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

Dominik Schrempf, Bui Quang Minh, Nicola De Maio, Arndt von Haeseler, Carolin Kosiol

Research output: Contribution to journalArticlepeer-review

50 Citations (Scopus)
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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.

Original languageEnglish
Pages (from-to)362-370
Number of pages9
JournalJournal of Theoretical Biology
Early online date29 Jul 2016
Publication statusPublished - 21 Oct 2016


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


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