Received: 2 December 2015 | Accepted: 25 July 2016 DOI: 10.1111/eva.12412 ORIGINAL ARTICLE Genomic signatures among Oncorhynchus nerka ecotypes to inform conservation and management of endangered Sockeye Salmon Krista M. Nichols1 | Christine C. Kozfkay2 | Shawn R. Narum3 1Conservation Biology Division, Northwest Fisheries Science Center, National Marine Abstract Fisheries Service, NOAA, Seattle, WA, USA Conservation of life history variation is an important consideration for many species 2 Idaho Department of Fish and Game, Eagle, with trade- offs in migratory characteristics. Many salmonid species exhibit both resi- ID, USA dent and migratory strategies that capitalize on benefits in freshwater and marine en- 3Columbia River Intertribal Fish Commission, Hagerman Fish Culture Experiment Station, vironments. In this study, we investigated genomic signatures for migratory life history Hagerman, ID, USA in collections of resident and anadromous Oncorhynchus nerka (Kokanee and Sockeye Correspondence Salmon, respectively) from two lake systems, using ~2,600 SNPs from restriction- site- Krista M. Nichols, Conservation Biology associated DNA sequencing (RAD- seq). Differing demographic histories were evident Division, Northwest Fisheries Science Center, National Marine Fisheries Service, in the two systems where one pair was significantly differentiated (Redfish Lake, NOAA, Seattle, WA, USA. FST = 0.091 [95% confidence interval: 0.087 to 0.095]) but the other pair was not Email:
[email protected] (Alturas Lake, FST = −0.007 [−0.008 to −0.006]). Outlier and association analyses iden- tified several candidate markers in each population pair, but there was limited evi- dence 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.