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J Theor Biol. 2016 Oct 21;407:362-370. doi: 10.1016/j.jtbi.2016.07.042. Epub 2016 Jul 29.

Reversible polymorphism-aware phylogenetic models and their application to tree inference.

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Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria; Vienna Graduate School of Population Genetics, Wien, Austria. Electronic address:
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Austria.
Nuffield Department of Medicine, University of Oxford, UK; Oxford Martin School, University of Oxford, UK.
Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria. Electronic address:


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.


Incomplete lineage sorting; Phylogenetics; Reversible polymorphism-aware phylogenetic model; Species tree; Substitution model

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