Genomics Facilitates Evaluation and Monitoring of McCloud River Redband Trout (Oncorhynchus mykiss stonei)
Authors: Ensieh Habibi 1; Michael Miller 1; Daphne Gill 2; Leigh Sanders 2; Jeff Rodzen 2; Molly Stephens 3; Amanda Finger 1
Affiliations: 1) University of California, Davis, CA; 2) California Department of Fish and Wildlife, Genetics Research Laboratory, Sacramento, CA ; 3) Natural Reserve System, University of California Merced, Merced, CA
Keywords: Ecological & conservation genetics
The McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei) is a unique subspecies of rainbow troutthat 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.