Subregional heatmaps of functional group spatial distributions.

Each functional group was broken out into the 15 subregions via survey data, fisheries landings data, or species distribution models (see Methods), or distributional assumptions when there was a lack of available information. The color of each subregional cell is a gradient denoting the proportion of biomass (for each functional group) that is within each subregional cell (with red being the highest and pale yellow being the lowest proportions, respectively). The proportion of biomass in each subregion sums to 1 across all subregions. See “SubRegions/” in supplemental data and code to reproduce this plot, and for plots of all functional groups). Adult Chinook, common murre, and sooty shearwater distributions are based off of the juvenile salmon and ocean ecosystem survey (JSOES); hake distributions are from the hake acoustic trawl survey; herring, jack mackerel, and sardine distributions are from the coastal pelagic species (CPS) acoustic trawl survey; and Southern resident killer whale (SRKW) distributions are based off of movement data from satellite-tagged Southern resident killer whales [130]. State outline data comes from US Department of Commerce, Census Bureau, Cartographic Boundary Files.</p

Primary production time series as both ecosystem model output and vertically generalized production model.

Satellite imagery-derived estimates of daily primary productivity via a vertically generalized production model (VGPM, blue lines) [50, 51] are plotted against ecosystem model-derived estimates of primary production driven by an upwelling time series (black lines are aggregated large and small phytoplankton functional groups). The average values of the final eight years of the VGPM (2014–2021) are used to inform the starting conditions (values) for the ecosystem model. After this point, the ecosystem model is driven entirely by nutrient inputs to the system as determined by the coastal upwelling transport index (CUTI) [42], and any resemblance to the VGPM time series is an indication that the ecosystem model is capturing the appropriate dynamics in primary productivity.</p

EcoTran trophic network of ecosystem model.

The EcoTran trophic network is visualized here as a weighted, directed graph. Numbered nodes are functional groups (see Table 1 for numbers), while arrows indicate directed edges (energy flows from producer groups towards consumer groups). The shade of green indicates strength of interaction (higher diet preference and prey biomass results in darker green network edges) up to a value of 0.10, at which point network edges get thicker with higher values, as in Fig 5. This graph includes detritus groups (86–90), which dominate the network.</p

Simplified Chinook salmon centric EcoTran trophic network.

The EcoTran trophic network is visualized here as a weighted, directed graph with detritus groups (86–90) and those without direct energy flow to or from Chinook salmon groups removed. That is, this is a simplified version of Fig 7, which allows for a focused perspective on Chinook salmon. Numbered nodes are functional groups (see Table 1 for numbers); arrows indicate directed edges (energy flows from producer groups towards consumer groups). The color intensity and line thickness indicates strength of interaction. Higher diet preference and prey biomass results in darker network edges up to a value of 0.025, at which point network edges get thicker with higher values (direct salmon connections are in red, all other connections in grey).</p

Fishery discards for each functional group.

The table contains information about the yearly discards (mt/km2) of each fishery in the model (columns in table; see Table 2 for descriptions) for each living functional group (rows of table) in the model. See https://doi.org/10.5281/zenodo.7079777 for a csv version of this table and see Table 1, S2–S5 Tables for other ecosystem model parameters. (CSV)</p

Cross-shelf physical model.

The EcoTran ecosystem model allows direct linking of physical oceanographic forcings to the food web model, which drives primary production and the transport of plankton, detritus, and nutrients across model domain boundaries. The currency of a time-dynamic EcoTran model (see Figs 9 and 10 for examples) is nitrogen input to the system as nitrate and ammonium at the base of the food web via upwelling and detritus remineralization by bacteria. The ecosystem model is driven by nutrient flux that is important for bottom-up food web processes using the coastal upwelling transport index (CUTI) [42]. The CUTI time series (in daily time steps) drives advection (red arrows) of nutrients across the shelf. Primary production is supported by nutrient uptake and, in turn, supports grazing and predation by higher trophic level groups and catch by fishing fleets. Adapted from Ruzicka et al., 2016 [33].</p

EcoTran trophic network of non-detritus groups by trophic level.

The EcoTran trophic network is visualized here as a weighted, directed graph with detritus groups (86–90) removed (see Fig 6). Numbered nodes are functional groups (see Table 1 for numbers); arrows indicate directed edges (energy flows from producer groups towards consumer groups). The shade of green indicates strength of interaction (higher diet preference and prey biomass results in darker green network edges) up to a value of 0.025, at which point network edges get thicker with higher values.</p

Coastal pelagic fish functional group time series as both ecosystem model output and independent estimates.

Independently derived estimates (blue points; blue lines = locally estimated scatterplot smoothing lines) of relative biomass of sardine, anchovy, jack mackerel, and Pacific chub mackerel via stock assessments [56, 84, 86, 87] are plotted against ecosystem model-derived estimates of matching functional groups (black lines).</p

Seabird and mammal functional group time series as both ecosystem model output and independent estimates.

Independently derived estimates (blue lines and points) of relative biomass via a Juvenile Salmon and Ocean Ecosystem Survey (JSOES; common murre and sooty shearwaters), a humpback whale mark-recapture study (baleen whales [88]), and counts of the well-monitored Southern resident killer whale population [https://www.whaleresearch.com/orca-population] are plotted against ecosystem model-derived estimates of matching functional groups (black lines).</p

Invertebrate functional group time series as both ecosystem model output and independent estimates.

Independently derived estimates (blue points; blue lines = locally estimated scatterplot smoothing lines) of relative biomass via a Juvenile Salmon and Ocean Ecosystem Survey (JSOES; large jellies), fisheries landings (small cephalopod aggregate = market squid), and a pre-season abundance model (Dungeness crabs [83]) are plotted against ecosystem model-derived estimates of matching functional groups (black lines). The ecosystem model is driven entirely by nutrient inputs to the system as determined by the coastal upwelling transport index (CUTI) [42] and trophic relationships, and any resemblance of the two time series is an indication that the ecosystem model is matching independently-observed dynamics.</p