Phylogenetic Relationships and Introgression Patterns in a Threatened Species: Conservation Genomics of California's Native Inland Rainbow Trout

The evolutionary relationships of native rainbow trout (Oncorhynchus mykiss) subspecies have been difficult to elucidate, given the relative recency of divergence, likely incidence of secondary contact among select groups, and human induced introgression through both the transfer of native fish and the introduction of hatchery O. mykiss. We used Restriction site Associated DNA Sequencing (RAD-seq) to develop over 16,000 SNP markers to investigate the phylogenetic relationships among native trout subspecies in California, USA, as well as among selected populations within each subspecies. We also developed a panel of ancestry-informative SNPs to evaluate introgression between native and introduced subspecies; SNP-based relationships and estimates of introgression are then compared to results of previous investigations using microsatellite, mtDNA, and smaller SNP panels for each species. Lastly, we look for genomic patterns in hybridized individuals and signatures of selection in native groups. Understanding historical phylogenetic affinities, anthropogenically altered relationships, extant diversity, and potential genomic effects of hybridization are critical to management of many of these native groups which are threatened or candidate species for listing under the U.S. Endangered Species Act.