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Objective: The Clark Fork–Pend Oreille River basin of northeastern Washington and the Idaho Panhandle historically supported a robust metapopulation of the Westslope Cutthroat Trout (WCT) Oncorhynchus lewisi, a western native salmonid of high cultural and economic value. The construction of impassible hydroelectric dams and smaller instream barriers has prevented the return of migratory WCT to spawning tributaries, leading to the fragmentation of this metapopulation over the past 100 years. One such impassible barrier is Albeni Falls Dam (AFD) near Newport, Washington, which was completed without fish passage capabilities in 1955. We sought to examine large‐scale genetic patterns in the study area and determine the most likely spawning tributary of origin for migratory WCT captured below AFD. Methods: We created a genetic baseline representative of populations within the Clark Fork–Pend Oreille River basin from upstream and downstream of the dam using 191 biallelic single‐nucleotide polymorphism genetic markers. Our data set included 124 collections, which allowed for an examination of population structure and hatchery influence across the study area and provided a robust tool for population assignment. Population assignment tests were conducted using the program RUBIAS. Result: Population assignment tests were successful for all pure WCT of unknown origin despite potential influence from hatchery lineages across the study area. Of 83 migratory WCT captured below AFD, approximately 80% were assigned to tributaries upstream of AFD with a posterior assignment probability of at least 90%. Only one fish was assigned to a tributary downstream of AFD. Conclusion: Our results indicate that AFD disrupts the natural metapopulation dynamics of WCT populations in the basin. Passage for WCT at this barrier would reestablish metapopulation connectivity within the basin by allowing migratory individuals to make genetic contributions to populations upstream of the dam. Impact statementMost Westslope Cutthroat Trout captured below Albeni Falls Dam were genetically assigned to regions upstream of the dam, indicating that this barrier disrupts their natural metapopulation structure. Fish passage facilities would likely benefit these salmonids. [ABSTRACT FROM AUTHOR]

Conservation of threatened and endangered species often involves large‐scale collaboration across jurisdictional boundaries, but such efforts are typically hampered by a lack of consistent monitoring data at local, regional, and species‐distributional scales. Contemporary methods of genetic monitoring that are grounded in sequencing‐based approaches offer a powerful means to achieve the data consistency necessary for conservation of high‐profile species. Here, we describe the collaborative, multiagency development of a genotyping‐in‐thousands by sequencing panel for genetic monitoring of threatened Bull Trout Salvelinus confluentus across its range in North America. The resulting panel consists of 266 single nucleotide polymorphisms, a subset of which differentiate Salvelinus species (Arctic Char S. alpinus, Brook Trout S. fontinalis, Bull Trout, Dolly Varden S. malma, Lake Trout S. namaycush, and Whitespotted Char S. leucomaenis), as well as one sex ID locus. We then used case studies from the Pacific Northwest and northern Rocky Mountains to demonstrate the efficacy of the panel for addressing local conservation needs (e.g., genetic variation, genetic differentiation, genetic assignment tests, and number of effective breeders) and compatibility with legacy data sets. Future genotyping with this panel will provide opportunities for improved conservation prioritization across the species range and collaboration among the numerous agencies charged with conserving this species. This effort provides framework to develop population genetic tools that will contribute to robust and efficient monitoring of biodiversity. [ABSTRACT FROM AUTHOR]

We examined genetic diversity patterns among 55 collections of Chum Salmon from the northeastern Pacific Ocean using 89 single nucleotide polymorphisms (SNPs). The distribution of Chum Salmon samples extended from the Nass River along the coast of British Columbia and along the coast of Washington as far south as the Columbia River. Chum Salmon represented three previously defined run-groups: fall (primarily), summer, and winter. Genetic variation at SNP loci, as measured byFST, ranged from 0.002 to 0.279 over all collections and averaged 0.062 over all loci. Similar to the genetic patterns detected with microsatellites and allozymes, genetic variation followed a regional structure along geographic distance, with genetic diversity being highest in the north and decreasing southward, then increasing in and near the Columbia River. Within Puget Sound, Washington, genetic variation was structured further according to run timing (fall, summer, and winter) and shared ancestry. Simulations indicated that this suite of SNPs is powerful for identifying regional components in a Chum Salmon mixed fishery. Because of the transferability of SNP data, the growing SNP baseline for Chum Salmon will be useful for multiple agencies managing Chum Salmon around the Pacific Rim. Received December 19, 2014; accepted May 20, 2015 [ABSTRACT FROM AUTHOR]

Programs to rebuild imperiled wild fish populations often include hatchery-born fish derived from wild populations to supplement natural spawner abundance. These programs require monitoring to determine their demographic, biological, and genetic effects. In 1990s in Washington State, the Summer Chum Salmon Conservation Initiative developed a recovery program for the threatened Hood Canal summer chum salmon Evolutionarily Significant Unit (ESU) (the metapopulation) that used in-river spawners (wild fish) for each respective supplementation broodstock in six tributaries. Returning spawners (wild-born and hatchery-born) composed subsequent broodstocks, and tributary-specific supplementation was limited to three generations. We assessed impacts of the programs on neutral genetic diversity in this metapopulation using 16 microsatellite loci and a thirty-year dataset spanning before and after supplementation, roughly eight generations. Following supplementation, differentiation among subpopulations decreased (but not significantly) and isolation by distance patterns remained unchanged. There was no decline in genetic diversity in wild-born fish, but hatchery-born fish sampled in the same spawning areas had significantly lower genetic diversity and unequal family representation. Despite potential for negative effects from supplementation programs, few were detected in wild-born fish. We hypothesize that chum salmon natural history makes them less vulnerable to negative impacts from hatchery supplementation. [ABSTRACT FROM AUTHOR]

It is widely recognized that genetic diversity within species is shaped by dynamic habitats. The quantitative and molecular genetic patterns observed are the result of demographics, mutation, migration, and adaptation. The populations of rainbow trout Oncorhynchus mykiss in the Columbia River basin (including both resident and anadromous forms and various subspecies) present a special challenge to understanding the relative roles of those factors. Standardized microsatellite data were compiled for 226 collections (15,658 individuals) from throughout the Columbia and Snake River basins to evaluate the genetic patterns of structure and adaptation. The data were primarily from fish of the anadromous life history form, and we used a population grouping procedure based on principal components and hierarchical k-means clustering to cluster populations into eight aggregates or groups with similar allele frequencies. These aggregates approximated geographic regions, and the two largest principal components corresponded to ancestral lineages of Sacramento redband trout O. m. stonei, coastal rainbow trout O. m. irideus, and interior Columbia River redband trout O. m. gairdneri. Genetic data were partitioned among primary aggregates (lower Columbia, middle–upper Columbia, and Snake rivers), and the magnitude of genetic divergence relative to genetic diversity was analyzed (per locus) to test for evidence of selection and subsequent signals of adaptation. Two loci showed higher divergence than expected by chance (i.e., positive selection); however, both of these loci were on the fringe of the 99% confidence level and are potential false positives. Genetic patterns were also significantly correlated with certain environmental and habitat parameters (e.g., precipitation), but the extent to which those correlations are causal as opposed to effectual remains unclear. Despite the remaining questions, these data provide a foundation for more detailed investigations of harvest, admixture, and introgression between hatcheryand natural-origin fish and differences in reproductive success among individuals as well as monitoring trends in productivity. [ABSTRACT FROM AUTHOR]

Lower Crab Creek (LCC) in eastern Washington is a groundwater-fed tributary to the Columbia River at river kilometer 661. The creek traverses agriculturally modified desert habitat, and in several reaches the water quality is poor, summer water temperatures are lethal to fish, and stream habitat is degraded. The creek was thought to be unsuitable for salmonids, yet fall-run Chinook salmon Oncorhynchus tshawytscha spawn and rear in it. The origin of these fish is uncertain since it is unclear whether LCC was a perennial creek prior to the hydrologic changes in the Columbia River basin stemming from the Columbia Basin Irrigation Project in the 1950s. We used genetic analyses to examine the hypotheses that these fish are (1) random strays, (2) a population founded since the 1950s (by wild or hatchery strays), or (3) an established native population. Chinook salmon juveniles and adults were collected in LCC and genetically characterized with the Chinook salmon microsatellite DNA locus suite in the Genetic Analysis of Pacific Salmonids database. The LCC population of Chinook salmon was found to be significantly different from interior Columbia River basin hatchery and wild populations and to have alleles that are absent from proximal populations. Lower Crab Creek Chinook salmon showed no evidence of recent founding and had genetic diversity, allelic richness, and effective population size similar to those of other Columbia River basin Chinook salmon. The data suggest that a genetically distinct, native population of Chinook salmon inhabits LCC that has adapted to the rigorous environment. [ABSTRACT FROM AUTHOR]

The bull trout Salvelinus confluentus is a broadly distributed char in northwestern North America that has undergone significant population declines. This species is currently protected under the Endangered Species Act across its range in the coterminous United States. To clarify patterns of phylogenetic structure and to assist with identification of conservation units, we examined genetic variation within and among 75 representative bull trout populations sampled throughout the USA. Genealogies from a 520-base-pair portion of the mitochondrially encoded NADH dehydrogenase 1 gene (ND-1) revealed reciprocal monophyly between coastal and interior lineages that differed by 1.34% in DNA sequence. The geographic distribution of the two lineages was divided by the Cascade Mountains, a pattern that likely reflects postglacial dispersal from separate glacial refugia. Analysis of microsatellite variation revealed that 76% of populations had an estimated effective population size less than 50 and indicated high divergence among populations caused by genetic drift (average genetic differentiation index FST = 0.32) and mutation (average genetic differentiation index RST = 0.58). Concordant phylogeographic and phylogenetic patterns observed with microsatellite and mitochondrial DNA analyses provided evidence for two to six bull trout lineages that largely reflect historic patterns of gene flow and isolation among populations. These lineages can be further subdivided into finer-scale units due to the extremely low dispersal among populations and small effective population sizes. In fact, Bayesian analysis of population structure identified an optimal solution of 69 genetically different groups. Based on these results, we believe that conservation efforts should ideally be focused on the 118 bull trout core areas originally identified in the draft Endangered Species Act recovery plan, which are broadly defined as metapopulations. We provide examples of how other data, such as unique life history forms and ecological setting, can be used in combination with our genetic results to refine the U.S. Fish and Wildlife Service's hierarchical conservation strategy for bull trout. [ABSTRACT FROM AUTHOR]

Stochastic fluctuation in allele frequencies may reflect microevolutionary processes responsible for genetic change, such as small effective population size ( Ne), which is a legitimate concern for imperiled populations affected by environmental or anthropogenic factors. In salmonids, recent empirical studies have provided conflicting results regarding the consistency of within-population genetic variation over time. In the present study, we surveyed the genetic variation at 14 microsatellite loci in two endemic populations of summer steelhead (Tucannon and Touchet) for seven consecutive years and the Lyons Ferry Hatchery stock (LFH) for 4 years. The LFH (mitigation) stock is used to enhance fishing opportunities in southeastern Washington State and not to aid in the recovery of natural populations. We observed statistically significant differences in allele frequencies between replicated collections from the same location. One of twenty-one genic tests for the Tucannon River collections, 9 of 21 genic tests for the Touchet River collections, and all genic tests regarding LFH collections were statistically significant. Temporal variation was larger than spatial variation (0.86% and 0.44%, respectively). We also used genetic data to infer effective population sizes for natural steelhead populations and the LFH mitigation hatchery stock, with point estimates of 729.7, 599.4, and 266.7 for the Tucannon, Touchet, and LFH populations, respectively. Despite the temporal variation observed, relative genetic differentiation was stable over time, replicated collections tending to cluster together in factorial correspondence analyses of allele frequency data. However, the genetic data were consistent with the potential for gene flow between the Tucannon River and LFH populations. The potential benefits of stocking genetically differentiated hatchery fish to enhance fishing opportunities in the Tucannon River may be offset by the negative effects of hatchery introgression and the small Ne in hatchery fish. [ABSTRACT FROM AUTHOR]

We used 13 microsatellite loci to examine population structure in rainbow trout collected from 20 tributaries and 3 main stems in the greater Spokane River drainage. Populations displayed some excess homozygosity and linkage disequilibrium, which was more pronounced in upper tributary collections and probably the result of small effective population sizes or structuring within tributaries. In general, population structure followed geographic structure; collections from creeks within sub-drainages were the most closely related, and collections from different tributaries were genetically distinct. Comparisons with cutthroat trout indicated little to no introgression. Comparisons with steelhead (anadromous rainbow trout), coastal rainbow trout O. mykiss irideus, and inland rainbow trout from hatcheries suggested introgression by hatchery fish into some wild populations. Introgression was suspected in populations from stocked tributaries and tributaries that lacked barriers to escaped hatchery fish. Populations from tributaries above barriers that had not been stocked were genetically distinct from hatchery fish and appeared to be native inland redband trout O. mykiss gairdneri. [ABSTRACT FROM AUTHOR]

We investigated temporal and spatial genetic variation in Pacific herring collections from six sites in Puget Sound (PS) and the southern Strait of Georgia (SOG), using 12 microsatellite loci. Loci were highly variable with up to 70 alleles per locus (mean = 30.67 alleles), and observed heterozygosity was high (mean = 0.823). Analysis of molecular variance (AMOVA) indicated significant structure, with over twice as much variance among sites as among collection years, although among-site variance was mainly due to Cherry Point and Squaxin Pass collections. In an AMOVA excluding Cherry Point and Squaxin Pass, only temporal variance was significant. With the exception of the Cherry Point and Squaxin Pass collections, pairwise genotypic and FST tests show some differences among collection years within a site and some genetic overlap among most PS and SOG collections. The Cherry Point and Squaxin Pass collections had no differences in genotypic distributions among collection years, and in cluster analyses the Cherry Point and Squaxin Pass collections each formed groups separate from other PS and SOG collections. Cherry Point herring have a later spawning time than other PS and SOG herring, and Squaxin Pass is physically isolated in southern Puget Sound. We hypothesize that spawn timing differences and spatial isolation generated genetic structure among some Pacific herring in PS and SOG. We suspect that, as in the case of Atlantic herring , population genetic structure in Pacific herring in PS and southern SOG is a combination of a larval retention model and a metapopulation model. Because Cherry Point and Squaxin Pass herring are genetically and behaviorally differentiated from other PS and SOG herring populations, this unique variation should be preserved through careful management. [ABSTRACT FROM AUTHOR]

Abstract American marten (Martes americana ) have a close association with mature temperate forests, a habitat that expanded throughout the Pacific Northwest as glaciers receded at the end of the Pleistocene. Similar to several other forest-associated mammals in North America (e.g. black bear), genetic analysis of the marten shows a deep phylogeographical subdivision that reflects populations with distinctive evolutionary histories. Using a suite of 14 microsatellite markers, we explored the genetic structure of marten populations in two reciprocally monophyletic clades in the Pacific Northwest identified previously as M. caurina and M. americana by mitochondrial haplotypes and morphology. Microsatellite phylogeographical patterns were congruent with mitochondrial analyses. These independent data sets shed light upon hybridization patterns, population structure and evolutionary histories. Hybridization between M. caurina and M. americana individuals was documented in two regions of sympatry (Kuiu Island in southeastern Alaska and southern Montana). Northern insular populations of M. caurina exhibited higher differentiation and lower variability relative to northern populations of M. americana . Greater divergence among M. caurina populations may reflect longer isolation and persistence in coastal forest habitat that was fragmented by rising sea level in the early Holocene. Lower differentiation among northern M. americana populations and close relationship to other continental M. americana populations may reflect more recent expansion into the Pacific Northwest and/or continued gene flow among populations. Differentiation among M. caurina populations was attributed to habitat fragmentation (i.e. rising sea level), as opposed to isolation-by-distance; oceanic straits pose significant barriers to gene flow among M. caurina populations and between populations of M. caurina and M. americana . [ABSTRACT FROM AUTHOR]