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Data from: Assessing conservation risks to populations of an anadromous Arctic salmonid, the northern Dolly Varden (Salvelinus malma malma), via estimates of effective and census population sizes and approximate Bayesian computation
Harris, Les N.; Palstra, Friso P.; Bajno, Rob; Gallagher, Colin P.; Howland, Kimberly L.; Taylor, Eric B.; Reist, James D.; Bajno, Robert — 2017-11-29 Census population size (Nc) is crucial to the development of resource management strategies, however, monitoring the effective population size (Ne) of managed populations has proliferated because of this parameter’s relationship to the short-term impacts of genetic stochasticity and long-term population viability. Thus, having a sound understanding of both Nc and Ne, including population connectivity, provides valuable insights into both the demographic and genetic risks to extinction. Here, we assessed microsatellite DNA variation in four (of five known) anadromous northern Dolly Varden (NDV, Salvelinus malma malma) populations from Canada’s western Arctic region, to estimate Ne using both temporal-based and single-sample estimators and to test for associations between Ne and Nc. We also employed approximate Bayesian computation (ABC) to evaluate several evolutionary scenarios that have potentially shaped contemporary population structure in this species, focusing particularly on population size and connectivity. We found evidence for moderate to large contemporary and historical Ne, suggesting that short- and long-term extinction risks are low for these populations. Estimates of contemporary and long-term Ne were variable within and among populations and overall estimates could not be reliably linked with Nc or available spawning habitat. The overall estimate of Ne/Nc, was 0.152 and ranged from 0.024 to 0.442 when including errors around the estimate of Ne and Nc. Finally, ABC analyses suggest that NDV had a common origin followed by divergence in isolation while maintaining large effective sizes, but also that these populations were bottlenecked in the past, likely the result of post-glacial colonization processes. These results corroborate indications of limited gene flow at present, indicating independent demographic and evolutionary trajectories that imply NDV is best managed on a per-river-population basis. Overall, the results of this study further our general understanding of Ne, Ne/Nc and demographic independence in NDV, and provide a comprehensive and quantitative assessment of the potential genetic and demographic risk status of Arctic anadromous salmonids, including baselines for future monitoring. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow and fine-scale population structure in Northern Dolly Varden (Salvelinus malma malma) in Canada
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Harris, Les N.; Bajno, Robert; Gallagher, Colin P.; Koizumi, Itsuro; Johnson, Lucy K.; Howland, Kimberly L.; Taylor, Eric B.; Reist, James D. — 2016-06-01 The Northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in Northern Dolly Varden from the western Canadian Arctic to resolve landscape and life history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls with stream-resident forms intermediate between the two. Anadromous and isolated populations were genetically divergent from each other while no genetic differentiation was detectable between sympatric anadromous and stream-resident forms. Population structure was stable over 25 years, hierarchically organized and conformed to an isolation-by-distance pattern, but stream-isolated forms often deviated from these patterns. Gene flow occurred primarily among Yukon North Slope populations and between sympatric anadromous and resident forms. These results were sex-dependent to some extent, but were influenced more by reproductive status and life history. Our study provides novel insights into the life history, population demographic and habitat variables that shape the distribution of genetic variation and population structure in Arctic fluvial habitats while providing a spatial context for management and conservation.
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Data from: Evolution and origin of sympatric shallow-water morphotypes of Lake Trout, Salvelinus namaycush, in Canada's Great Bear Lake
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Harris, Les N.; Chavarie, Louise; Bajno, Robert; Howland, Kimberly L.; Wiley, Simon H.; Tonn, William M.; Taylor, Eric B. — 2014-07-18 Range expansion in north-temperate fishes subsequent to the retreat of the Wisconsinan glaciers has resulted in the rapid colonization of previously unexploited, heterogeneous habitats and, in many situations, secondary contact among conspecific lineages that were once previously isolated. Such ecological opportunity coupled with reduced competition likely promoted morphological and genetic differentiation within and among post-glacial fish populations. Discrete morphological forms existing in sympatry, for example, have now been described in many species, yet few studies have directly assessed the association between morphological and genetic variation. Morphotypes of Lake Trout, Salvelinus namaycush, are found in several large-lake systems including Great Bear Lake (GBL), Northwest Territories, Canada, where several shallow-water forms are known. Here, we assess microsatellite and mitochondrial DNA variation among four morphotypes of Lake Trout from the five distinct arms of GBL, and also from locations outside of this system to evaluate several hypotheses concerning the evolution of morphological variation in this species. Our data indicate that morphotypes of Lake Trout from GBL are genetically differentiated from one another, yet the morphotypes are still genetically more similar to one another compared with populations from outside of this system. Furthermore, our data suggest that Lake Trout colonized GBL following dispersal from a single glacial refugium (the Mississippian) and support an intra-lake model of divergence. Overall, our study provides insights into the origins of morphological and genetic variation in post-glacial populations of fishes and provides benchmarks important for monitoring Lake Trout biodiversity in a region thought to be disproportionately susceptible to impacts from climate change.
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Data from: Genetic stock structure of Anadromous Arctic char in Canada’s Central Arctic: potential implications for the management of Canada’s largest Arctic char commercial fishery
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Harris, Les N.; Moore, Jean-Sébastien; Bajno, Robert; Tallman, Ross F. — 2017-10-19 The Arctic Char Salvelinus alpinus is widely considered the most important subsistence fish species in the Canadian Arctic. Throughout the species’ range, commercial fisheries for Arctic Char also exist, the management of which primarily follows river-specific harvest strategies. Such an approach, however, may not be appropriate if the management unit or stock does not accurately reflect a demographically independent population or if mixtures of populations are being harvested. We assayed microsatellite DNA variation among 744 Arctic Char from the Cambridge Bay region, Nunavut, where the largest commercial fishery for the species exists, in order to identify the most appropriate spatial scale at which these stocks should be managed. Our sampling design specifically mirrored that of the commercial fishery in order to describe patterns of genetic structure and genetic variation within and among the harvested component. We also included Arctic Char from more geographically distant sampling locations to provide a spatial context for genetic stock structuring in the region. Overall, we found moderate but significant structure across the entire study area. In contrast, commercially harvested stocks were weakly differentiated, especially among the stocks that are considered part of the Wellington Bay complex. We propose several hypotheses for this weak differentiation, including (1) our sampling design that mirrored the commercial harvest, (2) high rates of potential gene flow, and (3) large effective population sizes. Our results may have important implications for commercial and subsistence fisheries management, including the notion that there are several potential units of conservation below the species level.
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Size and bathymetry of Greiner Lake and other large lakes in its watershed, Nunavut
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Rautio, Milla; Lapeyre, Juliette; Ayala Borda, Paola; Grosbois, Guillaume; Moore, Jean-Sebastien; Harris, Les N.; Malley, Brendan K.; Blackburn-Desbiens, Pénélope — 2022 Most of the world’s lakes are in the Arctic, yet very little is known about these aquatic environments. We present here the size and depth data for five large lakes in the Greiner lake watershed near Cambridge Bay, southern Victoria Island, Nunavut. Using satellite imagery, a watershed digital surface model (WDSM) was generated to estimate surface area of Greiner lake, First lake, Second lake, Inuhuktok and Nakyulik. Bathymetry for each lake was generated using depth measures that were taken as point measures and a Biosonics or Humminbird echo sounder. La majorité des lacs du monde se trouvent en Arctique, mais on sait pourtant très peu de choses sur ces milieux aquatiques. Nous présentons ici des données sur la taille et la profondeur de cinq grands lacs du bassin versant du lac Greiner, près de Cambridge Bay, dans le sud de l'île Victoria, au Nunavut. À l'aide d'images satellitaires, un modèle numérique de surface du bassin versant (WDSM) a été généré pour estimer la superficie des lacs Greiner, First, du Second, Inuhuktok et Nakyulik. La bathymétrie de chaque lac a été générée à l'aide de mesures de profondeur prises sous forme de mesures ponctuelles et d'un échosondeur Biosonics ou Humminbird.
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Data from: Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems
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Benestan, Laura; Moore, Jean-Sébastien; Sutherland, Ben J. G.; Le Luyer, Jérémy; Maaroufi, Halim; Rougeux, Clément; Normandeau, Eric; Rycroft, Nathan; Atema, Jelle; Harris, Les N.; Tallman, Ross F.; Greenwood, Spencer J.; Clark, K. Fraser; Bernatchez, Louis — 2017-04-19 Using massively parallel sequencing data from two species with different life history traits, American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus), we highlight how an unbalanced sex ratio in the samples and a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Here, multivariate analyses revealed two genetic clusters separating samples by sex instead of by expected spatial variation; inshore and offshore locations in lobster, or east and west locations in Arctic Char. To further investigate this, we created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups, and then demonstrated that significant genetic differentiation could be observed despite panmixia in lobster, and that Fst values were overestimated in Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to non-significant genetic structure in lobster and a more accurate estimation of Fst in Arctic Char. The locations of these markers and putative identities of genes containing, or nearby the markers were determined using available transcriptomic and genomic data, and this provided new information related to sex determination in both species. Given that only 9.6% of all marine/diadromous population genomic studies to date have reported sex information, we urge researchers to collect and consider individual sex information. Sex information is therefore relevant for avoiding unexpected biases due to sex-linked markers as well as for improving our knowledge of sex determination systems in non-model species.

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(Author: Harris, Les N.)

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