Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest
Identifieur interne : 001780 ( Istex/Corpus ); précédent : 001779; suivant : 001781Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest
Auteurs : Timothy F. Sheehan ; Christopher M. Legault ; Timothy L. King ; Adrian P. SpidleSource :
- ICES Journal of Marine Science [ 1054-3139 ] ; 2010-04.
Abstract
Sheehan, T. F., Legault, C. M., King, T. L., and Spidle, A. P. 2010. Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest. ICES Journal of Marine Science, 67: 537550. A multistock Atlantic salmon (Salmo salar) fishery operates off the coast of West Greenland and harvests fish of North American and European origin. Annual landings peaked in 1971 at 2700 t, but declined to 22 t in 2003. Biological data are collected to characterize the catch and its stock composition. Multilocus genotypes, generated via microsatellite DNA analysis, are used to derive statistics on continent of origin and less accurate finer-scale assignments. We developed a probabilistic-based genetic assignment (PGA) model to estimate the contribution of salmon from individual North American rivers in the 20002003 West Greenland catch. Uncertainty associated with finer-scale assignments is addressed by incorporating estimated misclassification rates and by reporting results as distributions generated via Monte Carlo resampling. US-origin fish represented 1 (by number) of the salmon harvested at West Greenland during the years 20002003. The resulting loss of spawners to this stock complex was approximately half the estimated adult returns in 2001, but was below 4 in the other 3 years. This is the first attempt to partition the US component of the West Greenland mixed-stock fishery to its finer parts. The approach can be used to identify the effects of fishing on individual stocks within any multistock complex where genetic samples of known origin are available.
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DOI: 10.1093/icesjms/fsp247
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Sheehan</name><affiliation><mods:affiliation>United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: tim.sheehan@noaa.gov</mods:affiliation></affiliation></author><author><name sortKey="Legault, Christopher M" sort="Legault, Christopher M" uniqKey="Legault C" first="Christopher M." last="Legault">Christopher M. Legault</name><affiliation><mods:affiliation>United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA</mods:affiliation></affiliation></author><author><name sortKey="King, Timothy L" sort="King, Timothy L" uniqKey="King T" first="Timothy L." last="King">Timothy L. 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F., Legault, C. M., King, T. L., and Spidle, A. P. 2010. Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest. ICES Journal of Marine Science, 67: 537550. A multistock Atlantic salmon (Salmo salar) fishery operates off the coast of West Greenland and harvests fish of North American and European origin. Annual landings peaked in 1971 at 2700 t, but declined to 22 t in 2003. Biological data are collected to characterize the catch and its stock composition. Multilocus genotypes, generated via microsatellite DNA analysis, are used to derive statistics on continent of origin and less accurate finer-scale assignments. We developed a probabilistic-based genetic assignment (PGA) model to estimate the contribution of salmon from individual North American rivers in the 20002003 West Greenland catch. Uncertainty associated with finer-scale assignments is addressed by incorporating estimated misclassification rates and by reporting results as distributions generated via Monte Carlo resampling. US-origin fish represented 1 (by number) of the salmon harvested at West Greenland during the years 20002003. The resulting loss of spawners to this stock complex was approximately half the estimated adult returns in 2001, but was below 4 in the other 3 years. This is the first attempt to partition the US component of the West Greenland mixed-stock fishery to its finer parts. The approach can be used to identify the effects of fishing on individual stocks within any multistock complex where genetic samples of known origin are available.</div></front></TEI><istex><corpusName>oup</corpusName><author><json:item><name>Timothy F. Sheehan</name><affiliations><json:string>United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA</json:string><json:string>E-mail: tim.sheehan@noaa.gov</json:string></affiliations></json:item><json:item><name>Christopher M. Legault</name><affiliations><json:string>United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA</json:string></affiliations></json:item><json:item><name>Timothy L. King</name><affiliations><json:string>United States Geological Survey, Leetown Science Center, 11649 Leetown Road, Leetown, WV 25430, USA</json:string></affiliations></json:item><json:item><name>Adrian P. Spidle</name><affiliations><json:string>Northwest Indian Fisheries Commission, 6730 Martin Way East, Olympia, WA 98512, USA</json:string></affiliations></json:item></author><subject><json:item><value>Atlantic salmon</value></json:item><json:item><value>genetic stock identification</value></json:item><json:item><value>West Greenland</value></json:item></subject><articleId><json:string>fsp247</json:string></articleId><language><json:string>unknown</json:string></language><originalGenre><json:string>research-article</json:string></originalGenre><abstract>Sheehan, T. F., Legault, C. M., King, T. L., and Spidle, A. P. 2010. Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest. ICES Journal of Marine Science, 67: 537550. A multistock Atlantic salmon (Salmo salar) fishery operates off the coast of West Greenland and harvests fish of North American and European origin. Annual landings peaked in 1971 at 2700 t, but declined to 22 t in 2003. Biological data are collected to characterize the catch and its stock composition. Multilocus genotypes, generated via microsatellite DNA analysis, are used to derive statistics on continent of origin and less accurate finer-scale assignments. We developed a probabilistic-based genetic assignment (PGA) model to estimate the contribution of salmon from individual North American rivers in the 20002003 West Greenland catch. Uncertainty associated with finer-scale assignments is addressed by incorporating estimated misclassification rates and by reporting results as distributions generated via Monte Carlo resampling. US-origin fish represented 1 (by number) of the salmon harvested at West Greenland during the years 20002003. The resulting loss of spawners to this stock complex was approximately half the estimated adult returns in 2001, but was below 4 in the other 3 years. This is the first attempt to partition the US component of the West Greenland mixed-stock fishery to its finer parts. 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Published by Oxford Journals. All rights reserved. For Permissions, please email: journals.permissionsoxfordjournals.org</p></availability><date>2009-11-11</date></publicationStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a">Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest</title><author xml:id="author-1"><persName><forename type="first">Timothy F.</forename><surname>Sheehan</surname></persName><email>tim.sheehan@noaa.gov</email><affiliation>United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA</affiliation></author><author xml:id="author-2"><persName><forename type="first">Christopher M.</forename><surname>Legault</surname></persName><affiliation>United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA</affiliation></author><author xml:id="author-3"><persName><forename type="first">Timothy L.</forename><surname>King</surname></persName><affiliation>United States Geological Survey, Leetown Science Center, 11649 Leetown Road, Leetown, WV 25430, USA</affiliation></author><author xml:id="author-4"><persName><forename type="first">Adrian P.</forename><surname>Spidle</surname></persName><affiliation>Northwest Indian Fisheries Commission, 6730 Martin Way East, Olympia, WA 98512, USA</affiliation></author></analytic><monogr><title level="j">ICES Journal of Marine Science</title><idno type="pISSN">1054-3139</idno><idno type="eISSN">1095-9289</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2010-04"></date><biblScope unit="volume">67</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="537">537</biblScope><biblScope unit="page" to="550">550</biblScope></imprint></monogr><idno type="istex">CC021698FBA66ABC6F1190F7DA59197F694BEF1B</idno><idno type="DOI">10.1093/icesjms/fsp247</idno><idno type="ArticleID">fsp247</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2009-11-11</date></creation><abstract><p>Sheehan, T. F., Legault, C. M., King, T. L., and Spidle, A. P. 2010. Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest. ICES Journal of Marine Science, 67: 537550. A multistock Atlantic salmon (Salmo salar) fishery operates off the coast of West Greenland and harvests fish of North American and European origin. Annual landings peaked in 1971 at 2700 t, but declined to 22 t in 2003. Biological data are collected to characterize the catch and its stock composition. Multilocus genotypes, generated via microsatellite DNA analysis, are used to derive statistics on continent of origin and less accurate finer-scale assignments. We developed a probabilistic-based genetic assignment (PGA) model to estimate the contribution of salmon from individual North American rivers in the 20002003 West Greenland catch. Uncertainty associated with finer-scale assignments is addressed by incorporating estimated misclassification rates and by reporting results as distributions generated via Monte Carlo resampling. US-origin fish represented 1 (by number) of the salmon harvested at West Greenland during the years 20002003. The resulting loss of spawners to this stock complex was approximately half the estimated adult returns in 2001, but was below 4 in the other 3 years. This is the first attempt to partition the US component of the West Greenland mixed-stock fishery to its finer parts. The approach can be used to identify the effects of fishing on individual stocks within any multistock complex where genetic samples of known origin are available.</p></abstract><textClass><keywords scheme="keyword"><list><head>keywords</head><item><term>Atlantic salmon</term></item><item><term>genetic stock identification</term></item><item><term>West Greenland</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2009-11-11">Created</change><change when="2010-04">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/document/CC021698FBA66ABC6F1190F7DA59197F694BEF1B/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus oup" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" URI="journalpublishing.dtd" name="istex:docType"></istex:docType><istex:document><article article-type="research-article"><front><journal-meta><journal-id journal-id-type="publisher-id">icesjms</journal-id><journal-id journal-id-type="hwp">icesjms</journal-id><journal-title>ICES Journal of Marine Science</journal-title><issn pub-type="ppub">1054-3139</issn><issn pub-type="epub">1095-9289</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.1093/icesjms/fsp247</article-id><article-id pub-id-type="publisher-id">fsp247</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Sheehan</surname><given-names>Timothy F.</given-names></name><xref ref-type="aff" rid="af1">1</xref><xref ref-type="corresp" rid="cor1"></xref></contrib><contrib contrib-type="author"><name><surname>Legault</surname><given-names>Christopher M.</given-names></name><xref ref-type="aff" rid="af1">1</xref></contrib><contrib contrib-type="author"><name><surname>King</surname><given-names>Timothy L.</given-names></name><xref ref-type="aff" rid="af2">2</xref></contrib><contrib contrib-type="author"><name><surname>Spidle</surname><given-names>Adrian P.</given-names></name><xref ref-type="aff" rid="af3">3</xref></contrib></contrib-group><aff id="af1"><label>1</label><addr-line>United States Department of Commerce, National Oceanic and Atmospheric Administration</addr-line>, <institution>National Marine Fisheries Service, Northeast Fisheries Science Center</institution>, <addr-line>166 Water Street, Woods Hole, MA 02543</addr-line>, <country>USA</country></aff><aff id="af2"><label>2</label><institution>United States Geological Survey, Leetown Science Center</institution>, <addr-line>11649 Leetown Road, Leetown, WV 25430</addr-line>, <country>USA</country></aff><aff id="af3"><label>3</label><institution>Northwest Indian Fisheries Commission</institution>, <addr-line>6730 Martin Way East, Olympia, WA 98512</addr-line>, <country>USA</country></aff><author-notes><corresp id="cor1">Correspondence to T. F. Sheehan: Tel: <phone>+1 508 495 2215</phone>; fax: <fax>+1 508 495 2393</fax>; e-mail: <email>tim.sheehan@noaa.gov</email>.</corresp></author-notes><pub-date pub-type="ppub"><month>4</month><year>2010</year></pub-date><pub-date pub-type="epub"><day>11</day><month>11</month><year>2009</year></pub-date><volume>67</volume><issue>3</issue><fpage>537</fpage><lpage>550</lpage><history><date date-type="received"><day>5</day><month>3</month><year>2009</year></date><date date-type="accepted"><day>4</day><month>10</month><year>2009</year></date></history><copyright-statement>© 2009 International Council for the Exploration of the Sea. Published by Oxford Journals. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org</copyright-statement><copyright-year>2010</copyright-year><abstract><p><disp-quote><p>Sheehan, T. F., Legault, C. M., King, T. L., and Spidle, A. P. 2010. Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest. – ICES Journal of Marine Science, 67: 537–550.</p></disp-quote>A multistock Atlantic salmon (<italic>Salmo salar</italic>) fishery operates off the coast of West Greenland and harvests fish of North American and European origin. Annual landings peaked in 1971 at 2700 t, but declined to 22 t in 2003. Biological data are collected to characterize the catch and its stock composition. Multilocus genotypes, generated via microsatellite DNA analysis, are used to derive statistics on continent of origin and less accurate finer-scale assignments. We developed a probabilistic-based genetic assignment (PGA) model to estimate the contribution of salmon from individual North American rivers in the 2000–2003 West Greenland catch. Uncertainty associated with finer-scale assignments is addressed by incorporating estimated misclassification rates and by reporting results as distributions generated via Monte Carlo resampling. US-origin fish represented ∼1% (by number) of the salmon harvested at West Greenland during the years 2000–2003. The resulting loss of spawners to this stock complex was approximately half the estimated adult returns in 2001, but was below 4% in the other 3 years. This is the first attempt to partition the US component of the West Greenland mixed-stock fishery to its finer parts. The approach can be used to identify the effects of fishing on individual stocks within any multistock complex where genetic samples of known origin are available.</p></abstract><kwd-group><kwd>Atlantic salmon</kwd><kwd>genetic stock identification</kwd><kwd>West Greenland</kwd></kwd-group></article-meta></front></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest</title></titleInfo><name type="personal"><namePart type="given">Timothy F.</namePart><namePart type="family">Sheehan</namePart><affiliation>United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA</affiliation><affiliation>E-mail: tim.sheehan@noaa.gov</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Christopher M.</namePart><namePart type="family">Legault</namePart><affiliation>United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Timothy L.</namePart><namePart type="family">King</namePart><affiliation>United States Geological Survey, Leetown Science Center, 11649 Leetown Road, Leetown, WV 25430, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Adrian P.</namePart><namePart type="family">Spidle</namePart><affiliation>Northwest Indian Fisheries Commission, 6730 Martin Way East, Olympia, WA 98512, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="research-article"></genre><originInfo><publisher>Oxford University Press</publisher><dateIssued encoding="w3cdtf">2010-04</dateIssued><dateCreated encoding="w3cdtf">2009-11-11</dateCreated><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract>Sheehan, T. F., Legault, C. M., King, T. L., and Spidle, A. P. 2010. Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest. ICES Journal of Marine Science, 67: 537550. A multistock Atlantic salmon (Salmo salar) fishery operates off the coast of West Greenland and harvests fish of North American and European origin. Annual landings peaked in 1971 at 2700 t, but declined to 22 t in 2003. Biological data are collected to characterize the catch and its stock composition. Multilocus genotypes, generated via microsatellite DNA analysis, are used to derive statistics on continent of origin and less accurate finer-scale assignments. We developed a probabilistic-based genetic assignment (PGA) model to estimate the contribution of salmon from individual North American rivers in the 20002003 West Greenland catch. Uncertainty associated with finer-scale assignments is addressed by incorporating estimated misclassification rates and by reporting results as distributions generated via Monte Carlo resampling. US-origin fish represented 1 (by number) of the salmon harvested at West Greenland during the years 20002003. The resulting loss of spawners to this stock complex was approximately half the estimated adult returns in 2001, but was below 4 in the other 3 years. This is the first attempt to partition the US component of the West Greenland mixed-stock fishery to its finer parts. The approach can be used to identify the effects of fishing on individual stocks within any multistock complex where genetic samples of known origin are available.</abstract><subject><genre>keywords</genre><topic>Atlantic salmon</topic><topic>genetic stock identification</topic><topic>West Greenland</topic></subject><relatedItem type="host"><titleInfo><title>ICES Journal of Marine Science</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">1054-3139</identifier><identifier type="eISSN">1095-9289</identifier><identifier type="PublisherID">icesjms</identifier><identifier type="PublisherID-hwp">icesjms</identifier><part><date>2010</date><detail type="volume"><caption>vol.</caption><number>67</number></detail><detail type="issue"><caption>no.</caption><number>3</number></detail><extent unit="pages"><start>537</start><end>550</end></extent></part></relatedItem><identifier type="istex">CC021698FBA66ABC6F1190F7DA59197F694BEF1B</identifier><identifier type="DOI">10.1093/icesjms/fsp247</identifier><identifier type="ArticleID">fsp247</identifier><accessCondition type="use and reproduction" contentType="copyright">2009 International Council for the Exploration of the Sea. Published by Oxford Journals. All rights reserved. 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