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dc.contributor.authorDe Maio, Nicola
dc.contributor.authorSchrempf, Dominik
dc.contributor.authorKosiol, Carolin
dc.date.accessioned2017-02-09T13:30:19Z
dc.date.available2017-02-09T13:30:19Z
dc.date.issued2015-11
dc.identifier.citationDe Maio , N , Schrempf , D & Kosiol , C 2015 , ' PoMo : an allele frequency-based approach for species tree estimation ' , Systematic Biology , vol. 64 , no. 6 , pp. 1018-1031 . https://doi.org/10.1093/sysbio/syv048en
dc.identifier.issn1063-5157
dc.identifier.otherPURE: 249098610
dc.identifier.otherPURE UUID: 299eb682-af44-4826-aacf-153a43a2127f
dc.identifier.otherPubMed: 26209413
dc.identifier.otherPubMedCentral: PMC4604832
dc.identifier.otherScopus: 84946105401
dc.identifier.urihttp://hdl.handle.net/10023/10257
dc.descriptionThis work was supported by a grant from the Austrian Science Fund (FWF, P24551-B25 to C.K.). N.D.M. and D.S. were members of the Vienna Graduate School of Population Genetics which is supported by a grant of the Austrian Science Fund (FWF, W1225-B20). N.D.M. was partially supported by the Institute for Emerging Infections, funded by the Oxford Martin School.en
dc.description.abstractIncomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches.
dc.format.extent14
dc.language.isoeng
dc.relation.ispartofSystematic Biologyen
dc.rights© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.subjectIncomplete lineage sortingen
dc.subjectPhylogeneticsen
dc.subjectPoMoen
dc.subjectSpecies treeen
dc.subjectQH301 Biologyen
dc.subjectQH426 Geneticsen
dc.subjectBDCen
dc.subjectR2Cen
dc.subject.lccQH301en
dc.subject.lccQH426en
dc.titlePoMo : an allele frequency-based approach for species tree estimationen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.School of Biologyen
dc.contributor.institutionUniversity of St Andrews.Centre for Biological Diversityen
dc.identifier.doihttps://doi.org/10.1093/sysbio/syv048
dc.description.statusPeer revieweden


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