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

Two questions relevant to the management of species threatened by introgressive hybridization are whether results from different types of genetic marker are comparable, and whether all possible sources of introgression have been identified. We used recently-developed SNPs markers to quantify introgression from two non-native taxa: rainbow trout (Oncorhynchus mykiss) and cutthroat trout of the Yellowstone evolutionary lineage (O. clarkii subspp), into populations of the threatened Lahontan cutthroat trout (O. c. henshawi). Results for O. mykiss introgression were largely in agreement with those of previous studies using different markers. However, three populations contained substantial amounts of genetic material from the Yellowstone lineage, a source of introgression that had not previously been closely examined. This included one population previously proposed as a remnant of an extinct cutthroat trout subspecies.