<?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-04615570</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="2026-05-17T03:06:01+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation</title>
            <author role="aut">
              <persName>
                <forename type="first">Zachary</forename>
                <surname>Cohen</surname>
              </persName>
              <idno type="halauthorid">3176726-0</idno>
              <affiliation ref="#struct-1201169"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Olivier</forename>
                <surname>François</surname>
              </persName>
              <idno type="halauthorid">144536-0</idno>
              <affiliation ref="#struct-1135218"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Sean</forename>
                <surname>Schoville</surname>
              </persName>
              <idno type="idhal" notation="numeric">1393177</idno>
              <idno type="halauthorid" notation="string">731354-1393177</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-7364-434X</idno>
              <affiliation ref="#struct-1201169"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Olivier</forename>
                <surname>Francois</surname>
              </persName>
              <email type="md5">95c21f1836cf0251e0161d41adff8551</email>
              <email type="domain">imag.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2024-06-18 11:34:19</date>
              <date type="whenModified">2025-09-27 18:48:04</date>
              <date type="whenReleased">2024-06-18 11:34:19</date>
              <date type="whenProduced">2022-12-30</date>
              <ref type="externalLink" target="https://academic.oup.com/icb/article-pdf/62/6/1827/48448332/icac137.pdf"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="139275">
                <persName>
                  <forename>Olivier</forename>
                  <surname>Francois</surname>
                </persName>
                <email type="md5">95c21f1836cf0251e0161d41adff8551</email>
                <email type="domain">imag.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-04615570</idno>
            <idno type="halUri">https://hal.science/hal-04615570</idno>
            <idno type="halBibtex">cohen:hal-04615570</idno>
            <idno type="halRefHtml">&lt;i&gt;Integrative and Comparative Biology&lt;/i&gt;, 2022, 62 (6), pp.1827-1837. &lt;a target="_blank" href="https://dx.doi.org/10.1093/icb/icac137"&gt;&amp;#x27E8;10.1093/icb/icac137&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Integrative and Comparative Biology, 2022, 62 (6), pp.1827-1837. &amp;#x27E8;10.1093/icb/icac137&amp;#x27E9;</idno>
            <availability status="restricted"/>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="SDE">Sciences De l'Environnement</idno>
            <idno type="stamp" n="UGA">HAL Grenoble Alpes</idno>
            <idno type="stamp" n="IMAG">IMAG</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="INPG">Institut polytechnique de Grenoble</idno>
            <idno type="stamp" n="GIP-BE">GIP Bretagne Environnement</idno>
            <idno type="stamp" n="TIMC-IMAG">TIMC</idno>
            <idno type="stamp" n="UNIV-LYON">Université de Lyon</idno>
            <idno type="stamp" n="UGA-EPE">Université Grenoble Alpes [2020-*]</idno>
            <idno type="stamp" n="TIMC-MAGE" corresp="TIMC-IMAG">MAGe :  Modèles et Algorithmes pour la Génomique </idno>
            <idno type="stamp" n="TEST-UGA">TEST-UGA</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">Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Zachary</forename>
                    <surname>Cohen</surname>
                  </persName>
                  <idno type="halauthorid">3176726-0</idno>
                  <affiliation ref="#struct-1201169"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Olivier</forename>
                    <surname>François</surname>
                  </persName>
                  <idno type="halauthorid">144536-0</idno>
                  <affiliation ref="#struct-1135218"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Sean</forename>
                    <surname>Schoville</surname>
                  </persName>
                  <idno type="idhal" notation="numeric">1393177</idno>
                  <idno type="halauthorid" notation="string">731354-1393177</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-7364-434X</idno>
                  <affiliation ref="#struct-1201169"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">5553</idno>
                <idno type="issn">1540-7063</idno>
                <idno type="eissn">1557-7023</idno>
                <title level="j">Integrative and Comparative Biology</title>
                <imprint>
                  <publisher>Oxford University Press (OUP)</publisher>
                  <biblScope unit="volume">62</biblScope>
                  <biblScope unit="issue">6</biblScope>
                  <biblScope unit="pp">1827-1837</biblScope>
                  <date type="datePub">2022-12-30</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1093/icb/icac137</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="sde">Environmental Sciences</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>Abstract Despite extensive research on agricultural pests, our knowledge about their evolutionary history is often limited. A mechanistic understanding of the demographic changes and modes of adaptation remains an important goal, as it improves our understanding of organismal responses to environmental change and our ability to sustainably manage pest populations. Emerging genomic datasets now allow for characterization of demographic and adaptive processes, but face limits when they are drawn from contemporary samples, especially in the context of strong demographic change, repeated selection, or adaptation involving modest shifts in allele frequency at many loci. Temporal sampling, however, can improve our ability to reconstruct evolutionary events. Here, we leverage museum samples to examine whether population genomic diversity and structure has changed over time, and to identify genomic regions that appear to be under selection. We focus on the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say 1824; Coleoptera: Chrysomelidae), which is widely regarded as a super-pest due to its rapid, and repeated, evolution to insecticides. By combining whole genome resequencing data from 78 museum samples with modern sampling, we demonstrate that CPB expanded rapidly in the 19th century, leading to a reduction in diversity and limited genetic structure from the Midwest to Northeast United States. Temporal genome scans provide extensive evidence for selection acting in resistant field populations in Wisconsin and New York, including numerous known insecticide resistance genes. We also validate these results by showing that known selective sweeps in modern populations are identified by our genome scan. Perhaps most importantly, temporal analysis indicates selection on standing genetic variation, as we find evidence for parallel evolution in the two geographical regions. Parallel evolution involves a range of phenotypic traits not previously identified as under selection in CPB, such as reproductive and morphological functional pathways that might be important for adaptation to agricultural habitats.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="institution" xml:id="struct-1201169" status="INCOMING">
          <orgName>Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA.</orgName>
          <desc>
            <address>
              <country key="US"/>
            </address>
          </desc>
        </org>
        <org type="researchteam" xml:id="struct-1135218" status="VALID">
          <orgName>Modèles et Algorithmes pour la Génomique</orgName>
          <orgName type="acronym">TIMC-MAGe</orgName>
          <date type="start">2022-01-01</date>
          <desc>
            <address>
              <addrLine>Domaine de la Merci, 38706 La Tronche, France</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.timc.fr/MAGe</ref>
          </desc>
          <listRelation>
            <relation active="#struct-1043049" type="direct"/>
            <relation active="#struct-301767" type="indirect"/>
            <relation name="UMR5525" active="#struct-441569" type="indirect"/>
            <relation active="#struct-1042703" type="indirect"/>
            <relation active="#struct-1043329" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-1043049" status="VALID">
          <idno type="IdRef">14728936X</idno>
          <idno type="ISNI">0000 0004 4687 1979</idno>
          <idno type="RNSR">199511969L</idno>
          <idno type="ROR">https://ror.org/03985kf35</idno>
          <orgName>Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525</orgName>
          <orgName type="acronym">TIMC</orgName>
          <date type="start">2021-01-01</date>
          <desc>
            <address>
              <addrLine>Domaine de la Merci, 38706 La Tronche, France</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.timc.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-301767" type="direct"/>
            <relation name="UMR5525" active="#struct-441569" type="direct"/>
            <relation active="#struct-1042703" type="direct"/>
            <relation active="#struct-1043329" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-301767" status="VALID">
          <idno type="ROR">https://ror.org/01c7wz417</idno>
          <orgName>VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement</orgName>
          <orgName type="acronym">VAS</orgName>
          <date type="start">2010-01-01</date>
          <desc>
            <address>
              <addrLine>Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile (campus vétérinaire); Université de Clermont, VetAgro Sup, 63370 Lempdes (campus agronomique)</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.vetagro-sup.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="regroupinstitution" xml:id="struct-1042703" status="VALID">
          <idno type="IdRef">240648315</idno>
          <idno type="ROR">https://ror.org/02rx3b187</idno>
          <orgName>Université Grenoble Alpes</orgName>
          <orgName type="acronym">UGA</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <addrLine>Adresse CS 40700 - 38058 Grenoble cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-grenoble-alpes.fr</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-1043329" status="VALID">
          <idno type="IdRef">026388804</idno>
          <idno type="ROR">https://ror.org/05sbt2524</idno>
          <orgName>Institut polytechnique de Grenoble - Grenoble Institute of Technology</orgName>
          <orgName type="acronym">Grenoble INP</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <addrLine>46 avenue Félix Viallet 38031 Grenoble Cedex 1</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.grenoble-inp.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-1042703" type="direct"/>
          </listRelation>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>