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Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages
Moore, Jean-Sébastien; Bajno, Robert; Reist, James D.; Taylor, Eric B. — 2016-06-27 Aims: We investigated post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus) and examined potential hybridization between different glacial lineages upon secondary contact. Location: North American Arctic and adjacent areas. Methods: We collected mtDNA sequence data from 1355 individuals from 110 sampling locations and data from nine microsatellite loci from 931 individuals from 37 locations. We assessed the phylogenetic relationships and geographical distribution of mtDNA haplotypes and conducted historical demographic analyses. We used a Bayesian clustering analysis method to detect potential hybridization between glacial lineages. Results: Two highly divergent mtDNA lineages were identified in the Arctic region with distinct but overlapping geographic distributions: one in Beringia and the other over the entire Arctic Archipelago and coastal mainland east of Alaska. The microsatellite data also implied the existence of these two lineages. Evidence of hybridization was detected between the Arctic lineage and an Atlantic lineage in eastern North America. Main conclusions: Our data suggested survival and recolonization from two northern glacial refugia: one in Beringia and another in a smaller refugium, perhaps in the Arctic Archipelago itself or a separate refugium within Beringia. Patterns of hybridization detected supported the presence of a secondary contact zone between glacial lineages in the eastern Canadian Arctic.
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Data from: Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada
Beacham, Terry D.; Wallace, Colin; Jonsen, Kim; McIntosh, Brenda; Candy, John R.; Willis, David; Lynch, Cheryl; Moore, Jean-Sébastien; Bernatchez, Louis; Withler, Ruth E. — 2018-09-07 Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774–individual, 267–population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.
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Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci
Moore, Jean-Sébastien; Bourret, Vincent; Dionne, Mélanie; Bradbury, Ian; O’Reilly, Patrick; Kent, Matthew; Chaput, Gérald; Bernatchez, Louis; O'Reilly, Patrick — 2014-10-23 Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9,142 individuals from 149 sampling locations and data from a medium-density SNP array providing genotypes for >3,000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite dataset and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America.
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Data from: Assessing reproductive isolation using a contact zone between parapatric lake-stream stickleback ecotypes
Hanson, Dieta; Moore, Jean-Sébastien; Taylor, Eric B.; Barrett, Rowan D.H.; Hendry, Andrew P.; Moore, J.-S.; Barrett, R. D. H. — 2016-09-08 Ecological speciation occurs when populations evolve reproductive isolation as a result of divergent natural selection. This isolation can be influenced by many potential reproductive barriers, including selection against hybrids, selection against migrants, and assortative mating. How and when these barriers act and interact in nature is understood for relatively few empirical systems. We used a mark-recapture experiment in a contact zone between lake and stream three-spined sticklebacks (Gasterosteus aculeatus, Linnaeus) to evaluate the occurrence of hybrids (allowing inferences about reproductive isolation), the inter-annual survival of hybrids (allowing inferences about selection against hybrids), and the shift in lake-like versus stream-like characteristics (allowing inferences about selection against migrants). Genetic and morphological data suggest the occurrence of hybrids and no selection against hybrids in general, a result contradictory to a number of other studies of sticklebacks. However, we did find selection against more lake-like individuals, suggesting a barrier to gene flow from the lake into the stream. Combined with previous work on this system, our results suggest that multiple (most weakly and often asymmetric) barriers must be combining to yield substantial restrictions on gene flow. This work provides evidence of a reproductive barrier in lake-stream sticklebacks and highlights the value of assessing multiple reproductive barriers in natural contexts. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: The availability of research data declines rapidly with article age
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Vines, Timothy H.; Albert, Arianne Y. K.; Andrew, Rose L.; Débarre, Florence; Bock, Dan G.; Franklin, Michelle T.; Gilbert, Kimberly J.; Moore, Jean-Sébastien; Renaut, Sébastien; Rennison, Diana J. — 2014-11-05 Policies ensuring that research data are available on public archives are increasingly being implemented at the government, funding agency, and journal level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term, and indeed many studies have found that authors are often unable or unwilling to share their data. However, there are no systematic estimates of how the availability of research data changes with time since publication. We therefore requested datasets from a relatively homogenous set of 516 articles published between 2 and 22 years ago, and found that availability of the data was strongly affected by article age. For papers where the authors gave the status of their data, the odds of a dataset being extant fell by 17% per year. In addition, the odds that we could find a working email address for the first, last or corresponding author fell by 7% per year. Our results reinforce the notion that, in the long term, research data cannot be reliably preserved by individual researchers, and further demonstrate the urgent need for policies mandating data sharing via public archives.
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Data from: Mandated data archiving greatly improves access to research data
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Vines, Timothy H.; Andrew, Rose L.; Bock, Dan G.; Franklin, Michelle T.; Gilbert, Kimberly J.; Kane, Nolan C.; Moore, Jean-Sébastien; Moyers, Brook T.; Renaut, Sébastien; Rennison, Diana J.; Veen, Thor; Yeaman, Sam — 2013-01-04 The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, STRUCTURE. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost 1000-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with ∼8 d delay and some disagreement with authors. Given the long-term benefits of data accessibility to the academic community, we believe that journal-based mandatory data archiving policies and mandatory data availability statements should be more widely adopted.
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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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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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(auteur : Moore, Jean-Sébastien)

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