<?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-04265149</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="2026-05-23T00:56:22+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">GenAPoPop 1.0 : A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms</title>
            <title xml:lang="en" type="sub">Population genetic analyses of autopolyploids</title>
            <author role="crp">
              <persName>
                <forename type="first">Solenn</forename>
                <surname>Stoeckel</surname>
              </persName>
              <email type="md5">3a016298a8d69c45cb52e75adaa37a02</email>
              <email type="domain">inrae.fr</email>
              <idno type="idhal" notation="string">solenn-stoeckel</idno>
              <idno type="idhal" notation="numeric">736839</idno>
              <idno type="halauthorid" notation="string">10978-736839</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-6064-5941</idno>
              <idno type="IDREF">https://www.idref.fr/23029989X</idno>
              <affiliation ref="#struct-1096413"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Ronan</forename>
                <surname>Becheler</surname>
              </persName>
              <idno type="idhal" notation="numeric">779347</idno>
              <idno type="halauthorid" notation="string">1070211-779347</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-9322-0771</idno>
              <affiliation ref="#struct-1083968"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Ekaterina</forename>
                <surname>Bocharova</surname>
              </persName>
              <email type="md5">02b71092147299c35b2b6d600c8ccc94</email>
              <email type="domain">gmail.com</email>
              <idno type="idhal" notation="numeric">1301585</idno>
              <idno type="halauthorid" notation="string">2609772-1301585</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-9978-3006</idno>
              <affiliation ref="#struct-535179"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Dominique</forename>
                <surname>Barloy</surname>
              </persName>
              <email type="md5">0345df022275052d044f6cf422d85085</email>
              <email type="domain">agrocampus-ouest.fr</email>
              <idno type="idhal" notation="string">dominique-barloy</idno>
              <idno type="idhal" notation="numeric">752004</idno>
              <idno type="halauthorid" notation="string">2937578-752004</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-5810-4871</idno>
              <affiliation ref="#struct-1083968"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Solenn</forename>
                <surname>Stoeckel</surname>
              </persName>
              <email type="md5">3a016298a8d69c45cb52e75adaa37a02</email>
              <email type="domain">inrae.fr</email>
            </editor>
            <funder ref="#projanr-48590"/>
            <funder>- INVAMAT PROJECT (Plant Health and Environment Division of the French National Institute of Agricultural Research)- The French Embassy in the Russian Federation, METCHNIKOV 2019 grant- FEDER funds from Région Centre-Val de Loire and by Agence de l’eau Loire-Bretagne, grant Nature 2045, programme 9025 (AP 2015 9025)- IDB RAS Government basic research program № 0088-2021-0019</funder>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2023-10-30 16:41:48</date>
              <date type="whenModified">2026-05-05 16:37:43</date>
              <date type="whenReleased">2023-11-02 16:00:54</date>
              <date type="whenProduced">2024</date>
              <date type="whenEndEmbargoed">2023-10-30</date>
              <ref type="file" target="https://hal.science/hal-04265149v1/document">
                <date notBefore="2023-10-30"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.science/hal-04265149v1/file/2023-09-28_Stoeckel_et_al_GenAPoPop_HAL.pdf" id="file-4265149-3721585">
                <date notBefore="2023-10-30"/>
              </ref>
              <fs>
                <f name="inra_etatDocument_local" notation="numeric">
                  <numeric>0</numeric>
                </f>
                <f name="inra_etatDocument_local" notation="string" n="0">
                  <string>inra_etatDocument_local_0</string>
                </f>
                <f name="inra_publicVise_local" notation="string" n="SC">
                  <string>inra_publicVise_local_SC</string>
                </f>
              </fs>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="925565">
                <persName>
                  <forename>Solenn</forename>
                  <surname>Stoeckel</surname>
                </persName>
                <email type="md5">3a016298a8d69c45cb52e75adaa37a02</email>
                <email type="domain">inrae.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-04265149</idno>
            <idno type="halUri">https://hal.science/hal-04265149</idno>
            <idno type="halBibtex">stoeckel:hal-04265149</idno>
            <idno type="halRefHtml">&lt;i&gt;Molecular Ecology Resources&lt;/i&gt;, 2024, 24 (1), &lt;a target="_blank" href="https://dx.doi.org/10.1111/1755-0998.13886"&gt;&amp;#x27E8;10.1111/1755-0998.13886&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Molecular Ecology Resources, 2024, 24 (1), &amp;#x27E8;10.1111/1755-0998.13886&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://hal.science/licences/copyright/">Copyright - All rights reserved<ref corresp="#file-4265149-3721585"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="UNIV-RENNES1">Université de Rennes 1</idno>
            <idno type="stamp" n="IFREMER">IFREMER : Institut français de recherche pour l'exploitation de la mer</idno>
            <idno type="stamp" n="GIP-BE">GIP Bretagne Environnement</idno>
            <idno type="stamp" n="IGEPP">Institut de génétique, environnement et protection des plantes</idno>
            <idno type="stamp" n="UR1-UFR-SVE">UFR SVE Sciences de la vie et de l'environnement</idno>
            <idno type="stamp" n="UR1-HAL">Publications labos UR1 dans HAL-Rennes 1</idno>
            <idno type="stamp" n="UR1-SDV">UR1 - publications SDV</idno>
            <idno type="stamp" n="TEST-UR-CSS">TEST Université de Rennes CSS</idno>
            <idno type="stamp" n="UNIV-RENNES">Université de Rennes</idno>
            <idno type="stamp" n="INRAE">Institut National de Recherche en Agriculture, Alimentation et Environnement</idno>
            <idno type="stamp" n="ANR">ANR</idno>
            <idno type="stamp" n="UR1-ENV">Pôle UnivRennes - Environnement</idno>
            <idno type="stamp" n="INSTITUT-AGRO-RENNES-ANGERS-UMR-DECOD" corresp="INSTITUT-AGRO-RENNES-ANGERS">Institut Agro Rennes-Angers - UMR DECOD</idno>
            <idno type="stamp" n="INSTITUT-AGRO-RENNES-ANGERS" corresp="PUBLIS-EC-IA">Institut Agro Rennes-Angers</idno>
            <idno type="stamp" n="INSTITUT-AGRO-DECOD" corresp="INSTITUT-AGRO-RENNES-ANGERS">Institut Agro - DECOD</idno>
            <idno type="stamp" n="DPT_ECODIV">Ecologie et biodiversité</idno>
            <idno type="stamp" n="SANTE-PLANTES-ENVIRONNEMENT">Département Santé des Plantes et Environnement (SPE)</idno>
            <idno type="stamp" n="INSTITUT-AGRO">Institut Agro</idno>
            <idno type="stamp" n="PUBLIS-EC-IA">Publications des enseignants chercheurs de l'Institut Agro</idno>
            <idno type="stamp" n="DECOD">DECOD – Dynamique et durabilité des écosystèmes : de la source à l’océan</idno>
            <idno type="stamp" n="LINKED_RESEARCH_OUTPUTS">Publications linked to dataset and software</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">GenAPoPop 1.0 : A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms</title>
                <title xml:lang="en" type="sub">Population genetic analyses of autopolyploids</title>
                <author role="crp">
                  <persName>
                    <forename type="first">Solenn</forename>
                    <surname>Stoeckel</surname>
                  </persName>
                  <email type="md5">3a016298a8d69c45cb52e75adaa37a02</email>
                  <email type="domain">inrae.fr</email>
                  <idno type="idhal" notation="string">solenn-stoeckel</idno>
                  <idno type="idhal" notation="numeric">736839</idno>
                  <idno type="halauthorid" notation="string">10978-736839</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-6064-5941</idno>
                  <idno type="IDREF">https://www.idref.fr/23029989X</idno>
                  <affiliation ref="#struct-1096413"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Ronan</forename>
                    <surname>Becheler</surname>
                  </persName>
                  <idno type="idhal" notation="numeric">779347</idno>
                  <idno type="halauthorid" notation="string">1070211-779347</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-9322-0771</idno>
                  <affiliation ref="#struct-1083968"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Ekaterina</forename>
                    <surname>Bocharova</surname>
                  </persName>
                  <email type="md5">02b71092147299c35b2b6d600c8ccc94</email>
                  <email type="domain">gmail.com</email>
                  <idno type="idhal" notation="numeric">1301585</idno>
                  <idno type="halauthorid" notation="string">2609772-1301585</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-9978-3006</idno>
                  <affiliation ref="#struct-535179"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Dominique</forename>
                    <surname>Barloy</surname>
                  </persName>
                  <email type="md5">0345df022275052d044f6cf422d85085</email>
                  <email type="domain">agrocampus-ouest.fr</email>
                  <idno type="idhal" notation="string">dominique-barloy</idno>
                  <idno type="idhal" notation="numeric">752004</idno>
                  <idno type="halauthorid" notation="string">2937578-752004</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-5810-4871</idno>
                  <affiliation ref="#struct-1083968"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">103029</idno>
                <idno type="issn">1755-098X</idno>
                <idno type="eissn">1755-0998</idno>
                <title level="j">Molecular Ecology Resources</title>
                <imprint>
                  <publisher>Wiley/Blackwell</publisher>
                  <biblScope unit="volume">24</biblScope>
                  <biblScope unit="issue">1</biblScope>
                  <date type="datePub">2024</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1111/1755-0998.13886</idno>
              <idno type="wos">001094088000001</idno>
              <relatedItem target="https://doi.org/10.5281/zenodo.8164531" type="Cites" subtype="http://purl.org/coar/resource_type/c_ddb1"/>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">Bayesian</term>
                <term xml:lang="en">Autogamy</term>
                <term xml:lang="en">Asexual reproduction</term>
                <term xml:lang="en">Bayesian inference of reproductive modes</term>
                <term xml:lang="en">Unrooted tree of genetic distances</term>
                <term xml:lang="en">Genetic differentiation</term>
                <term xml:lang="en">Genotypic diversity</term>
                <term xml:lang="en">Polyploidy</term>
              </keywords>
              <classCode scheme="halDomain" n="sdv.gen.gpo">Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]</classCode>
              <classCode scheme="halDomain" n="sdv.bdlr">Life Sciences [q-bio]/Reproductive Biology</classCode>
              <classCode scheme="halDomain" n="sdv.bid.evo">Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]</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>Autopolyploidy is quite common in most clades of eukaryotes. The emergence of sequence‐based genotyping methods with individual and marker tags now enables confident allele dosage, overcoming the main obstacle to the democratization of the population genetic approaches when studying ecology and evolution of autopolyploid populations and species. Reproductive modes, including clonality, selfing and allogamy, have deep consequences on the ecology and evolution of population and species. Analysing genetic diversity and its dynamics over generations is one efficient way to infer the relative importance of clonality, selfing and allogamy in populations. GenAPoPop is a user‐friendly solution to compute the specific corpus of population genetic indices, including indices about genotypic diversity, needed to analyse partially clonal, selfed and allogamous polysomic populations genotyped with confident allele dosage. It also easily provides the posterior probabilities of quantitative reproductive modes in autopolyploid populations genotyped at two‐time steps and a graphical representation of the minimum spanning trees of the genetic distances between polyploid individuals, facilitating the interpretation of the genetic coancestry between individuals in hierarchically structured populations. GenAPoPop complements the previously existing solutions, including SPAGEDI and POLYGENE, to use genotypings to study the ecology and evolution of autopolyploid populations. It was specially developed with a simple graphical interface and workflow, and comes with a simulator to facilitate practical courses and teaching of population genetics for autopolyploid populations.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-1096413" status="VALID">
          <idno type="IdRef">183104226</idno>
          <idno type="RNSR">201220379D</idno>
          <idno type="ROR">https://ror.org/038kxsm48</idno>
          <orgName>Institut de Génétique, Environnement et Protection des Plantes</orgName>
          <orgName type="acronym">IGEPP</orgName>
          <date type="start">2022-01-01</date>
          <desc>
            <address>
              <addrLine>Domaine de la Motte au Vicomte BP 3532735653 Le Rheu</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.rennes.inra.fr/igepp</ref>
          </desc>
          <listRelation>
            <relation name="UMR1349" active="#struct-105160" type="direct"/>
            <relation name="UMR1349" active="#struct-577435" type="direct"/>
            <relation active="#struct-1091012" type="direct"/>
            <relation active="#struct-1042499" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-1083968" status="VALID">
          <idno type="RNSR">202224183V</idno>
          <orgName>Dynamique et durabilité des écosystèmes : de la source à l’océan</orgName>
          <orgName type="acronym">DECOD</orgName>
          <date type="start">2022-01-01</date>
          <desc>
            <address>
              <addrLine>Institut Agro Rennes Angers, 65 rue de Saint-BrieucF-35042 Rennes cedex</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-300022" type="direct"/>
            <relation name="UMR 0985" active="#struct-577435" type="direct"/>
            <relation active="#struct-1042499" type="direct"/>
            <relation active="#struct-1091012" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-535179" status="VALID">
          <orgName>Koltzov Institute of Developmental Biology</orgName>
          <date type="start">1967-01-01</date>
          <desc>
            <address>
              <addrLine>Moscou</addrLine>
              <country key="RU"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-534840" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-105160" status="VALID">
          <idno type="IdRef">26693823X</idno>
          <idno type="ROR">https://ror.org/015m7wh34</idno>
          <orgName>Université de Rennes</orgName>
          <orgName type="acronym">UR</orgName>
          <desc>
            <address>
              <addrLine>Campus de Beaulieu, 263 avenue Général Leclerc, CS 74205, 35042 RENNES CEDEX</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.univ-rennes.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-577435" status="VALID">
          <idno type="ROR">https://ror.org/003vg9w96</idno>
          <orgName>Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement</orgName>
          <orgName type="acronym">INRAE</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
          </desc>
        </org>
        <org type="institution" xml:id="struct-1091012" status="VALID">
          <idno type="IdRef">261039946</idno>
          <idno type="ROR">https://ror.org/01s3fs709</idno>
          <orgName>Institut Agro Rennes Angers</orgName>
          <date type="start">2022-01-01</date>
          <desc>
            <address>
              <addrLine>65 rue de Saint Brieuc CS 84215 35042 Rennes CEDEX</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-1042499" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-1042499" status="VALID">
          <idno type="IdRef">260373249</idno>
          <idno type="ROR">https://ror.org/01dkyve95</idno>
          <orgName>Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement</orgName>
          <orgName type="acronym">Institut Agro</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.institut-agro.fr</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-300022" status="VALID">
          <idno type="IdRef">027783073</idno>
          <idno type="ISNI">0000000121634107</idno>
          <idno type="ROR">https://ror.org/044jxhp58</idno>
          <orgName>Institut Français de Recherche pour l'Exploitation de la Mer</orgName>
          <orgName type="acronym">IFREMER</orgName>
          <date type="start">1984-01-01</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://wwz.ifremer.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-534840" status="VALID">
          <idno type="ROR">https://ror.org/02akkm420</idno>
          <orgName>Russian Academy of Sciences</orgName>
          <orgName type="acronym">RAS</orgName>
          <date type="start">1724-01-01</date>
          <desc>
            <address>
              <addrLine>Leninskii avenue, 14, Moscou V-17</addrLine>
              <country key="RU"/>
            </address>
            <ref type="url">https://www.ras.ru/indexeng.html</ref>
          </desc>
        </org>
      </listOrg>
      <listOrg type="projects">
        <org type="anrProject" xml:id="projanr-48590" status="VALID">
          <idno type="anr">ANR-18-CE32-0001</idno>
          <idno type="program">APPEL À PROJETS GÉNÉRIQUE 2018</idno>
          <orgName>Clonix2D</orgName>
          <desc>Les conséquences génétiques de reproduction partiellement clonale dans les populations colonisant de nouveaux territoires</desc>
          <date type="start">2018</date>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>