SNPs Reveal Previously Undocumented Non-Native Introgression within Lahontan Cutthroat Trout Populations

All eight recognized subspecies of interior cutthroat trout (Oncorhynchus clarkii) are threatened by hybridization with introduced congeners. These include rainbow trout (O. mykiss) and other cutthroat subspecies, such as Yellowstone cutthroat trout (O. c. bouvieri) which have been stocked outside their native range. We used recently-developed species- and subspecies-diagnostic SNP markers to investigate non-native introgression in 33 populations of Lahontan cutthroat trout (O. c. henshawi). Results for O. mykiss hybridization were largely in agreement with those of previous studies. However, three populations contained substantial amounts of genetic material from the Yellowstone cutthroat lineage.