Genomic signatures among Oncorhynchus nerka ecotypes to inform conservation and management of endangered Sockeye Salmon.

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 anadromous Oncorhynchus 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 of O. nerka, and conservation efforts to preserve this diversity are important for long-term resiliency of this species.

Adaptation of redband trout in desert and montane environments.

Natural populations that evolve under extreme climates are likely to diverge because of selection in local environments. To explore whether local adaptation has occurred in redband trout (Oncorhynchus mykiss gairdneri) occupying differing climate regimes, we used a limited genome scan approach to test for candidate markers under selection in populations occurring in desert and montane streams. An environmental approach to identifying outlier loci, spatial analysis method and linear regression of minor allele frequency with environmental variables revealed six candidate markers (P < 0.01). Putatively neutral markers identified high genetic differentiation among desert populations relative to montane sites, likely due to intermittent flows in desert streams. Additionally, populations exhibited a highly significant pattern of isolation by temperature (P< 0.0001) and those adapted to the same environment had similar allele frequencies across candidate markers, indicating selection for differing climates. These results imply that many genes are involved in the adaptation of redband trout to differing environments, and selection acts to reinforce localization. The potential to predict genetic adaptability of individuals and populations to changing environmental conditions may have profound implications for species that face extensive anthropogenic disturbances.