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The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon ( Oncorhynchus tshawytscha ) and southern resident killer whales ( Orcinus orca ). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 150-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.

Predation mortality can influence the distribution and abundance of fish populations. While predation is often assessed using direct observations of prey consumption, potential predation can be predicted from co-occurring predator and prey densities under varying environmental conditions. Juvenile Pacific salmon Oncorhynchus spp. (i.e., smolts) from the Columbia River Basin experience elevated mortality during the transition from estuarine to ocean habitat, but a thorough understanding of the role of predation remains incomplete. We used a Holling type II functional response to estimate smolt predation risk based on observations of piscivorous seabirds (sooty shearwater [ Ardenna griseus ] and common murre [ Uria aalge ]) and local densities of alternative prey fish including northern anchovy ( Engraulis mordax ) in Oregon and Washington coastal waters during May and June 2010–2012. We evaluated predation risk relative to the availability of alternative prey and physical factors including turbidity and Columbia River plume area, and compared risk to returns of adult salmon. Seabirds and smolts consistently co-occurred at sampling stations throughout most of the study area (mean = 0.79 ± 0.41, SD), indicating that juvenile salmon are regularly exposed to avian predators during early marine residence. Predation risk for juvenile coho ( Oncorhynchus kisutch ), yearling Chinook salmon ( O . tshawytscha ), and subyearling Chinook salmon was on average 70% lower when alternative prey were present. Predation risk was greater in turbid waters, and decreased as water clarity increased. Juvenile coho and yearling Chinook salmon predation risk was lower when river plume surface areas were greater than 15,000 km 2 , while the opposite was estimated for subyearling Chinook salmon. These results suggest that plume area, turbidity, and forage fish abundance near the mouth of the Columbia River, all of which are influenced by river discharge, are useful indicators of potential juvenile salmon mortality that could inform salmonid management.

Advances in telemetry and modeling of physical processes expand opportunities to assess relationships between marine predators and their dynamic habitat. The Columbia River plume (CRP) attracts sooty shearwaters Ardenna grisea and common murres Uria aalge, but how seabirds respond to variability in plume waters is unknown. We characterized seabird distributions in relation to hourly, daily, monthly, and seasonal variation in CRP location and surface area by attaching satellite telemetry tags to shearwaters in 2008 and 2009, and to murres in 2012 and 2013. We matched seabird locations to surface salinity from a high-resolution hydrodynamic model of the CRP and adjacent waters. Utilization distributions indicated high-use areas north of the Columbia River mouth and in continental shelf waters. Shearwater and murre occupancy of tidal (< 21 psu), recirculating (21–26 psu), and boundary (26–31 psu) plume waters was on average 31% greater than expected and positively correlated with CRP surface area. Seabird latitude was positively correlated with latitude of the geographic center of the CRP, indicating that birds move in phase with the plume. We detected a threshold response of seabirds to plume size, and birds were closer to the convergent CRP boundary (28 psu isohaline) after a surface area threshold between 1500 and 4000 km² was exceeded. We conclude that shearwaters and murres selectively occupy and track plume waters, particularly dynamic boundary waters where foraging opportunities may be enhanced by increases in surface area and associated biophysical coupling that aggregates zooplankton and attracts prey fishes.

Abstract Objective Because predation is thought to be the primary source of natural mortality for juvenile salmon first entering the ocean, we sought to identify regions where, on average, stock‐specific spatial overlap between the distribution of threatened and endangered juvenile Chinook Salmon Oncorhynchus tshawytscha and abundant fish‐eating seabirds (common murres Uria aalge and sooty shearwaters Ardenna grisea) suggests the greatest potential for ocean predation risk to juvenile Chinook Salmon. Methods The relative abundance and spatial distribution of seabird predators and juvenile Chinook Salmon were quantified as part of long‐term ecosystem surveys during May 2003–2012 and June 2003–2022. Genetic stock identification methods were used to assign individual fish to their respective stock groups. Stock‐specific species distribution models then generated maps and indices of average annual spatial overlap between predators and prey within the survey area. Result There is unequivocal evidence for spatial overlap between common murres, sooty shearwaters, and five genetic groups of interior and lower Columbia River juvenile Chinook Salmon. We found strongly positive (≥0.70) spatial correlations between predator and prey densities in both May and June, although spatial overlap was, in general, greater during May. The region of highest spatial overlap occurred on the inner continental shelf between the Columbia River mouth (46.2°N) and Grays Harbor (47.0°N), a region at the beginning of the juvenile salmon migratory pathway that is strongly affected by freshwater outflow from the river. Conclusion Our findings support the idea that ocean avian predation during early marine residence has the potential to affect marine survival of juvenile Chinook Salmon and should be further investigated to better inform and implement ecological models and possible recovery actions for Chinook Salmon populations of the Columbia River basin. Impact statement Our findings identify the geographical region where high numbers of fish‐eating seabirds occur along the migration pathway of juvenile salmon that recently entered the ocean. This information advances work to understand the role ocean predators play in affecting salmon survival.

Studies estimating species' distributions require information about animal locations in space and time. Location data can be collected using surveys within a predetermined frame of reference (i.e., Eulerian sampling) or from animal‐borne tracking devices (i.e., Lagrangian sampling). Integration of observations obtained from Eulerian and Lagrangian perspectives can provide insights into animal movement and habitat use. However, contemporaneous data from both perspectives are rarely available, making examination of biases associated with each sampling approach difficult. We compared distributions of a mobile seabird observed concurrently from ship, aerial, and satellite tag surveys during May, June, and July 2012 in the northern California Current. We calculated utilization distributions to quantify and compare variability in common murre (Uria aalge) space use and examine how sampling perspective and platform influence observed patterns. Spatial distributions of murres were similar in May, regardless of sampling perspective. Greatest densities occurred in coastal waters off southern Washington and northern Oregon, near large murre colonies and the mouth of the Columbia River. Density distributions of murres estimated from ship and aerial surveys in June and July were similar to those observed in May, whereas distributions of satellite‐tagged murres in June and July indicated northward movement into British Columbia, Canada, resulting in different patterns observed from Eulerian and Lagrangian perspectives. These results suggest that the population of murres observed in the northern California Current during spring and summer includes relatively stationary individuals attending breeding colonies and nonstationary, vagile adults and subadults. Given the expected growth of telemetry studies and advances in survey technology (e.g., unmanned aerial systems), these results highlight the importance of considering methodological approaches, spatial extent, and synopticity of distribution data sets prior to integrating data from different sampling perspectives. We compared distributions of a mobile seabird observed concurrently from ship, aerial, and satellite tag surveys during May, June, and July 2012 in the northern California Current. Spatial distributions of common murres (Uria aalge) were similar early in the study period, but sampling perspective influenced observed patterns later in the season. These results highlight the importance of considering methodological approaches, spatial extent, and synopticity of distribution data sets prior to integrating data from different sampling perspectives into habitat models.

Rare species are difficult to observe in the wild, particularly in the ocean where large spatial scales and accessibility hinder effective sampling. Environmental DNA (eDNA) is a non-destructive, scalable sampling method with the potential to inform the distribution of rare species in marine ecosystems. We sample eDNA within the California Current ecosystem to estimate the distribution of eulachon (Thaleichthys pacificus), a threatened anadromous smelt ranging along the coastal Northeast Pacific. We amplify eulachon DNA from thousands of water samples collected at night across two years and more than 200,000 square kilometers along the U.S. west coast. We then use spatiotemporal models to derive quantitative estimates of eulachon DNA across space, depth, and time relative to environmental covariates. We find that eulachon DNA has a distribution weighted towards the ocean surface, spatially associated with major river mouths and productive offshore banks. Temperature and prey density are key covariates, with eulachon more likely to be found in warmer waters with higher prey concentrations. We discuss how our results can augment the information currently used in eulachon recovery planning, and describe the wide applicability of our statistical models for estimating distribution and abundance for other species of conservation concern.

This article presents the findings of a qualitative study of multiracial individuals' understanding of identity, race and human genetic variation. The debate regarding the correlation between race, genetics and disease has expanded, but limited empirical data has been collected regarding the lay public's perspective. Participants in this study explore their identity and its relationships to their health care interactions. Participants also share their views on race-based therapeutics, health disparities and the connections between race, ancestry and genetics. Their voices highlight the limitations of racial categories in describing differences within our increasingly diverse communities. The genomic era will be a pivotal period in challenging current understandings and uses of racial categories in health.

Seabirds are known to be vulnerable to biotoxins produced by harmful algal blooms (HABs). The ingestion of prey contaminated with biotoxins such as domoic acid can cause disorientation, seizures, morbidity, and mortality. During Nov 2007 in Monterey Bay CA an unprecedented stranding of live and dead seabirds highlighted plumage fouling as an emerging mortality factor during HAB events. The fouling agent was a proteinaceous foam derived from the cellular breakdown of the dinoflagellate Akashiwo sanguinea. Here, Phillips et al summarize information of birds killed by a harmful algal bloom.

Oceanographic processes that aggregate prey and facilitate the transfer of energy to higher trophic levels often influence marine predator-prey interactions. Buoyant discharge from the Columbia River forms a large freshwater plume bounded by convergent fronts in the northern California Current. These oceanographic features aggregate zooplankton and attract coastal pelagic fish species (CPS) including northern anchovy (Engraulis mordax). Juvenile salmon (Oncorhynchus spp.) use the Columbia River plume as they migrate to sea and experience elevated mortality during early marine residence. Seabirds including sooty shearwaters (Ardenna grisea) and common murres (Uria aalge) use the plume to forage, consuming CPS and juvenile salmon, and the Columbia River plume may influence predator-prey interactions and juvenile salmon survival. This dissertation examined the influence of the Columbia River plume on distributions of seabirds and fish prey, and characterized conditions that influence juvenile salmon predation risk. Chapter 1 provides a general introduction to the Columbia River plume ecosystem. Chapter 2 demonstrates the disproportionate occurrence of murres, shearwaters, CPS, and juvenile salmon in plume waters, the positive relationship between turbid plume waters and seabird densities, and the aggregation of seabirds in the plume when surface area is low. Chapter 3 used satellite telemetry and a high resolution hydrodynamic model of plume circulation to demonstrate the ability of murres and shearwaters to track the north-south movements of the plume, and the movement of seabirds towards biophysically active plume boundaries when surface areas exceed a threshold of ~1,500–4,000 km 2. Chapter 4 compared murre distributions observed from ship, plane, and satellite telemetry data perspectives, and identified similarities and differences in seabird spatiotemporal distributions that can inform species distribution models. Chapter 5 documented a relationship between low plume surface areas and increased juvenile coho and Chinook salmon predation risk from seabirds, and the mediating role of CPS in predator-prey interactions near the plume. Taken together, the results of this dissertation demonstrate that variation in Columbia River plume surface area and river discharge influences predator-prey interactions and juvenile salmonid predation risk. Chapter 6 offers a synthesis of the results and recommendations for future research aimed at informing Pacific salmon ocean ecology, management, and conservation.