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Hybridization between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and steelhead (O. mykiss) was assessed in the Smith River, California. Individuals were categorized as pure or as 1 of 10 hybrid classes using 30 “diagnostic” single-nucleotide polymorphisms positioned on 26 separate chromosomes. Most of the individuals examined (n = 876), were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213), and 29 individuals were identified as having hybrid ancestry. Among hybrids, first generation hybrids (n = 15) and coastal cutthroat trout backcrosses (n = 12) were the most common. No individuals were identified as backcrosses to SH, suggesting the presence of genetic or behavioral mechanisms constraining such backcrosses, or the growth and survival of their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven primarily by sneak-mating of male coastal cutthroat trout with female steelhead. Evaluation of classical phenotypic characters for coastal cutthroat trout and steelhead (i.e. jaw slash, maxillary length, and hyoid teeth) were not reliable by themselves for identification of either pure parental fish or hybrids. In contrast, analysis with geometric morphometrics revealed distinctive body shapes for pure coastal cutthroat trout and steelhead, and the combination of classical traits and geometric morphology was mostly accurate in distinguishing them. However, first generation hybrids and backcrosses overlapped completely with parental types, highlighting challenges in hybrid identification using phenotypic traits.

Anadromous river herring (alewife and blueback herring) persist at historically low abundances and are caught as bycatch in commercial fisheries, potentially preventing recovery despite conservation efforts. We used newly established single-nucleotide polymorphism genetic baselines for alewife and blueback herring to define fine-scale reporting groups for each species. We then determined the occurrence of fish from these reporting groups in bycatch samples from a Northwest Atlantic fishery over four years. Within sampled bycatch events, the highest proportions of alewife were from the Block Island (34%) and Long Island Sound (22%) reporting groups, while for blueback herring the highest proportions were from the Mid-Atlantic (47%) and Northern New England (24%) reporting groups. We then quantified stock-specific mortality in a focal geographic area (∼3500 km2, including Block Island Sound) of high bycatch incidence and sampling effort, where the most accurate estimates of mortality could be made. During this period, we estimate that bycatch took about 4.6 million alewife and 1.2 million blueback herring, highlighting the need to reduce bycatch mortality for the most depleted river herring stocks.

Many juvenile fishes have specific habitat requirements, and while some habitats may be more important than others for growth and survival, habitat-specific growth and survival information is missing for the sensitive juvenile life stage of many species. Given the potential impact of habitat productivity on growth and the importance of growth to survival, we evaluated the influence of specific estuarine habitats on post-settlement growth of a marine fish. Juvenile black rockfish (Sebastes melanops) were collected from May to September over 2 years at both anthropogenic (dock) and natural (eelgrass) habitats in a marine-dominated estuary on the central Oregon coast. Recent growth decreased throughout each year, which correlates with an increase in fish size. Recent growth did not differ between habitats in 2016, a year of increased upwelling, but did differ between habitats in 2017, when upwelling was reduced. Recent growth remained high between years at the eelgrass habitat but greatly decreased at the dock habitat between years. During high upwelling years, Yaquina Bay may be an extension of nearshore waters, where a high diversity of prey resources and less variation in source of nutrients leads to high juvenile black rockfish growth rates regardless of habitat type. In years of variable ocean conditions, however, habitat type may become more important for growth, with eelgrass providing a higher quality and more consistent habitat compared to anthropogenic structures, and therefore contributing to consistent and higher interannual growth rates.

Genetic species identification is often necessary for species flocks, such as rockfishes in the genus Sebastes (Teleostei, Scorpaenidae), where traditional visual identification methods are challenged by the presence of many sympatric species with morphologically similar juveniles. Here we present a straightforward approach for performing species identification in rockfishes using 96 nuclear microhaplotype loci that can be efficiently genotyped using high-throughput DNA sequencing. Self-assignment of nearly 1 000 samples from 54 species resulted in > 99% accurate species identification at a 95% confidence threshold. Phylogenetic relationships of Sebastes uncovered with these same loci were highly concordant with relationships previously derived primarily with mitochondrial DNA. We also assessed ascertainment bias and consequent reduced nucleotide diversity and heterozygosity in non-ascertainment species to understand the potential utility of these markers for those species. The data and protocol presented here will be useful for research and management of rockfishes in the northeastern Pacific Ocean.

Recent climatic conditions are affecting biodiversity, particularly those species highly isolated and at their distribution limits such as trout (Oncorhynchus sp.) inhabiting the Northern Sierra Madre Occidental (NSMO) in Mexico, which is a current conservation concern due to their fragmented distribution and anthropogenic threads. Here, we compiled previously published data from 24 microsatellite loci from multiple localities of trout throughout the NSMO to construct geographic genetic structuring hypotheses. Our results confirm two genetically distinct subgroups within the NSMO corresponding to the northern populations from Rio Yaqui-Rio Bavispe and Rio Casas Grandes, and the southern population from Rio Yaqui-Rio Sirupa and Rio Conchos. In addition, we found a strong genetic differentiation between most of the locations sampled. We assembled species distribution models (SDM) to estimate the current distribution of trout. The SDM show that suitable environmental conditions may exist between northern and southern populations but are highly fragmented. In addition, association analyzes between FST and environmental factors show that the minimum temperature of the coldest month, the precipitation of wettest month, and the compound topographic index were responsible for the genetic structure. These results along with the limited mobility of the species, support limited connectivity as a possible explanation for current north and south arrangement of diversity. This study provides deep insights into the ecology and divergence processes within Northern Sierra Madre Occidental trout, and for the urgent development of effective conservation strategies for each of those lineages.

The expression of anadromy in partially migratory salmonid populations is influenced by sex-specific interactions among an individual’s genotype, condition, and environment, but genotype–phenotype relationships prior to the expression of migratory type are poorly understood. We examined whether juvenile growth and condition differed with respect to sex and a migration-associated genomic region (Omy05) in a coastal California population of steelhead and rainbow trout (Oncorhynchus mykiss). Sex and Omy05 genotype had additive effects on annual growth from age 0+ to age 1+ (∼6–18 months old), with higher growth in males and individuals with copies of the rearranged–resident haplotype. Condition at age 1+ increased with the number of copies of the rearranged–resident haplotype, with similar support for additive or interactive effects with sex; additive effects suggested that genotype differences occurred in both sexes and also that condition was slightly higher in males, while interactive effects suggested that the genotype differences occurred only in males. Our results indicate that phenotypic differences related to sex and Omy05 genotype occur well in advance of anadromous migration or freshwater maturation in this southern O. mykiss population.

Unexpectedly simple Chinook salmon are known to return to spawn at two distinct times of the year: spring and fall. Individuals that return during these times have generally been referred to as parts of distinct groups, or ecotypes, with traits specific to their timing and presumed divergence being caused by the lack of interbreeding. By looking at genomes across fish from both runs, Thompson et al. found that a single genomic region of interest was nearly perfectly associated with run timing but not with other traits such as maturity and fat reserves (see the Perspective by McKinney). Further, they conclude that the region operates as a Mendelian trait, with assortment dictating run timing and associated phenotypes being caused by the migration environment rather than genetics. Science , this issue p. 609 ; see also p. 526

In temperate climates, the recurring seasonal exigencies of winter represent a fundamental physiological challenge for a wide range of organisms. In response, many temperate insects enter diapause, an alternative developmental program, including developmental arrest, that allows organisms to synchronize their life cycle with seasonal environmental variation. Geographic variation in diapause phenology contributing to local climatic adaptation is well documented. However, few studies have examined how the rapid evolution of a suite of traits expressed across the diapause program may contribute to climatic adaptation on a contemporary timescale. Here, we investigate the evolution of the diapause program over the past 35 years by leveraging a “natural experiment” presented by the recent invasion of the Asian tiger mosquito, Aedes albopictus, across the eastern United States. We sampled populations from two distinct climatic regions separated by 6° of latitude (∼700 km). Using common‐garden experiments, we identified regional genetic divergence in diapause‐associated cold tolerance, diapause duration, and postdiapause starvation tolerance. We also found regional divergence in nondiapause thermal performance. In contrast, we observed minimal regional divergence in nondiapause larval growth traits and at neutral molecular marker loci. Our results demonstrate rapid evolution of the diapause program and imply strong selection caused by differences in winter conditions.

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.

Secondary contact may have important implications for ecological and evolutionary processes; however, few studies have tracked the outcomes of secondary contact from its onset in natural ecosystems. We evaluated an anadromous alewife (Alosa pseudoharengus ) reintroduction project in Rogers Lake (Connecticut, USA), which contains a landlocked alewife population that was isolated as a result of colonial‐era damming. After access to the ocean was restored, adult anadromous alewife were stocked into the lake. We assessed anadromous juvenile production, the magnitude and direction of introgression, and the potential for competition between ecotypes. We obtained fin clips from all adult alewife stocked into the lake during the restoration and a sample of juveniles produced in the lake two years after the stocking began. We assessed the ancestry of juveniles using categorical assignment and pedigree reconstruction with newly developed microhaplotype genetic markers. Anadromous alewives successfully spawned in the lake and hybridized with the landlocked population. Parentage assignments revealed that male and female anadromous fish contributed equally to juvenile F1 hybrids. The presence of landlocked backcrosses shows that some hybrids were produced within the first two years of secondary contact, matured in the lake, and reproduced. Therefore, introgression appears directional, from anadromous into landlocked, in the lake environment. Differences in estimated abundance of juveniles of different ecotypes in different habitats were also detected, which may reduce competition between ecotypes as the restoration continues. Our results illustrate the utility of restoration projects to study the outcomes of secondary contact in real ecosystems.

Este artículo contiene 10 páginas, 6 figuras, 1 tabla., Dispersal is one of the main determining factors of population structure. In the marine habitat, well-connected populations with large numbers of reproducing individuals are common but even so population structure can exist on a small-scale. Variation in dispersal patterns between populations or over time is often associated to geographic distance or changing oceanographic barriers. Consequently, detecting structure and variation in dispersal on a fine-scale within marine populations still remains a challenge. Here we propose and use a novel approach of combining a clustering model, early-life history trait information from fish otoliths, spatial coordinates and genetic markers to detect very fine-scale dispersal patterns. We collected 1573 individuals (946 adults and 627 juveniles) of the blackfaced blenny across a small-scale (2 km) coastline as well as at a larger-scale area (, We are grateful to the Southwest Fisheries Science Center Molecular Ecology and Genetic Analysis Team for support in the lab and helpful comments and Jinliang Wang for his help in converting relatedness into a distance measurement. This work was partially funded by the Spanish Ministry of Science and Innovation through the CTM2017-88080 (AEI/FEDER, UE) project. The authors C.S., M.P. and E.M. are part of the research groups 2017SGR-1120 and 2017SGR-378 of the Generalitat de Catalunya.

The construction of dams and water diversions has severely limited access to spawning habitat for anadromous fishes. To mitigate for these impacts, hatchery programs rear and release millions of juvenile salmonids, including steelhead, the anadromous ecotype of the species Oncorhynchus mykiss. These programs sometimes use nonindigenous broodstock sources that may have negative effects on wild populations. In California, however, only one anadromous fish hatchery program currently uses nonnative broodstock: the steelhead program at Nimbus Fish Hatchery on the American River, a tributary of the Sacramento River in the California Central Valley. The goal of this study was to determine if potentially appropriate sources to replace the broodstock for the Nimbus Hatchery steelhead program exist in the Upper American River, above Nimbus and Folsom dams. We show that all Upper American River O. mykiss sampled share ancestry with other populations in the Central Valley steelhead distinct population segment, with limited introgression from out-of-basin sources in some areas. Furthermore, some Upper American River populations retain adaptive genomic variation associated with a migratory life history, supporting the hypothesis that these populations display adfluvial migratory behavior. Together, these results provide insights into the evolution of trout populations above barrier dams. We conclude that some Upper American River O. mykiss populations represent genetically appropriate sources from which fisheries managers could potentially develop a new broodstock for the Nimbus Hatchery steelhead program to reestablish a native anadromous population in the Lower American River and contribute to recovery of the threatened Central Valley steelhead distinct population segment.

Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and nonparallel adaptation. All landlocked populations displayed an increased frequency of a large inversion on chromosome Omy05, while 3 of the 4 populations exhibited elevated frequencies of another inversion located on chromosome Omy20. In addition, we identified numerous regions outside these 2 inversions that also show significant shifts in allele frequencies consistent with adaptive evolution. However, there was little concordance among above-barrier populations in these specific genomic regions under selection. In part, the lack of concordance appears to arise from ancestral autopolyploidy in rainbow trout that provides duplicate genomic regions of similar functional composition for selection to act upon. Thus, while selection acting on landlocked populations universally favors the resident ecotype, outside of the major chromosomal inversions, the resulting genetic changes are largely distinct among populations. Our results indicate that selection on standing genetic variation is likely the primary mode of rapid adaptation, and that both supergene complexes and individual loci contribute to adaptive evolution, further highlighting the diversity of adaptive genomic variation involved in complex phenotypic evolution.

Non-invasive monitoring was used to evaluate the concentrations of forty contaminants in the blood plasma of the North American Green Sturgeon Acipenser medirostris caught and released from three estuaries in Washington State. The highest contaminant loads were found in fish caught in the most urbanized sites. Few statistical differences were found when evaluating contaminant levels according to sex, maturation stage, or distinct population segments of Green Sturgeon. The results indicate that recent exposure to legacy contaminants was reflected in Green Sturgeon plasma. Aldrin, 4,4-DDE, a-BHC, copper, and selenium were the most frequently detected contaminants. This study also explored the challenges of assessing toxicity in threatened species using non-lethal approaches. There is currently a lack of environmental contaminant monitoring data in estuaries frequented by Green Sturgeon and limited plasma to tissue toxicity correlations.

A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

Non-invasive monitoring was used to evaluate the concentrations of 40 contaminants in the blood plasma of the North American Green Sturgeon Acipenser medirostris caught and released from three estuaries in Washington State. The highest contaminant concentrations were found in fish caught in the most urbanized sites. Few statistical differences were found when evaluating contaminant levels according to sex, maturation stage, or distinct population segments of Green Sturgeon. The results indicate that recent exposure to legacy contaminants was reflected in Green Sturgeon plasma. Aldrin, 4,4-DDE, α-HCH, copper, and selenium were the most frequently detected contaminants. This study also explored the challenges of assessing toxicity in threatened species using non-lethal approaches. There is currently a lack of environmental contaminant monitoring data in estuaries frequented by Green Sturgeon and limited plasma to tissue toxicity correlations.

Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 x 10(-9) after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.

Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait – Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46×10−9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.

A stronger correlation between heterozygosity and fitness or its components (e.g., life-history traits such as survival, growth, morphology) is expected in harsher environments, but few studies have investigated whether the effects of heterozygosity on life-history traits vary with environmental conditions in natural populations. Here, the hypothesis that the effects of heterozygosity vary with environmental conditions was tested using six populations of marble trout Salmo marmoratus from Western Slovenia as a model system. Specifically, the tested hypotheses were: stronger effects of heterozygosity on survival in populations characterized by low average survival, no effects of heterozygosity on probability of surviving flash floods owing to their largely non-selective effects across traits, and stronger effects of heterozygosity on survival for fish born after floods than fish born before. A significant effect of heterozygosity on survival was found in populations characterized by low average survival. There were no effects of heterozygosity on probability of surviving flash floods, but in one population a positive correlation between heterozygosity and survival for fish born after the extreme events was found, probably because crowding in a small section of the stream caused more intense competition for resources.

Anthropogenic activities are placing increasing pressure on many species, particularly those that rely on more than one ecosystem. River herring (alewife, Alosa pseudoharengus and blueback herring, A. aestivalis collectively) are anadromous fishes that reproduce in rivers and streams of eastern North America and migrate to the western Atlantic Ocean. Here, we use data from single nucleotide polymorphisms (SNPs) to provide a comprehensive analysis of population structure for both species of river herring throughout their native ranges. We sampled river herring spawning runs in rivers from Newfoundland to Florida, examining a total of 108 locations, and genotyping over 8000 fish. We identified geographic population groupings (regional genetic groups) in each species, as well as significant genetic differentiation between most populations and rivers. Strong correlations between geographic and genetic distances (i.e., isolation by distance) were found range-wide for both species, although the patterns were less consistent at smaller spatial scales. River herring are caught as bycatch in fisheries and estimating stock proportions in mixed fishery samples is important for management. We assessed the utility of the SNP datasets as reference baselines for genetic stock identification. Results indicated high accuracy of individual assignment (76–95%) to designated regional genetic groups, and some individual populations, as well as highly accurate estimates of mixing proportions for both species. This study is the first to evaluate genetic structure across the entire geographic range of these species and provides an important foundation for conservation and management planning. The SNP reference datasets will facilitate continued multi-lateral monitoring of bycatch, as well as ecological investigation to provide information about ocean dispersal patterns of these species.

The accelerating rate at which DNA sequence data are now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by these sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine "microhaplotypes" and then call these microhaplotypes as alleles at each locus. We then demonstrate how these multi-allelic marker data from such loci dramatically increase power for relationship inference. The microhaplotype approach decreases false-positive rates by several orders of magnitude, relative to calling bi-allelic SNPs, for two challenging analytical procedures, full-sibling and single parent-offspring pair identification. We also show how the identification of half-sibling pairs requires so much data that physical linkage becomes a consideration, and that most published studies that attempt to do so are dramatically underpowered. The advent of phased short-read DNA sequence data, in conjunction with emerging analytical tools for their analysis, promises to improve efficiency by reducing the number of loci necessary for a particular level of statistical confidence, thereby lowering the cost of data collection and reducing the degree of physical linkage amongst markers used for relationship estimation. Such advances will facilitate collaborative research and management for migratory and other widespread species.

Management and restoration planning for Pacific salmon is often characterized by efforts at broad multi-basin scales. However, finer-scale genetic and phenotypic variability may be present within individual basins and can be overlooked in such efforts, even though it may be a critical component for long-term viability. Here, we investigate Chinook salmon (Oncorhynchus tshawytscha) within the Siletz River, a small coastal watershed in Oregon, USA. Adult Chinook salmon were genotyped using neutral microsatellite markers, single nucleotide polymorphisms and “adaptive” loci, associated with temporal variation in migratory behavior in many salmon populations, to investigate genetic diversity based upon both spatial and temporal variation in migratory and reproductive behavior. Results from all three marker types identified two genetically distinct populations in the basin, corresponding to early returning fish that spawn above a waterfall, a spring-run population, and later returning fish spawning below the waterfall, a fall-run population. This finding is an important consideration for management of the species, as spring-run populations generally only have been recognized in large watersheds, and highlights the need to evaluate population structure of salmon within smaller watersheds, and thereby increase the probability of successful conservation of salmon species.

Polyploid organisms pose substantial obstacles to genetic analysis, as molecular assay data are usually difficult to evaluate in a Mendelian framework. Green sturgeon (Acipenser medirostris) is a tetraploid species and is facing significant conservation challenges, including bycatch in ocean fisheries. We present here novel molecular genetic assays and analytical methodology for green sturgeon that allow discrimination of fish from the two visually indistinguishable distinct population segments (DPSs), and also provide individual-specific genetic tags. We show how the relative fluorescence intensity data from a standard quantitative PCR assay, designed for a biallelic single nucleotide polymorphism, can be grouped into “genotype categories” using standard analytical software and post-processing manipulation. We then show how these genotype category data can be used to discriminate green sturgeon from the southern DPS, which is protected under the US Endangered Species Act, and the northern DPS, which is not. We also show how these data can be used to reliably identify individual green sturgeon, and can therefore be used in capture/recapture analyses. Both types of identification are extremely accurate even when fewer than half of the assays are successfully called. We then apply these new techniques to show that proportions of the two green sturgeon DPSs are extremely different in the two major fishery areas where they are encountered as bycatch. While these assays and methods do not provide data that can be used in pedigree-based analyses, they are an important advance in the application of genetic analysis to conservation and management of polyploid organisms.

A thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

Dispersal is a main determining factor of population structure and variation. In the marine habitat, well-connected populations with large numbers of reproducing individuals are common but even so population structure can exist on a small-scale. Variation in dispersal between populations or over time is often associated to both environmental and genetic variation. Nonetheless, detecting structure and dispersal variation on a fine-scale within marine populations still remains a challenge. Here we propose and use a novel approach of combining a clustering model, early-life history trait information from fish otoliths, spatial coordinates and genetic markers to detect very fine-scale dispersal patterns. We collected 1573 individuals (946 adults and 627 juveniles) of the black-faced blenny across a small-scale (2km) coastline as well as at a larger-scale area (

Pacific trout Oncorhynchus spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review the state of knowledge on these important issues, focusing on Pacific trout in the genus Oncorhynchus. Although most research on salmonid fishes emphasizes Pacific salmon, we focus on Pacific trout because they share a common evolutionary history, and many taxa in western North America have not been formally described, particularly in the southern extent of their ranges. Research in recent decades has led to the revision of many hypotheses concerning the origin and diversification of Pacific trout throughout their range. Although there has been significant success at addressing past threats to Pacific trout, contemporary and future threats represented by nonnativ...

The ability of salmon to navigate from the ocean back to their river of origin to spawn acts to reinforce local adaptation and maintenance of unique and heritable traits among salmon populations. Here, the extent to which Chinook salmon Oncorhynchus tshawytscha from the same freshwater breeding groups associate together in the ocean at regional and smaller-scale aggre- gations prior to homeward migration is evaluated. Natural variation in salmon otolith daily growth bands, strontium isotopes ( 87 Sr/ 86 Sr), and microsatellite DNA were used as intrinsic tags to link the distributions of fish caught in the ocean with their freshwater origins. Adults were caught from vessels by hook and line in small aggregations (7�18 ind.) at the same geographic location (1�24 km of coastline) and time (4�36 h) from 3 ocean regions along central California, USA. Salmon caught together in aggregations were from the same genetic group, and to a lesser extent, of the same natal origin (individual rivers or hatcheries). However, at regional scales, adult salmon mixed. Central Valley winter-run Chinook salmon caught together in the ocean varied in the duration of freshwater rearing for up to 2�3 mo prior to seaward migration, suggesting associa- tions within the group were not established in freshwater or maintained over the lifetime of the fish. Our findings are consistent with coarser information indicating stocks are distributed differ- ently in time and space, but larger sample sizes are required to evaluate the consistency of pat- terns at smaller spatial scales. This study uncovers freshwater associations prior to homeward migration, a principle and undocumented prerequisite of the collective navigation hypothesis.

Geoduck clams are a valuable natural resource along the northeast Pacific, which makes the assessment of the biological and genetic status of their populations a key element to provide a basis for their proper management and conservation. In the present study, we assess the genetic variability and connectivity of Panopea generosa Gould, 1850 among four localities in the northeast Pacific using mitochondrial (DNA sequences from COI and COIII) and nuclear (five microsatellite loci) data. We found no evidence of genetic differentiation among localities encompassing scales of 100s to 1000s of kilometers along the northeast Pacific, which is consistent with a large effective population size and extensive gene flow in the absence of significant barriers acting on the larval stages. Our genetic findings and phenotypic evidence are consistent with the existence of a single management unit shared by Canada, the United States and Mexico, but further studies with increased geographic and genetic sampling are warranted to better estimate the extent and direction of gene flow to help in international management and conservation measures of this valuable resource.

Steelhead (Oncorhynchus mykiss) populations have declined dramatically in many parts of their range in North America, most critically in Southern California, where these anadromous trout are now classified as ‘Endangered’ under the United States Endangered Species Act. The widespread introduction of hatchery rainbow trout, the domesticated freshwater resident form of the species O. mykiss, is one factor threatening the long-term persistence of native steelhead and other trout populations. To identify where native fish of coastal steelhead lineage remained, we performed a population genetic analysis of microsatellite and SNP genotypes from O. mykiss populations at the extreme southern end of their range in Southern California, USA and Baja California, Mexico. In the northern part of this region, nearly all populations appeared to be primarily descendants of native coastal steelhead. However, in the southern, more urbanized part of this region, the majority of the sampled populations were derived primarily from hatchery trout, indicating either complete replacement of native fish or a strong signal of introgression overlaying native ancestry. Nevertheless, these genetically introgressed populations represent potentially critical genetic resources for the continued persistence of viable networks of O. mykiss populations, given the limited native ancestry uncovered in this region and the importance of genetic variation in adaptation. This study elucidates the geographic distribution of native trout populations in this region, and serves as a baseline for evaluating the impacts of hatchery trout on native O. mykiss populations and the success of steelhead conservation and recovery efforts.

Extreme variability in abundance of California salmon populations is often ascribed to ocean conditions, yet relatively little is known about their marine life history. To investigate which ocean conditions influence their distribution and abundance, we surveyed juvenile Chinook salmon (Oncorhynchus tshawytscha) within the California Current (central California [37°30′N) to Newport, Oregon (44°00′N]) for a 2-week period over three summers (2010–2012). At each station, we measured chlorophyll-a as an indicator of primary productivity, acoustic-based metrics of zooplankton density as an indicator of potential prey availability and physical characteristics such as bottom depth, temperature and salinity. We also measured fork lengths and collected genetic samples from each salmon that was caught. Genetic stock identification revealed that the majority of juvenile salmon were from the Central Valley and the Klamath Basin (91–98%). We constructed generalized logistic-linear negative binomial hurdle models and chose the best model(s) using Akaike's Information Criterion (AIC) to determine which covariates influenced the salmon presence and, at locations where salmon were present, determined the variables that influenced their abundance. The probability of salmon presence was highest in shallower waters with a high chlorophyll-a concentration and close to an individual's natal river. Catch abundance was primarily influenced by year, mean fork length and proximity to natal rivers. At the scale of sampling stations, presence and abundance were not related to acoustic indices of zooplankton density. In the weeks to months after ocean entry, California's juvenile Chinook salmon population appears to be primarily constrained to coastal waters near natal river outlets.

Traits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolved in these species is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 56 Mb double-inversion supergene that mediates sex-specific migration through sex-dependent dominance, a mechanism that reduces sexual conflict. The double-inversion contains key photosensory, circadian rhythm, adiposity, and sexual differentiation genes and displays frequency clines associated with latitude and temperature, revealing environmental dependence. Our results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.

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.