untitled
<OAI-PMH schemaLocation=http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd>
<responseDate>2018-01-17T12:07:41Z</responseDate>
<request identifier=oai:HAL:hal-01544794v1 verb=GetRecord metadataPrefix=oai_dc>http://api.archives-ouvertes.fr/oai/hal/</request>
<GetRecord>
<record>
<header>
<identifier>oai:HAL:hal-01544794v1</identifier>
<datestamp>2018-01-12</datestamp>
<setSpec>type:ART</setSpec>
<setSpec>subject:sdv</setSpec>
<setSpec>collection:EVOLUTION_PARIS_SEINE</setSpec>
<setSpec>collection:UPMC</setSpec>
<setSpec>collection:EVOL_PARIS_SEINE-AIRE</setSpec>
<setSpec>collection:CNRS</setSpec>
<setSpec>collection:UNIV-AG</setSpec>
<setSpec>collection:UNICE</setSpec>
<setSpec>collection:SAE</setSpec>
<setSpec>collection:GIP-BE</setSpec>
<setSpec>collection:UPMC_POLE_4</setSpec>
<setSpec>collection:IBPS</setSpec>
<setSpec>collection:UCA-TEST</setSpec>
<setSpec>collection:UNIV-COTEDAZUR</setSpec>
</header>
<metadata><dc>
<publisher>HAL CCSD</publisher>
<title lang=en>A Pluralistic Account of Homology: Adapting the Models to the Data</title>
<creator>Haggerty, Leanne S.</creator>
<creator>Jachiet, Pierre-Alain</creator>
<creator>Hanage, William P.</creator>
<creator>Fitzpatrick, David A.</creator>
<creator>Lopez, Philippe</creator>
<creator>O'Connell, Mary J.</creator>
<creator>Pisani, Davide</creator>
<creator>Wilkinson, Mark</creator>
<creator>Bapteste, Eric</creator>
<creator>McInerney, James O.</creator>
<contributor>Adaptation, Intégration, Réticulation et Evolution (AIRE) ; Systématique, adaptation, évolution (SAE) ; Université Pierre et Marie Curie - Paris 6 (UPMC) - Centre National de la Recherche Scientifique (CNRS) - Université Pierre et Marie Curie - Paris 6 (UPMC) - Centre National de la Recherche Scientifique (CNRS) - Evolution Paris Seine ; Université Nice Sophia Antipolis (UNS) ; Université Côte d'Azur (UCA) - Université Côte d'Azur (UCA) - Centre National de la Recherche Scientifique (CNRS) - Université des Antilles et de la Guyane (UAG) - Université Pierre et Marie Curie - Paris 6 (UPMC) - Université Nice Sophia Antipolis (UNS) ; Université Côte d'Azur (UCA) - Université Côte d'Azur (UCA) - Université des Antilles et de la Guyane (UAG)</contributor>
<contributor>Science Foundation Ireland [RFP EOB2510, RFP EOB3106, RFP EOB2673]</contributor>
<contributor> Biotechnology and Biological Sciences Research Council [BB/K007440/1]</contributor>
<description>International audience</description>
<source>ISSN: 0737-4038</source>
<source>EISSN: 1537-1719</source>
<source>Molecular Biology and Evolution</source>
<publisher>Oxford University Press (OUP)</publisher>
<identifier>hal-01544794</identifier>
<identifier>https://hal.archives-ouvertes.fr/hal-01544794</identifier>
<source>https://hal.archives-ouvertes.fr/hal-01544794</source>
<source>Molecular Biology and Evolution, Oxford University Press (OUP), 2014, 31 (3), pp.501-516. 〈10.1093/molbev/mst228〉</source>
<identifier>DOI : 10.1093/molbev/mst228</identifier>
<relation>info:eu-repo/semantics/altIdentifier/doi/10.1093/molbev/mst228</relation>
<language>en</language>
<subject lang=en>homology</subject>
<subject lang=en> network</subject>
<subject lang=en> comparative genomics</subject>
<subject lang=en> epaktolog</subject>
<subject lang=en> ortholog</subject>
<subject lang=en> paralog</subject>
<subject>[SDV.BID] Life Sciences [q-bio]/Biodiversity</subject>
<type>info:eu-repo/semantics/article</type>
<type>Journal articles</type>
<description lang=en>Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ``public goods,'' subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define `` family resemblances'' to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.</description>
<date>2014-03</date>
</dc>
</metadata>
</record>
</GetRecord>
</OAI-PMH>
