Estimating species phylogenies using coalescence times among sequences

Liang Liu, Lili Yu, Dennis K. Pearl, Scott V. Edwards

Research output: Contribution to journalArticlepeer-review

326 Scopus citations

Abstract

The estimation of species trees (phylogenies) is one of the most important problems in evolutionary biology, and recently, there has been greater appreciation of the need to estimate species trees directly rather than using gene trees as a surrogate. A Bayesian method constructed under the multispecies coalescent model can consistently estimate species trees but involves intensive computation, which can hinder its application to the phylogenetic analysis of large-scale genomic data. Many summary statistics-based approaches, such as shallowest coalescences (SC) and Global LAteSt Split (GLASS), have been developed to infer species phylogenies for multilocus data sets. In this paper, we propose 2 methods, species tree estimation using average ranks of coalescences (STAR) and species tree estimation using average coalescence times (STEAC), based on the summary statistics of coalescence times. It can be shown that the 2 methods are statistically consistent under the multispecies coalescent model. STAR uses the ranks of coalescences and is thus resistant to variable substitution rates along the branches in gene trees. A simulation study suggests that STAR consistently outperforms STEAC, SC, and GLASS when the substitution rates among lineages are highly variable. Two real genomic data sets were analyzed by the 2 methods and produced species trees that are consistent with previous results.

Original languageEnglish (US)
Pages (from-to)468-477
Number of pages10
JournalSystematic Biology
Volume58
Issue number5
DOIs
StatePublished - Oct 2009

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Fingerprint

Dive into the research topics of 'Estimating species phylogenies using coalescence times among sequences'. Together they form a unique fingerprint.

Cite this