Reversible polymorphism-aware phylogenetic models and their application to tree inference
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We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction.
Schrempf , D , Minh , B Q , De Maio , N , von Haeseler , A & Kosiol , C 2016 , ' Reversible polymorphism-aware phylogenetic models and their application to tree inference ' Journal of Theoretical Biology , vol 407 , pp. 362-370 . DOI: 10.1016/j.jtbi.2016.07.042
Journal of Theoretical Biology
© 2016 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
This work is supported by the Austrian Science Fund (FWF-P24551 and I-2805-B29) and partially by the Vienna Graduate School of Population Genetics (FWF-W1225).
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