Population genomics of harbour seal Phoca vitulina from northern British Columbia through California and comparison to the Atlantic subspecies.

The harbour seal Phoca vitulina is a ubiquitous pinniped species found throughout coastal waters of the Northern Hemisphere. Harbour seal impacts on ecosystem dynamics may be significant due to their high abundance and food web position. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean and P. v. vitulina in the Atlantic. Strong natal philopatry of harbour seals can result in fine-scale genetic structure and isolation by distance. Management of harbour seals is expected to benefit from improved resolution of seal population structure and dynamics. Here, we use genotyping-by-sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e. British Columbia (BC), Oregon and California) and the western Atlantic Ocean (i.e. Québec, Newfoundland and Labrador). Using 12,742 identified variants, we confirm the recently identified elevated genetic diversity in the eastern Pacific relative to the western Atlantic and greatest differentiation between the subspecies. Further, we demonstrate that this is independent of reference genome bias or other potential technical artefacts. Coast-specific analyses with 8933 and 3828 variants in Pacific and Atlantic subspecies, respectively, identify divergence between BC and Oregon-California, and between Québec and Newfoundland-Labrador. Unexpected PCA outlier clusters were observed in two populations due to cryptic relatedness of individuals; subsequently, closely related samples were removed. Admixture analysis indicates an isolation-by-distance signature where Oregon seals contained some of the BC signature, whereas California did not. Additional sampling is needed in the central and north coast of BC to determine whether a discrete separation of populations exists within the region.

Geolocator tagging links distributions in the non-breeding season to population genetic structure in a sentinel North Pacific seabird.

We tested the hypothesis that segregation in wintering areas is associated with population differentiation in a sentinel North Pacific seabird, the rhinoceros auklet (Cerorhinca monocerata). We collected tissue samples for genetic analyses on five breeding colonies in the western Pacific Ocean (Japan) and on 13 colonies in the eastern Pacific Ocean (California to Alaska), and deployed light-level geolocator tags on 12 eastern Pacific colonies to delineate wintering areas. Geolocator tags were deployed previously on one colony in Japan. There was strong genetic differentiation between populations in the eastern vs. western Pacific Ocean, likely due to two factors. First, glaciation over the North Pacific in the late Pleistocene might have forced a southward range shift that historically isolated the eastern and western populations. And second, deep-ocean habitat along the northern continental shelf appears to act as a barrier to movement; abundant on both sides of the North Pacific, the rhinoceros auklet is virtually absent as a breeder in the Aleutian Islands and Bering Sea, and no tagged birds crossed the North Pacific in the non-breeding season. While genetic differentiation was strongest between the eastern vs. western Pacific, there was also extensive differentiation within both regional groups. In pairwise comparisons among the eastern Pacific colonies, the standardized measure of genetic differentiation (FꞌST) was negatively correlated with the extent of spatial overlap in wintering areas. That result supports the hypothesis that segregation in the non-breeding season is linked to genetic structure. Philopatry and a neritic foraging habit probably also contribute to the structuring. Widely distributed, vulnerable to anthropogenic stressors, and exhibiting extensive genetic structure, the rhinoceros auklet is fully indicative of the scope of the conservation challenges posed by seabirds.

Percent ash-free dry weight as a robust method to estimate energy density across taxa.

Determining how energy flows through ecosystems reveals underlying ecological patterns that drive processes such as growth and food web dynamics. Models that assess the transfer of energy from producers to consumers require information on the energy content or energy density (ED) of prey species. ED is most accurately measured through bomb calorimetry, but this method suffers from limitations of cost, time, and sample requirements that often make it unrealistic for many studies. Percent dry weight (DW) is typically used as a proxy for ED, but this measure includes an indigestible portion (e.g., bones, shell, salt) that can vary widely among organisms. Further, several distinct models exist for various taxonomic groups, yet none can accurately estimate invertebrate, vertebrate and plant ED with a single equation. Here, we present a novel method to estimate the ED of organisms using percent ash-free dry weight (AFDW). Using data obtained from 11 studies diverse in geographic, temporal and taxonomic scope, AFDW, DW as well as percent protein and percent lipid were compared as predictors of ED. Linear models were produced on a logarithmic scale, including dummy variables for broad taxonomic groups. AFDW was the superior predictor of ED compared to DW, percent protein content and percent lipid content. Model selection revealed that using correction factors (dummy variables) for aquatic animals (AA) and terrestrial invertebrates (TI) produced the best-supported model-log10(ED) = 1.07*log10(AFDW) - 0.80 (R 2 = 0.978, p < .00001)-with an intercept adjustment of 0.09 and 0.04 for AA and TI, respectively. All models including AFDW as a predictor had high predictive power (R 2 > 0.97), suggesting that AFDW can be used with high degrees of certainty to predict the ED of taxonomically diverse organisms. Our AFDW model will allow ED to be determined with minimal cost and time requirements and excludes ash-weight from estimates of digestible mass. Its ease of use will allow for ED to be more readily and accurately determined for diverse taxa across different ecosystems.

Validity of inferring size-selective mortality and a critical size limit in Pacific salmon from scale circulus spacing.

Size-selective mortality owing to lack of energy reserves during the first marine winter has been suggested to be a result of juvenile salmon failing to reach a critical size or condition by the end of their first marine summer and not surviving the following winter due to this presumed energy deficit. This hypothesis implies strong size dependency of mortality, and is subject to empirical data support for acceptance. Scale circulus spacing has been interpreted as an index for body size, and we reviewed the effect of size-selective mortality with a knife-edge mortality function on descriptive statistics for a scale circulus spacing index (SCSI). In order to invoke size selection as an important driver of mortality during the first year of ocean rearing, it is necessary to demonstrate not only that size-selective mortality is directed towards the smaller members of the population, but that the selective nature of the mortality can account for a substantial portion of the observed mortality. If the assumption is made that a random sample of a single juvenile population has been obtained, then studies that employ a SCSI to infer size-selective mortality coupled with a critical size limit must demonstrate a shift toward larger values of the SCSI, but also a concomitant reduction in the variance and range of the SCSI and an increase in the skewness and kurtosis of the SCSI values. Through simulation we found that the percentage of adults that displayed a SCSI value greater than the maximum observed in the juvenile sample was highly dependent on the initial juvenile sample size and size-selective mortality rate. Geographical distributions of juvenile Pacific salmon can be stratified by size, with larger individuals migrating earlier from local ocean entry locations than smaller individuals, and thus differential timing migration of juveniles based upon body size prior to the collection of the marine juvenile sample may be a more plausible explanation of published trends in the SCSI, rather than invoking substantial size-selective mortality and a critical size limit.

Distinct seasonal infectious agent profiles in life-history variants of juvenile Fraser River Chinook salmon: An application of high-throughput genomic screening.

Disease-causing infectious agents are natural components of ecosystems and considered a major selective force driving the evolution of host species. However, knowledge of the presence and abundance of suites of infectious agents in wild populations has been constrained by our ability to easily screen for them. Using salmon as a model, we contrasted seasonal pathogenic infectious agents in life history variants of juvenile Chinook salmon from the Fraser River system (N = 655), British Columbia (BC), through the application of a novel high-throughput quantitative PCR monitoring platform. This included freshwater hatchery origin fish and samples taken at sea between ocean entry in spring and over-winter residence in coastal waters. These variants currently display opposite trends in productivity, with yearling stocks generally in decline and sub-yearling stocks doing comparatively well. We detected the presence of 32 agents, 21 of which were at >1% prevalence. Variants carried a different infectious agent profile in terms of (1) diversity, (2) origin or transmission environment of infectious agents, and (3) prevalence and abundance of individual agents. Differences in profiles tended to reflect differential timing and residence patterns through freshwater, estuarine and marine habitats. Over all seasons, individual salmon carried an average of 3.7 agents. Diversity changed significantly, increasing upon saltwater entrance, increasing through the fall and decreasing slightly in winter. Diversity varied between life history types with yearling individuals carrying 1.3-times more agents on average. Shifts in prevalence and load over time were examined to identify agents with the greatest potential for impact at the stock level; those displaying concurrent decrease in prevalence and load truncation with time. Of those six that had similar patterns in both variants, five reached higher prevalence in yearling fish while only one reached higher prevalence in sub-yearling fish; this pattern was present for an additional five agents in yearling fish only.

Two forage fishes as potential conduits for the vertical transfer of microfibres in Northeastern Pacific Ocean food webs.

We assessed the potential role played by two vital Northeastern Pacific Ocean forage fishes, the Pacific sand lance (Ammodytes personatus) and Pacific herring (Clupea pallasii), as conduits for the vertical transfer of microfibres in food webs. We quantified the number of microfibres found in the stomachs of 734 sand lance and 205 herring that had been captured by an abundant seabird, the rhinoceros auklet (Cerorhinca monocerata). Sampling took place on six widely-dispersed breeding colonies in British Columbia, Canada, and Washington State, USA, over one to eight years. The North Pacific Ocean is a global hotspot for pollution, yet few sand lance (1.5%) or herring (2.0%) had ingested microfibres. In addition, there was no systematic relationship between the prevalence of microplastics in the fish stomachs vs. in waters around three of our study colonies (measured in an earlier study). Sampling at a single site (Protection Island, WA) in a single year (2016) yielded most (sand lance) or all (herring) of the microfibres recovered over the 30 colony-years of sampling involved in this study, yet no microfibres had been recovered there, in either species, in the previous year. We thus found no evidence that sand lance and herring currently act as major food-web conduits for microfibres along British Columbia's outer coast, nor that the local at-sea density of plastic necessarily determines how much plastic enters marine food webs via zooplanktivores. Extensive urban development around the Salish Sea probably explains the elevated microfibre loads in fishes collected on Protection Island, but we cannot account for the between-year variation. Nonetheless, the existence of such marked interannual variation indicates the importance of measuring year-to-year variation in microfibre pollution both at sea and in marine biota.

Detection and Assessment of the Distribution of Infectious Agents in Juvenile Fraser River Sockeye Salmon, Canada, in 2012 and 2013.

Infectious diseases may contribute to declines in Fraser River Sockeye salmon (Oncorhynchus nerka) stocks, but a clear knowledge gap exists around which infectious agents and diseases are important. This study was conducted to: (1) determine the presence and prevalence of 46 infectious agents in juvenile Fraser River Sockeye salmon, and (2) evaluate spatial patterns in prevalence and burden over initial seaward migration, contrasting patterns between 2 years of average and poor productivity. In total, 2,006 out-migrating Sockeye salmon were collected from four regions along their migration trajectory in British Columbia, in 2012 and 2013. High-throughput microfluidics quantitative PCR was employed for simultaneous quantitation of 46 different infectious agents. Twenty-six agents were detected at least once, including nine with prevalence >5%. Candidatus Brachiomonas cysticola, Myxobolus arcticus, and Pacific salmon parvovirus were the most prevalent agents. Infectious agent diversity and burden increased consistently upon smolts entry into the ocean, but they did not substantially change afterwards. Notably, both freshwater- and saltwater-transmitted agents were more prevalent in 2013 than in 2012, leading to an overall higher infection burden in the first two sampling regions. A reduction in the prevalence of two agents, erythrocytic necrosis virus and Paraneuclospora theridion, was observed between regions 2 and 3, which was speculated to be associated with mortality during the 1st month at sea. The most prevalent infectious agents were all naturally occurring. In a small number of samples (0.9%), seven agents were only detected around and after salmon farming regions, including four important pathogens: piscine orthoreovirus, Piscirickettsia salmonis, Tenacibaculum maritimum, and Moritella viscosa. As the first synoptic survey of infectious agents in juvenile Sockeye salmon in British Columbia, this study provides the necessary baseline for further research on the most prevalent infectious agents and their potential pathogenicity, which may adversely affect the productivity of valuable Sockeye salmon stocks. In addition, our findings are informative to the decision makers involved in conservation programs.

Size- and condition-dependent predation: a seabird disproportionately targets substandard individual juvenile salmon.

Selection of prey that are small and in poor body condition is a widespread phenomenon in terrestrial predator-prey systems and may benefit prey populations by removing substandard individuals. Similar selection is widely assumed to operate in aquatic systems. Indeed, size-selective predation is a longstanding and central tenet of aquatic food web theory. However, it is not known if aquatic predators select prey based on their condition or state, compared to their size. Surprisingly, no comparable information is available for marine systems because it is exceedingly difficult to make direct observations in this realm. Thus the role of body condition in regulating susceptibility to predation remains a black box in the marine environment. Here we have exploited an ideal model system to evaluate selective predation on pelagic marine fish: comparing characteristics (fork length, mass corrected for fork length) of fresh, whole, intact juvenile Pacific salmon delivered by a seabird to its single nestling with salmon collected concurrently in coastal trawl surveys. Three species of juvenile salmon (Oncorhynchus spp.) are consumed by provisioning Rhinoceros Auklets (Cerorhinca nionocerata); an abundant, colonial, pursuit-diving seabird. Samples were collected from multiple colonies and fisheries surveys in coastal British Columbia in two years. As predicted, Auklets preyed on small individuals in poor condition and consistently selected them at levels higher than their relative availability. This is the first study to provide direct evidence for both size- and condition-selective predation on marine fish in the wild. We anticipate that our results will be a starting point in evaluating how selective predation may structure or influence marine fish populations and bridges a fundamental incongruity between ecological theory and application; although "bigger is better" is considered a fundamental tenet of marine food webs, marine predators are often assumed to consume indiscriminately.

Hitting the moving target: modelling ontogenetic shifts with stable isotopes reveals the importance of isotopic turnover.

Ontogenetic niche shifts are widely prevalent in nature and are important in shaping the structure and dynamics of ecosystems. Stable isotope analysis is a powerful tool to assess these shifts, with δ(15) N providing a measure of trophic level and δ(13) C a measure of energy source. Previous applications of stable isotopes to study ontogenetic niche shifts have not considered the appreciable time lag between diet and consumer tissue associated with isotopic turnover. These time lags introduce significant complexity into field studies of ontogenetic niche shifts. Juvenile Chinook salmon (Oncorhynchus tshawytscha) migrate from freshwater to marine ecosystems and shift their diet from feeding primarily on invertebrates to feeding primarily on fish. This dual ontogenetic habitat and diet shift, in addition to the long time lag associated with isotopic turnover, suggests that there is potential for a disconnect between the prey sources that juvenile salmon are consuming, and the inferred prey sources from stable isotopes. We developed a model that considered ontogenetic niche shifts and time lags associated with isotopic turnover, and compared this 'ontogeny' model to one that considered only isotopic turnover. We used a Bayesian framework to explicitly account for parameter uncertainty. Data showed overwhelming support for the ontogeny model relative to the isotopic turnover model. Estimated variables from best model fits indicate that the ontogeny model predicts a much greater reliance on fish prey than does the stomach content data. Overall, we found that this method of quantifying ontogenetic niche shifts effectively accounted for both isotopic turnover and ontogenetic diet shifts; a finding that could be widely applicable to a variety of systems.

Infectious disease, shifting climates, and opportunistic predators: cumulative factors potentially impacting wild salmon declines.

Emerging diseases are impacting animals under high-density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.