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dc.contributor.authorBorges, Rui
dc.contributor.authorKosiol, Carolin
dc.date.accessioned2020-01-06T16:30:03Z
dc.date.available2020-01-06T16:30:03Z
dc.date.issued2020-02-07
dc.identifier.citationBorges , R & Kosiol , C 2020 , ' Consistency and identifiability of the polymorphism-aware phylogenetic models ' , Journal of Theoretical Biology , vol. 486 , 110074 , pp. 1-6 . https://doi.org/10.1016/j.jtbi.2019.110074en
dc.identifier.issn0022-5193
dc.identifier.otherPURE: 263615679
dc.identifier.otherPURE UUID: edf624b8-7fad-40ad-866b-483a2faed82f
dc.identifier.otherScopus: 85075174472
dc.identifier.otherWOS: 000508488900014
dc.identifier.urihttp://hdl.handle.net/10023/19229
dc.descriptionFunding: Vienna Science and Technology Fund (WWTF) [MA16-061].en
dc.description.abstractPolymorphism-aware phylogenetic models (PoMo) constitute an alternative approach for species tree estimation from genome-wide data. PoMo builds on the standard substitution models of DNA evolution but expands the classic alphabet of the four nucleotide bases to include polymorphic states. By doing so, PoMo accounts for ancestral and current intra-population variation, while also accommodating population-level processes ruling the substitution process (e.g. genetic drift, mutations, allelic selection). PoMo has shown to be a valuable tool in several phylogenetic applications but a proof of statistical consistency (and identifiability, a necessary condition for consistency) is lacking. Here, we prove that PoMo is identifiable and, using this result, we further show that the maximum a posteriori (MAP) tree estimator of PoMo is a consistent estimator of the species tree. We complement our theoretical results with a simulated data set mimicking the diversity observed in natural populations exhibiting incomplete lineage sorting. We implemented PoMo in a Bayesian framework and show that the MAP tree easily recovers the true tree for typical numbers of sites that are sampled in genome-wide analyses.
dc.format.extent6
dc.language.isoeng
dc.relation.ispartofJournal of Theoretical Biologyen
dc.rightsCopyright © 2019 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license. (http://creativecommons.org/licenses/by/4.0/)en
dc.subjectPolymorphism-aware modelsen
dc.subjectPhylogeneticsen
dc.subjectSpecies tree estimationen
dc.subjectConsistencyen
dc.subjectIdentifiabilityen
dc.subjectQH301 Biologyen
dc.subjectQH426 Geneticsen
dc.subjectSB Plant cultureen
dc.subjectT-NDASen
dc.subject.lccQH301en
dc.subject.lccQH426en
dc.subject.lccSBen
dc.titleConsistency and identifiability of the polymorphism-aware phylogenetic modelsen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.Centre for Biological Diversityen
dc.contributor.institutionUniversity of St Andrews.School of Biologyen
dc.identifier.doihttps://doi.org/10.1016/j.jtbi.2019.110074
dc.description.statusPeer revieweden


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