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.

For more than 100 years, two dams blocked upstream migration of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) on the Elwha River, Washington. Prior to the removal of both dams (completed in 2015), 30 spatiotemporal collections of resident Rainbow Trout, steelhead, hatchery steelhead, and hatchery-derived Rainbow Trout (1,949 individuals) were made from 17 sites in the river, and the pattern of genetic diversity and connectivity were evaluated using 13 microsatellite loci. Wild-origin steelhead spawned below the downstream dam and were genetically distinguishable from upriver (above dam) resident Rainbow Trout (F ST = 0.034), and the resident Rainbow Trout segregated into two distinct groups (F ST = 0.056). Nonnative-origin hatchery steelhead varied from the indigenous steelhead (F ST = 0.029), and the hatchery trout differed from the resident trout (F ST = 0.163). Collections of resident Rainbow Trout from the upper portion of the basin were distinguished by lower estimates of genetic variability (H e , A R , and A/L) and effective population size compared with resident Rainbow Trout in the middle reaches of the Elwha River. The break between the two trout groups coincided with Rica Canyon, 8 river kilometers upstream from the Glines Canyon Dam (the upstream dam), suggesting that the upper and middle trout groups represent historic O. mykiss groups separated by flow conditions in the canyon prior to dam construction. Anticipating the potential for genetic exchange between steelhead and resident Rainbow Trout following dam removal, we evaluated the ability of the microsatellite baseline to distinguish F 1 crosses between the life history groups with computer simulations. These results demonstrate how a genetic baseline can be used as a conservation management tool to measure potential genetic introgression among resident populations and recolonizing anadromous populations.

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In 2011, steelhead Oncorhynchus mykiss (anadromous rainbow trout) will be systematically transported above Howard Hanson Dam, Green River, Washington. We are interested in providing data to help manage the stock of fish that are selected to recolonize the upper river and to track how resident rainbow trout above the dam respond genetically after 80 years of isolation. We characterized relevant gene pools in the upper Green River before fish transportation with 11 microsatellite loci to evaluate the genetic variability within and among collections. We also examined morphometric and coloration patterns as potential indicators of adaptive variation. Hatchery steelhead are clearly different from wild steelhead (FST = 0.037); genetic assignment tests correctly distinguished 91% of the steelhead. While there was no reduction in the amount of genetic variability in the resident rainbow trout above Howard Hanson Dam compared with that of wild steelhead collections below the dam, the two groups had low but statistically significant differences (FST = 0.03). The transport of juvenile and adult steelhead above the dam in the last 20 years may have affected these genetic results. Two collections of hatchery rainbow trout were highly differentiated from all other collections, and a STRUCTURE analysis indicated that there was no introgression of their genes into Green River fish. Morphologically, significant differences were seen between juvenile resident rainbow trout and steelhead. Resident trout had a stout caudal peduncle and more parr marks, whereas juvenile steelhead had a more elongate tail and fewer parr marks. Given these genetic and phenetic measures of differentiation, managers can monitor and screen the upstream passage of steelhead, and will be able evaluate the level of participation of resident rainbow trout gene pools in the recolonization event.

Restoration of access to lost habitat for threatened and endangered fishes above currently impassable dams represents a major undertaking. Biological monitoring is critical to understand the dynamics and success of anadromous recolonization as, in the case of Oncorhynchus mykiss, anadromous steelhead populations are reconnected with their conspecific resident rainbow trout counterparts. We evaluate three river systems in the Lower Columbia River basin: the White Salmon, Sandy, and Lewis rivers that are in the process of removing and/or providing passage around existing human-made barriers in O. mykiss riverine habitat. In these instances, now isolated resident rainbow trout populations will be exposed to competition and/or genetic introgression with steelhead and vice versa. Our genetic analyses of 2,158 fish using 13 DNA microsatellite (mSAT) loci indicated that within each basin anadromous O. mykiss were genetically distinct from and significantly more diverse than their resident above-dam trout counterparts. Above long-standing natural impassable barriers, each of these watersheds also harbors unique rainbow trout gene pools with reduced levels of genetic diversity. Despite frequent releases of non-native steelhead and rainbow trout in each river, hatchery releases do not appear to have had a significant genetic effect on the population structure of O. mykiss in any of these watersheds. Simulation results suggest there is a high likelihood of identifying anadromous x resident individuals in the Lewis and White Salmon rivers, and slightly less so in the Sandy River. These genetic data are a prerequisite for informed monitoring, managing, and conserving the different life history forms during upstream recolonization when sympatry of life history forms of O. mykiss is restored.