Abstract Genetic stock identification (GSI) is an important tool in fisheries management. Microsatellites (μSATs) have been the dominant genetic marker for GSI; however, increasing availability and numerous advantages of single‐nucleotide polymorphism (SNP) markers make them appealing alternative. We tested performance 13 μSAT vs. 92 SNP loci a fine‐scale application GSI, using new baseline Chinook salmon consisting 49 collections ( n = 4014) distributed across Columbia River Basin. In...

Abstract Landscape genomics is a rapidly growing field with recent advances in both genotyping efficiency and statistical analyses that provide insight towards local adaptation of populations under varying environmental selective pressure. Chinook salmon ( Oncorhynchus tshawytscha ) are broadly distributed Pacific species, occupying diversity habitats throughout the northeastern pronounced variation climate features but little understood regarding this species. We used multivariate method,...

Abstract Mounting evidence of climatic effects on riverine environments and adaptive responses fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment local extinction risk, ecology, viability, genetic differentiation. While planning has been largely informed by neutral structure, there a dearth critical information regarding the role non‐neutral or functional variation. We evaluated variation among steelhead trout C olumbia R iver B...

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal human stressors influence connectivity, diversity and persistence. We used riverscape genetics modelling to assess whether climatic habitat variables were related neutral adaptive patterns of differentiation (population-specific pairwise FST ) within five metapopulations (79 populations, 4583 individuals) steelhead trout (Oncorhynchus mykiss) in the...

Abstract Organisms typically show evidence of adaptation to features within their local environment. However, many species undergo long‐distance dispersal or migration across larger geographic regions that consist highly heterogeneous habitats. Therefore, selection may influence adaptive genetic variation associated with landscape at residing sites and along routes in migratory species. We tested for genomic natal spawning paths the ocean anadromous steelhead trout ( Oncorhynchus mykiss)...

Abstract We examined 13 microsatellite loci from 51 collections of Chinook salmon Oncorhynchus tshawytscha throughout the Columbia River basin to determine membership in one three major genetic lineages, introgression lineages within specific populations, and structure at subbasin level. Results confirm those previous studies that persist drainage, representing two interior life histories (ocean stream types) lineage lower River. Novel observations were noted collections, including (Sandy...

Abstract It is widely recognized that genetic diversity within species shaped by dynamic habitats. The quantitative and molecular patterns observed are the result of demographics, mutation, migration, adaptation. populations rainbow trout Oncorhynchus mykiss in Columbia River basin (including both resident anadromous forms various subspecies) present a special challenge to understanding relative roles those factors. Standardized microsatellite data were compiled for 226 collections (15,658...

ABSTRACT Releasing fish at varied life stages is an underutilized hatchery‐rearing practice. Columbia River Treaty tribes have been working to reintroduce extirpated Coho Salmon historical habitats in upper watersheds. This effort has included the release of hatchery‐origin both parr and smolt Yakima Basin (Washington State USA), a tributary River. We evaluated releases smolts tagged with passive integrated transponders over 11 brood years. assessed emigration timing, survival, age‐at‐return...

Numerous studies in salmonids have demonstrated a fitness cost of producing and releasing hatchery-origin fish into the natural environment. One approach to reduce these costs is incorporate natural-origin hatchery broodstock, but this not always feasible may consistently buffer against domestication. In study, we used fifteen years spawning genetic data from upper Yakima River spring Chinook salmon (<i>Oncorhynchus tshawytscha</i>) population successfully assign approximately...

Adult sockeye salmon ( Oncorhynchus nerka) migrate past the largest breeding colony of American white pelicans Pelecanus erythrorhynchos) in Columbia River, USA. To investigate magnitude pelican predation on salmon, a state-space Bayesian model was used to estimate spatially and temporally explicit survival probabilities, total number consumed by each year. Results show that substantial source mortality some years, with median probabilities ranging annually from 0.015 0.084, resulting an...

Abstract Chinook salmon Oncorhynchus tshawytscha in the Columbia River basin (CRB) comprise three lineages—lower and sympatric interior ocean stream types—each with distinct biological attributes. To evaluate adaptive neutral genetic variation of this species CRB, we genotyped 54 populations using a panel 96 single‐nucleotide polymorphism (SNP) loci. All lineages were represented among collections widely distributed across locations, ranging from upper Salmon to near estuary. Our goal was...

Abstract The variation in mitochondrial DNA (mtDNA) and at eight microsatellite loci was analyzed 700 rougheye rockfish Sebastes aleutianus sampled along the Pacific Rim from Oregon coast to western Aleutian Islands Bering Sea. program STRUCTURE used analyze genotypes determine that samples probably came two genetically distinct sources (type I type II) by minimizing strong Hardy−Weinberg gametic disequilibria observed total sample. types had nearly fixed differences one locus (μ Sma 6 ),...

Abstract Both environmental and genetic factors influence anadromy in rainbow trout Oncorhynchus mykiss , but the mechanisms that contribute to migratory selection are not well understood. In this study, we used a limited genome scan approach identify candidate markers associated with 10 populations of O. from Klickitat River, Washington. From an initial panel 96 single‐nucleotide polymorphism (SNP) markers, identified 3 SNPs were significantly after accounting for underlying population...

Anadromous fishes often use various survival tactics while migrating through main stem rivers to successfully reach spawning grounds and reproduce. Mixed-stock assemblages of anadromous adult summer steelhead Oncorhynchus mykiss re-enter the Columbia River from late spring fall including period peak water temperatures, previous studies suggest that stocks alter migratory behaviour in response warm temperatures by seeking cool refuges. We combined parentage-based tagging with mixed stock...

Abstract We evaluated the genetic influence of hatchery supplementation on distinct naturally spawning populations Chinook salmon Oncorhynchus tshawytscha in South Fork Salmon River (SFSR), Idaho. Genetic tissue samples were collected from unmarked natural-origin and McCall Fish Hatchery (MFH)-reared carcasses, fish identified by an adipose fin clip at five main-stem sites located both upstream downstream a seasonal exclusionary weir upper SFSR. allele frequency data across 95...

Major lineages of anadromous salmonids show resilience to natural introgressive hybridization; however, Klickitat River spring-run Chinook salmon (KRSC, Oncorhynchus tshawytscha ) have an enigmatic origin because their intermediate genetic and geographic relationship among Columbia lineages. We used computer simulations evaluate four anthropogenic processes as likely causes the apparent introgressed composition KRSC: recent admixture (∼5 generations), historical (>200...

Abstract The historical distribution of Sockeye Salmon Oncorhynchus nerka in the Columbia River basin has been constrained by species’ dependence on nursery lakes for juvenile rearing. Several productive lake systems were impounded dams during last century leading to extirpation from many region. Recent efforts re‐establish populations historically natal areas are exemplified Cle Elum Lake reintroduction program. program is founded outplanting adult fish two middle donor with different...

Abstract To promote recovery of natural salmonid populations, managers are utilizing hatchery supplementation programs to increase abundance spawners on the spawning grounds. However, studies have provided evidence that captive breeding can result in domestication, demonstrated by lower fitness hatchery‐origin compared with natural‐origin fish. Supplementation programs, therefore, typically use broodstock an effort minimize long‐term negative impacts. Here we evaluated upper Yakima River...

Abstract Two cryptic species of rougheye rockfish Sebastes aleutianus , which we refer to as types I and II, have been identified independently from DNA (microsatellite mitochondrial [mtDNA]) markers distributions allozyme allele frequencies. Visual differences that discriminate between these in the field would improve their conservation management. To delineate species, used two microsatellite loci, μ Sma6 Sma7 conjunction with mtDNA site for restriction enzymes Cfo region NADH...

Abstract Efforts to rehabilitate threatened summer‐run (SR) and winter‐run (WR) populations of steelhead Oncorhynchus mykiss in the Hood River, Oregon, include operation two conservation hatchery programs. Annual collection discrete broodstocks relies on identification SR WR fish based return time, reproductive state, other physical behavioral characteristics. An increased likelihood misidentification occurs spring, when times overlap. The resulting interbreeding between ecotypes imposes...