Apr 13, 2016

Reversible Polymorphism-Aware Phylogenetic Models and their Application to Tree Inference

BioRxiv : the Preprint Server for Biology
Dominik SchrempfCarolin Kosiol

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.

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Mentioned in this Paper

Computer Software
Gene Polymorphism
Pongidae
Genome
Trees (plant)
Reconstructive Surgical Procedures
Hominidae
Phylogenetic Analysis
Heparin Reversal Agent [EPC]
Sorting - Cell Movement

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