Wild Salmon Center

Objective Many populations of wild steelhead Oncorhynchus mykiss along the west coast of North America have declined in abundance over the past several decades. This has led to increased interest in improving the monitoring of population parameters, such as abundance and diversity. The objective of this study was to describe demographic trends in age structure and life history diversity over the past three decades for wild winter-run steelhead returning to the Hoh River on the Olympic Peninsula, Washington.Methods We used age information derived from scale analysis (n = 5,420) to describe the trends in life history over run years 1994-2023. We define a life history as a unique combination of freshwater age, marine age, and spawning history. We generated three life history diversity indices for each run year-all returning fish, maiden spawners, and repeat-spawning steelhead-and tested for any temporal change across the study period.Results Over the entire study, we observed 35 unique life histories based on age at return of wild winter steelhead, and over half (63%) of the life histories observed were repeat spawners. We found that life history diversity has decreased over the past 30 years, and the decrease was primarily related to a decline in repeat spawner life histories and the oldest marine age of maiden spawners. Size at age, freshwater age, and marine age of the most common age-classes of maiden spawners have not changed over the study period. Annual survival rates for repeat spawners were positively related to the life history diversity index for repeat-spawning steelhead, highlighting the importance of conserving diversity in this population.Conclusions This study used scale age data to develop life history diversity indices for a population of wild adult steelhead and identified a demographic shift in repeat and maiden spawners. We observed a decline in the life history diversity of repeat spawners, which was related to a decrease in kelt survival. These results highlight that actions taken to minimize the mortality of migrating kelts should help to protect O. mykiss diversity and abundance and provide the greatest chance of meeting management objectives. Many populations of steelhead continue to lack adequate data for evaluating management actions that are intended to maintain population health. We developed life history diversity indices that demonstrated a demographic shift in repeat spawners and the oldest marine age of maiden spawners over the past 30 years.

Abstract Climate change is threatening ecologically and culturally important species. For species with broad ranges and complex life cycles, such as migratory Pacific salmon (Oncorhynchus spp.), climate exposure may vary across space and diverse life history strategies. Here, we quantify climate exposure and adaptive capacity across the North American range and remarkable phenological diversity of Chinook salmon (O. tshawytscha). We compiled data on adult freshwater migration timing and its environmental covariates for 295 populations of Chinook salmon spanning 29 degrees of latitude from California to Alaska. We linked this migration timing data to recent (1990s) and future (2040s) water temperatures to quantify thermal exposure during each population's timing of entrance to freshwater. At northern latitudes, Chinook migration timing was compressed to 3 months during the summer, while at southern latitudes, migration occurred across months before and after stressful peak summer water temperatures. Earlier migration timing was associated with longer migration distances and greater elevations gained. Thermal exposure was controlled by latitude and run‐timing, with lower latitude and summer and fall runs being most exposed to potentially harmful temperatures both now and into the future. However, potentially harmful climate exposure was predicted to increase the most in mid‐latitude populations (~45° to 55°) that have not yet adapted to migrate before and after peak summer temperatures. If Chinook salmon phenology were to keep pace with projected climate warming by the 2040s, the majority (75%) of populations would need to shift their migration timing earlier in the year, pulling their migration farther apart from their fall spawning phenology. Collectively, these findings showcase how latitude and life history diversity influence climate change risk and indicate the importance of preserving existing migration timing diversity and adaptive capacity across the broad range of a migratory species.

The Wild Salmon Policy was adopted in 2005, to safeguard salmon biodiversity and provide sustainable benefits to Canadians. Over the last 20 years the WSP has made important contributions to conservation, but many gaps remain. We find that many Conservation Units (83%; 324/390) have not had status assessments, a key element of the WSP. Changes in fisheries targeting Skeena and Nass sockeye, and Interior Fraser River coho salmon have promoted recovery of some CUs, but failure to robustly implement WSP strategies for north and central coast chum and coho salmon populations creates conservation risks with potentially devastating consequences for fisheries and ecosystems. Most Chinook salmon CUs in British Columbia are unassessed (81%; 65/80), and two out of the 15 assessed CUs are considered healthy (green status zone). Despite these risks, changes in the management of mixed-stock Chinook fisheries have been inadequate for reversing declines. A renewed commitment to WSP implementation, and an increased focus on transitioning harvest out of high-risk mixed-stock fisheries can support improved outcomes for Pacific salmon in Canada.

The loss of intraspecific diversity is a hidden crisis that threatens to disrupt ecological processes and ecosystem services, diminishing economic, subsistence, and cultural benefits to human communities. Conserving this diversity requires a deeper understanding of its evolutionary underpinnings and the ecological conditions necessary for its persistence amid rapid environmental change. Here, we integrate evolutionary principles and empirical evidence from recently developed genetic assays to examine the maintenance of run timing diversity within steelhead (Oncorhynchus mykiss), a widely distributed anadromous salmonid with distinct summer and winter adult migration timings. Using a GREB1L-based genetic assay, we analyzed nearly 2000 juvenile samples from the North Umpqua River, Oregon, USA to map watershed-scale distributions of run timing genotypes alongside climate-driven stream warming patterns. We found that summer-run genotypes dominate only in habitats located above seasonally passable barriers, such as natural waterfalls, that restrict or prevent passage by adult winter-run steelhead. This pattern supports the hypothesis that exclusive access to habitat provides a critical fitness advantage that compensates for the costs associated with summer run timing. Temperature modeling further revealed that habitats currently exclusive to summer-run steelhead are already thermally stressful and are projected to become increasingly so under end-of-century climate scenarios, reducing the quality of critical summer-run steelhead habitat. Because the persistence of summer-run steelhead under climate change depends on access to exclusive habitat of sufficient quality, we propose strategies to establish or maintain habitat exclusivity in more climate-resilient areas within the basin while minimizing impacts on winter-run steelhead and other anadromous species. More broadly, our study demonstrates how understanding the genetic basis of run timing and the fitness trade-offs associated with different life histories can inform the conservation of intraspecific diversity in migratory fish.

Reduced-representation sequencing methods, such as Restriction-site Associated DNA sequencing (RAD-seq), use restriction enzymes to achieve a cost-effective approach for generating genome-wide SNP data. However, a major limitation of these methods is their inability to directly assay specific loci of interest unless located near restriction sites. Here, we present ampliRAD, a novel method combining targeted (i.e., amplicon) and reduced-representation sequencing. AmpliRAD uses an initial multiplex PCR step to amplify target loci and append restriction enzyme recognition sites onto them. The PCR product is then combined with genomic DNA and used as input for a traditional RAD library preparation protocol, enabling the incorporation of virtually any target loci into a standard RAD dataset. We also introduce updates to an existing RAD protocol, including enzymatic shearing, that enhance its accessibility and efficiency. To demonstrate ampliRAD's utility, we investigate genetic associations with adult migration timing in Dean River Chinook salmon, revealing a clear link between the GREB1L locus and migration timing that extends previous findings from southern populations to this northern river. AmpliRAD provides a powerful new tool for genomic analyses, offering the combined benefits of both reduced representation and targeted sequencing approaches.