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 ϭ 30.67 alleles), and observed heterozygosity was high (mean ϭ 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, 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 C. harengus, 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.

No abstract

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.

The upper Columbia River in Washington State (main‐stem and tributary habitat between McNary and Chief Joseph dams) is inhabited by two major lineages of Chinook Salmon Oncorhynchus tshawytscha: endangered spring Chinook Salmon and summer Chinook Salmon, which are not Endangered Species Act (ESA) listed. The lineages are highly genetically divergent from one another, and historically, spatial and temporal isolating mechanisms maintained these genetic differences. Both lineages occur in the Entiat River, a system where anthropogenic activity has changed habitat, flows, species composition, and the distribution of the two lineages over the past century. We examined the spatial and temporal overlap in spawning distributions between Entiat River spring and summer Chinook Salmon, and we used genetic markers to assess the level of introgression between lineages. Redd surveys were conducted from 2003 to 2017 to describe spatial and temporal spawning patterns of both lineages. There was temporal overlap in spawning between lineages in several years and considerable spatial overlap in redd locations annually. We genotyped subyearling juvenile Chinook Salmon captured in the Entiat River from 2009 to 2014 at 90 single nucleotide polymorphism loci to determine lineage and hybridization status. Genetic analysis revealed that hybridization between lineages does occur, albeit at relatively low rates (2.6% of subyearling juveniles genotyped). We detected hybrids each year samples were collected, and they were distributed throughout the Entiat River basin. Hybridization between lineages of Chinook Salmon could result in introgression and a loss of genetic diversity between the lineages and/or a loss of production by ESA‐listed spring Chinook Salmon. The presence of hybrids warrants concern for ESA‐listed spring Chinook Salmon in both the Entiat River system and throughout the upper Columbia River basin.