Detection of human adaptation during the past 2000 years
Identifieur interne : 000A23 ( Pmc/Checkpoint ); précédent : 000A22; suivant : 000A24Detection of human adaptation during the past 2000 years
Auteurs : Yair Field [États-Unis] ; Evan A. Boyle [États-Unis] ; Natalie Telis [États-Unis] ; Ziyue Gao [États-Unis] ; Kyle J. Gaulton [États-Unis, Royaume-Uni] ; David Golan [États-Unis] ; Loic Yengo [France, Australie] ; Ghislain Rocheleau [France] ; Philippe Froguel [France, Royaume-Uni] ; Mark I. Mccarthy [Royaume-Uni] ; Jonathan K. Pritchard [États-Unis]Source :
- Science (New York, N.Y.) [ 0036-8075 ] ; 2016.
Abstract
Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.
Url:
DOI: 10.1126/science.aag0776
PubMed: 27738015
PubMed Central: 5182071
Affiliations:
- Australie, France, Royaume-Uni, États-Unis
- Angleterre, Californie, Grand Londres, Hauts-de-France, Nord-Pas-de-Calais, Oxfordshire
- Lille, Londres, Oxford
- Université d'Oxford
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Gaulton</name><affiliation wicri:level="2"><nlm:aff id="A1">Department of Genetics, Stanford University, Stanford, CA 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, CA 94305</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="A4">Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford</wicri:regionArea><placeName><settlement type="city">Oxford</settlement><region type="country">Angleterre</region><region type="comté" nuts="2">Oxfordshire</region><settlement type="city">Oxford</settlement></placeName><orgName type="university">Université d'Oxford</orgName></affiliation></author><author><name sortKey="Golan, David" sort="Golan, David" uniqKey="Golan D" first="David" last="Golan">David Golan</name><affiliation wicri:level="2"><nlm:aff id="A1">Department of Genetics, Stanford University, Stanford, CA 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, CA 94305</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Yengo, Loic" sort="Yengo, Loic" uniqKey="Yengo L" first="Loic" last="Yengo">Loic Yengo</name><affiliation wicri:level="3"><nlm:aff id="A5">Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Lille</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A6">Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Institute for Molecular Bioscience, The University of Queensland, Brisbane</wicri:regionArea><wicri:noRegion>Brisbane</wicri:noRegion></affiliation></author><author><name sortKey="Rocheleau, Ghislain" sort="Rocheleau, Ghislain" uniqKey="Rocheleau G" first="Ghislain" last="Rocheleau">Ghislain Rocheleau</name><affiliation wicri:level="1"><nlm:aff id="A5">Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille</wicri:regionArea><wicri:noRegion>59000 Lille</wicri:noRegion><wicri:noRegion>59000 Lille</wicri:noRegion></affiliation></author><author><name sortKey="Froguel, Philippe" sort="Froguel, Philippe" uniqKey="Froguel P" first="Philippe" last="Froguel">Philippe Froguel</name><affiliation wicri:level="1"><nlm:aff id="A5">Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille</wicri:regionArea><wicri:noRegion>59000 Lille</wicri:noRegion><wicri:noRegion>59000 Lille</wicri:noRegion></affiliation><affiliation wicri:level="3"><nlm:aff id="A7">Imperial College, Department of Genomics of Common Disease, London Hammersmith Hospital, London, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Imperial College, Department of Genomics of Common Disease, London Hammersmith Hospital, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Mccarthy, Mark I" sort="Mccarthy, Mark I" uniqKey="Mccarthy M" first="Mark I." last="Mccarthy">Mark I. Mccarthy</name><affiliation wicri:level="4"><nlm:aff id="A4">Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford</wicri:regionArea><placeName><settlement type="city">Oxford</settlement><region type="country">Angleterre</region><region type="comté" nuts="2">Oxfordshire</region><settlement type="city">Oxford</settlement></placeName><orgName type="university">Université d'Oxford</orgName></affiliation></author><author><name sortKey="Pritchard, Jonathan K" sort="Pritchard, Jonathan K" uniqKey="Pritchard J" first="Jonathan K." last="Pritchard">Jonathan K. Pritchard</name><affiliation wicri:level="2"><nlm:aff id="A1">Department of Genetics, Stanford University, Stanford, CA 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Stanford University, Stanford, CA 94305</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="A2">Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="A8">Department of Biology, Stanford University, Stanford, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">Science (New York, N.Y.)</title><idno type="ISSN">0036-8075</idno><idno type="eISSN">1095-9203</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 id="P1">Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">0404511</journal-id><journal-id journal-id-type="pubmed-jr-id">7473</journal-id><journal-id journal-id-type="nlm-ta">Science</journal-id><journal-id journal-id-type="iso-abbrev">Science</journal-id><journal-title-group><journal-title>Science (New York, N.Y.)</journal-title></journal-title-group><issn pub-type="ppub">0036-8075</issn><issn pub-type="epub">1095-9203</issn></journal-meta><article-meta><article-id pub-id-type="pmid">27738015</article-id><article-id pub-id-type="pmc">5182071</article-id><article-id pub-id-type="doi">10.1126/science.aag0776</article-id><article-id pub-id-type="manuscript">NIHMS835307</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Detection of human adaptation during the past 2000 years</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Field</surname><given-names>Yair</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref><xref rid="FN2" ref-type="author-notes">*</xref><xref rid="FN1" ref-type="author-notes">†</xref></contrib><contrib contrib-type="author"><name><surname>Boyle</surname><given-names>Evan A</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref rid="FN2" ref-type="author-notes">*</xref></contrib><contrib contrib-type="author"><name><surname>Telis</surname><given-names>Natalie</given-names></name><xref ref-type="aff" rid="A3">3</xref><xref rid="FN2" ref-type="author-notes">*</xref></contrib><contrib contrib-type="author"><name><surname>Gao</surname><given-names>Ziyue</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Gaulton</surname><given-names>Kyle J.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Golan</surname><given-names>David</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Yengo</surname><given-names>Loic</given-names></name><xref ref-type="aff" rid="A5">5</xref><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Rocheleau</surname><given-names>Ghislain</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Froguel</surname><given-names>Philippe</given-names></name><xref ref-type="aff" rid="A5">5</xref><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>McCarthy</surname><given-names>Mark I.</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Pritchard</surname><given-names>Jonathan K.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref><xref ref-type="aff" rid="A8">8</xref><xref rid="FN1" ref-type="author-notes">†</xref></contrib></contrib-group><aff id="A1"><label>1</label>Department of Genetics, Stanford University, Stanford, CA 94305, USA</aff><aff id="A2"><label>2</label>Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA</aff><aff id="A3"><label>3</label>Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA</aff><aff id="A4"><label>4</label>Wellcome Trust Center for Human Genetics, and Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK</aff><aff id="A5"><label>5</label>Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199–EGID, F-59000 Lille, France</aff><aff id="A6"><label>6</label>Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia</aff><aff id="A7"><label>7</label>Imperial College, Department of Genomics of Common Disease, London Hammersmith Hospital, London, UK</aff><aff id="A8"><label>8</label>Department of Biology, Stanford University, Stanford, CA, USA</aff><author-notes><corresp id="FN1"><label>†</label>Corresponding author. <email>yairf@stanford.edu</email> (Y.F.); <email>pritch@stanford.edu</email> (J.K.P.)</corresp><fn id="FN2" fn-type="equal"><label>*</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="nihms-submitted"><day>12</day><month>12</month><year>2016</year></pub-date><pub-date pub-type="epub"><day>13</day><month>10</month><year>2016</year></pub-date><pub-date pub-type="ppub"><day>11</day><month>11</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>23</day><month>12</month><year>2016</year></pub-date><volume>354</volume><issue>6313</issue><fpage>760</fpage><lpage>764</lpage><pmc-comment>elocation-id from pubmed: 10.1126/science.aag0776</pmc-comment>
<abstract><p id="P1">Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes. For polygenic adaptation, we find that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we identify shifts associated with other complex traits, suggesting that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.</p></abstract></article-meta></front></pmc><affiliations><list><country><li>Australie</li><li>France</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Californie</li><li>Grand Londres</li><li>Hauts-de-France</li><li>Nord-Pas-de-Calais</li><li>Oxfordshire</li></region><settlement><li>Lille</li><li>Londres</li><li>Oxford</li></settlement><orgName><li>Université d'Oxford</li></orgName></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Field, Yair" sort="Field, Yair" uniqKey="Field Y" first="Yair" last="Field">Yair Field</name></region><name sortKey="Boyle, Evan A" sort="Boyle, Evan A" uniqKey="Boyle E" first="Evan A" last="Boyle">Evan A. Boyle</name><name sortKey="Field, Yair" sort="Field, Yair" uniqKey="Field Y" first="Yair" last="Field">Yair Field</name><name sortKey="Gao, Ziyue" sort="Gao, Ziyue" uniqKey="Gao Z" first="Ziyue" last="Gao">Ziyue Gao</name><name sortKey="Gao, Ziyue" sort="Gao, Ziyue" uniqKey="Gao Z" first="Ziyue" last="Gao">Ziyue Gao</name><name sortKey="Gaulton, Kyle J" sort="Gaulton, Kyle J" uniqKey="Gaulton K" first="Kyle J." last="Gaulton">Kyle J. Gaulton</name><name sortKey="Golan, David" sort="Golan, David" uniqKey="Golan D" first="David" last="Golan">David Golan</name><name sortKey="Pritchard, Jonathan K" sort="Pritchard, Jonathan K" uniqKey="Pritchard J" first="Jonathan K." last="Pritchard">Jonathan K. Pritchard</name><name sortKey="Pritchard, Jonathan K" sort="Pritchard, Jonathan K" uniqKey="Pritchard J" first="Jonathan K." last="Pritchard">Jonathan K. Pritchard</name><name sortKey="Pritchard, Jonathan K" sort="Pritchard, Jonathan K" uniqKey="Pritchard J" first="Jonathan K." last="Pritchard">Jonathan K. Pritchard</name><name sortKey="Telis, Natalie" sort="Telis, Natalie" uniqKey="Telis N" first="Natalie" last="Telis">Natalie Telis</name></country><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Gaulton, Kyle J" sort="Gaulton, Kyle J" uniqKey="Gaulton K" first="Kyle J." last="Gaulton">Kyle J. Gaulton</name></region><name sortKey="Froguel, Philippe" sort="Froguel, Philippe" uniqKey="Froguel P" first="Philippe" last="Froguel">Philippe Froguel</name><name sortKey="Mccarthy, Mark I" sort="Mccarthy, Mark I" uniqKey="Mccarthy M" first="Mark I." last="Mccarthy">Mark I. Mccarthy</name></country><country name="France"><region name="Hauts-de-France"><name sortKey="Yengo, Loic" sort="Yengo, Loic" uniqKey="Yengo L" first="Loic" last="Yengo">Loic Yengo</name></region><name sortKey="Froguel, Philippe" sort="Froguel, Philippe" uniqKey="Froguel P" first="Philippe" last="Froguel">Philippe Froguel</name><name sortKey="Rocheleau, Ghislain" sort="Rocheleau, Ghislain" uniqKey="Rocheleau G" first="Ghislain" last="Rocheleau">Ghislain Rocheleau</name></country><country name="Australie"><noRegion><name sortKey="Yengo, Loic" sort="Yengo, Loic" uniqKey="Yengo L" first="Loic" last="Yengo">Loic Yengo</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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