Genomics Facilitates Evaluation and Monitoring of McCloud River Redband Trout ( Oncorhynchus mykiss stonei )

The McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei ) is a unique subspecies of rainbow trout that inhabits the isolated Upper McCloud River of Northern California. A major threat to MRRT is introgressive hybridization with non-native rainbow trout from historical stocking and contemporary unauthorized introductions . To help address this concern, we collected RAD-sequencing data on 308 total individuals from MRRT and other California O. mykiss populations and examined population structure using Principal Component and admixture analyses. Our results are consistent with previous studies; we found that populations of MRRT in Sheepheaven, Swamp, Edson, and Moosehead creeks are nonintrogressed. Additionally, we saw no evidence of introgression in Dry Creek, and suggest further investigation to determine if it can be considered a core MRRT conservation population. Sheepheaven Creek was previously thought to be the sole historical lineage of MRRT, but our analysis identified three: Sheepheaven, Edson, and Dry creeks, all of which should be preserved. Finally, we discovered diagnostic and polymorphic SNP markers for monitoring introgression and genetic diversity in MRRT. Collectively, our results provide a valuable resource for the conservation and management of MRRT.

Cutthroat Trout: Evolutionary Biology and Taxonomy

<em>Abstract</em>.—The fossil record of Cutthroat Trout <em>Oncorhynchus clarkii</em> enables us to see them as ancient fish adapted to mountain streams and lakes, with resilience to dramatic geologic and climatic changes over time scales of thousands to millions of years. Their natural habitat is in the Rocky Mountains and Great Basin of the United States and Canada, usually inland of their sisters, Rainbow Trout <em>O. mykiss</em> and Redband Trout. Earliest records of the lineage are from near the California–Nevada line in the 16-to-3-million-year-old tectonic trough between the Sierra Nevada and the Great Basin that predates the uplift of the Sierras. The first known member of the lineage is the Truckee Trout <em>O. belli</em>, 10 million years ago. This ancestral Cutthroat Trout and its eight known fossil descendants lived in lakes and tributaries in the trough between the Sierra Nevada and the Great Basin, from The Miocene Esmeralda Formation north to Pleistocene Honey Lake. These already possessed diagnostic Cutthroat Trout traits such as an abbreviated preopercle, deep subopercle, and A-shaped dermethmoid (bone on the snout), which differentiate them from chars and other salmonids. Five Pleistocene relatives have been found above 1,400 m in the Bonneville basin and four others have been found from 1,800 to 2,700 m in Colorado and Wyoming. Throughout their fossil history, Cutthroat Trout are not known to have coexisted with Rainbow Trout or Redband Trout, apparently being susceptible to genetic mixing and competitive elimination, although there is limited sympatry in northern coastal streams today. The other major threat to their persistence is habitat loss from anthropogenic dams, water withdrawal for agriculture, overgrazing, and deforestation, which disrupt natural dispersal within metapopulations and risks local extirpation. Maintenance of natural habitat, including historical immigration routes among populations, would contribute more to long-term survival of Cutthroat Trout than providing minimal habitat reserves.