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      Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic

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          Abstract

          Domestication is rife with episodes of interbreeding between cultured and wild populations, potentially challenging adaptive variation in the wild. In Atlantic salmon, Salmo salar, the number of domesticated individuals far exceeds wild individuals, and escape events occur regularly, yet evidence of the magnitude and geographic scale of interbreeding resulting from individual escape events is lacking. We screened juvenile Atlantic salmon using 95 single nucleotide polymorphisms following a single, large aquaculture escape in the Northwest Atlantic and report the landscape-scale detection of hybrid and feral salmon (27.1%, 17/18 rivers). Hybrids were reproductively viable, and observed at higher frequency in smaller wild populations. Repeated annual sampling of this cohort revealed decreases in the presence of hybrid and feral offspring over time. These results link previous observations of escaped salmon in rivers with reports of population genetic change, and demonstrate the potential negative consequences of escapes from net-pen aquaculture on wild populations.

          Abstract

          Brendan Wringe et al. find evidence of extensive hybridization between wild and domesticated salmon following a large escape event in the Northwest Atlantic in 2013. Genetic screening of juvenile salmon shows that > 27% of fish in 17 of 18 rivers examined are hybrids or feral, demonstrating a significant impact of escaped individuals on local populations.

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          Most cited references40

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            COLONY: a program for parentage and sibship inference from multilocus genotype data.

            Pedigrees, depicting genealogical relationships between individuals, are important in several research areas. Molecular markers allow inference of pedigrees in wild species where relationship information is impossible to collect by observation. Marker data are analysed statistically using methods based on Mendelian inheritance rules. There are numerous computer programs available to conduct pedigree analysis, but most software is inflexible, both in terms of assumptions and data requirements. Most methods only accommodate monogamous diploid species using codominant markers without genotyping error. In addition, most commonly used methods use pairwise comparisons rather than a full-pedigree likelihood approach, which considers the likelihood of the entire pedigree structure and allows the simultaneous inference of parentage and sibship. Here, we describe colony, a computer program implementing full-pedigree likelihood methods to simultaneously infer sibship and parentage among individuals using multilocus genotype data. colony can be used for both diploid and haplodiploid species; it can use dominant and codominant markers, and can accommodate, and estimate, genotyping error at each locus. In addition, colony can carry out these inferences for both monoecious and dioecious species. The program is available as a Microsoft Windows version, which includes a graphical user interface, and a Macintosh version, which uses an R-based interface. © 2009 Blackwell Publishing Ltd.
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              Evolution of crop species: genetics of domestication and diversification.

              Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.
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                Author and article information

                Contributors
                ian.bradbury@dfo-mpo.gc.ca
                Journal
                Commun Biol
                Commun Biol
                Communications Biology
                Nature Publishing Group UK (London )
                2399-3642
                9 August 2018
                9 August 2018
                2018
                : 1
                : 108
                Affiliations
                [1 ]ISNI 0000 0004 0449 2129, GRID grid.23618.3e, Science Branch, Fisheries and Oceans Canada, ; 80 East White Hills Road, St. John’s, Newfoundland, A1C 5X1 Canada
                [2 ]ISNI 0000 0000 9130 6822, GRID grid.25055.37, Department of Ocean Sciences, , Memorial University of Newfoundland, St. John’s, ; Newfoundland, A1C 5S7 Canada
                [3 ]ISNI 0000 0004 1936 8200, GRID grid.55602.34, Faculty of Computer Science, , Dalhousie University, ; Halifax, NS B3H 4R2 Canada
                [4 ]ISNI 0000 0001 2173 5688, GRID grid.418256.c, Science Branch, Fisheries and Oceans Canada, , Bedford Institute of Oceanography, ; Dartmouth, NS B2Y 4A2 Canada
                [5 ]ISNI 0000 0001 2173 5688, GRID grid.418256.c, Aquatic Biotechnology Laboratory, Fisheries and Oceans Canada, , Bedford Institute of Oceanography, ; Dartmouth, NS B2Y 4A2 Canada
                [6 ]ISNI 0000 0001 1266 2261, GRID grid.3532.7, Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, , National Oceanic and Atmospheric Administration, ; Santa Cruz, CA 95060 USA
                Author information
                http://orcid.org/0000-0002-8152-4943
                Article
                112
                10.1038/s42003-018-0112-9
                6123692
                29809203
                6454a15a-4dba-4e22-81a8-27ba08942bc0
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 6 December 2017
                : 16 July 2018
                Funding
                Funded by: This study was funded through the Program for Aquaculture Regulatory Research of Fisheries and Oceans Canada, the Genomics Research and Development Initiative of Canada, as well as the National Sciences and Engineering Research Council of Canada, and support from the Atlantic Salmon Federation.
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                © The Author(s) 2018

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