title: Genomic signatures amongOncorhynchus nerkaecotypes to inform conservation and management of endangered Sockeye Salmon.
abstract: Conservation of life history variation is an important consideration for many species with trade-offs in migratory characteristics. Many salmonid species exhibit both resident and migratory strategies that capitalize on benefits in freshwater and marine environments. In this study, we investigated genomic signatures for migratory life history in collections of resident and anadromousOncorhynchus nerka(Kokanee and Sockeye Salmon, respectively) from two lake systems, using ~2,600 SNPs from restriction-site-associated DNA sequencing (RAD-seq). Differing demographic histories were evident in the two systems where one pair was significantly differentiated (Redfish Lake,FST= 0.091 [95% confidence interval: 0.087 to 0.095]) but the other pair was not (Alturas Lake,FST= -0.007 [-0.008 to -0.006]). Outlier and association analyses identified several candidate markers in each population pair, but there was limited evidence for parallel signatures of genomic variation associated with migration. Despite lack of evidence for consistent markers associated with migratory life history in this species, candidate markers were mapped to functional genes and provide evidence for adaptive genetic variation within each lake system. Life history variation has been maintained in these nearly extirpated populations ofO. nerka,and conservation efforts to preserve this diversity are important for long-term resiliency of this species.
authors.affiliation: Conservation Biology Division Northwest Fisheries Science Center National Marine Fisheries Service, NOAA Seattle WA USA.
authors.forename: Krista M
authors.identifier: 0000-0003-3453-7239
authors.initials: KM
authors.lastname: Nichols
authors.affiliation: Idaho Department of Fish and Game Eagle ID USA.
authors.forename: Christine C
authors.initials: CC
authors.lastname: Kozfkay
authors.affiliation: Columbia River Intertribal Fish Commission, Hagerman Fish Culture Experiment Station Hagerman ID USA.
authors.forename: Shawn R
authors.initials: SR
authors.lastname: Narum
keywords: migration; natural selection; random forest; residency