Mysterious population structure confers a fitness advantage in Misty Outlet stickleback

Understanding adaptation requires detecting selection at both phenotypic and genotypic levels. However, detecting selection at the genotypic level is challenging when selection is weak and/or when the genetic basis of phenotypes under selection is polygenic. Here, we investigated selection on genotypes in threespine stickleback fish (Gasterosteus aculeatus Linnaeus, 1758) from a mark-recapture experiment performed in the outlet stream of Misty Lake on Vancouver Island, Canada. We performed restriction site associated DNA sequencing (RAD-seq) on 190 fish that were recaptured in the experiment (“survivor” fish) and 192 fish that were not recaptured (“random” fish). Although we did not identify individual loci with strong differentiation between survivor and random fish, we found that survival was associated with a multi-locus genetic signature of ancestry in a "mystery" population. These loci were distributed across the genome and were not found at high frequency in the inlet stream of Misty Lake, suggesting that Misty Inlet is not the source of the mystery population. Fish that survived in Misty Outlet tended to be female and have wider pectoral fins. Our findings highlight the complexities of detecting weak and polygenic selection and the importance of integrating genomic approaches with ecological studies to elucidate adaptive mechanisms in natural populations.