<?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-03813178</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="2026-05-16T13:48:15+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Correlated stabilizing selection shapes the topology of gene regulatory networks</title>
            <author role="aut">
              <persName>
                <forename type="first">Apolline</forename>
                <surname>Petit</surname>
              </persName>
              <email type="md5">adbfbc95b98c801cc3dd0eb5b792fa7f</email>
              <email type="domain">universite-paris-saclay.fr</email>
              <idno type="idhal" notation="string">apolline-j-r-petit</idno>
              <idno type="idhal" notation="numeric">1444263</idno>
              <idno type="halauthorid" notation="string">2611277-1444263</idno>
              <affiliation ref="#struct-1041768"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Jérémy</forename>
                <surname>Guez</surname>
              </persName>
              <email type="md5">532d814bb902be3919a729c37db3490e</email>
              <email type="domain">mnhn.fr</email>
              <idno type="idhal" notation="numeric">1399823</idno>
              <idno type="halauthorid" notation="string">2289776-1399823</idno>
              <idno type="IDREF">https://www.idref.fr/285003836</idno>
              <affiliation ref="#struct-1004942"/>
              <affiliation ref="#struct-1061259"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Arnaud</forename>
                <surname>Le Rouzic</surname>
              </persName>
              <email type="md5">c29d07c3f88f6dc8f10aec974822e762</email>
              <email type="domain">universite-paris-saclay.fr</email>
              <ptr type="url" target="https://www.egce.universite-paris-saclay.fr/?p=757"/>
              <idno type="idhal" notation="string">arnaud-le-rouzic</idno>
              <idno type="idhal" notation="numeric">180891</idno>
              <idno type="halauthorid" notation="string">427062-180891</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/A-4106-2008</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-2158-3458</idno>
              <idno type="GOOGLE SCHOLAR">https://scholar.google.fr/citations?user=HumZpaIAAAAJ&amp;hl=en</idno>
              <idno type="IDREF">https://www.idref.fr/094949697</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/A-4106-2008</idno>
              <affiliation ref="#struct-1041768"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Théo</forename>
                <surname>Rousselle</surname>
              </persName>
              <email type="md5">4dd8f309c0f72378cdf21feb75dfdf16</email>
              <email type="domain">inist.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2024-02-06 11:52:02</date>
              <date type="whenModified">2025-04-15 03:17:15</date>
              <date type="whenReleased">2024-02-06 11:54:17</date>
              <date type="whenProduced">2023-06-26</date>
              <date type="whenEndEmbargoed">2024-02-06</date>
              <ref type="file" target="https://hal.science/hal-03813178v1/document">
                <date notBefore="2024-02-06"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.science/hal-03813178v1/file/2022.08.29.505706.full.pdf" id="file-4441044-3855911">
                <date notBefore="2024-02-06"/>
              </ref>
              <ref type="externalLink" target="https://www.biorxiv.org/content/biorxiv/early/2022/08/29/2022.08.29.505706.full.pdf"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="887009">
                <persName>
                  <forename>Théo</forename>
                  <surname>Rousselle</surname>
                </persName>
                <email type="md5">4dd8f309c0f72378cdf21feb75dfdf16</email>
                <email type="domain">inist.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-03813178</idno>
            <idno type="halUri">https://hal.science/hal-03813178</idno>
            <idno type="halBibtex">petit:hal-03813178</idno>
            <idno type="halRefHtml">&lt;i&gt;Genetics&lt;/i&gt;, 2023, 224 (2), pp.iyad065. &lt;a target="_blank" href="https://dx.doi.org/10.1101/2022.08.29.505706"&gt;&amp;#x27E8;10.1101/2022.08.29.505706&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Genetics, 2023, 224 (2), pp.iyad065. &amp;#x27E8;10.1101/2022.08.29.505706&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-4441044-3855911"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="IRD">IRD - Institut de recherche pour le développement</idno>
            <idno type="stamp" n="MNHN">Muséum National d'Histoire Naturelle</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="CENTRALESUPELEC">Ecole CentraleSupélec</idno>
            <idno type="stamp" n="UNIV-PARIS-SACLAY">Université Paris-Saclay</idno>
            <idno type="stamp" n="UNIV-PARIS">Université Paris Cité</idno>
            <idno type="stamp" n="UNIVERSITE-PARIS-SACLAY" corresp="UNIV-PARIS-SACLAY">Université Paris-Saclay</idno>
            <idno type="stamp" n="EGCE">Evolution, Génomes, Comportement, Ecologie</idno>
            <idno type="stamp" n="LISN">Laboratoire Interdisciplinaire des Sciences du Numérique</idno>
            <idno type="stamp" n="GS-COMPUTER-SCIENCE">Graduate School Computer Science</idno>
            <idno type="stamp" n="GS-BIOSPHERA">Graduate School Biologie, Société, Ecologie &amp; Environnement, Ressources, Agriculture &amp; Alimentation</idno>
            <idno type="stamp" n="GS-LIFE-SCIENCES-HEALTH" corresp="UNIVERSITE-PARIS-SACLAY">Graduate School Life Sciences and Health</idno>
            <idno type="stamp" n="LISN-BIOINFO" corresp="LISN">BioInformatique </idno>
            <idno type="stamp" n="ALLIANCE-SU"> Alliance Sorbonne Université</idno>
            <idno type="stamp" n="TEST3-HALCNRS">TEST3-HALCNRS</idno>
            <idno type="stamp" n="TEST4-HALCNRS">collection test</idno>
            <idno type="stamp" n="TEST5-HALCNRS">collection test 5</idno>
            <idno type="stamp" n="INEE-CNRS">Institut écologie et environnement du CNRS</idno>
            <idno type="stamp" n="ECO-ANTHROPOLOGIE" corresp="MNHN">Éco-Anthropologie </idno>
            <idno type="stamp" n="APT_TEST">APT_TEST</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">Correlated stabilizing selection shapes the topology of gene regulatory networks</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Apolline</forename>
                    <surname>Petit</surname>
                  </persName>
                  <email type="md5">adbfbc95b98c801cc3dd0eb5b792fa7f</email>
                  <email type="domain">universite-paris-saclay.fr</email>
                  <idno type="idhal" notation="string">apolline-j-r-petit</idno>
                  <idno type="idhal" notation="numeric">1444263</idno>
                  <idno type="halauthorid" notation="string">2611277-1444263</idno>
                  <affiliation ref="#struct-1041768"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Jérémy</forename>
                    <surname>Guez</surname>
                  </persName>
                  <email type="md5">532d814bb902be3919a729c37db3490e</email>
                  <email type="domain">mnhn.fr</email>
                  <idno type="idhal" notation="numeric">1399823</idno>
                  <idno type="halauthorid" notation="string">2289776-1399823</idno>
                  <idno type="IDREF">https://www.idref.fr/285003836</idno>
                  <affiliation ref="#struct-1004942"/>
                  <affiliation ref="#struct-1061259"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Arnaud</forename>
                    <surname>Le Rouzic</surname>
                  </persName>
                  <email type="md5">c29d07c3f88f6dc8f10aec974822e762</email>
                  <email type="domain">universite-paris-saclay.fr</email>
                  <ptr type="url" target="https://www.egce.universite-paris-saclay.fr/?p=757"/>
                  <idno type="idhal" notation="string">arnaud-le-rouzic</idno>
                  <idno type="idhal" notation="numeric">180891</idno>
                  <idno type="halauthorid" notation="string">427062-180891</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/A-4106-2008</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-2158-3458</idno>
                  <idno type="GOOGLE SCHOLAR">https://scholar.google.fr/citations?user=HumZpaIAAAAJ&amp;hl=en</idno>
                  <idno type="IDREF">https://www.idref.fr/094949697</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/A-4106-2008</idno>
                  <affiliation ref="#struct-1041768"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">171552</idno>
                <idno type="issn">1943-2631</idno>
                <title level="j">Genetics</title>
                <imprint>
                  <publisher>Oxford University Press</publisher>
                  <biblScope unit="volume">224</biblScope>
                  <biblScope unit="issue">2</biblScope>
                  <biblScope unit="pp">iyad065</biblScope>
                  <date type="datePub">2023-06-26</date>
                </imprint>
              </monogr>
              <idno type="biorxiv">2022.08.29.505706</idno>
              <idno type="doi">10.1101/2022.08.29.505706</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">Evolutionary Systems Biology</term>
                <term xml:lang="en">Evolution of Pleiotropy</term>
                <term xml:lang="en">Mutation Covariance Matrix</term>
                <term xml:lang="en">Evolvability</term>
                <term xml:lang="en">Genetical analysis</term>
                <term xml:lang="en">Quantitative genetics model</term>
                <term xml:lang="en">Stabilizing correlated fitness function</term>
                <term xml:lang="en">Genetic architectures</term>
                <term xml:lang="en">Genomics and evolution</term>
                <term xml:lang="en">Gene mutations</term>
                <term xml:lang="en">Gene expression</term>
                <term xml:lang="en">Gene regulatory networks</term>
              </keywords>
              <classCode scheme="halDomain" n="sdv.bid.evo">Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]</classCode>
              <classCode scheme="halDomain" n="sdv.bbm">Life Sciences [q-bio]/Biochemistry, Molecular Biology</classCode>
              <classCode scheme="halDomain" n="sdv.gen">Life Sciences [q-bio]/Genetics</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>The evolution of gene expression is constrained by the topology of gene regulatory networks, as co-expressed genes are likely to be affected together by mutations. Conversely, co-expression can also be an advantage when genes are under joint selection. Here, we assessed theoretically whether correlated selection (selection for a combination of traits) was able to affect the pattern of correlated gene expressions and the underlying gene regulatory networks. We ran individual based simulations, applying a stabilizing correlated fitness function to two genetic architectures: a quantitative genetics (multilinear) model featuring epistasis and pleiotropy, and a gene regulatory model, mimicking the mechanisms of gene expression regulation. Simulations showed that correlated mutational effects evolved in both genetic architecture as a response to correlated selection, but the response in gene networks was less precise due to the mechanistic constraints of gene regulation. The intensity of gene co-expression was mostly explained by the regulatory distance between genes (largest correlations being associated to genes directly interacting with each other), and the sign of co-expression was associated with the nature of the regulatory interaction (transcription activation or inhibition). These results concur to the idea that gene network topologies could partly reflects past correlated selection patterns on gene expression.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-1041768" status="VALID">
          <idno type="IdRef">187405794</idno>
          <idno type="RNSR">201521302U</idno>
          <idno type="ROR">https://ror.org/011abem59</idno>
          <orgName>Evolution, génomes, comportement et écologie</orgName>
          <orgName type="acronym">EGCE</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <addrLine>Avenue de la Terrasse, bâtiment 13, boite postale 1, 91198, Gif-sur-Yvette cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.egce.cnrs-gif.fr/?lang=fr</ref>
          </desc>
          <listRelation>
            <relation active="#struct-67872" type="direct"/>
            <relation active="#struct-419361" type="direct"/>
            <relation name="UMR 9191" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-1004942" status="VALID">
          <idno type="IdRef">192039423</idno>
          <idno type="ISNI">000000040370736X</idno>
          <idno type="RNSR">200311825V</idno>
          <idno type="ROR">https://ror.org/03x0yny97</idno>
          <orgName>Éco-Anthropologie</orgName>
          <orgName type="acronym">EA 7206</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <addrLine>Musée de l’Homme - 17 place du Trocadéro - 75016 Paris</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.ecoanthropologie.cnrs.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-7512" type="direct"/>
            <relation name="UMR7206" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-1061259" status="VALID">
          <idno type="IdRef">253160316</idno>
          <idno type="RNSR">202123711L</idno>
          <idno type="ROR">https://ror.org/00rd81916</idno>
          <idno type="Wikidata">Q109620676</idno>
          <orgName>Laboratoire Interdisciplinaire des Sciences du Numérique</orgName>
          <orgName type="acronym">LISN</orgName>
          <date type="start">2021-01-01</date>
          <desc>
            <address>
              <addrLine>Campus Universitaire bât 507Rue du Belvédère91405 Orsay cedexet Campus Universitaire bât 6401 rue Raimond Castaing91190 Gif-sur-Yvette</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.lisn.upsaclay.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-300009" type="direct"/>
            <relation active="#struct-411575" type="direct"/>
            <relation active="#struct-419361" type="direct"/>
            <relation name="UMR9015" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-67872" status="VALID">
          <idno type="IdRef">050165224</idno>
          <idno type="ROR">https://ror.org/05q3vnk25</idno>
          <orgName>Institut de Recherche pour le Développement</orgName>
          <orgName type="acronym">IRD</orgName>
          <desc>
            <address>
              <addrLine>SiègeLe Sextant 44, bd de DunkerqueCS 9000913572 Marseille cedex 02</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.ird.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-419361" status="VALID">
          <idno type="IdRef">241345251</idno>
          <idno type="ROR">https://ror.org/03xjwb503</idno>
          <orgName>Université Paris-Saclay</orgName>
          <desc>
            <address>
              <addrLine>Bâtiment Bréguet, 3 Rue Joliot Curie 2e ét, 91190 Gif-sur-Yvette</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.universite-paris-saclay.fr/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>
        <org type="institution" xml:id="struct-7512" status="VALID">
          <idno type="IdRef">026394944</idno>
          <idno type="ROR">https://ror.org/03wkt5x30</idno>
          <orgName>Muséum national d'Histoire naturelle</orgName>
          <orgName type="acronym">MNHN</orgName>
          <desc>
            <address>
              <addrLine>57, rue Cuvier - 75231 Paris Cedex 05</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.mnhn.fr</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-300009" status="VALID">
          <idno type="ROR">https://ror.org/02kvxyf05</idno>
          <orgName>Institut National de Recherche en Informatique et en Automatique</orgName>
          <orgName type="acronym">Inria</orgName>
          <desc>
            <address>
              <addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inria.fr/en/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-411575" status="VALID">
          <idno type="IdRef">184443237</idno>
          <idno type="ROR">https://ror.org/019tcpt25</idno>
          <orgName>CentraleSupélec</orgName>
          <desc>
            <address>
              <addrLine>3, rue Joliot Curie,Plateau de Moulon,91192 GIF-SUR-YVETTE Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.centralesupelec.fr</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>