Identifying introgressive hybridization in native populations of California golden trout based on molecular markers

The California golden trout Oncorhynchus mykiss aguabonita is one of three subspecies within the rainbow trout-redband trout complex endemic to the Kern River basin and historically restricted to Golden Trout Creek and the South Fork Kern River. Past allozyme studies have indicated that native populations of California golden trout in the Golden Trout Creek drainage may have become introgressed with rainbow trout alleles through interaction with hybrids of rainbow trout and California golden trout stocked into nearby headwater lakes that are connected to tributaries in the drainage. We used six microsatellites and a minisatellite marker to estimate the genetic diversity and levels of introgression in approximately 700 California golden trout taken from 23 locations in Golden Trout Creek, its tributaries, and surrounding lakes. Indications of introgression were found in all but one of the sampled Golden Trout Creek drainage locations, the lowest average levels (0-8%) occurring in the lower reaches of Golden Trout Creek. The highest levels (12-17%) were in the Cottonwood Lakes populations that have been used as California golden trout broodstock by the California Department of Fish and Game. Evidence of introgression was also found in fish sampled from the upper reaches of the South Fork Kern River. This suggests that past and present stocking policies and hybridization with introduced rainbow trout currently threaten the genetic integrity of California golden trout populations across all of their native range.