{
"USGS Publications Warehouse": { "@context": "https://schema.org", "@type": "Article", "additionalType": "Journal Article", "name": "Genomics and introgression: Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing", "identifier": [ { "@type": "PropertyValue", "propertyID": "USGS Publications Warehouse IndexID", "value": "70141019", "url": "https://pubs.usgs.gov/publication/70141019" }, { "@type": "PropertyValue", "propertyID": "USGS Publications Warehouse Internal ID", "value": 70141019 }, { "@type": "PropertyValue", "propertyID": "DOI", "value": "10.1093/czoolo/61.1.146", "url": "https://doi.org/10.1093/czoolo/61.1.146" } ], "journal": { "@type": "Periodical", "name": "Current Zoology", "volumeNumber": "61", "issueNumber": "1" }, "inLanguage": "en", "isPartOf": [ { "@type": "CreativeWorkSeries", "name": "Current Zoology" } ], "datePublished": "2015", "dateModified": "2020-12-18", "abstract": "Invasive hybridization and introgression pose a serious threat to the persistence of many native species. Understanding the effects of hybridization on native populations (e.g., fitness consequences) requires numerous species-diagnostic loci distributed genome-wide. Here we used RAD sequencing to discover thousands of single-nucleotide polymorphisms (SNPs) that are diagnostic between rainbow trout (RBT,\u00a0Oncorhynchus mykiss), the world\u2019s most widely introduced fish, and native westslope cutthroat trout (WCT,\u00a0O. clarkii lewisi) in the northern Rocky Mountains, USA. We advanced previous work that identified 4,914 species-diagnostic loci by using longer sequence reads (100 bp\u00a0vs. 60 bp) and a larger set of individuals (n =\u00a084). We sequenced RAD libraries for individuals from diverse sampling sources, including native populations of WCT and hatchery broodstocks of WCT and RBT. We also took advantage of a newly released reference genome assembly for RBT to align our RAD loci. In total, we discovered 16,788 putatively diagnostic SNPs, 10,267 of which we mapped to anchored chromosome locations on the RBT genome. A small portion of previously discovered putative diagnostic loci (325 of 4,914) were no longer diagnostic (i.e., fixed between species) based on our wider survey of non-hybridized RBT and WCT individuals. Our study suggests that RAD loci mapped to a draft genome assembly could provide the marker density required to identify genes and chromosomal regions influencing selection in admixed populations of conservation concern and evolutionary interest.", "description": "9 p.", "publisher": { "@type": "Organization", "name": "Oxford University Press" }, "author": [ { "@type": "Person", "name": "Kovach, Ryan P. rkovach@usgs.gov", "givenName": "Ryan P.", "familyName": "Kovach", "email": "rkovach@usgs.gov", "affiliation": [ { "@type": "Organization", "name": "Northern Rocky Mountain Science Center", "url": "https://www.usgs.gov/centers/norock" } ] }, { "@type": "Person", "name": "Hand, Brian K.", "givenName": "Brian K.", "familyName": "Hand", "affiliation": [ { "@type": "Organization", "name": "Flathead Lake Biological Station, Fish and Wildlife Genomics Group, University of Montana, Polson, MT 59860" } ] }, { "@type": "Person", "name": "Hether, Tyler D", "givenName": "Tyler D", "familyName": "Hether", "affiliation": [ { "@type": "Organization", "name": "Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID 83844" } ] }, { "@type": "Person", "name": "Muhlfeld, Clint C. cmuhlfeld@usgs.gov", "givenName": "Clint C.", "familyName": "Muhlfeld", "email": "cmuhlfeld@usgs.gov", "identifier": { "@type": "PropertyValue", "propertyID": "ORCID", "value": "0000-0002-4599-4059", "url": "https://orcid.org/0000-0002-4599-4059" }, "affiliation": [ { "@type": "Organization", "name": "Northern Rocky Mountain Science Center", "url": "https://www.usgs.gov/centers/norock" }, { "@type": "Organization", "name": "Coop Res Unit Seattle", "url": "https://www1.usgs.gov/coopunits/unit/Washington" } ] }, { "@type": "Person", "name": "Amish, Stephen J.", "givenName": "Stephen J.", "familyName": "Amish", "affiliation": [ { "@type": "Organization", "name": "University of Montana, Division of Biological Sciences" } ] }, { "@type": "Person", "name": "Boyer, Matthew C.", "givenName": "Matthew C.", "familyName": "Boyer", "affiliation": [ { "@type": "Organization", "name": "Montana Fish, Wildlife and Parks, Kalispell, Montana 59901, USA" } ] }, { "@type": "Person", "name": "O\u2019Rourke, Sean M.", "givenName": "Sean M.", "familyName": "O\u2019Rourke", "affiliation": [ { "@type": "Organization", "name": "Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA" } ] }, { "@type": "Person", "name": "Miller, Michael R.", "givenName": "Michael R.", "familyName": "Miller", "affiliation": [ { "@type": "Organization", "name": "Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA" } ] }, { "@type": "Person", "name": "Hohenlohe, Paul A.", "givenName": "Paul A.", "familyName": "Hohenlohe", "affiliation": [ { "@type": "Organization", "name": "Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID 83844" } ] }, { "@type": "Person", "name": "Luikart, Gordon", "givenName": "Gordon", "familyName": "Luikart", "affiliation": [ { "@type": "Organization", "name": "University of Montana, Flathead Lake Biological Station, Polson, Montana 59860, USA" } ] }, { "@type": "Person", "name": "Lowe, Winsor H.", "givenName": "Winsor H.", "familyName": "Lowe", "affiliation": [ { "@type": "Organization", "name": "University of Montana, Division of Biological Sciences" } ] } ], "funder": [ { "@type": "Organization", "name": "Northern Rocky Mountain Science Center", "url": "https://www.usgs.gov/centers/norock" } ], "spatialCoverage": [ { "@type": "Place", "additionalType": "country", "name": "United States", "url": "https://geonames.org/4074035" }, { "@type": "Place", "additionalType": "state", "name": "Montana" }, { "@type": "Place", "geo": [ { "@type": "GeoShape", "additionalProperty": { "@type": "PropertyValue", "name": "GeoJSON", "value": { "type": 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Hand", "orcid": "https://orcid.org/0000-0003-1152-665X" }, "institutions": [ { "id": "https://openalex.org/I6750721", "display_name": "University of Montana", "ror": "https://ror.org/0078xmk34", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I6750721" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Brian K. 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Geological Survey, Northern Rocky Mountain Science Center, Glacier National Park, West Glacier, Montana 59936, USA" ], "affiliations": [ { "raw_affiliation_string": "Flathead Lake Biological Station, Fish and Wildlife Genomics Group, University of Montana, Polson, MT 59860, USA", "institution_ids": [ "https://openalex.org/I6750721" ] }, { "raw_affiliation_string": "U. S. Geological Survey, Northern Rocky Mountain Science Center, Glacier National Park, West Glacier, Montana 59936, USA", "institution_ids": [ "https://openalex.org/I1286329397" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5029284700", "display_name": "Clint C. 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Amish", "raw_affiliation_strings": [ "Fish and Wildlife Genomics Group, Division of Biological Sciences, The University of Montana, Missoula, Montana 59812, USA" ], "affiliations": [ { "raw_affiliation_string": "Fish and Wildlife Genomics Group, Division of Biological Sciences, The University of Montana, Missoula, Montana 59812, USA", "institution_ids": [ "https://openalex.org/I6750721" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5061312845", "display_name": "Matthew Boyer", "orcid": null }, "institutions": [ { "id": "https://openalex.org/I4210126201", "display_name": "Montana Fish, Wildlife & Parks", "ror": "https://ror.org/0398xj847", "country_code": "US", "type": "government", "lineage": [ "https://openalex.org/I4210126201" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Matthew C. 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