<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-01544803</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-17T15:33:19+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Evolutionary analyses of non-genealogical bonds produced by introgressive descent</title>
            <author role="aut">
              <persName>
                <forename type="first">Eric</forename>
                <surname>Bapteste</surname>
              </persName>
              <email type="md5">179f9bee5d53636931acdd2091848e5d</email>
              <email type="domain">gmail.com</email>
              <idno type="idhal" notation="string">eric-bapteste</idno>
              <idno type="idhal" notation="numeric">740361</idno>
              <idno type="halauthorid" notation="string">52006-740361</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-1966-1215</idno>
              <idno type="IDREF">https://www.idref.fr/08148724X</idno>
              <idno type="VIAF">https://viaf.org/viaf/214199413</idno>
              <idno type="ISNI">http://isni.org/isni/0000000358987234</idno>
              <affiliation ref="#struct-495435"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Philippe</forename>
                <surname>Lopez</surname>
              </persName>
              <email type="md5">9f24217719c1301029b00555565087c3</email>
              <email type="domain">upmc.fr</email>
              <idno type="idhal" notation="string">philippe-lopez</idno>
              <idno type="idhal" notation="numeric">13940</idno>
              <idno type="halauthorid" notation="string">12984-13940</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-3410-9744</idno>
              <idno type="IDREF">https://www.idref.fr/180850075</idno>
              <affiliation ref="#struct-495435"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Frederic</forename>
                <surname>Bouchard</surname>
              </persName>
              <idno type="halauthorid">1185604-0</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Fernando</forename>
                <surname>Baquero</surname>
              </persName>
              <idno type="halauthorid">991776-0</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">James O.</forename>
                <surname>Mcinerney</surname>
              </persName>
              <idno type="halauthorid">1185594-0</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Richard M.</forename>
                <surname>Burian</surname>
              </persName>
              <idno type="halauthorid">692820-0</idno>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Charlotte</forename>
                <surname>Mazalérat</surname>
              </persName>
              <email type="md5">360be9468dfc49ea1ede7731d130b534</email>
              <email type="domain">upmc.fr.invalid</email>
            </editor>
            <funder>Social Sciences and Humanities Research Council of Canada</funder>
            <funder> European Union [PAR-241476, EvoTAR-282004]</funder>
            <funder> Carlos III Institute Research Fund [FIS-PI10-02588]</funder>
            <funder> Science Foundation Ireland Research Frontiers Programme [09/RFP/EOB2510]</funder>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2017-06-22 10:49:11</date>
              <date type="whenModified">2023-09-06 10:42:12</date>
              <date type="whenReleased">2017-06-22 10:49:11</date>
              <date type="whenProduced">2012-11</date>
              <ref type="externalLink" target="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494893"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="531834">
                <persName>
                  <forename>Charlotte</forename>
                  <surname>Mazalérat</surname>
                </persName>
                <email type="md5">360be9468dfc49ea1ede7731d130b534</email>
                <email type="domain">upmc.fr.invalid</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-01544803</idno>
            <idno type="halUri">https://hal.science/hal-01544803</idno>
            <idno type="halBibtex">bapteste:hal-01544803</idno>
            <idno type="halRefHtml">&lt;i&gt;Proceedings of the National Academy of Sciences of the United States of America&lt;/i&gt;, 2012, 109 (45), pp.18266-18272. &lt;a target="_blank" href="https://dx.doi.org/10.1073/pnas.1206541109"&gt;&amp;#x27E8;10.1073/pnas.1206541109&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (45), pp.18266-18272. &amp;#x27E8;10.1073/pnas.1206541109&amp;#x27E9;</idno>
            <availability status="restricted"/>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="UNICE">Université Nice Sophia Antipolis</idno>
            <idno type="stamp" n="UPMC" corresp="SORBONNE-UNIVERSITE">Université Pierre et Marie Curie</idno>
            <idno type="stamp" n="UNIV-AG">Université des Antilles</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="GIP-BE">GIP Bretagne Environnement</idno>
            <idno type="stamp" n="EVOLUTION_PARIS_SEINE" corresp="SORBONNE-UNIVERSITE">Evolution Paris Seine</idno>
            <idno type="stamp" n="EVOL_PARIS_SEINE-AIRE" corresp="EVOLUTION_PARIS_SEINE">Adaptation, Integration, Réticulation, Evolution</idno>
            <idno type="stamp" n="UPMC_POLE_4" corresp="UPMC">UPMC Pôle 4</idno>
            <idno type="stamp" n="UNIV-COTEDAZUR">Université Côte d'Azur</idno>
            <idno type="stamp" n="SORBONNE-UNIVERSITE">Sorbonne Université</idno>
            <idno type="stamp" n="SU-SCIENCES" corresp="SORBONNE-UNIVERSITE">Faculté des Sciences de Sorbonne Université</idno>
            <idno type="stamp" n="SU-TI">Sorbonne Université - Texte Intégral</idno>
            <idno type="stamp" n="ALLIANCE-SU"> Alliance Sorbonne Université</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Evolutionary analyses of non-genealogical bonds produced by introgressive descent</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Eric</forename>
                    <surname>Bapteste</surname>
                  </persName>
                  <email type="md5">179f9bee5d53636931acdd2091848e5d</email>
                  <email type="domain">gmail.com</email>
                  <idno type="idhal" notation="string">eric-bapteste</idno>
                  <idno type="idhal" notation="numeric">740361</idno>
                  <idno type="halauthorid" notation="string">52006-740361</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-1966-1215</idno>
                  <idno type="IDREF">https://www.idref.fr/08148724X</idno>
                  <idno type="VIAF">https://viaf.org/viaf/214199413</idno>
                  <idno type="ISNI">http://isni.org/isni/0000000358987234</idno>
                  <affiliation ref="#struct-495435"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Philippe</forename>
                    <surname>Lopez</surname>
                  </persName>
                  <email type="md5">9f24217719c1301029b00555565087c3</email>
                  <email type="domain">upmc.fr</email>
                  <idno type="idhal" notation="string">philippe-lopez</idno>
                  <idno type="idhal" notation="numeric">13940</idno>
                  <idno type="halauthorid" notation="string">12984-13940</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-3410-9744</idno>
                  <idno type="IDREF">https://www.idref.fr/180850075</idno>
                  <affiliation ref="#struct-495435"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Frederic</forename>
                    <surname>Bouchard</surname>
                  </persName>
                  <idno type="halauthorid">1185604-0</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Fernando</forename>
                    <surname>Baquero</surname>
                  </persName>
                  <idno type="halauthorid">991776-0</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">James O.</forename>
                    <surname>Mcinerney</surname>
                  </persName>
                  <idno type="halauthorid">1185594-0</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Richard M.</forename>
                    <surname>Burian</surname>
                  </persName>
                  <idno type="halauthorid">692820-0</idno>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">7969</idno>
                <idno type="issn">0027-8424</idno>
                <idno type="eissn">1091-6490</idno>
                <title level="j">Proceedings of the National Academy of Sciences of the United States of America</title>
                <imprint>
                  <publisher>National Academy of Sciences</publisher>
                  <biblScope unit="volume">109</biblScope>
                  <biblScope unit="issue">45</biblScope>
                  <biblScope unit="pp">18266-18272</biblScope>
                  <date type="datePub">2012-11</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1073/pnas.1206541109</idno>
              <idno type="pubmedcentral">PMC3494893</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en"> symbiosis</term>
                <term xml:lang="en"> network of life</term>
                <term xml:lang="en"> lateral gene transfer</term>
                <term xml:lang="en"> evolutionary transitions</term>
                <term xml:lang="en">biodiversity structure</term>
              </keywords>
              <classCode scheme="halDomain" n="sdv.bid">Life Sciences [q-bio]/Biodiversity</classCode>
              <classCode scheme="halTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halOldTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halTreeTypology" n="ART">Journal articles</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="researchteam" xml:id="struct-495435" status="OLD">
          <orgName>Adaptation, Intégration, Réticulation et Evolution</orgName>
          <orgName type="acronym">AIRE</orgName>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.ibps.upmc.fr/en/research/evolution/aire</ref>
          </desc>
          <listRelation>
            <relation active="#struct-247242" type="direct"/>
            <relation active="#struct-93016" type="indirect"/>
            <relation active="#struct-93591" type="indirect"/>
            <relation active="#struct-117617" type="indirect"/>
            <relation name="UMR7138" active="#struct-441569" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-247242" status="OLD">
          <idno type="RNSR">200918444N</idno>
          <orgName>Evolution Paris Seine</orgName>
          <desc>
            <address>
              <addrLine>UPMC 4 place Jussieu 75005 Paris, France</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-93016" type="direct"/>
            <relation active="#struct-93591" type="direct"/>
            <relation active="#struct-117617" type="direct"/>
            <relation name="UMR7138" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-93016" status="OLD">
          <idno type="IdRef">026603136</idno>
          <idno type="ROR">https://ror.org/02ryfmr77</idno>
          <orgName>Université des Antilles et de la Guyane</orgName>
          <orgName type="acronym">UAG</orgName>
          <date type="start">1982-07-02</date>
          <date type="end">2015-06-24</date>
          <desc>
            <address>
              <addrLine>Fouillole - BP 250 - 97157 Pointe-à-Pitre</addrLine>
              <country key="GP"/>
            </address>
            <ref type="url">http://www.univ-ag.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-93591" status="OLD">
          <idno type="ROR">https://ror.org/02en5vm52</idno>
          <orgName>Université Pierre et Marie Curie - Paris 6</orgName>
          <orgName type="acronym">UPMC</orgName>
          <date type="end">2017-12-31</date>
          <desc>
            <address>
              <addrLine>4 place Jussieu - 75005 Paris</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.upmc.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-117617" status="VALID">
          <idno type="IdRef">026403498</idno>
          <idno type="ISNI">0000000123372892</idno>
          <idno type="ROR">https://ror.org/02k9vew78</idno>
          <orgName>Université Nice Sophia Antipolis (1965 - 2019)</orgName>
          <orgName type="acronym">UNS</orgName>
          <date type="start">1965-10-23</date>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <addrLine>Parc Valrose, 06100 Nice</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://unice.fr/</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>