Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon

The genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and can provide insights into the role of pathogen‐mediated selection in wild populations. Here, we examined variation at the MHC class II peptide‐binding region in 27 populations of sockeye salmon (Oncorhynchus nerka), distributed among three distinct spawning ecotypes, from a complex of interconnected rivers and lakes in south‐western Alaska. We also obtained genotypes from 90 putatively neutral single nucleotide polymorphisms for each population to compare the relative roles of demography and selection in shaping the observed MHC variation. We found that MHC divergence was generally partitioned by spawning ecotype (lake beaches, rivers and streams) and was 30 times greater than variation at neutral markers. Additionally, we observed substantial differences in modes of selection and diversity among ecotypes, with beach populations displaying higher levels of directional selection and lower MHC diversity than the other two ecotypes. Finally, the level of MHC differentiation in our study system was comparable to that observed over much larger geographic ranges, suggesting that MHC variation does not necessarily increase with increasing spatial scale and may instead be driven by fine‐scale differences in pathogen communities or pathogen virulence. The low levels of neutral structure and spatial proximity of populations in our study system indicate that MHC differentiation can be maintained through strong selective pressure even when ample opportunities for gene flow exist.     

Maternal and environmental influences on egg size and juvenile life‐history traits in Pacific salmon

Life‐history traits such as fecundity and offspring size are shaped by investment trade‐offs faced by mothers and mediated by environmental conditions. We use a 21‐year time series for three populations of wild sockeye salmon (Oncorhynchus nerka) to test predictions for such trade‐offs and responses to conditions faced by females during migration, and offspring during incubation. In years when their 1100 km upstream migration was challenged by high water discharges, females that reached spawning streams had invested less in gonads by producing smaller but not fewer eggs. These smaller eggs produced lighter juveniles, and this effect was further amplified in years when the incubation water was warm. This latter result suggests that there should be selection for larger eggs to compensate in populations that consistently experience warm incubation temperatures. A comparison among 16 populations, with matching migration and rearing environments but different incubation environments (i.e., separate spawning streams), confirmed this prediction; smaller females produced larger eggs for their size in warmer creeks. Taken together, these results reveal how maternal phenotype and environmental conditions can shape patterns of reproductive investment and consequently juvenile fitness‐related traits within and among populations.     

Alaskan brown bears (Ursus arctos) aggregate and display fidelity to foraging neighborhoods while preying on Pacific salmon along small streams

The interaction between brown bears (Ursus arctos) and Pacific salmon (Oncorhynchus spp.) is important to the population dynamics of both species and a celebrated example of consumer‐mediated nutrient transport. Yet, much of the site‐specific information we have about the bears in this relationship comes from observations at a few highly visible but unrepresentative locations and a small number of radio‐telemetry studies. Consequently, our understanding of brown bear abundance and behavior at more cryptic locations where they commonly feed on salmon, including small spawning streams, remains limited. We employed a noninvasive genetic approach (barbed wire hair snares) over four summers (2012–2015) to document patterns of brown bear abundance and movement among six spawning streams for sockeye salmon, O. nerka, in southwestern Alaska. The streams were grouped into two trios on opposite sides of Lake Aleknagik. Thus, we predicted that most bears would forage within only one trio during the spawning season because of the energetic costs associated with swimming between them or traveling around the lake and show fidelity to particular trios across years because of the benefits of familiarity with local salmon dynamics and stream characteristics. Huggins closed‐capture models based on encounter histories from genotyped hair samples revealed that as many as 41 individuals visited single streams during the annual 6‐week sampling season. Bears also moved freely among trios of streams but rarely moved between these putative foraging neighborhoods, either during or between years. By implication, even small salmon spawning streams can serve as important resources for brown bears, and consistent use of stream neighborhoods by certain bears may play an important role in spatially structuring coastal bear populations. Our findings also underscore the efficacy of noninvasive hair snagging and genetic analysis for examining bear abundance and movements at relatively fine spatial and temporal scales.     

Carcass analogues provide marine subsidies for macroinvertebrates and juvenile Atlantic salmon in temperate oligotrophic streams

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Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared with the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome–environment associations (GEA) to understand the relationship between landscape and environmental conditions driving selection in seven populations of the anadromous Chinook salmon (Oncorhynchus tshawytscha)—a species of important economic, social, cultural, and ecological value—in the Columbia River basin. We extracted environmental variables for the shared migration corridors and at distinct spawning sites for each population, and used a Pool‐seq approach to perform whole genome resequencing. Bayesian and univariate GEA tests with migration‐specific and spawning site‐specific environmental variables indicated many more candidate SNPs associated with environmental conditions at the migration corridor compared with spawning sites. Specifically, temperature, precipitation, terrain roughness, and elevation variables of the migration corridor were the most significant drivers of environmental selection. Additional analyses of neutral loci revealed two distinct clusters representing populations from different geographic regions of the drainage that also exhibit differences in adult migration timing (summer vs. fall). Tests for genomic regions under selection revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1 region that has been identified previously in salmonids as a region associated with adult migration timing. Our results show that environmental variation experienced throughout migration corridors imposed a greater selective pressure on Chinook salmon than environmental conditions at spawning sites.     

Quantitative Links Between Pacific Salmon and Stream Periphyton

Species’ impacts on primary production can have strong ecological consequences. In freshwater ecosystems, Pacific salmon (Oncorhynchus spp.) may influence stream periphyton through substrate disturbance during spawning and nutrient subsidies from senescent adults. The shape of relationships between the abundance of spawning salmon and stream periphyton, as well as interactions with environmental variables, are incompletely understood and may differ across the geographic range of salmon. We examined these relationships across 24 sockeye salmon (Oncorhynchus nerka) spawning streams in north-central British Columbia, Canada. The influence of salmon abundance and environmental variables (temperature, light, dissolved nutrients, water velocity, watershed size, and invertebrate grazer abundance) on post-spawning periphyton abundance and nitrogen stable isotope signatures, which can indicate the uptake of salmon nitrogen, was evaluated using linear regression models and Akaike Information Criterion. Periphyton nitrogen stable isotope signatures were best described by a positive log-linear relationship with an upstream salmon abundance metric that includes salmon from earlier years. This suggests the presence of a nutrient legacy. In contrast, periphyton abundance was negatively related to the spawning-year salmon density, which likely results from substrate disturbance during spawning, and positively related to dissolved soluble reactive phosphorus prior to spawning, which may indicate phosphorus limitation in the streams. These results suggest that enrichment from salmon nutrients does not always translate into elevated periphyton abundance. This underscores the need to directly assess the outcome of salmon impacts on streams rather than extrapolating from stable isotope evidence for the incorporation of salmon nutrients into food webs.     

Watershed‐scale climate influences productivity of Chinook salmon populations across southcentral Alaska

The ecosystems supporting Pacific salmon (Oncorhynchus spp.) are changing rapidly as a result of climate change and habitat alteration. Understanding how—and how consistently—salmon populations respond to changes at regional and watershed scales has major implications for fisheries management and habitat conservation. Chinook salmon (O. tshawytscha) populations across Alaska have declined over the past decade, resulting in fisheries closures and prolonged impacts to local communities. These declines are associated with large‐scale climate drivers, but uncertainty remains about the role of local conditions (e.g., precipitation, streamflow, and stream temperature) that vary among the watersheds where salmon spawn and rear. We estimated the effects of these and other environmental indicators on the productivity of 15 Chinook salmon populations in the Cook Inlet basin, southcentral Alaska, using a hierarchical Bayesian stock‐recruitment model. Salmon spawning during 2003–2007 produced 57% fewer recruits than the previous long‐term average, leading to declines in adult returns beginning in 2008. These declines were explained in part by density dependence, with reduced population productivity following years of high spawning abundance. Across all populations, productivity declined with increased precipitation during the fall spawning and early incubation period and increased with above‐average precipitation during juvenile rearing. Above‐average stream temperatures during spawning and rearing had variable effects, with negative relationships in many warmer streams and positive relationships in some colder streams. Productivity was also associated with regional indices of streamflow and ocean conditions, with high variability among populations. The cumulative effects of adverse conditions in freshwater, including high spawning abundance, heavy fall rains, and hot, dry summers may have contributed to the recent population declines across the region. Identifying both coherent and differential responses to environmental change underscores the importance of targeted, watershed‐specific monitoring and conservation efforts for maintaining resilient salmon runs in a warming world.     

Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska

Understanding the genetic mechanisms that facilitate adaptive radiation is an important component of evolutionary biology. Here, we genotyped 82 neutral SNPs, seven SNPs in islands of divergence identified in a previous study (island SNPs), and a region of the major histocompatibility complex (MHC) in 32 populations of sockeye salmon to investigate whether conserved genes and genomic regions are involved in adaptive radiation. Populations representing three ecotypes were sampled from seven drainages with differing habitats and colonization histories spanning a range of 2,000 km. We found strong signatures of parallel selection across drainages at the island SNPs and MHC, suggesting that the same loci undergo divergent selection during adaptive radiation. However, patterns of differentiation at most island SNPs and the MHC were not associated with ecotypes, suggesting that these loci are responding differently to a mosaic of selective pressures. Our study provides some of the first evidence that conserved genomic islands may be involved in adaptive divergence of salmon populations. Additionally, our data provide further support for the hypothesis that sockeye salmon inhabiting rivers unconnected to lakes harbour similar genetic diversity across large distances, are likely the ancestral form of the species, and have repeatedly recolonized lake systems as they have become available after glacial recession. Finally, our results highlight the value and importance of validating outlier loci by screening additional populations and regions, a practice that will hopefully become more common in the future.     

Biotic disturbance and benthic community dynamics in salmon-bearing streams

1. Organisms can impact ecosystems via multiple pathways, often with positive and negative impacts on inhabitants. Understanding the context dependency of these types of impacts remains challenging. For example, organisms may perform different functions at different densities. 2. Anadromous salmon accumulate > 99% of their lifetime growth in marine ecosystems, and then return to spawn, often at high densities, in relatively confined freshwaters. While previous research has focused on how salmon nutrients can fertilize benthic communities, we examined how an ecosystem engineer, sockeye salmon Oncorhynchus nerka, influences seasonal dynamics of stream benthic communities through their nest-digging activities in south-western Alaska, USA. Benthic invertebrate and algal abundance were quantified every 7-14 days during the open water seasons of 10 streams in riffle and run habitats across multiple years, leading to 25 different stream-year combinations that spanned a large gradient of salmon density. 3. In streams with few or no salmon, benthic algal and insect biomass were fairly constant throughout the season. However, in streams with more than 0.1 salmon m(-2), algal and insect biomass decreased by an average of 75-85% during salmon spawning. Algal biomass recovered quickly following salmon disturbance, occasionally reaching pre-salmon biomass. In contrast, in streams with more than 0.1 salmon m(-2), aquatic insect populations did not recover to pre-salmon levels within the same season. We observed no positive impacts of salmon on algae or insects via fertilization from carcass nutrients. 4. Salmon, when their populations exceed thresholds in spawning density, are an important component of stream disturbance regimes and influence seasonal dynamics of benthic communities. Human activities that drive salmon densities below threshold densities, as has likely happened in many streams, will lead to altered seasonal dynamics of stream communities. Human activities that alter animal populations that are sources of biogenic disturbance can result in shifts in community dynamics.     

Effects of Salmon-Derived Nutrients and Habitat Characteristics on Population Densities of Stream-Resident Sculpins

Movement of nutrients across ecosystem boundaries can have important effects on food webs and population dynamics. An example from the North Pacific Rim is the connection between productive marine ecosystems and freshwaters driven by annual spawning migrations of Pacific salmon (Oncorhynchus spp). While a growing body of research has highlighted the importance of both pulsed nutrient subsidies and disturbance by spawning salmon, their effects on population densities of vertebrate consumers have rarely been tested, especially across streams spanning a wide range of natural variation in salmon densities and habitat characteristics. We studied resident freshwater prickly (Cottus asper), and coastrange sculpins (C. aleuticus) in coastal salmon spawning streams to test whether their population densities are affected by spawning densities of pink and chum salmon (O. gorbuscha and O. keta), as well as habitat characteristics. Coastrange sculpins occurred in the highest densities in streams with high densities of spawning pink and chum salmon. They also were more dense in streams with high pH, large watersheds, less area covered by pools, and lower gradients. In contrast, prickly sculpin densities were higher in streams with more large wood and pools, and less canopy cover, but their densities were not correlated with salmon. These results for coastrange sculpins provide evidence of a numerical population response by freshwater fish to increased availability of salmon subsidies in streams. These results demonstrate complex and context-dependent relationships between spawning Pacific salmon and coastal ecosystems and can inform an ecosystem-based approach to their management and conservation.     

Application of otolith analyses to investigate broad size distributions of young yellow perch in temperate lakes

Otolith analyses were used to back-calculate young-of-the-year (YOY) yellow perch Perca flavescens hatch-date estimates to interpret broad length distributions observed within a small Great Lake, Lake St. Clair, and a small inland lake, Lake Opinicon, during 1998. For the Great Lake, the earliest observed hatch date occurred 2 weeks after suitable water temperatures and latest hatch dates occurred the same week temperatures were considered too warm for spawning. For the inland lake, the earliest hatch date occurred 4 weeks after suitable water temperatures and the latest hatch dates occurred 2 weeks after the water temperatures were considered too warm for spawning. It is inferred that spawning in each lake had a duration of >9 weeks. This suggests that natural perch populations can protract their spawning season opportunistically under the appropriate environmental cues. During 1998, these cues involved a shortened winter, earlier spring, and slow warming to typical summer temperatures, caused by the El Niño-Southern Oscillation. Time of YOY hatch determined the absolute opportunity for growth and resulted in a match or mismatch with optimal foraging conditions and contributed to the development of the observed YOY length distributions.     

Divergence of mitochondrial DNA in a population of sockeye salmon (Oncorhynchus nerka Walbaum) from Azabache'e lake (Kamchatka)

Variability of three PCR-amplified mtDNA regions was examined in five populations of sockeye salmon from Azabach'e Lake. Eighteen haplotypes were detected in 144 fish. Significant differences were found between seasonal races of sockeye salmon spawning in the lake. The short time of independent divergence between the seasonal races indicates that these races formed independently in each spawning region. No difference in mtDNA between lake samples of early sockeye salmon (subisolates) was revealed, which confirms the existence of gene flow between them. A high level of differences between the sockeye salmon spawning in the lake and spawning in the tributaries of the lake, the Bushuev and Lotnaya rivers, suggests that there were no migration between them during many generations and that the nature of spawning grounds (lake or river) is essential for within species differentiation in this species.     

Juvenile coho salmon track a seasonally shifting thermal mosaic across a river floodplain

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Divergence of Mitochondrial DNA in Populations of Sockeye Salmon Oncorhynchus nerka Walbaum from Azabach'e Lake (Kamchatka)

Variability of three PCR-amplified mtDNA regions was examined in five populations of sockeye salmon from Azabach'e Lake. Eighteen haplotypes were detected in 144 fish. Significant differences were found between seasonal races of sockeye salmon spawning in the lake. The short time of independent divergence between the seasonal races indicates that these races formed independently in each spawning region. No difference in mtDNA between lake samples of early sockeye salmon (subisolates) was revealed, which confirms the existence of gene flow between them. A high level of differences between the sockeye salmon spawning in the lake and spawning in the tributaries of the lake, the Bushuev and Lotnaya rivers, suggests that there were no migration between them during many generations and that the nature of spawning grounds (lake or river) is essential for within-species differentiation in this species.     

Asynchrony in population dynamics of sockeye salmon in southwest Alaska

Ecologists have examined the synchronization of population dynamics across space as a means to understand how populations respond to climate variation. However, response diversity may reflect important variation among local population dynamics driven by population‐specific responses to regional environmental change. We used long‐term data on sockeye salmon Oncorhynchus nerka from pristine watersheds of southwestern Alaska to show that populations spawning in close proximity (<40 km) to one another have a limited degree of synchrony in their dynamics, even after accounting for density‐dependent processes. In fact, the dynamics of local populations of stream‐spawning sockeye salmon were no more coherent than those of stocks at a much coarser resolution across this region of Alaska. We examined four hypotheses to explain the observed patterns of asynchrony among stream‐spawning populations, and found that populations spawning in dissimilar habitats, and using different nursery lakes were less synchronized in their productivity. Similarity in the age structure of spawning adults was less correlated with synchrony in productivity. These results emphasize the importance of maintaining diverse spawning and rearing habitat for the conservation of Pacific salmon, and should guide conservation planning for Pacific salmon populations in regions where natural dynamics have been altered by habitat loss, hatchery practices, and over‐fishing.     

Sea to sky: impacts of residual salmon-derived nutrients on estuarine breeding bird communities

Pacific salmon (Oncorhynchus spp.) returning to streams around the North Pacific Rim provide a nutrient subsidy to these ecosystems. While many species of animals feed directly on salmon carcasses each autumn, salmon-derived nutrients can also be stored in coastal habitats throughout the year. The effects of this storage legacy on vertebrates in other seasons are not well understood, especially in estuaries, which can receive a large portion of post-spawning salmon nutrients. We examine the effects of residual salmon-derived nutrients, forest habitats and landscape features on summer breeding birds in estuary forests. We compared models containing environmental variables and combined chum (Oncorhynchus keta) and pink (Oncorhynchus gorbuscha) salmon biomass to test predictions concerning bird density and diversity. We discovered that total bird, insectivore, golden-crowned kinglet and Pacific wren densities and Shannon's diversity in the summer were strongly predicted by salmon biomass in the autumn. For most metrics, this relationship approaches an asymptote beyond 40 000 kg of salmon biomass. Foliage height diversity, watershed catchment area and estuary area were also important predictors of avian communities. Our study suggests that the legacy of salmon nutrients influences breeding bird density and diversity in estuaries that vary across a wide gradient of spawning salmon biomass.     

TEMPORAL VARIATION AT THE MHC CLASS IIB IN WILD POPULATIONS OF THE GUPPY (POECILIA RETICULATA)

Understanding genetic diversity in natural populations is a fundamental objective of evolutionary biology. The immune genes of the major histocompatibility complex (MHC) are excellent candidates to study such diversity because they are highly polymorphic in populations. Although balancing selection may be responsible for maintaining diversity at these functionally important loci, temporal variation in selection pressure has rarely been examined. We examine temporal variation in MHC class IIB diversity in nine guppy (Poecilia reticulata) populations over two years. We found that five of the populations changed significantly more at the MHC than at neutral (microsatellite) loci as measured by F_ST, which suggests that the change at the MHC was due to selection and not neutral processes. Additionally, pairwise population differentiation measures at the MHC were higher in 2007 than in 2006, with the signature of selection changing from homogenizing to diversifying selection or neutral evolution. Interestingly, within the populations the magnitude of the change at the MHC between years was related to the change in the proportion of individuals infected by a common parasite, indicating a link between genetic structure and the parasite. Our data thereby implicate temporal variation in selective pressure as an important mechanism maintaining diversity at the MHC in wild populations.     

Thermal regime,predation danger and the early marine exit of sockeye salmon Oncorhynchus nerka

Marine exit timing of sockeye salmon Oncorhynchus nerka populations on the Haida Gwaii Archipelago, British Columbia, Canada, is described, with specific focus on Copper Creek. Marine exit in Copper Creek occurs > 130 days prior to spawning, one of the longest adult freshwater residence periods recorded for any O. nerka population. Copper Creek presents an easy upstream migration, with mild water temperatures (7 to 14° C), short distance (13·1 km) and low elevation gain (41 m) to the lake where fish hold prior to spawning. An energetic model estimates that <1% of the initial energy reserve is required for upstream migration, compared with 62% for lake holding and 38% for reproductive development. Historical records suggest that it is unlikely that water temperature in any of the O.nerka streams in Haida Gwaii has ever exceeded the presumed temperature threshold (19° C) for early marine exit. Although it is not impossible that the thermal tolerance of Copper Creek O.nerka is very low, the data presented here appear inconsistent with thermal avoidance as an explanation for the early marine exit timing in Copper Creek and in three other populations on the archipelago with early marine exit.     

Divergence of the seasonal races of chum salmon, <Emphasis Type="Italic">Oncorhynchus keta</Emphasis> Walbaum, 1792, in the Amur and Poronai rivers: Ecology,genetics, and morphology

The chum salmon of the Amur River (the mainland part of the Far East) and the Poronai River (Terpeniya Bay, Sakhalin Island) are historically related to one another, as the drainage basins of these rivers are the remnants of a formerly single river system, the Paleoamur, which existed when Sakhalin Island was a part of the continent. Both river populations of chum salmon consist of the early-run and late-run ecological forms (seasonal races), which are also referred to as the summer and autumn races. They are reproductively isolated from each other due to their spawning at different times and in different types of spawning grounds. To assess the direction, pattern, and degree of divergence between these chum salmon races in the both river fragments since the Paleoamur, it is necessary to compare them using two types of traits: selectively neutral DNA markers and morphological and physiological traits, variations in which may have an adaptive value. For this, we have studied chum salmon from both rivers in terms of microsatellite DNA markers, body counts and measurements, body weight, and fecundity. Both in the Amur River and in the Poronai River, the autumn race of chum salmon prevails over the summer race in body length and weight, fecundity, number of pyloric caeca, and several other meristic traits. The intra-basin differences between the races are much more pronounced in the Amur chum salmon. The inter-race differences in microsatellites are also greater in the Amur chum salmon compared to the Poronai chum salmon. Using microsatellites, three levels of differentiation have been revealed: (1) between the basins of the Amur and Poronai rivers, (2) between the races within each of the river basins, (3) and between population samples within each race of each basin. A hypothesis is proposed that the currently existing races of chum salmon in the Amur and Poronai rivers have evolved since the breakup of the Paleoamur, and the intra-basin divergence of the races started in the Amur River earlier than in the Poronai River. An analysis of our own data and the published data suggests that the adaptation of the seasonal races of chum salmon to the conditions of their spawning grounds is determined by a complex of morphological and physiological traits, including the number of pyloric caeca, which is an adaptive and highly heritable trait associated with the incubation temperature of the water.     

Effects of river temperature and climate warming on stock‐specific survival of adult migrating Fraser River sockeye salmon (Oncorhynchus nerka)

Mean summer water temperatures in the Fraser River (British Columbia, Canada) have increased by ～1.5 °C since the 1950s. In recent years, record high river temperatures during spawning migrations of Fraser River sockeye salmon (Oncorhynchus nerka) have been associated with high mortality events, raising concerns about long‐term viability of the numerous natal stocks faced with climate warming. In this study, the effect of freshwater thermal experience on spawning migration survival was estimated by fitting capture–recapture models to telemetry data collected for 1474 adults (captured in either the ocean or river between 2002 and 2007) from four Fraser River sockeye salmon stock‐aggregates (Chilko, Quesnel, Stellako‐Late Stuart and Adams). Survival of Adams sockeye salmon was the most impacted by warm temperatures encountered in the lower river, followed by that of Stellako‐Late Stuart and Quesnel. In contrast, survival of Chilko fish was insensitive to the encountered river temperature. In all stocks, in‐river survival of ocean‐captured sockeye salmon was higher than that of river‐captured fish and, generally, the difference was more pronounced under warm temperatures. The survival–temperature relationships for ocean‐captured fish were used to predict historic (1961–1990) and future (2010–2099) survival under simulated lower river thermal experiences for the Quesnel, Stellako‐Late Stuart and Adams stocks. A decrease of 9–16% in survival of all these stocks was predicted by the end of the century if the Fraser River continues to warm as expected. However, the decrease in future survival of Adams sockeye salmon would occur only if fish continue to enter the river abnormally early, towards warmer periods of the summer, as they have done since 1995. The survival estimates and predictions presented here are likely optimistic and emphasize the need to consider stock‐specific responses to temperature and climate warming into fisheries management and conservation strategies.