The copper rockfish (Sebastes caurinus) is a benthic, nonmigratory, rocky reef species with pelagic larval and juvenile stages lasting several months. Adults are commonly distributed in temperate coastal waters of the Pacific Ocean from British Columbia to southern California, including the inland waterways of Puget Sound, Washington, a semi-enclosed fjord system of known postglacial origin. Here, we report the distribution of genetic variation at six microsatellite DNA loci from six locations throughout the species' range. Among four coastal samples, significant population subdivision was detected (FST = 0.007), and a significant correlation between genetic and geographic distance was observed. Divergence was large and significant between Puget Sound proper and coastal samples (FST = 0.087). A sample taken only 100 km north of Puget Sound (the Canadian Gulf Islands) was also highly divergent from Puget Sound and coastal samples and was genetically intermediate between the two. The Puget Sound sample also displayed significantly lower allelic diversity and a more substantial presence of private alleles. The patterns of genetic divergence and diversity are most consistent with a historical colonization followed by limited oceanographic exchange among geographically proximate locations.

A recent phylogenetic review of the genus Sebastes suggested the existence of a cryptic species of vermilion rockfish (Sebastes miniatus). To evaluate the geographical and bathymetric range of the Type 1 and Type 2 forms reported in that study, cytochrome b sequences were examined from 548 fish. Type 1 fish were found primarily south of Point Conception on reefs deeper than 100 m. Type 2 fish were common range-wide at sites shallower than 100 m. Reproductive isolation between the two types was tested using nine microsatellite loci. Estimates of genetic divergence were made using the fixation index (F(ST)) and correspondence between haplotype and genotype was tested by Bayesian population assignment and multivariate plotting of individual genotypes. Microsatellite analyses gave strong support for the presence of two distinct groups of genotypes. All fish with Type 1 haplotypes and fish with Type 2 haplotypes from < 100 m depth had genotypes unique to their haplotype group. However, most (68%) fish with Type 2 haplotypes from > 100 m depth assigned strongly to the Type 1 genotype group. Morphometric comparisons between the two genotypic groups revealed significant differences at three of the six examined measurements. Differences in both genetics, depth of occurrence, and morphology suggest these are separate species. This observation along with evidence of depth segregation in many recent species pairs led us to hypothesize a speciation model for Sebastes spp. by which the loss or truncation of a depth-related ontogenetic migration can lead to the creation of reproductively isolated populations.

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