Ancestry and Adaptation of Rainbow Trout in Yosemite National Park

Abstract

California's Central Valley contains an abundance of rivers with historical and potential productivity for anadromous salmonids, which are currently limited by impacts such as dams, water diversions, and high temperatures. We surveyed genetic variation in Rainbow Trout Oncorhynchus mykiss within the upper Tuolumne and Merced rivers in and around Yosemite National Park to evaluate both population origins (ancestry) and the evolutionary response to natural and artificial barriers to migration (adaptation). This analysis revealed that despite extensive stocking with hatchery Rainbow Trout strains throughout the study area, most populations retained largely indigenous ancestry. Adaptive genomic variation associated with anadromy was distributed throughout the study area, with higher frequencies observed in populations connected to reservoirs that are known to support adfluvial life history variants. Fish in southern Central Valley rivers experience temperatures near the upper thermal limit for salmonids and represent an important reservoir of genomic diversity for adaptation to climate change. These results highlight the importance of local adaptation as well as the potential for resident Rainbow Trout populations above barrier dams to contribute to the recovery of steelhead (anadromous Rainbow Trout) once migratory connectivity is restored between upstream spawning and rearing habitats and the ocean.