The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA
Identifieur interne : 000006 ( Pmc/Curation ); précédent : 000005; suivant : 000007The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA
Auteurs : Andrea Splendiani [Italie] ; Tatiana Fioravanti [Italie] ; Massimo Giovannotti [Italie] ; Alessandra Negri [Italie] ; Paolo Ruggeri [Italie] ; Luigi Olivieri [Italie] ; Paola Nisi Cerioni [Italie] ; Massimo Lorenzoni [Italie] ; Vincenzo Caputo Barucchi [Italie]Source :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
In this pilot study for the first time, ancient DNA has been extracted from bone remains of
Url:
DOI: 10.1371/journal.pone.0157975
PubMed: 27331397
PubMed Central: 4917132
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PMC:4917132Le document en format XML
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type="wicri:source">PMC</idno><idno type="pmid">27331397</idno><idno type="pmc">4917132</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917132</idno><idno type="RBID">PMC:4917132</idno><idno type="doi">10.1371/journal.pone.0157975</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000006</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000006</idno><idno type="wicri:Area/Pmc/Curation">000006</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000006</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA</title><author><name sortKey="Splendiani, Andrea" sort="Splendiani, Andrea" uniqKey="Splendiani A" first="Andrea" last="Splendiani">Andrea Splendiani</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Dipartimento di 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sortKey="Giovannotti, Massimo" sort="Giovannotti, Massimo" uniqKey="Giovannotti M" first="Massimo" last="Giovannotti">Massimo Giovannotti</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona</wicri:regionArea></affiliation></author><author><name sortKey="Negri, Alessandra" sort="Negri, Alessandra" uniqKey="Negri A" first="Alessandra" last="Negri">Alessandra Negri</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona</wicri:regionArea></affiliation></author><author><name sortKey="Ruggeri, Paolo" sort="Ruggeri, Paolo" uniqKey="Ruggeri P" first="Paolo" last="Ruggeri">Paolo Ruggeri</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona</wicri:regionArea></affiliation></author><author><name sortKey="Olivieri, Luigi" sort="Olivieri, Luigi" uniqKey="Olivieri L" first="Luigi" last="Olivieri">Luigi Olivieri</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona</wicri:regionArea></affiliation></author><author><name sortKey="Nisi Cerioni, Paola" sort="Nisi Cerioni, Paola" uniqKey="Nisi Cerioni P" first="Paola" last="Nisi Cerioni">Paola Nisi Cerioni</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona</wicri:regionArea></affiliation></author><author><name sortKey="Lorenzoni, Massimo" sort="Lorenzoni, Massimo" uniqKey="Lorenzoni M" first="Massimo" last="Lorenzoni">Massimo Lorenzoni</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 06123 Perugia, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 06123 Perugia</wicri:regionArea></affiliation></author><author><name sortKey="Caputo Barucchi, Vincenzo" sort="Caputo Barucchi, Vincenzo" uniqKey="Caputo Barucchi V" first="Vincenzo" last="Caputo Barucchi">Vincenzo Caputo Barucchi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Istituto Italiano di Paleontologia Umana, Is.I.P.U., Convitto Nazionale Regina Margherita, Piazza Ruggero Bonghi 2. 03012 Anagni, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto Italiano di Paleontologia Umana, Is.I.P.U., Convitto Nazionale Regina Margherita, Piazza Ruggero Bonghi 2. 03012 Anagni</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In this pilot study for the first time, ancient DNA has been extracted from bone remains of <italic>Salmo trutta</italic>. These samples were from a stratigraphic succession located in a coastal cave of Calabria (southern Italy) inhabited by humans from upper Palaeolithic to historical times. Seven pairs of primers were used to PCR-amplify and sequence from 128 to 410 bp of the mtDNA control region of eleven samples. Three haplotypes were observed: two (ADcs-1 and MEcs-1) already described in rivers from the Italian peninsula; one (ATcs-33) belonging to the southern Atlantic clade of the AT <italic>Salmo trutta</italic> mtDNA lineage (<italic>sensu</italic> Bernatchez). The prehistoric occurrence of this latter haplotype in the water courses of the Italian peninsula has been detected for the first time in this study. Finally, we observed a correspondence between frequency of trout remains and variation in haplotype diversity that we related with ecological and demographic changes resulting from a period of rapid cooling known as the Younger Dryas.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cohen, K" uniqKey="Cohen K">K Cohen</name></author><author><name sortKey="Finney, S" uniqKey="Finney S">S Finney</name></author><author><name sortKey="Gibbard, P" uniqKey="Gibbard P">P Gibbard</name></author><author><name sortKey="Fan, J" uniqKey="Fan J">J Fan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hewitt, Gm" uniqKey="Hewitt G">GM Hewitt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hewitt, Gm" uniqKey="Hewitt G">GM Hewitt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Bruyn, M" uniqKey="De Bruyn M">M de 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27331397</article-id><article-id pub-id-type="pmc">4917132</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0157975</article-id><article-id pub-id-type="publisher-id">PONE-D-15-54894</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Evolutionary Biology</subject><subj-group><subject>Population Genetics</subject><subj-group><subject>Haplotypes</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Population Genetics</subject><subj-group><subject>Haplotypes</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Population Biology</subject><subj-group><subject>Population Genetics</subject><subj-group><subject>Haplotypes</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Earth Sciences</subject><subj-group><subject>Atmospheric Science</subject><subj-group><subject>Climatology</subject><subj-group><subject>Paleoclimatology</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Paleontology</subject><subj-group><subject>Paleoclimatology</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Earth Sciences</subject><subj-group><subject>Paleontology</subject><subj-group><subject>Paleoclimatology</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Animals</subject><subj-group><subject>Vertebrates</subject><subj-group><subject>Fishes</subject><subj-group><subject>Osteichthyes</subject><subj-group><subject>Trout</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>DNA</subject><subj-group><subject>Forms of DNA</subject><subj-group><subject>Mitochondrial DNA</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Nucleic acids</subject><subj-group><subject>DNA</subject><subj-group><subject>Forms of DNA</subject><subj-group><subject>Mitochondrial DNA</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Paleontology</subject><subj-group><subject>Paleogenetics</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Earth Sciences</subject><subj-group><subject>Paleontology</subject><subj-group><subject>Paleogenetics</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Animals</subject><subj-group><subject>Vertebrates</subject><subj-group><subject>Fishes</subject><subj-group><subject>Freshwater Fish</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Artificial Gene Amplification and Extension</subject><subj-group><subject>Polymerase Chain Reaction</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Artificial Gene Amplification and Extension</subject><subj-group><subject>Polymerase Chain Reaction</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Earth Sciences</subject><subj-group><subject>Atmospheric Science</subject><subj-group><subject>Climatology</subject><subj-group><subject>Climate Change</subject></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA</article-title><alt-title alt-title-type="running-head">Pelistocene-Holocene mtDNA Variability in Brown Trout</alt-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Splendiani</surname><given-names>Andrea</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Fioravanti</surname><given-names>Tatiana</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Giovannotti</surname><given-names>Massimo</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Negri</surname><given-names>Alessandra</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ruggeri</surname><given-names>Paolo</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Olivieri</surname><given-names>Luigi</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Nisi Cerioni</surname><given-names>Paola</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lorenzoni</surname><given-names>Massimo</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Caputo Barucchi</surname><given-names>Vincenzo</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff003"><sup>3</sup></xref><xref ref-type="corresp" rid="cor001">*</xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy</addr-line></aff><aff id="aff002"><label>2</label><addr-line>Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 06123 Perugia, Italy</addr-line></aff><aff id="aff003"><label>3</label><addr-line>Istituto Italiano di Paleontologia Umana, Is.I.P.U., Convitto Nazionale Regina Margherita, Piazza Ruggero Bonghi 2. 03012 Anagni, Italy</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Consuegra</surname><given-names>Sofia</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Swansea University, UNITED KINGDOM</addr-line></aff><author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: AS VCB. Performed the experiments: AS TF LO PNC. Analyzed the data: AS TF AN PR. Contributed reagents/materials/analysis tools: VCB MG. Wrote the paper: AS TF AN MG PR ML VCB.</p></fn><corresp id="cor001">* E-mail: <email>v.caputo@univpm.it</email></corresp></author-notes><pub-date pub-type="epub"><day>22</day><month>6</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>11</volume><issue>6</issue><elocation-id>e0157975</elocation-id><history><date date-type="received"><day>21</day><month>12</month><year>2015</year></date><date date-type="accepted"><day>8</day><month>6</month><year>2016</year></date></history><permissions><copyright-statement>© 2016 Splendiani et al</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Splendiani et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="pone.0157975.pdf"></self-uri><abstract><p>In this pilot study for the first time, ancient DNA has been extracted from bone remains of <italic>Salmo trutta</italic>. These samples were from a stratigraphic succession located in a coastal cave of Calabria (southern Italy) inhabited by humans from upper Palaeolithic to historical times. Seven pairs of primers were used to PCR-amplify and sequence from 128 to 410 bp of the mtDNA control region of eleven samples. Three haplotypes were observed: two (ADcs-1 and MEcs-1) already described in rivers from the Italian peninsula; one (ATcs-33) belonging to the southern Atlantic clade of the AT <italic>Salmo trutta</italic> mtDNA lineage (<italic>sensu</italic> Bernatchez). The prehistoric occurrence of this latter haplotype in the water courses of the Italian peninsula has been detected for the first time in this study. Finally, we observed a correspondence between frequency of trout remains and variation in haplotype diversity that we related with ecological and demographic changes resulting from a period of rapid cooling known as the Younger Dryas.</p></abstract><funding-group><funding-statement>This work was financed by: 1) Università Politecnica delle Marche (grant number 2014/472 “Divergenza genetica e speciazione in vertebrati ectotermi” awarded to Vincenzo Caputo Barucchi) <ext-link ext-link-type="uri" xlink:href="http://www.univpm.it/Entra/Engine/RAServePG.php/P/250010010603/T/Universita-Politecnica-delle-Marche">http://www.univpm.it/Entra/Engine/RAServePG.php/P/250010010603/T/Universita-Politecnica-delle-Marche</ext-link>; 2) Università Politecnica delle Marche grant number 2015/342 "Aspetti dell'evoluzione del genoma in Vertebrati ectotermi (Pesci ossei, Rettili squamati)" awarded to Massimo Giovannotti (Ricerca scientifica d'ateneo 2015; and 3) Prog n. 85 RFO2014 "SAPROPEL AND THE MEDITERRANEAN CLIMATE" awarded to Alessandra Negri.</funding-statement></funding-group><counts><fig-count count="5"></fig-count><table-count count="4"></table-count><page-count count="15"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All relevant data are within the paper and its Supporting Information files.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All relevant data are within the paper and its Supporting Information files.</p></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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