High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation
Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few dist...
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| creator | Speller, Camilla F Hauser, Lorenz Lepofsky, Dana Moore, Jason Rodrigues, Antonia T Moss, Madonna L McKechnie, Iain Yang, Dongya Y |
| description | Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often |
| doi_str_mv | 10.1371/journal.pone.0051122 |
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Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0051122</identifier><identifier>PMID: 23226474</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Anthropogenic factors ; Archaeology ; Bioinformatics ; Biology ; Bone and Bones - metabolism ; Bones ; Clupea ; Clupea pallasii ; Coastal ecosystems ; Coasts ; Commercial fishing ; Conservation ; Conservation of Natural Resources ; Deoxyribonucleic acid ; Differentiation ; DNA ; DNA - genetics ; DNA, Mitochondrial - genetics ; Ecology ; Ecosystem biology ; Feasibility studies ; Fish populations ; Fisheries ; Fisheries management ; Fishery management ; Fishes - genetics ; Fishing ; Fossils ; Genetic diversity ; Genetic Markers ; Genetic research ; Geography ; Haplotypes ; Haplotypes - genetics ; Historical structures ; Information management ; Laboratories ; Linux ; Local population ; Management ; Marine ecosystems ; Metapopulations ; Microsatellite Repeats ; Microsatellites ; Mitochondrial DNA ; Phylogeography ; Polymorphism, Single Nucleotide - genetics ; Population ; Population genetics ; Population structure ; Populations ; Protection and preservation ; Science ; Single-nucleotide polymorphism ; Social and Behavioral Sciences</subject><ispartof>PloS one, 2012-11, Vol.7 (11), p.e51122-e51122</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Speller et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2012 Speller et al 2012 Speller et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a781t-2d258cab47c83ccc09aa41059c13aa1198bf67d4b996c0ed1e0ec69c2a02bad73</citedby><cites>FETCH-LOGICAL-a781t-2d258cab47c83ccc09aa41059c13aa1198bf67d4b996c0ed1e0ec69c2a02bad73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511397/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511397/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23226474$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Orlando, Ludovic</contributor><creatorcontrib>Speller, Camilla F</creatorcontrib><creatorcontrib>Hauser, Lorenz</creatorcontrib><creatorcontrib>Lepofsky, Dana</creatorcontrib><creatorcontrib>Moore, Jason</creatorcontrib><creatorcontrib>Rodrigues, Antonia T</creatorcontrib><creatorcontrib>Moss, Madonna L</creatorcontrib><creatorcontrib>McKechnie, Iain</creatorcontrib><creatorcontrib>Yang, Dongya Y</creatorcontrib><title>High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation.</description><subject>Analysis</subject><subject>Animals</subject><subject>Anthropogenic factors</subject><subject>Archaeology</subject><subject>Bioinformatics</subject><subject>Biology</subject><subject>Bone and Bones - metabolism</subject><subject>Bones</subject><subject>Clupea</subject><subject>Clupea pallasii</subject><subject>Coastal ecosystems</subject><subject>Coasts</subject><subject>Commercial fishing</subject><subject>Conservation</subject><subject>Conservation of Natural Resources</subject><subject>Deoxyribonucleic acid</subject><subject>Differentiation</subject><subject>DNA</subject><subject>DNA - genetics</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Ecology</subject><subject>Ecosystem biology</subject><subject>Feasibility studies</subject><subject>Fish populations</subject><subject>Fisheries</subject><subject>Fisheries management</subject><subject>Fishery management</subject><subject>Fishes - genetics</subject><subject>Fishing</subject><subject>Fossils</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Genetic research</subject><subject>Geography</subject><subject>Haplotypes</subject><subject>Haplotypes - genetics</subject><subject>Historical structures</subject><subject>Information management</subject><subject>Laboratories</subject><subject>Linux</subject><subject>Local population</subject><subject>Management</subject><subject>Marine ecosystems</subject><subject>Metapopulations</subject><subject>Microsatellite Repeats</subject><subject>Microsatellites</subject><subject>Mitochondrial DNA</subject><subject>Phylogeography</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Population</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Populations</subject><subject>Protection and preservation</subject><subject>Science</subject><subject>Single-nucleotide polymorphism</subject><subject>Social and Behavioral Sciences</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk1uL1DAUx4so7jr6DUQDgujDjLn0MnkRhvWyA4sL3l7DaZp2srTJbNIu-u09dbrLVPZB-pCS8zv_c8tJkueMrpgo2LsrPwQH7WrvnVlRmjHG-YPklEnBlzmn4uHR_0nyJMYrhMQ6zx8nJ1xwnqdFepq4c9vsyN73xvUWWlL7QIZoXUM-fNmQOviOgNMWrWRnQhgNJQaMpPfEOqQ70vnKBEdqG5GwaOrAQWO60QdcRbR30YQb6K13T5NHNbTRPJvORfLj08fvZ-fLi8vP27PNxRKKNeuXvOLZWkOZFnottNZUAqSMZlIzAcCYXJd1XlRpKWWuqamYoUbnUnOgvISqEIvk5UF33_qoplZFxUSGKgIPJLYHovJwpfbBdhB-Kw9W_b3woVEQeqtbo0zKaZ3xkqUZw6YxyXWqi1qaVNMMG4pa76doQ9mZSmPlAdqZ6Nzi7E41_kZhOkzIMd03k0Dw14OJveps1KZtwRk_YN5cFIhmOMpF8uof9P7qJqoBLGAcFMbVo6japEUupcizMe_VPRR-leksjs3UFu9nDm9nDsj05lffwBCj2n77-v_s5c85-_qI3Rlo-1307TA-mTgH0wOog48xmPquyYyqcS1uu6HGtVDTWqDbi-MB3Tnd7oH4A4wmCC8</recordid><startdate>20121130</startdate><enddate>20121130</enddate><creator>Speller, Camilla F</creator><creator>Hauser, Lorenz</creator><creator>Lepofsky, Dana</creator><creator>Moore, Jason</creator><creator>Rodrigues, Antonia T</creator><creator>Moss, Madonna L</creator><creator>McKechnie, Iain</creator><creator>Yang, Dongya Y</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20121130</creationdate><title>High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation</title><author>Speller, Camilla F ; Hauser, Lorenz ; Lepofsky, Dana ; Moore, Jason ; Rodrigues, Antonia T ; Moss, Madonna L ; McKechnie, Iain ; Yang, Dongya Y</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a781t-2d258cab47c83ccc09aa41059c13aa1198bf67d4b996c0ed1e0ec69c2a02bad73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Anthropogenic factors</topic><topic>Archaeology</topic><topic>Bioinformatics</topic><topic>Biology</topic><topic>Bone and Bones - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Speller, Camilla F</au><au>Hauser, Lorenz</au><au>Lepofsky, Dana</au><au>Moore, Jason</au><au>Rodrigues, Antonia T</au><au>Moss, Madonna L</au><au>McKechnie, Iain</au><au>Yang, Dongya Y</au><au>Orlando, Ludovic</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-11-30</date><risdate>2012</risdate><volume>7</volume><issue>11</issue><spage>e51122</spage><epage>e51122</epage><pages>e51122-e51122</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23226474</pmid><doi>10.1371/journal.pone.0051122</doi><tpages>e51122</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2012-11, Vol.7 (11), p.e51122-e51122 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1351053135 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Animals Anthropogenic factors Archaeology Bioinformatics Biology Bone and Bones - metabolism Bones Clupea Clupea pallasii Coastal ecosystems Coasts Commercial fishing Conservation Conservation of Natural Resources Deoxyribonucleic acid Differentiation DNA DNA - genetics DNA, Mitochondrial - genetics Ecology Ecosystem biology Feasibility studies Fish populations Fisheries Fisheries management Fishery management Fishes - genetics Fishing Fossils Genetic diversity Genetic Markers Genetic research Geography Haplotypes Haplotypes - genetics Historical structures Information management Laboratories Linux Local population Management Marine ecosystems Metapopulations Microsatellite Repeats Microsatellites Mitochondrial DNA Phylogeography Polymorphism, Single Nucleotide - genetics Population Population genetics Population structure Populations Protection and preservation Science Single-nucleotide polymorphism Social and Behavioral Sciences |
| title | High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-18T19%3A59%3A45IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=High%20potential%20for%20using%20DNA%20from%20ancient%20herring%20bones%20to%20inform%20modern%20fisheries%20management%20and%20conservation&rft.jtitle=PloS%20one&rft.au=Speller,%20Camilla%20F&rft.date=2012-11-30&rft.volume=7&rft.issue=11&rft.spage=e51122&rft.epage=e51122&rft.pages=e51122-e51122&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0051122&rft_dat=%3Cgale_plos_%3EA476993656%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1351053135&rft_id=info:pmid/23226474&rft_galeid=A476993656&rft_doaj_id=oai_doaj_org_article_e420f52b1451474192c4c7f9e4c05866&rfr_iscdi=true |