Riverscape genetics identifies a cryptic lineage of speckled dace (Rhinichthys osculus) in the Klamath-Trinity Basin

Cataloging biodiversity is of utmost importance given that habitat destruction has dramatically increased extinction rates. While the presence of cryptic species poses challenges for biodiversity assessment, molecular analysis has proven useful in uncovering this hidden diversity. Using nuclear microsatellite markers and mitochondrial DNA (mtDNA), I investigated the genetic structure of Klamath speckled dace (Rhinichthys osculus klamathensis), a subspecies endemic to the Klamath-Trinity Basin. Analysis of 25 populations within the basin uncovered a cryptic lineage of speckled dace restricted to the Trinity River system and a possible contact zone between this lineage and speckled dace occurring in the Klamath Basin. The extent of mtDNA divergence between the Klamath and Trinity speckled dace was consistent with levels observed between sibling fish species (~3%). Trinity River system populations exhibited significantly lower levels of microsatellite genetic diversity (He=0.49, Ar=9.46) compared to Klamath Basin populations (He=0.64, Ar=12.35). Levels of hybridization between the lineages appeared to be low and confined to areas near the confluence of the Klamath and Trinity Rivers. The deep divergence between the lineages suggests that historical biogeographical processes are responsible. The precise mechanism that generated these lineages and currently maintains them as distinct in the absence of physical barriers is unknown. This study highlights the importance of incorporating molecular analysis into biodiversity research to uncover cryptic diversity.