RT Journal Article
SR Electronic
T1 Reversible Polymorphism-Aware Phylogenetic Models and their Application to Tree Inference
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 048496
DO 10.1101/048496
A1 Dominik Schrempf
A1 Bui Quang Minh
A1 Nicola De Maio
A1 Arndt von Haeseler
A1 Carolin Kosiol
YR 2016
UL http://biorxiv.org/content/early/2016/04/13/048496.abstract
AB 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 specia-tion dating to species tree reconstruction.