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Ancestry and adaptation of resident, adfluvial, and anadromous rainbow trout (Oncorhynchus mykiss) in Putah Creek, an ecotone crossing watershed

Goetz, Laura12; Chapman, Eric3; Michel, Cyril21; Correa, Elena21; Pearse, Devon12

Published Jul 23, 2026 on Dryad. https://doi.org/10.5061/dryad.1c59zw49w

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Abstract

Evaluating patterns in the distribution of genetic variation across heterogeneous landscapes provides perspectives on how environmental features contribute to molecular evolution, and how human activities influence populations. Impassable barriers, such as hydroelectric dams, and human-directed movement or propagation of individuals across riverscapes have had strong impacts on the genetic diversity observed in natural populations. We considered the population structure and distribution of adaptive genetic variation in the salmonid species Oncorhynchus mykiss throughout Putah Creek, a watershed near Napa Valley, California that was transformed by the 1950’s construction of multiple dams and a large artificial reservoir (Lake Berryessa). In addition, hatchery-raised O. mykiss have been introduced throughout the watershed over many years, which may have introduced genetic variation into existing Putah Creek populations. To explore the population structure and distribution of adaptive genetic variation in Putah Creek, we analyzed microhaplotypes from 196 individuals from eight O. mykiss populations above Lake Berryessa and two populations below Lake Berryessa, and compared them with 2,075 samples from 40 reference populations from California Central Valley, coastal, inland, and hatchery rainbow trout lineages. We found distinct patterns of neutral and adaptive variation between populations above Lake Berryessa and those below. Populations below Lake Berryessa resembled various Central Valley populations and hatchery rainbow trout strains, while those above were more similar to coastal O. mykiss populations. Additionally, Putah Creek populations below Lake Berryessa possessed significantly different proportions of adaptive variants associated with life-history compared to populations above Lake Berryessa, consistent with studies in other populations located above and below barriers to migration.