The lahontan cutthroat trout (LCT) oncorhynchus clarkii henshawi has been listed as a threatened species under the U.S. Endangered species act (ESA) since 1974

This Project Grant award, provided by the U.S. Fish and Wildlife Service under the Cooperative Endangered Species Conservation Fund (CFDA 15.615) program, supports efforts to restore the genetic integrity of the Lahontan cutthroat trout (LCT) population at Independence Lake in California. The $283,540 award, with a performance period from January 2025 to January 2028, will fund a program to selectively remove non-native rainbow trout (RT) and LCT-RT hybrids from Independence Lake and its tributary, Independence Creek. This will be accomplished through population monitoring, genetic testing, and targeted removal of hybrid fish. The project will also install a spawning weir to control the upstream migration of LCT during spawning season. Additionally, environmental DNA (eDNA) sampling will be used to monitor for the presence of non-native trout. The California Department of Fish and Wildlife is the primary awardee, working in partnership with The Nature Conservancy to provide field assistance and resources. The overarching goal is to reduce the introgressive hybridization rate between LCT and RT to less than 5%, thereby restoring the genetic purity of this critical LCT population.

The LCT population at independence lake in eastern california is of particular conservation interest from a species recovery standpoint because IT is the only extant native population of lacustrine LCT in california and is one of only two extant adfluvial populations in the lahontan basin. The independence lake LCT population has declined by at least two orders of magnitude over the past several decades, reportedly due to competition and predation by introduced, non-native salmonids. The depressed LCT population has been further threatened in recent years by an accidental invasion of rainbow trout (RT) 0. Mykiss into the lake. LCT readily hybridize with RT and introgressive hybridization between LCT and RT threatens the genetic integrity of this important part of the LCT evolutionary legacy. A selective removal program for RT and LCT:RT hybrids began under a previous ESA section 6 grant and has been successful in driving the introgressive hybridization rate in the adult LCT population down to 0.8%, based on genetics samples collected in 2023. The current proposal is for a continuation of the selective removal and genetic monitoring program that is currently in place at independence lake. The basic approach to this work involves a combination of population sampling and monitoring in the field augmented with genetics support studies. The fact that upper independence creek is the only spawning tributary available to LCT at independence lake is a major advantage for controlling the composition of the spawning population. We will achieve this control by installing a fence in the stream, called a spawning weir, which blocks the upstream migration of LCT as they attempt to move into the creek to spawn. We will integrate a trap into the weir that holds the intercepted fish and allows US to sample them for information and to give each LCT an individual identifying passive integrated transponder (PIT) tag. We will take a small piece of tissue from the tail FIN of each captured LCT, which will then be analyzed in a genetics lab to determine whether the fish is a genetically pure LCT or hybridized with RT. If a tagged fish is captured during a subsequent capture event, its genetic status will be checked and if a LCT:RT hybrid, IT will be removed from the population. We are proposing to add a new element to this monitoring, a PIT tag array, which will allow for passive monitoring of both the upstream and downstream movement of LCT spawners in independence creek. Finally, we will collect samples of environmental DNA, or edna, from upper independence creek during the fall to monitor for the presence of RT, LCT:RT hybrids, and other non-native trout residing in the creek. We will use the locational information that goes along with the edna results to inform where in-stream removal work of non-native trout and hybrids should be focused, as applicable. The overarching goal of this project is to restore and ensure the genetic integrity of the unique LCT resource at independence lake, as evidenced in the estimated introgressive hybridization rate approaching 0%. This work will be accomplished by california department of fish and wildlife (cdfw) working in partnership with the nature conservancy (TNC), who will provide on-site field assistance and other resources to the project. This project will culminate with the development of a long-term monitoring concept for maintenance of the native lacustrine LCT genetic resource at independence lake.