title: Reversible polymorphism-aware phylogenetic models and their application to tree inference.
abstract: 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.
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria; Vienna Graduate School of Population Genetics, Wien, Austria. Electronic address: dominik.schrempf@vetmeduni.ac.at.
authors.forename: Dominik
authors.initials: D
authors.lastname: Schrempf
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Austria.
authors.forename: Bui Quang
authors.initials: BQ
authors.lastname: Minh
authors.affiliation: Nuffield Department of Medicine, University of Oxford, UK; Oxford Martin School, University of Oxford, UK.
authors.forename: Nicola
authors.initials: N
authors.lastname: De Maio
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Austria.
authors.forename: Arndt
authors.initials: A
authors.lastname: von Haeseler
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria. Electronic address: carolin.kosiol@vetmeduni.ac.at.
authors.forename: Carolin
authors.initials: C
authors.lastname: Kosiol
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004058:Diffusion; D015186:Hominidae / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D011110:Polymorphism, Genetic; D013045:Species Specificity
keywords: Incomplete lineage sorting; Phylogenetics; Reversible polymorphism-aware phylogenetic model; Species tree; Substitution model