UC Santa Cruz

Genetic assessments serve as powerful tools to evaluate the effects of anthropogenic habitat fragmentation on natural populations. In the Klamath River Basin, construction of four dams from 1912 to 1962 had a profound impact on the distribution of anadromous fishes, blocking access to over 751 river kilometers of critical habitat. To characterize the genetic diversity and connectivity among Oncorhynchus mykiss in the basin prior to the historic removal of the four dams in 2024, we genotyped 2466 samples at 193 presumably neutral and 105 putatively adaptive markers. Using complementary population genetic analyses, we found a clear division between coastal and inland O. mykiss lineages located primarily downstream and upstream of the outlet of Upper Klamath Lake, and little genetic structure associated with dams. Further, we detected distinct inland and coastal genetic lineages upstream of the lake outlet supporting the hypothesis that ancestral inland O. mykiss were secondarily invaded by a coastal lineage. We found that neutral genetic diversity was significantly greater in collections consisting primarily of anadromous O. mykiss compared to collections of adfluvial, fluvial, and resident fish while genetic diversity was significantly lower in adfluvial collections. Based on the chromosome Omy5 markers associated with anadromous/resident phenotypes, we found that anadromous and heterozygous genotypes were more prevalent downstream of the lake outlet while resident genotypes were prevalent upstream of the outlet. Based on the chromosome Omy28 markers associated with adult migration timing, we found that late-migration timing and heterozygous genotypes were numerous downstream of the lake outlet while early-migration timing genotypes were prevalent upstream of the outlet. The results of our population genetic analyses highlight the genetic diversity and structure of O. mykiss in the Klamath River Basin and will serve as a critical baseline for future assessments post dam removal.