The Search for the Kern River Rainbow: Conservation Genetics of a Native Trout

The Kern River rainbow trout (Oncorhynchus mykiss gilberti, "KRRT"), like many freshwater fish, has been heavily impacted by the introduction of non-native species into its native range. Angling interest in the region beginning over a century ago led to rampant transplantation of several different types of trout into lakes and streams throughout KRRT's range, the upper Kern River basin in southern California. These introductions resulted in hybridization and introgression with KRRT, and a dwindling number of purely native fish. In the following chapters I use genetic tools to examine the impact of this history of introductions, to measure current genetic characteristics of wild populations, and to provide guidance for the development of KRRT hatchery broodstock with the hope of helping to preserve one of California's native fish. In Chapter 1, I used SNP (single nucleotide polymorphism) and microsatellite markers to determine if a consistent genetic signature of KRRT within the upper Kern River basin still exists. I then measured introgression between KRRT and non-native trout, including coastal rainbow trout ( O. mykiss), Little Kern golden trout (O. m. whitei), and California golden trout (O. m. aguabonita). We found that there is indeed still a genetic signature distinct from the non-native trout that have been introduced, but that introgression with those fish is widespread. Nonetheless, we did find several populations with very little introgression, and discovered that a number of populations in the upper Kern River basin still largely represent the native genotype, despite the lengthy history of stocking.;In Chapter 2, I used microsatellites to examine gene flow and genetic diversity, particularly as they related to introgression. I found that those populations that have escaped introgression seem to have done so by being reproductively isolated from other populations. This isolation, however, coincides with reduced genetic diversity and genetic signs of population bottlenecks. In this way, avoidance of the primary threat to KRRT has exposed isolated populations to the threats of small population size and reduced genetic diversity.;In Chapter 3, I present a Hatchery Genetic Management Plan for KRRT. This plan details recommendations for the collection of wild KRRT, and the development and maintenance of a hatchery broodstock to be planted back into the Kern River in areas currently planted with non-native trout. I describe the genetic factors germane to maximizing genetic diversity, limiting inbreeding, and limiting adaptation to captivity. I also provide guidelines for planting the resulting fish, and for monitoring both existing wild populations as well as hatchery-origin fish. This plan is an important part of helping to restore KRRT to its native range, while ensuring proper management of KRRT populations that still exist.;Although this research focuses on KRRT, the issues addressed are relevant to a broader array of taxa threatened by the introduction of non-native species. In particular, the retention of a KRRT genetic signal despite a long history of introductions indicates some degree of resistance on the part of native taxa, and has implications for invasion biology. In addition, the balance between the competing threats of introgression and low genetic diversity provides an example of the many challenges involved in the attempt to preserve biodiversity in a changing world.