Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, ...potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single‐nucleotide polymorphisms using restriction‐site‐associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high‐resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.
Chinook salmon (Oncorhynchus tshawytscha) are migratory fish that are highly valued for subsistence, sport, and commercial fisheries throughout their native range. Populations of Chinook salmon in ...western Alaska have exhibited long-term declines, leading to restrictions on harvests. Management priorities require greater resolution for genetic stock identification (GSI) than is available with current methods. We leveraged RADseq, TaqMan, and GT-seq data originating from multiple sources, collected through time, to develop a set of GT-seq panels containing 1092 single nucleotide polymorphisms (SNPs) that improved GSI resolution in western Alaska for at-sea and in-river sampling. We generated a dense linkage map to ensure that markers selected for panels spanned the entire genome. In addition, we identified multiple RADseq markers that were associated with sex; these aligned to a 5-centimorgan (cM) region on the sex chromosome. Finally, we developed a bioinformatic pipeline to streamline analysis of GT-seq data that is capable of genotyping microhaplotypes and paralogs, both of which can improve GSI resolution over traditional single-SNP data. Our panels and pipeline provide tools for management agencies to rapidly and easily analyze large-scale genotyping projects.
Pink salmon, the most abundant Pacific salmon, have an obligate 2-year life cycle that leads to reproductively isolated even- and odd-year lineages. Using new and existing data, we examined the ...genetic structure of both lineages across their distributional range by genotyping 16 681 single-nucleotide polymorphisms for 383 individuals originating from seven pairs of even- and odd-year populations. Distinct differences in standing pools of genetic variation were identified between the lineages; we observed higher levels of heterozygosity, allelic richness, and significantly more private alleles in the odd-year lineage. However, the patterns of population structure were concordant between lineages: the Asian and northern Alaska populations displayed little differentiation but differed significantly from populations in southcentral Alaska and the Pacific Northwest. Our population structure results, in the context of known paleoecological information, suggest that both lineages occupied a northern Beringial refugium as well as a Cascadian refugium in North America during the Last Glacial Maximum. These results highlight the influence of historical patterns of habitat availability on contemporary population structure and support the hypothesis of a pre-glacial origin of the lineages.
Genetic stock identification (GSI), an important tool for fisheries management that relies upon the ability to differentiate stocks of interest, can be difficult when populations are closely related. ...Here we genotyped 11 850 single-nucleotide polymorphisms (SNPs) from existing DNA sequence data available in five closely related populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. We then converted a subset of 96 of these SNPs displaying high differentiation into high-throughput genotyping assays. These 96 SNPs (RAD96) and 191 SNPs developed previously (CTC191) were screened in 28 populations from western Alaska. Regional assignment power was evaluated for five different SNP panels, including a panel containing the 96 SNPs with the highest F
ST
across the CTC191 and RAD96 panels (F
ST
96). Assignment tests indicated that SNPs in the RAD96 were more useful for GSI than those in the CTC191 and that increasing the number of reporting groups in western Alaska from one to three was feasible with the F
ST
96. Our approach represents an efficient way to discover SNPs for GSI and should be applicable to other populations and species.
Previous studies generally report that hatchery‐origin Pacific Salmon (Oncorhynchus spp.) have lower relative reproductive success (RRS) than their natural‐origin counterparts. We estimated the RRS ...of Pink Salmon (O. gorbuscha) in Prince William Sound (PWS), Alaska using incomplete pedigrees. In contrast to other RRS studies, Pink Salmon have a short freshwater life history, freshwater habitats in PWS are largely unaltered by development, and sampling was conducted without the aid of dams or weirs resulting in incomplete sampling of spawning individuals. Pink Salmon released from large‐scale hatchery programs in PWS have interacted with wild populations for more than 15 generations. Hatchery populations were established from PWS populations but have subsequently been managed as separate broodstocks. Gene flow is primarily directional, from hatchery strays to wild populations. We used genetic‐based parentage analysis to estimate the RRS of a single generation of stray hatchery‐origin Pink Salmon in two streams, and across the odd‐ and even‐year lineages. Despite incomplete sampling, we assigned 1745 offspring to at least one parent. Reproductive success (RS), measured as sampled adult offspring that returned to their natal stream, was significantly lower for hatchery‐ vs. natural‐origin parents in both lineages, with RRS ranging from 0.03 to 0.47 for females and 0.05 to 0.86 for males. Generalized linear modeling for the even‐year lineage indicated that RRS was lower for hatchery‐origin fish, ranging from 0.42 to 0.60, after accounting for sample date (run timing), sample location within the stream, and fish length. Our results strongly suggest that hatchery‐origin strays have lower fitness in the wild. The consequences of reduced RRS on wild productivity depend on whether the mechanisms underlying reduced RRS are environmentally driven, and likely ephemeral, or genetically driven, and likely persistent across generations.
Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, ...new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.
Juvenile Chinook Salmon (Oncorhynchus tshawytscha) abundance in the northern Bering Sea is used to provide insight into future returns and fisheries in the Yukon River. The status of Yukon River ...Chinook Salmon is of concern due to recent production declines and subsequent closures of commercial, sport, and personal use fisheries, and severe restrictions on subsistence fisheries in the Yukon River. Surface trawl catch data, mixed layer depth adjustments, and genetic stock mixtures are used to estimate juvenile abundance for the Canadian-origin stock group from the Yukon River. Abundance ranged from a low of 0.62 million in 2012 to a high of 2.58 million in 2013 with an overall average of 1.5 million from 2003 to 2015. Although abundance estimates indicate that average survival is relatively low (average of 5.2%), juvenile abundance was significantly correlated (r=0.87, p=0.005) with adult returns, indicating that much of the variability in survival occurs during early life-history stages (freshwater and initial marine). Juvenile abundance in the northern Bering Sea has increased since 2013 due to an increase in early life-history survival (average juveniles-per-spawner increased from 29 to 59). The increase in juvenile abundance is projected to produce larger runs and increased subsistence fishing opportunities for Chinook Salmon in the Yukon River as early as 2016.
Most information about Chinook salmon genetic diversity and life history originates from studies from the West Coast USA, western Canada and southeast Alaska; less is known about Chinook salmon from ...western and southcentral Alaska drainages. Populations in this large area are genetically distinct from populations to the south and represent an evolutionary legacy of unique genetic, phenotypic and life history diversity. More genetic information is necessary to advance mixed stock analysis applications for studies involving these populations. We assembled a comprehensive, open‐access baseline of 45 single nucleotide polymorphisms (SNPs) from 172 populations ranging from Russia to California. We compare SNP data from representative populations throughout the range with particular emphasis on western and southcentral Alaska. We grouped populations into major lineages based upon genetic and geographic characteristics, evaluated the resolution for identifying the composition of admixtures and performed mixed stock analysis on Chinook salmon caught incidentally in the walleye pollock fishery in the Bering Sea. SNP data reveal complex genetic structure within Alaska and can be used in applications to address not only regional issues, but also migration pathways, bycatch studies on the high seas, and potential changes in the range of the species in response to climate change.
We genotyped Chinook salmon (Oncorhynchus tshawytscha) from the Bering Sea and North Pacific Ocean for 43 single-nucleotide polymorphisms (SNPs) to investigate seasonal distribution and migration ...patterns. We analyzed 3563 immature fish from 22 spatiotemporal strata; composition analyses were performed using genotype data from spawning stocks spanning the species range. Substantial variation in stock composition existed among spatial and seasonal strata. We inferred patterns of seasonal migration based upon these data along with data from previous tag, scale, and parasite studies. We found that stocks from western Alaska and Yukon River overwinter on the Alaska continental shelf then travel to the middle and western Bering Sea during spring-fall. Stocks from California to Southeast Alaska were distributed in Gulf of Alaska year-round, with a substantial portion of this group migrating northward to the eastern Bering Sea during spring-fall. Proportions of Russian stocks increase when moving east to west in both the Bering Sea and North Pacific Ocean. These data can be used to better understand the impacts of fisheries and climate change on this valuable resource.
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