Exploring the space of gene/species reconciliations with transfers.
Identifieur interne : 002E16 ( Main/Exploration ); précédent : 002E15; suivant : 002E17Exploring the space of gene/species reconciliations with transfers.
Auteurs : Yao-Ban Chan [Australie] ; Vincent Ranwez [France] ; Céline Scornavacca [France]Source :
- Journal of mathematical biology [ 1432-1416 ] ; 2015.
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Abstract
Reconciliations between gene and species trees have important applications in the study of genome evolution (e.g. sequence orthology prediction or quantification of transfer events). While numerous methods have been proposed to infer them, little has been done to study the underlying reconciliation space. In this paper, we characterise the reconciliation space for two evolutionary models: the [Formula: see text] (duplication, loss and transfer) model and a variant of it-the no-[Formula: see text] model-which does not allow [Formula: see text] events (a transfer immediately followed by a loss). We provide formulae to compute the size of the corresponding spaces and define a set of transformation operators sufficient to explore the entire reconciliation space. We also define a distance between two reconciliations as the minimal number of operations needed to transform one into the other and prove that this distance is easily computable in the no-[Formula: see text] model. Computing this distance in the [Formula: see text] model is more difficult and it is an open question whether it is NP-hard or not. This work constitutes an important step toward reconciliation space characterisation and reconciliation comparison, needed to better assess the performance of reconciliation inference methods through simulations.
DOI: 10.1007/s00285-014-0851-2
PubMed: 25502987
Affiliations:
- Australie, France
- Languedoc-Roussillon, Occitanie (région administrative)
- Montpellier
- Université Montpellier 2
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Bataillon-CC 064, Montpellier Cedex 5, 34095, France. celine.scornavacca@univ-montp2.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E. Bataillon-CC 064, Montpellier Cedex 5, 34095</wicri:regionArea><wicri:noRegion>34095</wicri:noRegion><orgName type="university">Université Montpellier 2</orgName><placeName><settlement type="city">Montpellier</settlement><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author></analytic><series><title level="j">Journal of mathematical biology</title><idno type="eISSN">1432-1416</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Computer Simulation</term><term>Evolution, Molecular</term><term>Gene Deletion</term><term>Gene Duplication</term><term>Gene Transfer, Horizontal</term><term>Genetic Speciation</term><term>Mathematical Concepts</term><term>Models, Genetic</term><term>Multigene Family</term><term>Phylogeny</term><term>Species Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Concepts mathématiques</term><term>Duplication de gène</term><term>Délétion de gène</term><term>Famille multigénique</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Simulation numérique</term><term>Spéciation génétique</term><term>Spécificité d'espèce</term><term>Transfert horizontal de gène</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Computer Simulation</term><term>Evolution, Molecular</term><term>Gene Deletion</term><term>Gene Duplication</term><term>Gene Transfer, Horizontal</term><term>Genetic Speciation</term><term>Mathematical Concepts</term><term>Models, Genetic</term><term>Multigene Family</term><term>Phylogeny</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Concepts mathématiques</term><term>Duplication de gène</term><term>Délétion de gène</term><term>Famille multigénique</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Simulation numérique</term><term>Spéciation génétique</term><term>Spécificité d'espèce</term><term>Transfert horizontal de gène</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Reconciliations between gene and species trees have important applications in the study of genome evolution (e.g. sequence orthology prediction or quantification of transfer events). While numerous methods have been proposed to infer them, little has been done to study the underlying reconciliation space. In this paper, we characterise the reconciliation space for two evolutionary models: the [Formula: see text] (duplication, loss and transfer) model and a variant of it-the no-[Formula: see text] model-which does not allow [Formula: see text] events (a transfer immediately followed by a loss). We provide formulae to compute the size of the corresponding spaces and define a set of transformation operators sufficient to explore the entire reconciliation space. We also define a distance between two reconciliations as the minimal number of operations needed to transform one into the other and prove that this distance is easily computable in the no-[Formula: see text] model. Computing this distance in the [Formula: see text] model is more difficult and it is an open question whether it is NP-hard or not. 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