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Systematic Biology Advance Access originally published online on July 16, 2009
Systematic Biology 2009 58(5):468-477; doi:10.1093/sysbio/syp031
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© The Author(s) 2009. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Estimating Species Phylogenies Using Coalescence Times among Sequences

Liang Liu1,*, Lili Yu2, Dennis K. Pearl3 and Scott V. Edwards1

1 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: lliu{at}oeb.harvard.edu, sedwards{at}fas.harvard.edu
2 Department of Biostatistics, Georgia Southern University, Statesboro, GA 30460, USA; E-mail: lyu{at}georgiasouthern.edu
3 Department of Statistics,The Ohio State University, Columbus, OH 43210, USA; E-mail: dkp{at}stat.osu.edu

* Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; E-mail: lliu{at}oeb.harvard.edu.


  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.

Keywords: Coalescent model; gene tree; species tree

Received November 12, 2008; Revised December 22, 2008; Accepted May 11, 2009

Associate Editor: L. Lacey Knowles


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L. L. Knowles
Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes
Syst Biol, October 1, 2009; 58(5): 463 - 467.
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