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ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps

hal.structure.identifierEvolutionary Biology and Ecology of Algae [EBEA]
hal.structure.identifierUniversité Pierre et Marie Curie - Paris 6 [UPMC]
hal.structure.identifierSorbonne Université [SU]
dc.contributor.authorBECHELER, Ronan
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorMASSON, Jean-Pierre
hal.structure.identifierMARine Biodiversity Exploitation and Conservation [UMR MARBEC]
dc.contributor.authorARNAUD-HAOND, Sophie
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorHALKETT, Fabien
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorMARIETTE, Stéphanie
hal.structure.identifierEvolutionary Biology and Ecology of Algae [EBEA]
hal.structure.identifierUniversité Pierre et Marie Curie - Paris 6 [UPMC]
hal.structure.identifierSorbonne Université [SU]
hal.structure.identifierFacultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas
dc.contributor.authorGUILLEMIN, Marie-Laure
hal.structure.identifierEvolutionary Biology and Ecology of Algae [EBEA]
hal.structure.identifierUniversité Pierre et Marie Curie - Paris 6 [UPMC]
hal.structure.identifierSorbonne Université [SU]
dc.contributor.authorVALERO, Myriam
hal.structure.identifierEvolutionary Biology and Ecology of Algae [EBEA]
hal.structure.identifierUniversité Pierre et Marie Curie - Paris 6 [UPMC]
hal.structure.identifierSorbonne Université [SU]
dc.contributor.authorDESTOMBE, Christophe
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorSTOECKEL, Solenn
dc.date.issued2017-11
dc.identifier.issn1755-098X
dc.description.abstractEnPartial clonality is commonly used in eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal vs. sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent populations, using an extended Wright–Fisher model explicitly integrating reproductive modes. Our model provides posterior probability distribution of inferred c, given the assumed rates of mutation, as well as inbreeding and selfing when occurring. Tested under various conditions, this model provided accurate inferences of c, especially when the amount of information was modest, that is low sample sizes, few loci, low polymorphism and strong linkage disequilibrium. Inferences remained robust when mutation models and rates were misinformed. However, the method was sensitive to moderate frequencies of null alleles and when the time interval between required samplings exceeding two generations. Misinformed rates on mating modes (inbreeding and selfing) also resulted in biased inferences. Our method was tested on eleven data sets covering five partially clonal species, for which the extent of clonality was formerly deciphered. It delivered highly consistent results with previous information on the biology of those species. ClonEstiMate represents a powerful tool for detecting and inferring clonality in finite populations, genotyped with SNPs or microsatellites. It is freely available at https://www6.rennes.inra.fr/igepp_eng/Productions/Software.
dc.description.sponsorshipUne révision en profondeur de la Génétique des Populations et de la Génomique des Organismes clonaux - ANR-11-BSV7-0007
dc.language.isoen
dc.publisherWiley/Blackwell
dc.subjectautoincompatibilité
dc.subjecteucaryote
dc.subjectapproche bayésienne
dc.subjectreproduction clonale
dc.subjectécologie végétale
dc.subjectendogamie
dc.subjectclonalite
dc.subjectlogiciel
dc.subject.eninstantaneous inference
dc.subject.eninbreeding
dc.subject.enpopulation genetics model
dc.subject.ensoftware
dc.subject.enselfing
dc.subject.enrate of asexuality
dc.subject.enselfincompatibility
dc.title.enClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps
dc.typeArticle de revue
dc.identifier.doi10.1111/1755-0998.12698
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalMolecular Ecology Resources
bordeaux.pagee251–e267
bordeaux.volume17
bordeaux.issue6
bordeaux.peerReviewedoui
hal.identifierhal-01608371
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01608371v1
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