Population genomic analysis of the Speckled Dace species complex identifies three distinct lineages in California

Abstract

AbstractObjectiveSpeckled Dace Rhinichthys osculus is small cyprinoid fish that is widespread in western North America. In California and elsewhere it is currently treated as a single species with multiple subspecies, many undescribed. However, these subspecies may represent evolutionary lineages that are cryptic species because they cannot be distinguished using standard morphometric techniques. In this study, we attempt to determine evolutionary lineages within California populations of Speckled Dace using the population genetic and genomic information.MethodsWe used restriction site‐associated DNA sequencing to extract thousands of single‐nucleotide polymorphisms across the genome to identify genetic differences among all the samples from 38 locations in the western USA, with a focus on California. We performed principal component analysis, admixture analysis, estimated pairwise values of the genetic differentiation index FST, and constructed molecular phylogenies to characterize population genetic and phylogenetic relationships among sampled Speckled Dace populations.ResultOur analyses detected three major lineages of Speckled Dace in California that align with geography: (1) Sacramento River, central California coast, Klamath River, and Warner Basin; (2) Death Valley and Lahontan Basin; and (3) Santa Ana River basin, in southern California. These lineages fit well with the geologic history of California, which has promoted long isolation of populations of Speckled Dace and other fishes.ConclusionThe presence of distinct evolutionary lineages indicates that Speckled Dace in California should be managed with distinct population segments to preserve within‐species diversity. This study highlights the importance of genetic analyses for conservation and management of freshwater fishes.