Genetic analysis of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) in the Walker Basin, California and Nevada

For more information contact Dr. Mandi Finger:

Background and Significance of Study


In 1975, California Department of Fish and Game (CDFG, now California Department of Fish and Wildlife, CDFW) discovered a remnant population of Lahontan cutthroat trout (LCT) in By-Day Creek, a small, degraded tributary of the East Walker River. Impending threats from drought soon led to translocations of LCT to other waters. Of these initial transfers, only one population is known to remain: Murphy Creek. In the late 1980s and early 1990s, four headwater streams were restored with LCT stocked directly from the natal stream (or from previously restored streams—primarily Slinkard, which was the first water treated) into these newly-fishless waters upstream of manmade and/or natural barriers: Slinkard, Mill, Wolf, and Silver creeks (in that chronological order), all tributaries to the West Walker River. Presumably, these LCT populations are non-hybrid; however, genetic analysis (Peacock et al. 2007) suggests that their phylogenetic signal has been lost due to low levels of heterozygosity as a result of low population sizes, random genetic drift, and/or repeated bottlenecks.

Prior to translocating LCT to new waters, their genetic purity must be confirmed. Currently, all Walker LCT populations persist in small headwater streams with no interconnection. No additional waters have been restored since 1996. Research has shown that for long term population viability, populations cannot be isolated—meta-population structure is needed.

The information acquired from this project will be used to determine the best modes of translocation: which populations to use; which, if any sections of streams to take the fish from; numbers to transfer; and age classes. The genetic analysis proposes to answer the following:

1. Is there population genetic structure in Lahontan cutthroat trout populations within streams? If so, what is causing this genetic structure?

2. What are the genetic differences between streams in the Walker Basin? Can these differences be attributed to habitat or population history?

3. What are the levels of introgression with rainbow trout in Walker Basin LCT populations? If funds allow, their major histocompatibility complex (MHC) functional genetic marker which deals with fish’ immunity to disease will be examined

Specific objectives of this project are to:

a. Evaluate two potential recipient streams in Nevada for LCT restoration.

b. Write a Walker Basin Lahontan cutthroat trout genetic management plan, outlining which populations may need infusions from additional fish to augment genetic variation, or which populations can withstand take in order to supplement declining populations.

Use RADseq and Rapture analysis to assess variation within and among LCT Walker Basin headwater populations and to characterize introgression with rainbow trout.

The results of these findings will be published in peer-reviewed journals and present at appropriate conferences. The SNP type assay will be published and shared with other labs to facilitate further genetic monitoring of LCT populations.



Nevada Division of Wildlife

California Department of Fish and Wildlife


More information:

Hydrology of the Walker Basin – USGS

National Fish and Wildlife Foundation’s Walker Basin Restoration Program

Walker Basin hydro mapper – USGS