Genomic Regions Potentially Under Selection in a Hybridized Population of Westslope Cutthroat Trout (Oncorhynchus clarkii Lewisi)

Hybridization among taxa is increasingly influenced by anthropogenic activities. This outcome is especially true in fish populations where stocking and external fertilization often encourage hybridization among previously isolated populations and species. Our knowledge of the effect of the introgressed genome on physiological function and population fitness and dynamics is largely unknown. In the North Fork Flathead River, Montana, introduced rainbow trout (Oncorhynchus mykiss) have readily hybridized with native westslope cutthroat trout (O. clarkii lewisi). Previous work has suggested that hybridization between the two species could have negative effects on population dynamics of cutthroat trout through a reducing in fitness in the hybrid genome. Here, we investigated the genomic mechanisms explaining this response using approaches based on genotyping by sequencing. We assayed the previously studied adult spawning fish (rainbow, westslope cutthroat, and hybrid trout) from the North Fork Flathead River, and determined the degree of admixture at the genomic level within individuals, using reference genome maps. Using this information, we describe the genomic architecture of hybridization between these two species, and the relationship between admixture and individual fitness.