Introgressive Hybridization of Redband Trout in the Upper McCloud River Watershed

Introgressive hybridization is an obstacle to the conservation of many species and subspecies. Diagnostic genetic markers or markers with high allele frequency differentials, such as single-nucleotide polymorphisms (SNPs), are becoming increasingly useful for detecting introgression between species or subspecies, such as subspecies of rainbow trout Oncorhynchus mykiss known as redband trout in the upper McCloud River watershed. Using a diagnostic mitochondrial SNP as well as nine nuclear SNPs, we quantified introgression levels between native redband trout and nonnative rainbow trout at 14 locations in the upper McCloud watershed and two locations in the lower McCloud region. Our analyses suggest that Sheepheaven, Edson, Moosehead, and Swamp creeks contain a large portion of the nonintrogressed redband trout individuals remaining in the upper McCloud watershed, implying a dramatic loss of populations free from introgressive hybridization. The results of this study have key management implications, such as the need to erect migration barriers and cease all stocking in the area. However, for managers to make fully informed decisions, additional research is needed on the population genetic structure and phylogenetics of these populations to clarify the issues of low genetic variation, inbreeding, or both and to define an appropriate management unit.