Molecular markers distinguish coastal cutthroat trout from coastal rainbow trout/steelhead and their hybrids

A major cause of population declines among interior cutthroat trout subspecies Oncorhynchus clarki ssp.is hybridization with introduced rainbow trout O. mykiss ssp. Coastal cutthroat trout O. c. clarki have also experienced population declines in recent decades and are known to hybridize with coastal rainbow trout/steelhead O. m. irideus. However, unlike interior cutthroat trout, coastal cutthroat trout are naturally sympatric with coastal rainbow trout/steelhead, and the role of hybridization in their population declines remains unclear. Further, little is known about the spatial and temporal distributions of hybridization in these coastal subspecies. As a step toward better characterization of this hybridization, we developed a suite of species-specific DNA markers for coastal cutthroat trout and coastal rainbow trout/steelhead. Of 11 loci presented here, 8 exhibit fixed differences between coastal cutthroat trout and coastal rainbow trout/steelhead. The other three loci revealed frequency differences great enough to make them useful as species markers. To demonstrate their utility, five of the markers developed here were used to assay a coastal cutthroat trout hatchery broodstock for the presence of hybrids. DNA-based markers can be assayed using nonlethal fin clips or archived samples and hence offer advantages for the study of historical and threatened contemporary populations.