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When females prefer mates with rare phenotypes, sexual selection can maintain rather than deplete genetic variation. However, there is no consensus on why this widespread and frequently observed preference might evolve and persist. We examine the fitness consequences of female preference for rare male color patterns in a natural population of Trinidadian guppies, using a pedigree that spans 10 generations. We demonstrate (i) a rare male reproductive advantage, (ii) that females that mate with rare males gain an indirect fitness advantage through the mating success of their sons, and (iii) the fitness benefit that females accrue through their “sexy sons” evaporates for their grandsons as their phenotype becomes common. Counter to prevailing theory, we show that female preference can be maintained through indirect selection.

Funding: This work was supported by Fisheries and Oceans Canada (DFO) Maritimes and National Geographic emerging explorer grant to L.J.F, with support by and Natural Sciences and Engineering Research Council of Canada (NSERC) and Killam Nova Scotia Doctoral Scholarships. Work was also supported by US Office of Naval Research and US Strategic Environmental Research and Development Program (SERDP), DFO, University of Windsor, Crown-Indigenous Relations and Northern Affairs Canada, Nunavut Fisheries Association, Government of Nunavut, and NSERC. Funding and resources for sequencing the northern bottlenose whale genome was supported by the CanSeq150 program of Canada’s Genomics Enterprise. Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole-genome resequencing data (n = 37) from five regions across the North Atlantic Ocean. We found a range-wide pattern of isolation-by-distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long-term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes. Publisher PDF

Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.

Atlantic salmon (Salmo salar) populations throughout the North Atlantic have declined in recent decades largely due to reduced marine survival, yet our understanding of marine distribution patterns and migratory routes remains limited. Here, we assigned archived individual samples (n = 3891) collected over a half century (1968–2018) throughout the North Atlantic to region of origin using range-wide genetic assignment. In the Northwest Atlantic, the distribution of assignments reinforced the importance of the Labrador Sea as an aggregation area, with 73% of all reporting groups detected. Moreover, individuals from six European reporting groups were identified in the Northwest Atlantic, and detections decreased with decreasing latitude spanning an area from Greenland to southern Newfoundland. In the Northeast Atlantic, six North American reporting groups were detected in samples from around the Faroe Islands. Based on the distribution of samples, estimates of trans-Atlantic migration distance averaged 3861 and 2889 km for North American and European salmon respectively. Our analysis highlights the widespread importance of the Labrador Sea and Faroe Islands to the species marine distribution patterns, and the prevalence of long-distance trans-Atlantic migration. Ultimately, the results suggest that environmental conditions experienced by many Atlantic salmon populations span much of the North Atlantic Ocean.

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.

The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next‐generation sequencing, several methods now exist for resolving fine‐scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine‐scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29‐year tagging dataset. Self‐assignment and simulation‐based analyses of 111 genome‐wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north‐eastern Canada identified largely river‐specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self‐assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery‐collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence‐based microsatellite genotyping to advance understanding of fine‐scale population structure and harvest composition in northern and understudied species.

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) in the western and eastern Atlantic diverged >600,000 years before present, with the two lineages isolated in different southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic divergence. Here, we investigate the genomic consequences of glacial isolation and trans-Atlantic secondary contact using 108,870 single nucleotide polymorphisms genotyped in 80 North American and European populations. Throughout North America, we identified extensive interindividual variation and discrete linkage blocks within and between chromosomes with known trans-Atlantic differences in rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post-glacial trans-Atlantic secondary contact, contrasting with low European ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intrapopulation diversity, suggesting a derived chromosome fusion polymorphism that evolved within North America. Evidence of potential selection on both genomic regions suggests that the adaptive role of rearrangements warrants further investigation in Atlantic salmon. Our study highlights how Pleistocene glaciations can influence large-scale intraspecific variation in genomic architecture of northern species.

In dendritic river systems, gene flow is expected to occur primarily within watersheds. Yet, rare cross‐watershed transfers can also occur, whether mediated by (often historical) geological events or (often contemporary) human activities. We explored these events and their potential evolutionary consequences by analyzing patterns of neutral genetic variation (microsatellites) and adaptive phenotypic variation (male color) in wild guppies (Poecilia reticulata) distributed across two watersheds in northern Trinidad. We found the expected signatures of within‐watershed gene flow; yet we also inferred at least two instances of cross‐watershed gene flow—one in the upstream reaches and one further downstream. The upstream cross‐watershed event appears to be very recent (41 ± 13 years), suggesting dispersal via recent flooding or undocumented human‐mediated transport. The downstream cross‐watershed event appears to be considerably older (577 ± 265 years), suggesting a role for rare geological or climatological events. Alongside these strong signatures of both contemporary and historical gene flow, we found little evidence of impacts on presumably adaptive phenotypic differentiation, except perhaps in the one instance of very recent cross‐watershed gene flow. Selection in this system seems to overpower gene flow—at least on the spatiotemporal scales investigated here.

Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net‐pen salmon aquaculture. Although domestic–wild hybrid offspring have shown reduced fitness in laboratory and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context‐dependent. Here, we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in‐river proportions of hybrids and feral individuals over time using genetically based hybrid identification. Over a three‐year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1% and 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within‐cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively) and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual‐based salmon eco‐genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short‐term to long‐term invasion and three relative survival scenarios. Modelling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall, this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long‐term impact of farmed salmon escape events on wild populations.

Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using FSTrankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.

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.

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.

Restriction‐site associated DNA sequencing (RAD‐seq) can identify and score thousands of genetic markers from a group of samples for population‐genetics studies. One challenge of de novo RAD‐seq analysis is to distinguish paralogous sequence variants (PSVs) from true single‐nucleotide polymorphisms (SNPs) associated with orthologous loci. In the absence of a reference genome, it is difficult to differentiate true SNPs from PSVs, and their impact on downstream analysis remains unclear. Here, we introduce a network‐based approach, PMERGE that connects fragments based on their DNA sequence similarity to identify probable PSVs. Applying our method to de novo RAD‐seq data from 150 Atlantic salmon (Salmo salar) samples collected from 15 locations across the Southern Newfoundland coast allowed the identification of 87% of total PSVs identified through alignment to the Atlantic salmon genome. Removal of these paralogs altered the inferred population structure, highlighting the potential impact of filtering in RAD‐seq analysis. PMERGE is also applied to a green crab (Carcinus maenas) data set consisting of 242 samples from 11 different locations and was successfully able to identify and remove the majority of paralogous loci (62%). The PMERGE software can be run as part of the widely used Stacks analysis package.

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.

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.

Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry have received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites, we examined hybridization between sympatric populations of alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) to test whether the frequency of hybridization and pattern of introgression have been impacted by the construction of a dam that isolated formerly anadromous populations of both species in a landlocked freshwater reservoir. The frequency of hybridization and pattern of introgression differed markedly between anadromous and landlocked populations. The rangewide frequency of hybridization among anadromous populations was generally 0-8%, whereas all landlocked individuals were hybrids. Although neutral introgression was observed among anadromous hybrids, directional introgression leading to increased prevalence of alewife genotypes was detected among landlocked hybrids. We demonstrate that habitat alteration can lead to hybrid swarm formation between divergent species that naturally occur sympatrically, and provide empirical evidence that reinforcement does not always sustain reproductive isolation under such circumstances.

Gyrodactylus patersoni n. sp. is described from the gills of the Atlantic silverside, Menidia menidia (L.) (Atherinidae), from Kingsport, Nova Scotia, Canada. The new species is the second species of Gyrodactylus to be reported from this host and is characterized by having small hamuli with short hamuli roots, a ventral bar with anterolateral processes of moderate size and a linguiform membrane, a dorsal bar with medial notch, and a male copulatory organ with 1 large spine and 5–6 terminal spines arranged in a single arched row. Gyrodactylus patersoni n. sp. most closely resembles Gyrodactylus stephanus Mueller, 1937 described from the mummichog, Fundulus heteroclitus L., from the northeastern coast of North America. The 2 species can be differentiated by the size of the hamuli (32.5 µm vs. 40.0 µm), length of the anterolateral processes (4.5 µm vs. 8.5 µm), number of copulatory spines (5–6 vs. 6–8) and, to a lesser degree, the shape of the marginal hook in that members of Gyrodactylus patersoni n. sp. have a slightly reduced heel and a more upright shaft. The description includes 438 sequenced base pairs (bp) of the 18S gene (including the V4 region) as well as 936 bp of the ITS region (ITS-1/5.8S/ITS-2). Basic Local Alignment Search Tool (BLAST) queries for the ITS and 18S fragments returned G. stephanus as most genetically similar (97.6% and 99.1%, respectively). Gyrodactylus patersoni n. sp. is a member of the Gyrodactylus arcuatus-group, a lineage that has successfully radiated through phylogenetically diverse fishes of the northern hemisphere, most of which share a littoral marine habitat.

Gyrodactylus laevisoides n. sp. is described from the gill rakers of red belly dace, Phoxinus eos Cope (Cyprinidae), from Nova Scotia, Canada. Gyrodactylus laevisoides n. sp. is the second species of Gyrodactylus Nordmann, 1832 described from this host and is characterised by weakly curving hamuli, a small ventral bar lacking anterolateral processes, stout dorsal bar, small marginal hooks with sickles larger proximally than distally and having a small circular process on the heel, a MCO with spines arranged in two arched rows, and lack of obvious excretory bladders. The new species most closely resembles Gyrodactylus laevis Malmberg, 1957, a Eurasian species whose principle host is Phoxinus phoxinus (L.). The two species are separated by Gyrodactylus laevisoides n. sp. having less divergent and longer hamulus root and marginal hook sickle toe with a steeper continuous angle and heel that is less prominent. The morphological description is supplemented with sequences of the 18S gene (449 bp, including the V4 region) and of the ITS region (821 bp). Gyrodactylus sedelnikowi Gvosdev, 1950 infecting Barbatula barbatula (L.) and Gyrodactylus neili Leblanc, Hansen, Burt & Cone, 2006 infecting Esox niger Lesueur are the most genetically similar species on GenBank for the 18S rRNA gene and ITS regions respectively (c.96% and c.92%). Gyrodactylus laevisoides n. sp. belongs to Malmberg’s subgenus Gyrodactylus (Gyrodactylus) and phylogenetic analysis of the ITS region groups this species with other members of the subgenus. The phylogeny has two main clades, one comprised of Eurasian species and the other of North American species, specifically Gyrodactylus laevisoides n. sp. and Gyrodactylus neili. It is suspected that this lineage, which is seemingly underrepresented in North America, likely colonised the new world with an ancestral species of Phoxinus via the Bering land connection around the time of the Pliocene.