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Freshwater-resident coastal rainbow trout Oncorhynchus mykiss irideus and the anadromous form of the subspecies, coastal steelhead (summer and winter runs), are present throughout the lower Klamath River–Trinity River system. Although coastal steelhead and other anadromous salmonids historically migrated into the Upper Klamath Basin (which encompasses the upper Klamath River and Upper Klamath Lake) and associated tributaries, the construction of Copco Dam in 1918 and Iron Gate Dam in 1962 stopped all upstream migration of fish past these barriers. In the Upper Klamath Lake basin, native Upper Klamath Lake redband trout O. mykiss newberrii are found along with coastal rainbow trout that were trapped above the dams or stocked from hatchery sources. However, relatively little is known about the genetic relationships among the O. mykiss populations within the Upper Klamath Basin. A population genetic analysis based on data from 17 variable microsatellite loci was conducted for samples collected in th...

Novel genetic resources now make it possible to directly assess the effects of natural selection on specific regions of the salmonid genome. Natural selection on specific genetic loci will also affect the variation in linked flanking regions through “hitchhiking” effects, causing greater differentiation between populations than would be expected from purely neutral processes. Here we identify candidate genomic regions for the effects of differential natural selection in two closely related populations of steelhead–rainbow trout Oncorhynchus mykiss separated for the last century following anthropogenic introduction above a barrier waterfall in a coastal California stream. A set of 110 expressed sequence tag (EST)-linked and 188 anonymous microsatellite loci, most of which are mapped, were chosen to provide distributed coverage of all linkage groups in the O. mykiss genome. A genome screen was then performed to identify genomic regions under divergent selection. Multiple complementary statistical m...

Molecular genetic analysis has long been used to identify species or populations that otherwise may be difficult to distinguish. More than 100 species of rockfish (genus Sebastes) occur worldwide, and more than 50 species may be found in relatively small regions, such as the Monterey Bay or Channel Islands in central and southern California. Many species are morphologically similar, particularly during the early larval stages, and identification to the species level is time-consuming and problematic for some groups. We describe a simple genetic method for the rapid identification of rockfish species by means of multilocus nuclear genotypes from a panel of six microsatellite loci. Application to a set of known rockfish tissue samples, including fish collected in different parts of their geographic ranges and species not represented in the reference data set, resulted in high assignment accuracy for the represented species and exclusion of the nonrepresented species. Members of the subgenus Pteropo...