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Understanding the conservation status of native fish populations is increasingly important because they are put at risk by mounting anthropogenic pressures, including climate change. Conventional approaches to assess fish populations can be logistically challenging and cost-prohibitive. As a result, resource managers often make assumptions about the status of fish populations based on limited information. The watersheds of Washington’s San Juan Islands were considered too small to support wild salmonid populations. Many streams flow only seasonally, and all have been subjected to varying degrees of anthropogenic impacts affecting their ecological integrity. Nonetheless, we found that at least five watersheds in the archipelago support populations of coastal cutthroat trout (Oncorhynchus clarki clarki). To better understand the conservation status of coastal cutthroat trout populations there, we genotyped approximately fifty trout in each of three watersheds: Cascade and Doe Bay creeks on Orcas Island and Garrison Creek on San Juan Island. Results suggest that two watersheds support native populations and one supports naturalized hatchery fish. The likely native coastal cutthroat trout diversity documented in the two watersheds contributes to the overall diversity of the species, demonstrates that species’ resiliency, and provides justification for conservation measures. Effective management and conservation planning in data-limited situations requires the use of a precautionary approach. Population genetics provide a useful tool for identifying vulnerable fish populations and understanding their relationships with other conspecific populations. This information can inform restoration goals and help identify and prioritize restoration and protection measures.

Technological advancements have allowed geneticists to exploit an increasing array of molecular markers, many of which have different properties and may provide contrasting insights into the evolutionary history and structure of populations. This has important consequences for conservation managers attempting to identify units at which to conserve intraspecific diversity. In this study we compared the inferences derived from nuclear microsatellites and restriction-site associated DNA (RADseq) data for a threatened freshwater fish, the bull trout Salvelinus confluentus. For both marker types we generated data for the same suite of individuals collected from 24 populations distributed across the species range. The RADseq data were low coverage (mean site coverage

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 by FST, 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 th...

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.

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 componen...

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 Ge...

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...

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 Oncorhynchus mykiss (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 ...

In supplementation programs, hatcheries employ wild-origin fish as brood stock and their offspring are allowed into wild spawning areas. Resource managers use supplementation to support imperiled salmonid populations, seeking to in- crease census size and possibly effective population size (Ne), while minimizing risks of genetic diversity loss and domesti- cation from hatchery intervention. Here we document impacts of 5-10 years of supplementation on threatened summer-run chum salmon (Oncorhynchus keta) in Hood Canal (HC) and Strait of Juan de Fuca (SJF) in Washington State and compare them genetically with unsupplemented summer- and fall-run chum salmon from HC and South Puget Sound. Microsatellite allele frequencies identified four run-timing and geographic groups. HC and SJF summer chum salmon genetic relationships followed a metapopulation pattern of isolation by distance, similar to patterns prior to supplementation, suggesting that sup- plementation minimally impacted population structure. In most supplemented subpopulations, we detected no effects on di- versity and Ne, but high variance in individual pairwise relatedness values indicated over-representation of family groups. In two subpopulations, hatchery impacts (decreased diversity and lower Ne) were confounded with extreme bottlenecks. Re- bounds in census sizes in all subpopulations suggest that general survivorship has improved and that possible hatchery ef- fects on genetic diversity will be overcome. Resume´ : Dans les programmes de supplementation, les piscicultures utilisent des poissons d'origine sauvage comme stock

We genetically characterized seven species of Pacific salmonids in the Elwha River and in selected neighboring rivers prior to the impending removal of two dams. Monitoring the genetics of recolonization of the watershed by remnant native, hatchery, and/or adjacent watershed populations is a critical element to further our understanding of ecosystem restoration. By pooling data from independent studies, we assessed intraspecific diversity for pink salmon (Oncorhynchus gorbuscha), chum salmon (O. keta), coho salmon (O. kisutch), sockeye salmon (O. nerka), Chinook salmon (O. tshawytscha), rainbow trout (O. mykiss) and bull trout (Salvelinus confluentus). Levels and patterns of genetic variability within and among collections were evaluated at 6–15 microsatellite (mSAT) loci per species. Each species had 3–8 loci with 20 or more alleles. In all species, an Elwha collection was statistically different from one or more nearest-neighbor population. In addition, the native in-river collections of Chinoo...

We demonstrate an efficient model for standardizing microsatellite DNA data among laboratories studying Oncorhynchus mykiss. Eight laboratories standardized 13 microsatellite loci following allele nomenclature of a central laboratory (average inter-laboratory genotyping concordance >98%). Following this central model, we have currently standardized 298 alleles from throughout the species native range. Although we focus here on O. mykiss, our experiences and recommendation apply equally to other broadly distributed species that may benefit from multi-laboratory collaborative data collection.

We used 13 microsatellite loci to examine population structure in rainbow trout Oncorhynchus mykiss 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 O. clarkii 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 barr...

The lower Columbia River drainage once supported a run of over a million chum salmon. By the late 1950s, the run had decreased to often a few hundred fish. With the exception of Grays River near the coast and an aggregation of chum salmon spawning in creeks and the main stem near Bonneville Dam in the Columbia Gorge, most populations were thought to be extinct. However, chum salmon consistently return in low numbers to tributaries originating in the Cascade Range: the Cowlitz, Lewis, and Washougal rivers. To assess whether Cascade spawners were strays or remnants of former populations, chum salmon from the Coastal, Cascade and Gorge ecoregional zones were characterized at 17 microsatellite loci. Significant heterogeneity in genotype distributions was detected between zones and collections formed regional groups in a neighbor-joining tree. Cascade collections had higher allelic richness and private alleles, and the Cowlitz River supported genetically divergent fall and summer runs, the only summer chum salmon run extant in the Columbia River drainage. We propose that chum salmon in the Cascade zone are remnants of original populations. We attribute the divergence between zonal groups to diverse ecological conditions in each zone, which promoted regional genetic adaptation, and to genetic drift experienced in small populations.

We investigated temporal and spatial genetic variation in Pacific herring Clupea pallasii 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 F ST 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, an...

For over a century, Washington State Department of Fish and Wildlife has implemented hatchery programs as a means to boost salmon abundance. Concerns have developed that native populations may be replaced by hatchery strains, decreasing the genetic diversity required to respond to environmental changes. We report a comparison of microsatellite DNA variation in wild-spawning and hatchery-strain coho salmon from the Nooksack and Samish rivers in northern Puget Sound. Significant heterogeneity in genotype frequencies was detected between wild-spawning coho salmon from the upper North Fork (NF) Nooksack River and hatchery-strain coho salmon from the Nooksack River (descendants of primarily Nooksack River broodstock). Little difference in genotype frequencies was detected between wild-spawning coho salmon from the Samish River and hatchery-strain coho salmon from the Nooksack River. The 13-locus suite provided high resolution: in assignment tests over 85% of wild-spawning coho salmon from the upper NF Nooksack River were assigned to source. Wild-spawning coho salmon collected below hatcheries in the Nooksack River and 50% of wild-spawning Samish River coho salmon were assigned to hatchery collections. The genetic divergence of wild-spawning coho salmon in the upper NF Nooksack River is remarkable given the extensive stocking history and proximity of a hatchery. We suggest that these upper river fish are native coho salmon and that wild spawners in the lower Nooksack and Samish River are descendants of hatchery productions. We attribute divergence to earlier run timing in upper NF Nooksack River wild spawners, availability of extensive spawning and rearing habitat upstream of a hatchery in the upper NF Nooksack River, and a longer stocking history in the Samish River.

The intertidal snail Littorina,saxntilis displays a range of shell morphologies associated with a variety of habitats. Since morphology has an environmental and genetic basis, shell-based taxonomy may not accurately reflect genetic relationships. We explored genetic structure among adjacent populations of L. saxatilis (the robust open-shore type). L. neglecta (the tiny barnacle-dwelling type) and L. tenebrosa (the fragile brackish-water type), at nine sites in Britain. Using single-strand conformational polymorphism analysis of a 375bp fragment of cytochrome-b we found no evidence of species distinction. In AMOVA tests significant variation was contained among populations (68%;,) and among individuals (32%, both P < 0.001), and insignificant variation was found among ecotypes. Genetic patterns suggested gene flow among ecotypes over small scales and a strong random input over larger scales.

Snails of the Littorina saxatilis species complex are ubiquitous and important members of hard shore intertidal communities in the North Atlantic. The complex includes L. arcana, L. compressa and L. saxatilis. We investigated species and population structure among these species from six locations in Ireland and Britain using a nonradioactive single strand conformational polymorphism analysis of a 375 base pair fragment of the cytochrome-b gene. Variability was high with 38 haplotypes found in 591 individuals. The most common haplotype in L. arcana and L. compressa was absent from L. saxatilis and the most common haplotype in L. saxatilis was found in low numbers in L. arcana and L. compressa. Haplotypes restricted to L. arcana and L. compressa formed a cluster separate from L. saxatilis haplotypes in maximum parsimony and multidimensional scaling analyses. In analyses examining populations, L. arcana and L. compressa formed a group separate from L. saxatilis. Both the populations in the L. arcana/L. compressa group and in L. saxatilis show similar geographical structuring in that the North England populations were separated from a cluster of Cornwall (South-west England) and Irish populations. We suggested that Pleistocene sea level changes accounted for these congruent genetic patterns. We concluded that L. arcana and L. compressa are more closely related to each other than either is to L. saxatilis and offer this as a resolution to a previous trichotomy.

A series of experiments at two tropical locations tested the ability of land hermit crabs Coenobitu perlatus (H. Milne Edwards) and Coenobita compressus (H. Milne Edwards) to detect and respond to odors of dead conspecifics. An attraction array compared numbers of crabs attending hidden food odors and dead conspecific odors. Pit experiments tested crab shell-acquisition behaviors at different hidden odors. Bucket experiments confined crabs collected from various categories (feeding crabs, wandering crabs and crabs aggregated at dead conspecific odors) and tested behavioral responses to odors and an empty shell. Land hermit crab behavior at both sites was similar. Crabs were attracted to dead conspecific odors up to 10 times more than to food odors. Crabs attracted to dead conspecifics displayed significantly more shell-acquisition behaviors: touching other crab’s shells in an exploratory manner and switching shells if an empty shell was available. In buckets, crabs from each category switched into shells. Results are compared to previous reports of similar shell-seeking behaviors by marine hermit crabs in response to dead conspecific odors. It is suggested that responding to dead conspecilic odors for shell source location is an evolutionarily conserved behavior developed before hermit crabs became terrestrial.

We have isolated a yolk glycoprotein complex from eggs and early embryos of the sea urchin, Strongylocentrotus purpuratus. Sodium dodecyl sulfate polyacrylamide gel electrophoresis of these complexes and peptide mapping of their individual glycoprotein components indicate that developmental stage-specific changes in molecular composition of the complex are due to proteolytic processing events. Our data revealed that a 180 kDa glycoprotein of the egg complex is separated by a single proteolytic cleavage into intermediate glycoproteins of 115 and 76 kDa early in development. By the hatched blastula stage, each of these intermediate glycoproteins has been further processed to lower molecular weight forms: the 115 kDa protein is proteolytically clipped to a 84 kDa form, perhaps through 110 and 105 kDa intermediaries, while the 76 kDa molecule is directly processed to a 65 kDa form.