Isolation, Migration, and Local Recruitment Drive Persistence of Cutthroat Trout in Tributaries near American Falls Reservoir

Abstract

We analyzed 67 SNPs to describe the genetics of Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri in seven tributaries near American Falls Reservoir, Idaho. We detected Yellowstone Cutthroat Trout in all but one site despite significant historical stocking of Rainbow Trout O. mykiss. Three of four relatively low-elevation sites near the reservoir contained Yellowstone Cutthroat Trout in sympatry with early-generation hybrids and Rainbow Trout yet contained no physical barriers to admixture. A posteriori assignment tests suggested that migrants from a nearby headwater population in Ross Fork Creek and possibly recruitment by local-origin Yellowstone Cutthroat Trout with fluvial or adfluvial life histories drive persistence in these sites. In contrast, hybridization was rare or absent in headwater populations and was associated with complete or apparent physical isolation. We also compared genetic diversity of our samples with Yellowstone basin Yellowstone Cutthroat Trout and Bear River Bonneville Cutthroat Trout O. c. utah to examine possible historical gene flow resulting from hydrogeological connections during the Pleistocene. Multivariate analysis showed that most genetic variation among individuals was explained by divergence of Yellowstone basin Yellowstone Cutthroat Trout from our samples and Bear River Bonneville Cutthroat Trout, which supports recent mtDNA studies and a possible change in taxonomic nomenclature. Our results indicate that, due to relative isolation and downstream emigration, headwater populations are critical to the persistence of Yellowstone Cutthroat Trout and thus loss of such populations would likely threaten the subspecies throughout the region. Management actions to reduce threats from established, nonnative Rainbow Trout populations will likely have to be multifaceted and may include a combination of targeted removal of Rainbow Trout and hybrids and the use of physical barriers to prevent further dispersal.

Received April 19, 2015; accepted February 7, 2016 Published online May 31, 2016

Acknowledgments

This research was funded by a grant from the Bonneville Power Administration to the Shoshone-Bannock Tribes, Bonneville Power Administration project Number 2008-906-00. We thank the many Shoshone-Bannock Tribal biologists, technicians, and staff for sample collection and project organization. We acknowledge the valuable efforts of the staff at the University of Montana Conservation Genetics Laboratory: Sally Painter, Angella Lodmell, and Steve Amish. We thank Montana Fish, Wildlife, and Parks and Dr. Robb Leary for development of the SNP assays used in this study. We thank Victoria O’Byrne for Figure 1 and three reviewers for helpful comments.