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Despite widespread biodiversity losses, an understanding of how most taxa will respond to future climate change is lacking. Here we integrate genomics and environmental modelling to assess climate change responses in an ecologically and economically important Arctic species. Environmentally associated genomic diversity and machine learning are used to identify highly vulnerable populations of anadromous (migratory) Arctic charr, and we reconstruct estimates of effective population size spanning the twentieth century to identify past climate-associated declines. We uncover past region-wide declines in effective population size that correspond to decreases in temperature and community biomass in the Northwest Atlantic. We find vulnerable populations near the southern range limit, indicating northward shifts and a possible loss of commercially important life-history variation in response to climate change. The genomic approach used here to investigate climate change response identifies past and future declines that impact species persistence, ecosystem stability and food security in the Arctic. Genomics and environmental modelling are integrated to assess past and future changes in Arctic charr populations in response to changing climate. Southern population vulnerability suggests climate change may lead to northward shifts and the loss of important life-history variation.

Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long‐term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been stocked since the early 1900s, and despite continued stocking efforts, populations have suffered declines in recent decades. Before this study, the genetic structure of brook trout populations in the province was unknown; however, given the potential negative consequences associated with hatchery stocking, it is possible that hatchery programs have adversely affected the genetic integrity of wild populations. To assess the influence of hatchery supplementation on wild populations, we genotyped wild brook trout from 12 river systems and hatchery brook trout from two major hatcheries using 100 microsatellite loci. Genetic analyses of wild trout revealed extensive population genetic structure among and within river systems and significant isolation‐by‐distance. Hatchery stocks were genetically distinct from wild populations, and most populations showed limited to no evidence of hatchery introgression (

Interpretation of conservation status should be informed by an appreciation of genetic diversity, past demography, and overall trends in population size, which contribute to a species' evolutionary potential and resilience to genetic risks. Low genetic diversity can be symptomatic of rapid demographic declines and impose genetic risks to populations, but can also be maintained by natural processes. The northern bottlenose whale Hyperoodon ampullatus has the lowest known mitochondrial diversity of any cetacean and was intensely whaled in the Northwest Atlantic over the last century, but whether exploitation imposed genetic risks that could limit recovery is unknown. We sequenced full mitogenomes and genotyped 37 novel microsatellites for 128 individuals from known areas of abundance in the Scotian Shelf, Northern and Southern Labrador, Davis Strait, and Iceland, and a newly discovered group off Newfoundland. Despite low diversity and shared haplotypes across all regions, both markers supported the Endangered Scotian Shelf population as distinct from the combined northern regions. The genetic affinity of Newfoundland was uncertain, suggesting an area of mixing with no clear population distinction for the region. Demographic reconstruction using mitogenomes suggests that the northern region underwent population expansion following the last glacial maximum, but for the peripheral Scotian Shelf population, a stable demographic trend was followed by a drastic decline over a temporal scale consistent with increasing human activity in the Northwest Atlantic. Low connectivity between the Scotian Shelf and the rest of the Atlantic likely compounded the impact of intensive whaling for this species, potentially imposing genetic risks affecting recovery of this population. We highlight how the combination of historical environmental conditions and modern exploitation of this species has had very different evolutionary impacts on structured populations of northern bottlenose whales across the western North Atlantic.

Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in a wild population of Trinidadian guppies. Crucially, we tested our predictions against evolutionary change observed in common-garden experiments performed on samples from the same population. We show that standard quantitative genetic models underestimated or failed to detect the cryptic evolution of this trait as demonstrated by the common-garden experiments. The models failed because (1) size at maturity and fitness both decreased with increases in population density, (2) offspring experienced higher population densities than their parents, and (3) selection on size was strongest at high densities. When we accounted for environmental change, predictions better matched observations in the common-garden experiments, although substantial uncertainty remained. Our results demonstrate that predictions of evolution are unreliable if environmental change is not appropriately captured in models.

Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multi-tissue transcriptomes, and reduced representation population data for the Atlantic halibut (Hippoglossus hippoglossus), which has an XY/XX sex determination mechanism and has recently diverged (0.9-3.8 MYA) from the Pacific halibut (Hippoglossus stenolepis), which has a ZZ/ZW system. We used frequency and coverage-based population approaches to identify a putative sex-determining factor, GSDF. We characterized regions with elevated heterozygosity and linkage disequilibrium indicating suppression of recombination across a nascent sex chromosome. We detected testis-specific expression of GSDF, the sequence of which is highly conserved across flatfishes. Based on evidence from genome-wide association, coverage, linkage disequilibrium, testis and brain transcriptomes, and sequence conservation with other flatfishes, we propose a mechanism for the recent evolution of an XY sex-determination mechanism in Atlantic halibut. Changes to the ancestral sex-determining gene DMRT1 in regulating the downstream gene GSDF likely coincided with GSDF, or a proximal regulatory element of it, becoming the primary sex-determining factor. Our results suggest changes to a small number of elements can have drastic repercussions for the genomic substrate available to sex-specific evolutionary forces, providing insight into how certain elements repeatedly evolve to control sex across taxa. Our chromosome-level assembly, multi-tissue transcriptomes, and population genomic data provide a valuable resource and understanding of the evolution of sexual systems in fishes.

Rare extreme "black swan" disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so-called "50-year floods") can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population's ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events - perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods - one in 2005 and another in 2016. For each river, we selected four sites and used archived "historical" samples to compare levels of genetic and phenotypic diversity before vs. after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) colour. We found that genetic diversity and population structure was mostly "resistant" to even these extreme floods; whereas the larger impacts on phenotypic diversity were short-lived, suggesting additional "resilience". We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances.

Restriction site-associated DNA sequencing (RADseq) is a powerful tool for genotyping of individuals, but the identification of loci and assignment of sequence reads is a crucial and often challenging step. The optimal parameter settings for a given de novo RADseq assembly vary between data sets and can be difficult and computationally expensive to determine. Here, we introduce RADProc, a software package that uses a graph data structure to represent all sequence reads and their similarity relationships. Storing sequence-comparison results in a graph eliminates unnecessary and redundant sequence similarity calculations. De novo locus formation for a given parameter set can be performed on the precomputed graph, making parameter sweeps far more efficient. RADProc also uses a clustering approach for faster nucleotide-distance calculation. The performance of RADProc compares favourably with that of the widely used Stacks software. The run-time comparisons between RADProc and Stacks for 32 different parameter settings using 20 green-crab (Carcinus maenas) samples showed that RADProc took as little as 2 hr 40 min compared to 78 hr by Stacks, while 16 brown trout (Salmo trutta L.) samples were processed by RADProc and Stacks in 23 and 263 hr, respectively. Comparisons of the de novo loci formed, and catalog built using both the methods demonstrate that the improvement in processing speeds achieved by RADProc does not affect much the actual loci formed and the results of downstream analyses based on those loci.

Brazilian native meliponines are currently threatened by increased human impacts. The assessment of their genetic variation by microsatellite DNA markers can assist in the conservation of populations and help in the planning and establishment of efficient management strategies. The purpose of this study was to develop the first set of microsatellite markers for Melipona fasciculata, selected from partial genome assembly of Illumina paired-end reads. Primer pairs were designed for each detected locus at their flanking regions. Bee samples were genotyped from two different populations of Northeastern Brazil for marker characterization and validation. A total of 17 microsatellite loci displayed polymorphism. Mean HE and HO heterozygosities were 0.453 and 0.536, respectively. PIC across all loci ranged from 0.108 to 0.714. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.194, RST = 0.230, and Dest = 0.162) within the investigated region. PCoA and Bayesian clustering showed a separation of the species into two distinct clusters. These microsatellite markers have demonstrated strong potential for population-level genetic studies. Moreover, the preliminary analysis of the genetic diversity in M. fasciculata provides provisional evidence of significant population differentiation between the two studied populations.

Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations. The mechanisms influencing the differentiation of embayment populations were investigated using both multivariate and machine-learning landscape genetic approaches. We identified temperature as the strongest correlate with genetic structure, particularly warm temperature extremes and wider annual temperature ranges. The genomic basis of this divergence was further explored using a subset of locations (n = 17) and a 220K SNP array. SNPs associated with spatial structuring and temperature mapped to a diverse set of genes and molecular pathways, including regulation of gene expression, immune response, and cell development and differentiation. The results spanning molecular marker types and both novel and established methods clearly show climate-associated, fine-scale population structure across an environmental gradient in Atlantic salmon near its range limit in North America, highlighting valuable approaches for predicting population responses to climate change and managing species sustainability.

Biological invasions provide opportunities to examine contemporary evolutionary processes in novel environments. American shad, an anadromous fish native to the Atlantic Coast of North America, was introduced to California in 1871 and established spawning populations along the Pacific Coast that may provide insights into the dynamics of dispersal, colonization, and the establishment of philopatry. Using 13 neutral microsatellite loci we genotyped anadromous, freshwater resident and landlocked American shad from 14 locations along the US Pacific Coast to resolve population genetic structure. We observed significant differences in multilocus allele frequency distributions in nearly all (61/66; 92%) pairwise comparisons of non-native anadromous, freshwater resident and landlocked populations, and detected significant genetic differentiation for most (55/66; 83%) of these comparisons. Genetic divergence between landlocked and anadromous populations is due to genetic drift in isolation because of a physical migration barrier. However, some reproductive isolating mechanism maintains genetic differentiation between sympatric populations in the Columbia River exhibiting alternative life history strategies (i.e. anadromous vs. ‘freshwater-type’). Non-native populations possessed genetic variants that were not observed in the species’ native range and were strongly differentiated from Atlantic Coast populations ( $${\text{G}}^{{\prime }}_{\text{ST}}$$ = 0.218). Our results indicate that philopatry became established shortly after dispersal and colonization along the Pacific Coast. This study contributes to our understanding of dynamic evolutionary processes during invasions.

Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome-wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analysed genome-wide polymorphisms to measure genetic differentiation between an offshore migratory and a nonmigratory population and to define conservation units of Atlantic Cod (Gadus morhua) in coastal Labrador. A total of 141 individuals, collected from offshore sites and from a coastal site within Gilbert Bay, Labrador, were genotyped using an ~11k single nucleotide polymorphism array. Analyses of population structure revealed strong genetic differentiation between migratory offshore cod and nonmigratory Gilbert Bay cod. Genetic differentiation was elevated for loci within a chromosomal rearrangement found on linkage group 1 (LG1) that coincides with a previously found double inversion associated with migratory and nonmigratory ecotype divergence of cod in the northeast Atlantic. This inverted region includes several genes potentially associated with adaptation to differences in salinity and temperature, as well as influencing migratory behaviour. Our work provides evidence that a chromosomal rearrangement on LG1 is associated with parallel patterns of divergence between migratory and nonmigratory ecotypes on both sides of the Atlantic Ocean.

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine‐learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with F ST ranking for selection of single nucleotide polymorphisms (SNP) for fine‐scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self‐assignment accuracy of at least 90% using each method to create panels of 50–700 markers Panels of SNPs identified using random forest‐based methods performed up to 7.8 and 11.2 percentage points better than F ST‐selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self‐assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using F ST‐selected panels. Our results demonstrate a role for machine‐learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species' evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake. To investigate patterns of adaptive immunogenetic variation among lake trout ecomorphs, we used Illumina high-throughput sequencing. The population's genetic structure of the major histocompatibility complex (MHC Class IIβ exon 2) and 18 microsatellite loci were compared to disentangle neutral and selective processes at a small geographic scale. Both MHC and microsatellite variation were partitioned more by water depth stratum than by ecomorph. Several metrics showed strong clustering by water depth in MHC alleles, but not microsatellites. We report a 75% increase in the number of MHC alleles shared between the predominant shallow and deep water ecomorphs since a previous lake trout MHC study at the same locale (c. 1990s data). This result is consistent with the reverse speciation hypothesis, although adaptive MHC polymorphisms persist along an ecological gradient. Finally, results suggested that the lake trout have multiple copies of the MHC II locus consistent with a historic genomic duplication event. Our findings indicated that conservation approaches for this species could focus on managing various ecological habitats by depth, in addition to regulating the fisheries specific to ecomorphs.

Organisms can change their environment and in doing so change the selection they experience and how they evolve. Population density is one potential mediator of such interactions because high population densities can impact the ecosystem and reduce resource availability. At present, such interactions are best known from theory and laboratory experiments. Here we quantify the importance of such interactions in nature by transplanting guppies from a stream where they co-occur with predators into tributaries that previously lacked both guppies and predators. If guppies evolve solely because of the immediate reduction in mortality rate, the strength of selection and rate of evolution should be greatest at the outset and then decline as the population adapts to its new environment. If indirect effects caused by the increase in guppy population density in the absence of predation prevail, then there should be a lag in guppy evolution because time is required for them to modify their environment. The duration of this lag is predicted to be associated with the environmental modification caused by guppies. We observed a lag in life-history evolution associated with increases in population density and altered ecology. How guppies evolved matched predictions derived from evolutionary theory that incorporates such density effects.

Predicting population colonisations requires understanding how spatio‐temporal changes in density affect dispersal. Density can inform on fitness prospects, acting as a cue for either habitat quality, or competition over resources. However, when escaping competition, high local density should only increase emigration if lower‐density patches are available elsewhere. Few empirical studies on dispersal have considered the effects of density at the local and landscape scale simultaneously. To explore this, we analyze 5 years of individual‐based data from an experimental introduction of wild guppies Poecilia reticulata. Natal dispersal showed a decrease in local density dependence as density at the landscape level increased. Landscape density did not affect dispersal among adults, but local density‐dependent dispersal switched from negative (conspecific attraction) to positive (conspecific avoidance), as the colonisation progressed. This study demonstrates that densities at various scales interact to determine dispersal, and suggests that dispersal trade‐offs differ across life stages. peerReviewed

Microsporidia are emerging as a threat to productivity of commercial finfish aquaculture because of high-prevalence infections facilitated by direct transmission. Infection dynamics are poorly understood for most microsporidians and inability to reliably quantify differential infections impedes disease mitigation strategies that could select broodstock with inherent disease-resistant phenotypes. Moreover, investigations of suitable biomarkers that link immune function with disease susceptibility of fishes are limited. Herein, we observe an inverse relationship between fish growth and infection status with the microsporidium Loma morhua among 50 different Atlantic cod (Gadus morhua) family lines. We present a standardized template for quantifying parasite infection intensity, with the spleen being the most reliable organ for comparing natural infections and for monitoring experimental infections. Variability in infection intensities among 50 cod families suggests that differential susceptibility to L. morhua has a genetic basis. Ultra-deep Illumina sequencing identified 299 major histocompatibility class I (MH-I) variants from this regionally restricted 50-family cod population. Variation in Atlantic cod susceptibility might reflect hyper-diversification of MH-I genes and individual variability in the ability to present endogenous pathogen antigens during cell-mediated immune responses. Relevance of MH-I expansion to selective breeding for disease resistance remains poorly characterized. Importantly, differential susceptibility to L. morhua revealed impaired fish growth, resulting in a 14% reduction in fillet mass in susceptible individuals. These data imply that relative resistance to L. morhua exists in cod, that it is heritable, and that broodstock selection could be used to limit the impact of microsporidian infections on growth during finfish aquaculture.

Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability., The Atlantic salmon has suffered widespread population declines over the last century. Here, Lehnert et al. reconstruct changes in effective population size of 172 populations based on genomic linkage information revealing mostly temperature-associated population declines with over 60% of populations in decline since 1975.

The ability of populations to rapidly adapt to new environments will determine their future in an increasingly human-modified world. Although meta-analyses do frequently uncover signatures of local adaptation, they also reveal many exceptions. We suggest that particular constraints on local adaptation might arise when organisms are exposed to novel stressors, such as anthropogenic pollution. To inform this possibility, we studied the extent to which guppies (Poecilia reticulata) show local adaptation to oil pollution in southern Trinidad. Neutral genetic markers revealed that paired populations in oil-polluted versus not-polluted habitats diverged independently in two different watersheds. Morphometrics revealed some divergence (particularly in head shape) between these environments, some of which was parallel between rivers. Reciprocal transplant experiments in nature, however, found little evidence of local adaptation based on survival and growth. Moreover, subsequent laboratory experiments showed that the two populations from oil-polluted sites showed only weak local adaptation even when compared to guppies from oil-free northern Trinidad. We conclude that guppies show little local adaptation to oil pollution, which might result from the challenges associated with adaptation to particularly stressful environments. It might also reflect genetic drift owing to small population sizes and/or high gene flow between environments.

Stocking programs have been used extensively to mitigate declines in anadromous fishes, but these programs can have long-term unintended genetic consequences. Stocking can homogenize population structure, impede local adaptation, and hinder the use of genetic stock identification as a fishery management tool. Using 12 microsatellite loci, we evaluate the spatiotemporal genetic structure of 16 anadromous alewife (Alosa pseudoharengus) populations in Maine, USA, to determine whether inter-basin stocking practices have influenced population structure and the genetic diversity of the species in this region. Although, no pre-supplementation samples exist, comparative analyses of stocked and non-stocked populations show that stock transfers have influenced alewife population genetic structure. Genetic isolation by distance (IBD) was non-significant among stocked populations, but significant among non-stocked populations. However, two populations, Dresden Mills and Sewell Pond, appear to have resisted genetic homogenization despite stocking. Non-significant genic and genetic differentiations were broadly distributed among alewife populations. Hierarchical AMOVA indicated highly significant differentiation among temporal replicates within populations, and Bayesian clustering analysis revealed weak population structure. A significant correlation was observed between stocking (time and events) and pairwise $${\text{F}}_{\text{ST}}^{{\prime }}$$ among alewife collections, and an analysis of IBD residuals showed a significant decline in the amount of genetic differentiation among populations as the extent of stocking activity increased. These findings call for an increased awareness of evolutionary processes and genetic consequences of restoration activities such as inter-basin stock transfers by fisheries management and conservation practitioners.

American Shad Alosa sapidissima in the Hudson River, New York, and coastwide have shown major long-term declines. A possible contributing factor is commercial fisheries that harvest this population outside of the Hudson River estuary. Using previously published and new reference microsatellite data from 33 baseline populations, our goals were (1) to estimate the proportion of Hudson River American Shad contributing to the two remaining major mixed-stock fisheries along the Atlantic coast in Delaware Bay and the Bay of Fundy and (2) to estimate the proportions of other American Shad stocks contributing to these two fisheries at the highest level of stock specificity. Stock composition estimates for 2009 and 2010 Delaware Bay collections were made using three models that ranged from the most simple question (Hudson River and Delaware Bay populations) to one with all 33 baseline populations included. In all cases, a Hudson River contribution nearly equal to that of the Delaware Bay contribution w...

Alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), also known collectively as either river herring or gaspereau, are anadromous clupeid fishes that display spatiotemporal overlap during riverine spawning migrations. Both species have experienced severe population declines within portions of their ranges. Evidence that they home to their natal rivers to spawn suggests the likelihood of ecologically significant population structure, yet this hypothesis has not been rigorously tested. We examined genetic diversity, differentiation and population structure in 34 alewife and four blueback herring populations spanning a 2,500 km portion of their northern range, using 14 microsatellite loci. Significant differentiation was detected among most rivers, and eight genetically defined alewife population clusters that largely corresponded to hydrographic regions were identified. Similar population structure was seen for blueback herring. Genetic isolation by distance was not significant among alewife populations in regions that have been historically influenced by dams, and/or stock transfers, but was highly significant in two regions that have not been subject to these influences. Genetic differentiation of alewife populations was strongest in the Bay of Fundy. Bottleneck tests revealed evidence of demographic bottlenecks in all of the alewife populations. Lastly, our results indicated that hybridization between alewife and blueback herring is common.

Marine fishes from the northwest Atlantic Ocean were analysed to determine whether barcoding was effective at identifying species. Our data included 177 species, 136 genera, 81 families and 28 orders. Overall, 88% of nominal species formed monophyletic clusters based on >500 bp of the CO1 region, and the average bootstrap value for these species was 98%. Although clearly effective, the percentage of species that were distinguishable with barcoding based on the criterion of reciprocal monophyletic clusters was slightly lower than has been documented in other studies of marine fishes. Eelpouts, sculpins and rocklings proved to be among the most challenging groups for barcoding, although we suspect that difficult identifications based on traditional (morphology based) taxonomy played a role. Within several taxa, speciation may have occurred too recently for barcoding to be effective (e.g. within Sebastes, Thunnus and Ammodytes) or the designation of distinct species may have been erroneous (e.g. within Antimora and Macrourus). Results were consistent with previous work recognizing particularly high levels of divergence within certain taxa, some of which have been recognized as distinct species (e.g. Osmerus mordax and Osmerus dentex; and Liparis gibbus and Liparis bathyarcticus), and some of which have not (e.g. within Halargyreus johnsonii and within Mallotus villosus). The results from this study suggest that morphology-based identification and taxonomy can be challenging in marine fishes, even within a region as well characterized as Atlantic Canada. Barcoding proved to be a very useful tool for species identification that will likely find a wide range of applications, including the fisheries trade, studies of range expansion, ecological analyses and population assessments.

Northern and Spotted Wolffishes (Anarhichas denticulatus and A. minor) are demersal marine fishes listed as “threatened” in Canadian waters. Both species have unusually large benthic eggs and large size at hatch, which should reduce passive dispersal. We examined population differentiation with microsatellite and AFLP loci across the ranges of both species in the North Atlantic Ocean. Although significant population structure was documented, differentiation was less than expected based on knowledge of life history characteristics. Significant differentiation was found in Northern Wolffish between the Barents Sea and other samples based on both microsatellite and AFLP data. In contrast, population structure in the Spotted Wolffish was notably weaker, particularly with microsatellites. Both species were characterized by low genetic diversity for marine fishes and had significantly lower genetic diversity than the congeneric Atlantic Wolffish. This finding was consistent with the conservation status of these three species and suggests potential vulnerability to over-exploitation in Northern and Spotted Wolffishes.

Fine-scale genetic diversity and contemporary evolution can theoretically influence ecological dynamics in the wild. Such eco-evolutionary effects might be particularly relevant to the persistence of populations facing acute or chronic environmental change. However, experimental data on wild populations is currently lacking to support this notion. One way that ongoing evolution might influence the dynamics of threatened populations is through the role that selection plays in mediating the ‘rescue effect’, the ability of migrants to contribute to the recovery of populations facing local disturbance and decline. Here, we combine experiments with natural catastrophic events to show that ongoing evolution is a major determinant of migrant contributions to population recovery in Trinidadian guppies (Poecilia reticulata). These eco-evolutionary limits on migrant contributions appear to be mediated by the reinforcing effects of natural and sexual selection against migrants, despite the close geographic proximity of migrant sources. These findings show that ongoing adaptive evolution can be a double-edged sword for population persistence, maintaining local fitness at a cost to demographic risk. Our study further serves as a potent reminder that significant evolutionary and eco-evolutionary dynamics might be at play even where the phenotypic status quo is largely maintained generation to generation.

The increasing use of single nucleotide polymorphisms (SNPs) in studies of nonmodel organisms accentuates the need to evaluate the influence of ascertainment bias on accurate ecological or evolutionary inference. Using a panel of 1641 expressed sequence tag-derived SNPs developed for northwest Atlantic cod (Gadus morhua), we examined the influence of ascertainment bias and its potential impact on assignment of individuals to populations ranging widely in origin. We hypothesized that reductions in assignment success would be associated with lower diversity in geographical regions outside the location of ascertainment. Individuals were genotyped from 13 locations spanning much of the contemporary range of Atlantic cod. Diversity, measured as average sample heterozygosity and number of polymorphic loci, declined (c. 30%) from the western (H(e) = 0.36) to eastern (H(e) = 0.25) Atlantic, consistent with a signal of ascertainment bias. Assignment success was examined separately for pools of loci representing differing degrees of reductions in diversity. SNPs displaying the largest declines in diversity produced the most accurate assignment in the ascertainment region (c. 83%) and the lowest levels of correct assignment outside the ascertainment region (c. 31%). Interestingly, several isolated locations showed no effect of assignment bias and consistently displayed 100% correct assignment. Contrary to expectations, estimates of accurate assignment range-wide using all loci displayed remarkable similarity despite reductions in diversity. Our results support the use of large SNP panels in assignment studies of high geneflow marine species. However, our evidence of significant reductions in assignment success using some pools of loci suggests that ascertainment bias may influence assignment results and should be evaluated in large-scale assignment studies.

Diversification of freshwater fishes on islands is considered unlikely because the traits that enable successful colonization—specifically, broad salinity tolerances and the potential for oceanic dispersal—may also constrain post-colonization genetic differentiation. Some secondary freshwater fish, however, exhibit pronounced genetic differentiation and geographic structure on islands, whereas others do not. It is unclear what conditions give rise to contrasting patterns of differentiation because few comparative reconstructions of population history have been carried out for insular freshwater fishes. In this study, we examined the phylogeography of Hart’s killifish (Rivulus hartii) across Trinidad, with reference to neighboring islands and northern South America, to test hypotheses of colonization and differentiation derived from comparable work on cooccurring guppies (Poecilia reticulata). Geographic patterns of mitochondrial DNA haplotype variation and microsatellite genotype variation provide evidence of genetic differentiation of R. hartii among islands and across Trinidad. Our findings are largely consistent with patterns of geographically structured ancestry and admixture found in Trinidadian guppies, which suggests that both species share a history of colonization and differentiation and that post-colonization diversification may be more common among members of insular freshwater fish assemblages than has been previously thought.

Molecular markers, such as mitochondrial DNA and microsatellite loci, are widely studied to assess population genetics and phylogeography; however, the selective neutrality of these markers is increasingly being questioned. Given the importance of molecular markers in fisheries science and conservation, we evaluated the neutrality of both mtDNA and microsatellite loci through their associations with population size. We surveyed mtDNA and microsatellite data from the primary literature and determined whether genetic diversity increased with abundance across a total of 105 marine and freshwater fishes, with both global fisheries catch data and body size as proxies for abundance (with an additional 57 species for which only body size data were assessed). We found that microsatellite data generally yielded higher associations with abundance than mtDNA data, and within mtDNA analyses, number of haplotypes and haplotype diversity were more strongly associated with abundance than nucleotide diversity, particularly for freshwater fishes. We compared genetic diversity between freshwater and marine fishes and found that marine fishes had higher values of all measures of genetic diversity than freshwater fishes. Results for both mtDNA and microsatellites generally conformed to neutral expectations, although weaker relationships were often found between mtDNA nucleotide diversity and 'abundance' compared to any other genetic statistic. We speculate that this is because of historical events unrelated to natural selection, although a role for selection cannot be ruled out.

Genetic variation was assessed in Atlantic wolffish, Anarhichas lupus, across the North Atlantic Ocean using microsatellite and amplified fragment length polymorphism (AFLP) markers. Despite unusual life history attributes such as large benthic eggs, large larvae, a limited pelagic stage and relatively sedentary adults, which suggest potential for strong population structure, range-wide FST values were comparable to other marine fishes (≤0.035). Nevertheless, both significant genetic differentiation among regions and isolation by distance were observed, suggesting limited dispersal in this species. AFLP loci, evaluated on a subset of samples, revealed slightly higher FST values, but similar patterns of differentiation and isolation-by-distance estimates, compared to microsatellites. The genetic structure of Atlantic wolffish has likely been shaped by its post-glacial history of recolonization, North Atlantic current patterns and continuity of habitat on continental shelves.

Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise F(ST) values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. F(ST) outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations.

The interplay between structural connectivity (i.e. habitat continuity) and functional connectivity (i.e. dispersal probability) in marine fishes was examined in a coastal fjord (Holyrood Pond, Newfoundland, Canada) that is completely isolated from the North Atlantic Ocean for most of the year. Genetic differentiation was described in three species (rainbow smelt Osmerus mordax, white hake Urophycis tenuis and Atlantic cod Gadus morhua) with contrasting life histories using seven to 10 microsatellite loci and a protein-coding locus, PanI (G. morhua). Analysis of microsatellite differentiation indicated clear genetic differences between the fjord and coastal regions; however, the magnitude of difference was no more elevated than adjacent bays and was not enhanced by the fjord's isolation. Osmerus mordax was characterized by the highest structure overall with moderate differentiation between the fjord and St Mary's Bay (F(ST)c.0.047). In contrast, U. tenuis and G. morhua displayed weak differentiation (F(ST) < 0.01). Nonetheless, these populations did demonstrate high rates (< 75%) of Bayesian self-assignment. Furthermore, elevated differentiation was observed at the PanI locus in G. morhua between the fjord and other coastal locations. Interestingly, locus-specific genetic differentiation and expected heterozygosity were negatively associated in O. mordax, in contrast to the positive associations observed in U. tenuis and G. morhua. Gene flow in these species is apparently unencumbered by limited structural connectivity, yet the observed differentiation suggests that population structuring exists over small scales despite high dispersal potential.

The Lake Washington watershed (Washington, USA) has been the recipient of numerous transplantations of nonnative Oncorhynchus nerka (both sockeye salmon and their landlocked form, kokanee) over the past century and currently contains self-sustaining populations of both ecotypes. Microsatellite DNA markers were used to identify native and introduced groups while characterizing population structure. This study confirmed that Baker Lake sockeye transplantations during the 20th century contributed to three current sockeye populations: Cedar River, Issaquah Creek, and Pleasure Point Beach in the Lake Washington watershed. Distinctive allele distributions at two loci, One101 and One114, provide evidence that a fourth Lake Washington sockeye population, Bear Creek, is divergent from other Lake Washington sockeye and may be of substantially native origin despite heavy stocking activity in the watershed over the past century. Data from these loci also suggest the presence of native genes in populations that had been regarded as entirely of introduced origin.

Conservation programs that release captive-bred individuals into the wild to mix with naturally produced individuals are an increasingly common method of supporting or enhancing weak or reduced populations that otherwise may not be self-sustaining. Captive and supportive breeding can be important conservation tools for species with small or declining populations; however, in the case of hatcheries producing salmonid fishes, detailed evaluation of spawning programs is rare. We examined variation in reproductive success, measured by adult offspring production, from three parental generations of hatchery-bred steelhead trout (Oncorhynchus mykiss) using an exclusion-based method of genetic parentage assignment. Reproductive success varied greatly among individuals (especially males) and was correlated with fecundity and maternal spawning date. Estimates of egg to smolt survival for the population as a whole among years ranged from 64% to 95%, marine survival ranged from 0.32% to 2.30%, and the number of adults produced per female ranged from 0 to 18 and the number of adults produced per male ranged from 0 to 32. The effective number of breeders ranged from 11% to 31% of the census population size for that brood year. These ratios fell within estimates from estimates of Ne/N in chinook (O. tshawytscha) and rainbow trout (O. mykiss) hatchery populations.

Evolutionary analyses of population translocations (experimental or accidental) have been important in demonstrating speed of evolution because they subject organisms to abrupt environmental changes that create an episode of selection. However, the strength of selection in such studies is rarely measured, limiting our understanding of the evolutionary process. This contrasts with long-term, mark–recapture studies of unmanipulated populations that measure selection directly, yet rarely reveal evolutionary change. Here, we present a study of experimental evolution of male colour in Trinidadian guppies where we tracked both evolutionary change and individual-based measures of selection. Guppies were translocated from a predator-rich to a low-predation environment within the same stream system. We used a combination of common garden experiments and monthly sampling of individuals to measure the phenotypic and genetic divergence of male coloration between ancestral and derived fish. Results show rapid evolutionary increases in orange coloration in both populations (1 year or three generations), replicating the results of previous studies. Unlike previous studies, we linked this evolution to an individual-based analysis of selection. By quantifying individual reproductive success and survival, we show, for the first time, that males with more orange and black pigment have higher reproductive success, but males with more black pigment also have higher risk of mortality. The net effect of selection is thus an advantage of orange but not black coloration, as reflected in the evolutionary response. This highlights the importance of considering all components of fitness when understanding the evolution of sexually selected traits in the wild.

Three Arctic marine fishes Icelus spatula, Aspidophoroides olrikii and Leptoclinus maculatus have been identified as target species for investigating the effects of ocean warming on population patterns in high-latitude marine habitats around Canada. In preparation for this research, we have resolved whole mitochondrial genome sequences of 16 384, 17 200 and 16 384 bp for each species, respectively. GC content for each species was 47.5%, 44.2% and 45.3%, respectively. Mitogenome gene composition included 13 protein-encoding genes, 2 rRNA and 22 tRNA genes, for I. spatula and L. maculatus, consistent with other teleosts. Only 20 tRNA genes were annotated for A. olrikii, because tRNA-Pro and tRNA-Thr are poorly characterized and aberrantly located in this species.

Genetic differentiation was greater between 'early' and 'late' spawning rainbow smelt Osmerus mordax separated by a hiatus in spawning activity compared to a continuously spawning population over a similar time period. This magnitude of temporal differentiation was comparable to that seen among spatially separated populations.

Samples of walleye pollock (Theragra chalcogramma) from the North Pacific Ocean and Bering Sea were screened for variation at the pantophysin (PanI) locus. Global genetic differentiation across samples (FST = 0.038) was considerably greater than reported in previous population studies using allozymes, mtDNA, or microsatellite loci and significantly greater than FSTdistributions of neutral loci simulated over a large range of locus heterozygosity. PanI allele frequencies varied over a broad latitudinal gradient and were correlated with estimated mean surface temperatures, resulting in the greatest levels of genetic divergence between the northern Bering Sea and the southernmost locations in the temperate Pacific Ocean (Puget Sound, Japan). The discordance between estimates of population differentiation estimated from PanI and other neutral marker classes, both in magnitude and in geographic patterns, could arise from temperature-mediated effects of natural selection over broad geographic scales. Our empirical results suggest that loci subject to directional selection may prove to be useful markers for stock identification in weakly structured marine fishes.

Heritability estimates were calculated for body size and shape, day of entry onto the spawning grounds, and egg size for two brood years (1997 and 1998) of a wild population of pink salmon Oncorhynchus gorbuscha based on parentage analysis of DNA samples from breeding adults and their mature offspring in a small creek in Southeast Alaska. The majority of heritability estimates for size and shape were not significantly different from zero, probably as a result of the close association of these variables with fitness. The even- and odd-year brood lines are genetically isolated but heritability estimates from the two lines were significantly correlated, suggesting similar selection histories. Consistent with heritability estimates from controlled breeding and captive rearing of pink and other species of salmon, day of entry onto the spawning grounds had the highest heritabilities of the traits examined in this study, especially for males (h 2 = 0.6– 1.38). One plausible method for the maintenance of...

Hatcheries have been built and operated to buffer salmon and trout populations from overfishing and to compensate for habitat lost or degraded by human activities. These facilities are now so prevalent that in some cases hatchery-produced salmon outnumber salmon produced in the wild. By default, this makes them an important component in the current ecology and evolution of salmonids. Hatcheries differ from natural environments in many ways, and among the most fundamental is the necessity that humans select fish for breeding instead of allowing natural processes of mate choice and competition. We examined the mating system for steelhead trout (Oncorhynchus mykiss) at Forks Creek Hatchery in southwest Washington and investigated factors affecting selection of individual steelhead for spawning by the hatchery staff. Despite efforts by the staff to not spawn selectively, data on steelhead spawned over 7 years revealed selection for large adult body size and early reproductive timing and a tendency for size-assortative mating (i.e., large with large). Selection on size was related to selection on reproductive timing because early returning fish tended to be larger than those returning later. To improve the fitness of both hatchery fish destined to spawn in the wild and hatchery fish designated to be spawned in the hatchery, a better understanding of factors associated with the range of reproductive success and mate-choice mechanisms in the wild is vital. This knowledge may then be applied to artificial propagation programs designed for conservation or enhancement. Resumen: Los criaderos de peces se han construido y operado para amortiguar el exceso de pesca en poblaciones de salmon y trucha y para mitigar la perdida o degradacion de habitat por actividades humanas. Estas instalaciones son tan prevalecientes actualmente, que en algunos casos el salmon producido en criaderos sobrepasa al producido en el medio silvestre. Por defecto, esto las hace un importante componente en la ecologia y evolucion actual de salmonidos. Los criaderos difieren del medio natural en muchas formas, entre las mas fundamentales esta la necesidad de que humanos seleccionen a los peces reproductores, en lugar de permitir procesos naturales de seleccion de pareja y competencia. Examinamos el sistema de apareamiento de la trucha arco iris (Oncorhynchus mykiss) en el Criadero Forks Creek en el suroeste de Washington e investigamos los factores que afectan la seleccion de individuos para desove por parte de trabajadores del criadero. A pesar de los esfuerzos de los trabajadores por no desovar selectivamente, los datos de desove de truchas a lo largo de 7 anos revelo la seleccion de talla corporal adulta grande y sincronizacion reproductiva temprana y una tendencia al apareamiento por clases de tamano (i. e., grande con grande). La seleccion de la talla se relaciono con la seleccion de la sincronia reproductiva debido a que peces que retornaban temprano tendian a ser mas grandes que los que retornaban mas tarde. Para mejorar la adaptabilidad de peces de criadero destinados a desovar en el medio natural y de los designados para desovar en el criadero, es vital un mejor entendimiento de los factores asociados con la gama de mecanismos de exito reproductivo y seleccion de pareja en el medio natural. Este conocimiento puede ser aplicado a programas de propagacion artificial disenados para la conservacion o mejoramiento.

The importance of body size to reproductive success has often been emphasized, but timing of arrival to the breeding grounds may also be important. To assess the relative roles of size and timing, we investigated the influence of life history and of behavioral and morphological traits on realized reproductive success in wild pink salmon, Oncorhynchus gorbuscha, during the 1997 and 1998 spawning seasons. Reproductive success was quantified by the number of adult offspring returning to spawn (1999 and 2000; parentage determined via DNA microsatellite genotyping). Males that arrived earlier, lived longer in the stream, and were more often observed in dominant courtship positions had significantly more offspring, although the importance of dominance was overshadowed by timing. Female reproductive success was not closely linked to any measured trait, but stabilizing selection on arrival timing and length is possible, as 1998 fish showing intermediate values of these traits were the most productive. Bear predation accounted for up to 50% of the mortality on the spawning grounds, yet did not have detectable effects on reproductive success. The absence of strong linear relationships between reproductive success and such traits as body size and fecundity may indicate that selection has driven the population to equilibrium values.

Driven by competition and mate choice, size-assortative mating has been seen in many organisms. The breeding system of salmonid fish, Oncorhynchus spp., has been extensively investigated and many examples of size-assortative mating have been found. However, assortative mating is not always observed and many reported examples involved cases with a large dichotomy in size classes or were conducted in artificial arenas where other factors influencing mate choice and competition were controlled. This study investigated size-assortative mating in a population of naturally reproducing pink salmon, O. gorbuscha. We made direct observations of courtship behaviour over 3 years on fish of known sizes. To determine the extent to which these observations corresponded to reproductive success, we assessed the parentage of the offspring produced by the fish in the first 2 years of the study using DNA fingerprinting. Size-assortative mating was not seen in the behavioural observations. Parentage results showed that our measure of dominance (proximity of males to ripe females) corresponded with successful matings, suggesting that the fish that we observed as dominant were in fact involved in more matings or more successful matings. We also saw no size-assortative mating in male and female pairs that produced adult offspring. We are not suggesting that the processes that can lead to size-assortative mating are not occurring, but that many other factors, such as female ripeness, male availability, predation threat and changing environmental conditions, may minimize the importance or mask the occurrence of size-assortative mating under natural conditions.

Microsatellites have proved to be useful for the detection of weak population structure in marine fishes and other species characterized by large populations and high gene flow. None the less, uncertainty remains about the net effects of the particular mutational properties of these markers, and the wide range of locus polymorphism they exhibit, on estimates of differentiation. We examined the effect of varying microsatellite polymorphism on the magnitude of observed differentiation in a population survey of walleye pollock, Theragra chalcogramma . Genetic differentiation at 14 microsatellite loci among six putative populations from across the North Pacific Ocean and Bering Sea was weak but significant on large geographical scales and conformed to an isolation-by-distance pattern. A negative relationship was found between locus variability and the magnitude of estimated population subdivision. Estimates of F ST declined with locus polymorphism, resulting in diminished power to discriminate among samples, and we attribute this loss to the effects of size homoplasy. This empirical result suggests that mutation rates of some microsatellite loci are sufficiently high to limit resolution of weak genetic structure typical of many marine fishes.

Salmonid fishes aggregate for breeding at spatially defined, suitable habitats. These aggregations may evolve into discrete populations when precise natal homing leads to reproductive isolation, and local regimes of selection lead to adaptation. Population structure is often defined by persistent differences in selectively neutral genetic markers and in mean values of morphological and life-history traits between locations. This approach is limited by the spatial scale at which traits diverge; low levels of reproductively successful straying, combined with similar selective pressures on life-history traits resulting from similar habitat features and environmental conditions, can significantly reduce the power of these discriminatory methods. We compared data on three life-history traits and polymorphism of DNA microsatellites for evidence of population subdivision among sockeye salmon spawning on spatially discrete but physically similar beaches on islands in Iliamna Lake, Alaska. We found small but significant differences in average body length, body depth and age composition between sites as well as significant interactions between site and year. These interactions, reflecting random variation in growth or recruitment among sites, are a powerful tool for discriminating populations with similar mean trait values. These results suggest fine-scale homing to natal sites, but the microsatellite data revealed no evidence of restricted gene flow among sites. There seems to be enough straying among the populations to prevent differentiation at neutral traits but enough homing for them to be functionally distinct.

Five tetranucleotide microsatellite loci developed from Atlantic haddock (Melanogrammus aeglefinus) are presented. Loci were isolated using a modified magnetic bead-hybridization selection procedure that enriched for tetranucleotide microsatellites. Loci were polymorphic (3-99 alleles per locus; mean, 33.2) and exhibited high levels of observed heterozygosity (0.07-0.99; mean, 0.73) in a sample of 70 haddock collected from the Scotian Shelf in the Northwest Atlantic Ocean. Primer sets for 5 tetranucleotide microsatellites, originally developed from cod (Gmo34), were also tested in Atlantic haddock; one pair yielded readily detectable product and was variable in the population assayed (29 alleles; heterozygosity, 0.96). These loci are suitable for kinship analyses in aquaculture-related applications, and are potentially useful for resolving population structure in the wild.

All existing sea otter (Enhydra lutris) populations have suffered at least 1, and in some cases 2, population bottlenecks. The 1st occurred during the 18th and 19th centuries as a result of commercial hunting that eliminated sea otters from much their native range and reduced surviving populations to small remnants. The 2nd bottleneck occurred when small numbers of otters were reintroduced, via translocation, to areas where the species had been eliminated. We examined genetic variation at 7 microsatellite loci and the mitochondrial DNA (mtDNA) control region in 3 remnant populations, Amchitka Island (Aleutian Islands, Alaska), central coastal California, and Prince William Sound (Alaska), and in 2 reintroduced populations, southeast Alaska and Washington, that were founded with transplants from Amchitka, and in the case of southeast Alaska, individuals from Prince William Sound as well. We found no evidence of reduced genetic diversity in translocated populations. Average expected microsatellite heterozygosities (H E) were similar in all populations (range, 0.40‐0.47), and mtDNA haplotype diversities were higher in reintroduced populations (0.51 for both Washington and southeast Alaska) than in remnant populations (X ¯ 5 0.35; range, 0.18‐0.45). The levels of genetic diversity we observed within sea otter populations were relatively low when compared with other mammals and are thought to be the result of fur trade exploitation.

A major cause of population declines among interior cutthroat trout subspecies Oncorhynchus clarki ssp.is hybridization with introduced rainbow trout O. mykiss ssp. Coastal cutthroat trout O. c. clarki have also experienced population declines in recent decades and are known to hybridize with coastal rainbow trout/steelhead O. m. irideus. However, unlike interior cutthroat trout, coastal cutthroat trout are naturally sympatric with coastal rainbow trout/steelhead, and the role of hybridization in their population declines remains unclear. Further, little is known about the spatial and temporal distributions of hybridization in these coastal subspecies. As a step toward better characterization of this hybridization, we developed a suite of species-specific DNA markers for coastal cutthroat trout and coastal rainbow trout/steelhead. Of 11 loci presented here, 8 exhibit fixed differences between coastal cutthroat trout and coastal rainbow trout/steelhead. The other three loci revealed frequency diff...

Newly established or perturbed populations are often the focus of conservation concerns but they pose special challenges for population genetics because drift-migration equilibrium is unlikely. To advance our understanding of the evolution of such populations, we investigated structure and gene flow among populations of chinook salmon that formed via natural straying following introduction to New Zealand in the early 1900s. We examined 11 microsatellite loci from samples collected in several sites and years to address two questions: (i) what population differentiation has arisen in the approximately 30 generations since salmon were introduced to New Zealand, relative to temporal variation within populations; and (ii) what are the approximate effective population sizes and amounts of gene flow in these populations? These questions are routinely addressed in studies of indigenous populations, but less often in the case of new populations and rarely with consideration of equilibrium assumptions. We show that despite the recent introduction, continued gene flow and high temporal variability among samples, detectable population structure has arisen among the New Zealand populations, consistent with their colonization pattern and isolation by geographical distance. Furthermore, we use simple individual-based simulations and estimates of effective population sizes to estimate the effective gene flow among drainages under likely nonequilibrium conditions. Similar methodology may be broadly applicable to other studies of population structure and phenotypic evolution under similar nonequilibrium, high gene flow conditions.

Using a genetic and tag–recapture study, we assessed the geographic scale of population structuring and dynamics of gene flow in collections of coastal cutthroat trout Oncorhynchus clarki clarki in Washington State. Tests for genotypic differentiation at 10 microsatellite loci were significant for all pairwise comparisons among 10 collections from Hood Canal creeks separated by about 2–100 km. Similarly, F-statistic analogues indicated that low but significant population structure existed among the nine anadromous collections (ϑST = 0.030, ρST = 0.029). Results from tests for isolation by distance revealed significant correlation between genetic and geographic distances. Previously published genetic data at six common loci from 14 coastal cutthroat trout collections across Washington were incorporated for some additional analyses. When analyzing all 22 anadromous collections at the six common loci, estimates of population structure increased to 0.088 for ϑST and 0.081 for ρST. All collections wer...

This study used simulations and a known two-generation pedigree of chinook salmon (Oncorhynchus tshawytscha) to evaluate the effect of full sibs of parents on pedigree reconstruction. Parentage analysis was conducted on 100 parent pair-offspring relationships from pedigrees with unrelated (simulation) and related (chinook salmon) candidate parents. Parentage assignment success for the chinook salmon was lower than in the simulated populations. For example, the six most variable loci (mean H(E) = 0.87) provided a mean of 97% unambiguous assignments in the simulated population and 67% unambiguous assignments for the chinook salmon. Estimates of the pairwise relatedness coefficient ((xy)) for most nonexcluded false parents and true parents of chinook salmon offspring exceeded 0.50. These results support the conclusion that closely related candidate parents decrease the power of genetic markers for pedigree reconstruction based on exclusion. Ambiguous parentage may be resolved using single parent- and parent pair-offspring likelihood analysis, however, these methods should be used with caution and they are not replacements for using more loci when many candidate parents are full sibs.

The examination of population-specific adaptations of introduced salmonids to the wide range of environments found in Patagonia (southern South America) can help unveil some of the genetic and environmental contributions to life history variation. The rainbow trout Oncorhynchus mykiss introduced into Argentina originated from a few parental stocks. Although some of these stocks were anadromous, all of the dozens of established populations described until now have been freshwater resident. In this paper we provide the first documentation of the presence of an anadromous run of rainbow trout in the Santa Cruz River, the second largest river of Argentinean Patagonia. Microsatellite analysis revealed that anadromous and resident fish from the Santa Cruz River are genetically indistinguishable, probably representing alternative life histories within the same population. Both wild types are very different from the fish of Danish origin that were reared in a local hatchery, suggesting that they are desc...