Persistence of Yellowstone Cutthroat Trout in Tributaries to American Falls Reservoir Despite Massive Historical Stocking of Rainbow Trout

Yellowstone cutthroat trout (YCT) are native to the Bear, Snake, and Yellowstone River drainages in the Rocky Mountains of the United States and are of substantial importance to the Shoshone-Bannock Tribes of Idaho.  American Falls Reservoir is the largest reservoir in the Snake River basin and is located within Tribal territory.  The reservoir may be a conduit of introgression from rainbow trout (RBT), given its stocking history and abundant tributaries.  Tributaries to the reservoir contain a range of environments, creating a situation where YCT, hybrids, and RBT may persist or invade in different areas and proportions.  We analyzed 71 SNP assays to describe hybridization and the genetic population structure of YCT.  Higher-elevation tributaries contained almost exclusively YCT.  In many lower, more impacted locations, the parental species, F1-hybrids, and early-generation backcrosses occurred sympatrically, suggesting active invasions.  YCT showed substantial divergence among populations and were more similar to YCT in the Bear River than the Yellowstone, which supports recent mtDNA analyses and hypotheses about historical hydrological connections.  Sympatry of RBT, YCT, and early generation hybrids indicates that invasions are relatively recent and management action focused on eliminating RBT and hybrids could reduce genetic introgression.  Secondly, preventing upstream spread of introgression is critical.