j FDF Small flatfish 1.00 1.00 0.01 1.00 1.00 1j  a FDF Small flatfish 1.00 1.00 0.01 1.00 1.00 1a  a FDF Small flatfish 1.00 1.00 0.01 1.00 1.00 1j  j SHD Large demer. 

sharks 

1.00 1.00 1.00 1.00 1.00 1

a  j SHD Large demer. 

sharks 

1.00 1.00 1.00 1.00 1.00 1

j  a SHD Large demer. 

sharks 

1.00 1.00 1.00 1.00 1.00 1

a  a SHD Large demer. 

sharks 

1.00 1.00 1.00 1.00 1.00 1

j  j SHP Misc. pelagic 

sharks 

1.00 

a  j SHP Misc. pelagic 

sharks 

1.00 

141
Table B-12 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Consumed groups here include macroalgae, seagrass, bacteria, detritus, and c

indicates that we did not change consumption parameters from their initial values. Ratios equal to or greater than 1italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that predator does not 

Prey group 

Predator 

Stagesa Code Group 

Macro algae MA 

Sea grassSG 

Pelagic bacteriaPB 

Sed. bacteriaBBb

MeiobenthosBO 

Labile detritusDL 

Refr. detritus DRc

Carrion DC 

Labile detritusin sed. DLsedd

Refr. detritus in sed. DRsede

Cin D

j  a SHP Misc. pelagic 

sharks 

1.00 

a  a SHP Misc. pelagic 

sharks 

1.00 

j  j SHB Sm. Demersal 

sharks 

1.00 1.00 1.00 1.00 1.00 1

a  j SHB Sm. Demersal 

sharks 

1.00 1.00 1.00 1.00 1.00 1

j  a SHB Sm. Demersal 

sharks 

1.00 1.00 1

a  a SHB Sm. Demersal 

sharks 

1.00 1.00 1

j  j SHR Shallow lg. 

rockfish 

1.00 1.00 1.00 1.00 1.00 1

a  j SHR Shallow lg. 

rockfish 

1.00 1.00 1.00 1.00 1.00 1

j  a SHR Shallow lg. 

rockfish 

1.00 

a  a SHR Shallow lg. 

rockfish 

1.00 

j  j SSK Skates, rays 1.00 1.00 1.00 1.00 1.00 1a  j SSK Skates, rays 1.00 1.00 1.00 1.00 1.00 1j  a SSK Skates, rays 1.00 1.00 1.00 1.00 1.00 1a  a SSK Skates, rays 1.00 1.00 1.00 1.00 1.00 1j  j SB Surface 

seabirds 

1.00 

a  j SB Surface 

seabirds 

1.00 1.00 

j  a SB Surface 

seabirds 

1.00 

a  a SB Surface 

seabirds 

1.00 

142
Table B-12 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Consumed groups here include macroalgae, seagrass, bacteria, detritus, and c

indicates that we did not change consumption parameters from their initial values. Ratios equal to or greater than 1italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that predator does not 

Prey group 

Predator 

Stagesa Code Group 

Macro algae MA 

Sea grassSG 

Pelagic bacteriaPB 

Sed. bacteriaBBb

MeiobenthosBO 

Labile detritusDL 

Refr. detritus DRc

Carrion DC 

Labile detritusin sed. DLsedd

Refr. detritus in sed. DRsede

Cin D

j  j SP Diving 

seabirds 

1.00 1.00 1.00 1.00 1.00 1

a  j SP Diving 

seabirds 

1.00 1.00 1.00 1.0 1.00 1

j  a SP Diving 

seabirds 

1.00 1.00 1.00 1.00 1.00 1

a  a SP Diving 

seabirds 

1.00 1.00 1.00 1.00 1.00 1

j  j REP Transient 

orcas 

1.00 

a  j REP Transient 

orcas 

1.00 

j  a REP Transient 

orcas 

1.00 

a  a REP Transient 

orcas 

1.00 

j  j PIN Pinnipeds 1.00 a  j PIN Pinnipeds 1.00 j  a PIN Pinnipeds 1.00 a  a PIN Pinnipeds 1.00 j  j WHB Baleen whales 1.00 0.01 1.00 1

a  j WHB Baleen whales 1.00 0.01 1.00 1j  a WHB Baleen whales 1.00 0.01 1.00 1a  a WHB Baleen whales 1.00 0.01 1.00 1j  j WHT Toothed 

whales 

1.00 1

a  j WHT Toothed 

whales 

1.00 1

j  a WHT Toothed 

whales 

1.00 1

a  a WHT Toothed 

whales 

1.00 1

143
Table B-12 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Consumed groups here include macroalgae, seagrass, bacteria, detritus, and c

indicates that we did not change consumption parameters from their initial values. Ratios equal to or greater than 1italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that predator does not 

Prey group 

Predator 

Stagesa Code Group 

Macro algae MA 

Sea grassSG 

Pelagic bacteriaPB 

Sed. bacteriaBBb

MeiobenthosBO 

Labile detritusDL 

Refr. detritus DRc

Carrion DC 

Labile detritusin sed. DLsedd

Refr. detritus in sed. DRsede

Cin D

j  j WDG Otters 1.00 1a  j WDG Otters 1.00 1j  a WDG Otters 1.00 1a  a WDG Otters 1.00 1

ZG Gelatinous 

zooplankton 

0.01 0.01 1.00 

ZL Large 

zooplankton 

0.01 0.01 

ZM Mesozooplankton 0.01 0.01 1.00 

ZS Microzooplankton 0.01 0.01 1.00 

BD Deposit 

feeders 

1.00 0.01 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1

BO Meiobenthos 0.01 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1

BC Carnivorous 

infauna 

1.00 1.00 0.01 0.10 1.00 1.00 1.00 1

BFS Shall. benthic 

filter feeders 

0.1 1.00 1.00 0.01 1.00 1.00 1.00 

BFF Other benthic 

filter feeders 

0.01 1.00 1.00 0.01 1.00 1.00 1.00 

BFD Deep benthic 

filter feeders 

0.01 1.00 1.00 1.00 1.00 1.00 1.00 1

BMS Shall. macrozoobenthos 1.00 1.00 0.01 1.00 1.00 1.00 1.00 1

BML Megazoobenthos 0.01 1.00 1.00 0.01 1.00 1.00 1.00 1.00 1

BMD Deep macrozoobenthos 1.00 1.00 1.00 1.00 1.00 1

BG Benthic 

grazers 

1.00 1.00 1.00 1.00 1

CEP Cephalopods 1.00 1.00 

144
Table B-12 continued. Ratio of final values/initial values for consumption parameter (variable a in Equation 10) to compar

calibration versus before calibration. Consumed groups here include macroalgae, seagrass, bacteria, detritus, and c

indicates that we did not change consumption parameters from their initial values. Ratios equal to or greater than 1italics, and ratios less than or equal to 0.1 are in light gray. Blank cells indicate cases where that predator does not 

Prey group 

Predator 

Stagesa Code Group 

Macro algae MA 

Sea grassSG 

Pelagic bacteriaPB 

Sed. bacteriaBBb

MeiobenthosBO 

Labile detritusDL 

Refr. detritus DRc

Carrion DC 

Labile detritusin sed. DLsedd

Refr. detritus in sed. DRsede

Cin D

PWN Shrimp 1.00 1.00 1.00 0.1 1.00 1.00 1.00 1.00 1PWM Shrimp 1.00 1.00 1.00 0.1 1.00 1.00 1.00 1.00 1

a In the stages column, jj signifies juvenile predation on juveniles, aj signifies adult predation on juveniles, ja signifies juvenile predation on adu

predation on adults. 

b BB = sedimentary bacteria. c DR = refractory detritus. d DLsed = labile detritus in sediment. e DRsed = refractory detritus in sediment. f DCsed = carrion in sediment. g PL = large phytoplankton. 

145h PS = small phytoplankton. 

Most NOAA Technical Memorandums NMFS-NWFSC are available online at the

Northwest Fisheries Science Center web site (http://www.nwfsc.noaa.gov)

NOAA Technical Memorandum NMFS-NWFSC83 Hecht, S.A., D.H. Baldwin, C.A. Mebane, T. Hawkes, S.J. Gross, and N.L. Scholz. 2007. An overview 

of sensory effects on juvenile salmonids exposed to dissolved copper: Applying a benchmark concentration 

approach to evaluate sublethal neurobehavioral toxicity. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-83, 39 p. NTIS number pending.

82 Helser, T.E., I.J. Stewart, C.E. Whitmire, and B.H. Horness. 2007. Model-based estimates of abundance 

for 11 species from the NMFS slope surveys. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC82, 145 p. NTIS number pending.

81 Hard, J.J., J.M. Myers, M.J. Ford, R.G. Cope, G.R. Pess, R.S. Waples, G.A. Winans, B.A. Berejikian, 

F.W. Waknitz, P.B. Adams. P.A. Bisson, D.E. Campton, and R.R. Reisenbichler. 2007. Status review of 

Puget Sound steelhead (Oncorhynchus mykiss). U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC81, 117 p. NTIS number PB2008-100451.

80 Berntson, E.A., P.S. Levin, and P.C. Moran (editors). 2007. Conservation of North Pacific rockfishes: 

Ecological genetics and stock structure. Proceedings of the workshop, March 2-3, 2004, Seattle, Washington. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-80, 80 p. NTIS number PB2007-111137.

79 Lawson, P.W., E.P. Bjorkstedt, M.W. Chilcote, C.W. Huntington, J.S. Mills, K.M.S. Moore, T.E.

 Nickelson, G.H. Reeves, H.A. Stout, T.C. Wainwright, and L.A. Weitkamp. 2007. Identification of 

 historical populations of coho salmon (Oncorhynchus kisutch) in the Oregon coast evolutionarily significant 

 unit. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-79, 129 p. NTIS number PB2007-111607.

78 Ruckelshaus, M.H., K.P. Currens, W.H. Graeber, R.R. Fuerstenberg, K. Rawson, N.J. Sands, and J.B. 

Scott. 2006. Independent populations of Chinook salmon in Puget Sound. U.S. Dept. Commer., NOAA 

Tech. Memo. NMFS-NWFSC-78, 125 p. NTIS number PB2007-104920.

77 Sloan, C.A., D.W. Brown, G.M. Ylitalo, J. Buzitis, D.P. Herman, D.G. Burrows, G. Yanagida, R.W. 

Pearce, J.L. Bolton, R.H. Boyer, and M.M. Krahn. 2006. Quality assurance plan for analyses of environmental samples for polycyclic aromatic compounds, persistent organic pollutants, fatty acids, stable isotope ratios, 

lipid classes, and metabolites of polycyclic aromatic compounds. U.S. Dept. Commer., NOAA Tech. Memo. 

NMFS-NWFSC-77, 30 p. NTIS number PB2007-104919.

76 Gustafson R.G., J. Drake, M.J. Ford, J.M. Myers, E.E. Holmes, and R.S. Waples. 2006. Status review 

of Cherry Point Pacific herring (Clupea pallasii) and updated status review of the Georgia Basin Pacific 

herring distinct population segment under the Endangered Species Act. U.S. Dept. Commer., NOAA Tech. 

Memo. NMFS-NWFSC-76, 182 p. NTIS number PB2007-104918.

Recent NOAA Technical Memorandums

published by the

Northwest Fisheries Science Center