Modeling ocean distributions and abundances of natural- and hatchery-origin Chinook salmon stocks with integrated genetic and tagging data

Background

Considerable resources are spent to track fish movement in marine environments, often with the intent of estimating behavior, distribution, and abundance. Resulting data from these monitoring efforts, including tagging studies and genetic sampling, often can be siloed. For Pacific salmon in the Northeast Pacific Ocean, predominant data sources for fish monitoring are coded wire tags (CWTs) and genetic stock identification (GSI). Despite their complementary strengths and weaknesses in coverage and information content, the two data streams rarely have been integrated to inform Pacific salmon biology and management. Joint, or integrated, models can combine and contextualize multiple data sources in a single statistical framework to produce more robust estimates of fish populations.

Methods

We introduce and fit a comprehensive joint model that integrates data from CWT recoveries and GSI sampling to inform the marine life history of Chinook salmon stocks at spatial and temporal scales relevant to ongoing fisheries management efforts. In a departure from similar models based primarily on CWT recoveries, modeled stocks in the new framework encompass both hatchery- and natural-origin fish. We specifically model the spatial distribution and marine abundance of four distinct stocks with spawning locations in California and southern Oregon, one of which is listed under the U.S. Endangered Species Act.

Results

Using the joint model, we generated the most comprehensive estimates of marine distribution to date for all modeled Chinook salmon stocks, including historically data poor and low abundance stocks. Estimated marine distributions from the joint model were broadly similar to estimates from a simpler, CWT-only model but did suggest some differences in distribution in select seasons. Model output also included novel stock-, year-, and season-specific estimates of marine abundance. We observed and partially addressed several challenges in model convergence with the use of supplemental data sources and model constraints; similar difficulties are not unexpected with integrated modeling. We identify several options for improved data collection that could address issues in convergence and increase confidence in model estimates of abundance. We expect these model advances and results provide management-relevant biological insights, with the potential to inform future mixed-stock fisheries management efforts, as well as a foundation for more expansive and comprehensive analyses to follow.

Fine-scale diversity of prey detected in humpback whale feces

Predator diets are largely influenced by prey availability and abundance. Yet, in heterogenous marine environments, identifying the prey species consumed by diving mammals remains a fundamental challenge. For rorqual whales, the energetic constraints of prey engulfment require that the whales seek areas of high prey abundance and execute discrete lunge feeding events on patches of high-density prey. Prey occurrences in feces should therefore provide meaningful insight into the dominant taxa in food patches selected by the animal. We investigated the prey consumed by humpback whales in three regions in southern British Columbia (BC), Canada, using opportunistic fecal sampling, microscopy, and DNA metabarcoding of 14 fecal samples. Fish including Pacific herring (Clupea pallasii), hake (Merluccius productus), and eulachon (Thaleichthys pacificus) were the most common fish species potentially targeted by humpback whales in two regions. The krill Euphausia pacifica was the most prevalent invertebrate DNA detected in all three regions, while sergestid and mysid shrimp may also be important. High DNA read abundances from walleye pollock (Gadus chalcogrammus) and sablefish (Anoplopoma fimbria) were also recovered in one sample each, suggesting that juveniles of these semi-pelagic species may occasionally be targeted. In general, we observed heavily digested fecal material that drove substantial dissimilarities in taxonomic resolution between polymerase chain reaction-based and morphological analyses of the feces. Pacific herring and walleye pollock were the only prey species confirmed by both methods. Our results highlight that molecular and visual analyses of fecal samples provide a complementary approach to diet analysis, with each method providing unique insight into prey diversity.

Synchrony erodes spatial portfolios of an anadromous fish and alters availability for resource users

Environmental forces can create spatially synchronous dynamics among nearby populations. However, increased climate variability, driven by anthropogenic climate change, will likely enhance synchrony among spatially disparate populations. Population synchrony may lead to greater fluctuations in abundance, but the consequences of population synchrony across multiple scales of biological organization, including impacts to putative competitors, dependent predators or human communities, are rarely considered in this context. Chinook salmon Oncorhynchus tshawytscha stocks distribute across the Northeast Pacific, creating spatially variable portfolios that support large ocean fisheries and marine mammal predators, such as killer whales Orcinus orca. We rely on a multi-population model that simulates Chinook salmon ocean distribution and abundance to understand spatial portfolios, or variability in abundance within and among ocean distribution regions, of Chinook salmon stocks across 17 ocean regions from Southeast Alaska to California. We found the expected positive correlation between the number of stocks in an ocean region and spatial portfolio strength; however, increased demographic synchrony eroded Chinook salmon spatial portfolios in the ocean. Moreover, we observed decreased resource availability within ocean fishery management jurisdictions but not within killer whale summer habitat. We found a strong portfolio effect across both Southern Resident and Northern Resident killer whale habitats that was relatively unaffected by increased demographic synchrony, likely a result of the large spatial area included in these habitats. However, within the areas of smaller fishing management jurisdictions we found a weakening of Chinook salmon portfolios and increased but inconsistent likelihood of low abundance years as demographic synchrony increased. We suggest that management and conservation actions that reduce spatial synchrony can enhance short-term ecosystem resilience by promoting the stabilizing effect multiple stocks have on aggregate Chinook salmon populations and overall resource availability.

Aquaculture mediates global transmission of a viral pathogen to wild salmon

Global expansion of aquaculture and agriculture facilitates disease emergence and catalyzes transmission to sympatric wildlife populations. The health of wild salmon stocks critically concerns Indigenous peoples, commercial and recreational fishers, and the general public. Despite potential impact of viral pathogens such as Piscine orthoreovirus-1 (PRV-1) on endangered wild salmon populations, their epidemiology in wild fish populations remains obscure, as does the role of aquaculture in global and local spread. Our phylogeographic analyses of PRV-1 suggest that development of Atlantic salmon aquaculture facilitated spread from Europe to the North and South East Pacific. Phylogenetic analysis and reverse transcription polymerase chain reaction surveillance further illuminate the circumstances of emergence of PRV-1 in the North East Pacific and provide strong evidence for Atlantic salmon aquaculture as a source of infection in wild Pacific salmon. PRV-1 is now an important infectious agent in critically endangered wild Pacific salmon populations, fueled by aquacultural transmission.

Direction and magnitude of natural selection on body size differ among age-classes of seaward-migrating Pacific salmon

Due to the mediating role of body size in determining fitness, the "bigger-is-better" hypothesis still pervades evolutionary ecology despite evidence that natural selection on phenotypic traits varies in time and space. For Pacific salmon (genus Oncorhynchus), most individual studies quantify selection across a narrow range of sizes and ages; therefore, uncertainties remain concerning how selection on size may differ among diverse life histories. Here, we quantify the direction and magnitude of natural selection on body size among age-classes of multiple marine cohorts of O. nerka (sockeye salmon). Across four cohorts of seaward migrants, we calculated standardized selection differentials by comparing observed size distributions of out-migrating juvenile salmon to back-calculated smolt length from the scales of surviving, returning adults. Results reveal the magnitude of selection on size was very strong (>90th percentile compared to a database of 3,759 linear selection differentials) and consistent among years. However, the direction of selection on size consistently varied among age-classes. Selection was positive for fish migrating to sea after two years in freshwater (age 2) and in their first year of life (age 0), but negative for fish migrating after 1 year in freshwater (age 1). The absolute magnitude of selection was negatively correlated to mean ocean-entry timing, which may underpin negative selection favoring small age-1 fish, given associations between size and timing of seaward migration. Collectively, these results indicate that "bigger is not always better" in terms of survival and emphasize trade-offs that may exist between fitness components for organisms with similarly diverse migratory life histories.