Marine species with pelagic larvae typically exhibit little population structure, suggesting long‐distance dispersal and high gene flow. Directly quantifying dispersal of marine fishes is challenging but important, particularly for the design of marine protected areas (MPAs). Here, we studied kelp rockfish (Sebastes atrovirens) sampled along ~25 km of coastline in a boundary current‐dominated ecosystem and used genetic parentage analysis to identify dispersal events and characterize them, because the distance between sedentary parents and their settled offspring is the lifetime dispersal distance. Large sample sizes and intensive sampling are critical for increasing the likelihood of detecting parent–offspring matches in such systems and we sampled more than 6,000 kelp rockfish and analysed them with a powerful set of 96 microhaplotype markers. We identified eight parent–offspring pairs with high confidence, including two juvenile fish that were born inside MPAs and dispersed to areas outside MPAs, and four fish born in MPAs that dispersed to nearby MPAs. Additionally, we identified 25 full‐sibling pairs, which occurred throughout the sampling area and included all possible combinations of inferred dispersal trajectories. Intriguingly, these included two pairs of young‐of‐the‐year siblings with one member each sampled in consecutive years. These sibling pairs suggest monogamy, either intentional or accidental, which has not been previously demonstrated in rockfishes. This study provides the first direct observation of larval dispersal events in a current‐dominated ecosystem and direct evidence that larvae produced within MPAs are exported both to neighbouring MPAs and to proximate areas where harvest is allowed.

Steelhead Oncorhynchus mykiss are the most widespread of the Pacific salmonids Oncorhynchus spp. and are found in nearly all basins within their native range around the northern Pacific Rim. Here, we elucidate genetic population structure of steelhead in coastal basins from most of their coastal‐California range using variation at 15 microsatellite loci. Juvenile fish from 60 streams in 40 river basins were sampled in a single year from a single cohort. As samples of juvenile salmonids often contain sibling groups, a method was implemented to identify and eliminate all but one member of larger sibships. This, in conjunction with a rigorous sampling protocol and hierarchical sampling design, provided substantially improved resolution for understanding patterns of migration and demography. A pattern of isolation by distance was evident, as indicated by both phylograms that were largely concordant with geography and a significant regression of genetic distance on geographic distance, indicating that population structure is largely determined by migration that is dependent upon geographic distance. Within‐basin genetic distances tended to be smaller than those between basins, although there was substantial overlap between them. Using a Bayesian clustering method to evaluate signals of population structure above the level of a river basin, four geographic sites were identified where genetic composition shifted abruptly. These areas largely correspond to major geographic features of the coastline: San Francisco and Humboldt bays and two extended sections of coast (the so‐called Lost Coast and Russian Gulch areas) with no streams reaching inland more than several kilometers. Only one of these boundaries is concordant with the current delineation of steelhead Distinct Population Segments designated under the U.S. Endangered Species Act. Finally, there was a strong correlation between latitude and genetic variation, with fewer alleles present in the south, a pattern consistent with generally smaller population sizes in the south.

Analysis of multilocus microsatellite genotypes revealed multiple paternity for all of the seven viable broods of larvae produced by kelp rockfish, Sebastes atrovirens (Jordan and Gilbert 1880), held jointly in a large aquarium tank (n = eight females and eight males). Only two of the eight experimental males were identified as fathers, and alleles not found in any of the captive males were present in all seven broods, demonstrating paternity by wild males external to the experiment. Thus, all of the females mated with one or more males prior to capture, confirming that female kelp rockfish are capable of storing sperm and controlling the overall timing of egg fertilization. These results highlight the potential for a paternal influence on larval quality through female mate choice and sperm competition.

Pelagic dispersal of marine organisms provides abundant opportunity for gene flow and presumably inhibits population genetic divergence. However, ephemeral, fine-scale, temporal and spatial genetic heterogeneity is frequently observed in settled propagules of marine species that otherwise exhibit broad-scale genetic homogeneity. A large variance in reproductive success is one explanation for this phenomenon. Here, genetic analyses of 16 microsatellite loci are used to examine temporal patterns of variation in young-of-year kelp rockfish (Sebastes atrovirens) recruiting to nearshore habitat in Monterey Bay, California, USA. Population structure of adults from central California is also evaluated to determine if spatial structure exists and might potentially contribute to recruitment patterns. Genetic homogeneity was found among 414 young-of-year sampled throughout the entire 1998 recruitment season. No substantial adult population structure was found among seven populations spanning 800 km of coastline that includes the Point Conception marine biogeographic boundary. Comparison of young-of-year and adult samples revealed no genetic differentiation and no measurable reduction in genetic variation of offspring, indicating little variance in reproductive success and no reduction in effective population size for this year class. Simulation analyses determined that the data set was sufficiently powerful to detect both slight population structure among adults and a small reduction in effective number of breeders contributing to this year class. The findings of high gene flow and low genetic drift have important implications for fisheries management and conservation efforts.

Rockfishes of the genus Sebastes are extensively distributed in the Pacific and Atlantic oceans. Although the occurrence of two morphologically similar species in the Southern Hemisphere, Sebastes oculatus and Sebastes capensis, is now clearly established, the taxonomic status and phylogeographic patterns for the genus in the region have not yet been completely resolved. In this study, we provide new insights into the taxonomy and evolutionary relationships of rockfishes inhabiting the Southwestern Atlantic Ocean, off the coast of mainland Argentina, by combining mitochondrial DNA (mtDNA) control region sequences, microsatellite data, and color pattern analyses. Differences in coloration ("dark" and "light" fish) together with bathymetric segregation between color morphotypes were evident from fish collection and literature review. In addition, the mtDNA phylogenetic analysis and Bayesian clustering analysis using microsatellite data separated the fish into two distinct groups (F ST = 0.041), most likely representing incipient species. Our results suggest that speciation-by-depth in the absence of physical barriers could be a widespread mechanism of speciation in Sebastes from both the Northern and Southern Hemispheres. Nevertheless, the degree of genetic differentiation found, added to the large number of individuals displaying high levels of admixture, points to the occurrence of incomplete reproductive barriers between color morphotypes. Beyond the taxonomic and phylogeographic implications of our findings, the occurrence of distinct groups of Sebastes off the coast of Argentina being targeted by different fisheries (angling and trawling) has consequences for the design and implementation of appropriate fishery regulations to avoid overharvest of either group.

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Conservation of the evolutionary legacy of endangered species is a key component for long-term persistence. Totoaba is a long-lived fish endemic to the Gulf of California and is considered critically endangered. There is currently a debate concerning its conservation status and whether it can be used as a fishery resource. Unfortunately, basic information on biological and genetic population structure of the species is lacking. We sampled 313 individuals and employed 16 microsatellite loci and 3 mitochondrial DNA markers (16S, 547 pb; COI, 619 pb; control region, 650 pb) to assess population structure and demography of totoaba in the Gulf of California, with samples from locations that encompass nearly all of its recognized geographic distribution. We could not reject a hypothesis of panmixia for totoaba, using nuclear or mitochondrial markers. Demographic analysis of mtDNA suggests a sudden population expansion model. The results have important implications for totoaba conservation because poaching is a significant conservation challenge and could have additive negative effects over the single population of totoaba in the Gulf of California.

Evaluation of population genetic structure and variation is an important part of planning for the recovery and management of protected species. Data from 18 polymorphic microsatellite DNA markers were used to analyze the phylogeographic structure of protected Coho Salmon Oncorhynchus kisutch from populations throughout California. Fish from 30 locations in two evolutionarily significant units (ESUs) representing most of the extant populations in the state were studied. Multiple analyses indicated a hierarchical pattern of population structure: the greatest divergence was found at the broadest geographic scale (ESU), followed by the divergences between basins and populations within basins. The populations of the large Klamath River basin were consistently identified as a distinct phylogenetic group, nearly as divergent from all other populations as the two ESUs were from each other. All populations in different basins were differentiated from each other and a pattern of isolation by distance was found at a California‐wide scale, but not at smaller spatial scales. Similarly, most individuals were accurately assigned to their population of origin, and almost all misassignments were to an adjacent or geographically proximal basin, indicating that there is substantial gene flow within each region but much less between regions. The number of parents contributing to each population was highly variable and reflected larger patterns of genetic variation, which was found to be generally higher in the southerly, low‐elevation coastal populations than in the northern, interior, higher‐elevation populations. The results strongly support the current boundary between the two ESU regions, and the detailed understanding of phylogeographic structure provided here will help to guide the management and recovery of Coho Salmon at the southern end of their geographic range. Received August 25, 2015; accepted May 4, 2016 Published online August 12, 2016