Genomic Signatures of Adaptive Divergence Between Migratory and Non-Migratory Population Pairs of Oncorhynchus Nerka

Sockeye and kokanee salmon include both migratory and non-migratory life history forms, respectively, that further exhibit differences in spawning location and timing with the lakes and associated streams in which they rear and spawn.  In this study, we examine the genomic signatures of natural selection in two population pairs of sockeye and kokanee in central Idaho in two different lake systems:  Redfish Lake (n=150) and Alturas Lake (n=63).  RAD sequencing yielded 2593 genome-wide SNP markers that collectively suggest there are very different demographic histories for these populations.  The resident-migratory pair in Alturas Lake shows no significant population differentiation, while the population pair in Redfish Lake shows a strong signal of population differentiation (F_ST=0.15).  Despite no population differentiation in a global analysis in the Alturas Lake pair, 71 loci showed signatures consistent with divergent natural selection.  In Redfish Lake, outlier analysis revealed 104 loci consistent with divergent natural selection.  Only two loci showing divergent natural selection were in common, and may represent markers linked to genes influencing the migratory life histories of these population pairs.  Overall, our results suggest very different population histories, while providing important information to inform management and possible supplementation strategies in each lake.