Fish have evolved a variety of sex-determining (SD) systems including male heterogamy (XY), female heterogamy (ZW) and environmental SD. Little is known about SD mechanisms of Sebastes rockfishes, a highly speciose genus of importance to evolutionary and conservation biology. Here, we characterize the sex determination system in the sympatrically distributed sister species Sebastes chrysomelas and Sebastes carnatus. To identify sex-specific genotypic markers, double digest restriction site - associated DNA sequencing (ddRAD-seq) of genomic DNA from 40 sexed individuals of both species was performed. Loci were filtered for presence in all of the individuals of one sex, absence in the other sex and no heterozygosity. Of the 74 965 loci present in all males, 33 male-specific loci met the criteria in at least one species and 17 in both. Conversely, no female-specific loci were detected, together providing evidence of an XY sex determination system in both species. When aligned to a draft reference genome from Sebastes aleutianus, 26 sex-specific loci were interspersed among 1168 loci that were identical between sexes. The nascent Y chromosome averaged 5% divergence from the X chromosome and mapped to reference Sebastes genome scaffolds totalling 6.9Mbp in length. These scaffolds aligned to a single chromosome in three model fish genomes. Read coverage differences were also detected between sex-specific and autosomal loci. A PCR-RFLP assay validated the bioinformatic results and correctly identified sex of five additional individuals of known sex. A sex-determining gene in other teleosts gonadal soma-derived factor (gsdf) was present in the model fish chromosomes that spanned our sex-specific markers.

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.

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.

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Understanding patterns of connectivity among marine fish populations with demersal adults and pelagic larvae is critical for effective conservation of west coast rockfishes. The brown rockfish (Sebastes auriculatus) occurs in nearshore habitat and is common from northern Baja California, Mexico to northern California, rare off the outer coast of Oregon and Washington and again common in the inland waters of Puget Sound, Washington. Here we examine patterns of microsatellite DNA diversity from throughout the species' range as an indirect measure of long-term trends in larval dispersal. Genetic divergence was large and highly significant over all populations (F ST =0.056, P<0.0001), and was significantly correlated with geographic distance when considering coastal populations. The best estimates of mean coastal dispersal distance were on the order of 10 km or less per generation. Diversity was relatively low in the Puget Sound, suggesting that Puget Sound rockfish populations experienced a post-glacial founder effect followed by genetic isolation and low effective population size. Puget Sound individuals appeared to have recent mixed ancestry as a result of introgression with S. maliger and S. caurinus. Genetic isolation of Puget Sound fish provides a basis for consideration as a Distinct Population Segment (DPS) under the provisions of the Endangered Species Act. We recommend that coastal brown rockfish fisheries be managed at regional rather than coast-wide scales, and that design of marine reserve networks considers the surprisingly low realized dispersal distance of some species with high dispersal potential.

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The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with isolation-by-distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly-spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole-coast scale (approximately 2200 km), significant population subdivision (F(ST) = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (approximately 450 km, F(ST) = 0.001). Hierarchical amova identified a weak but significant 130-km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (N(e)m) is half that of the coast-wide average. However, individual-based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.

This study presents a comparative hierarchical analysis of variance applied to three classes of molecular markers within the blue marlin (Makaira nigricans). Results are reported from analyses of four polymorphic allozyme loci, four polymorphic anonymously chosen single-copy nuclear DNA (scnDNA) loci, and previously reported restriction fragment length polymorphisms (RFLPs) of mitochondrial DNA (mtDNA). Samples were collected within and among the Atlantic and Pacific Oceans over a period of several years. Although moderate levels of genetic variation were detected at both polymorphic allozyme (H = 0.30) and scnDNA loci (H = 0.37), mtDNA markers were much more diverse (h = 0.85). Allele frequencies were significantly different between Atlantic and Pacific Ocean samples at three of four allozyme loci and three of four scnDNA loci. Estimates of allozyme genetic differentiation (θ ) ranged from 0.00 to 0.15, with a mean of 0.08. The θ values for scnDNA loci were similar to those of allozymes, ranging from 0.00 to 0.12 with a mean of 0.09. MtDNA RFLP divergence between oceans (θ = 0.39) was significantly greater than divergence detected at nuclear loci (95% nuclear confidence interval = 0.04-0.11). The fourfold smaller effective population size of mtDNA and male-mediated gene flow may account for the difference observed between nuclear and mitochondrial divergence estimates.