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Systematic Biology Advance Access originally published online on June 12, 2009
Systematic Biology 2009 58(2):167-183; doi:10.1093/sysbio/syp018
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© Society of Systematic Biologists

A Method for Investigating Relative Timing Information on Phylogenetic Trees

Daniel Ford1, Frederick A. Matsen2,* and Tanja Stadler3

1 Google Inc., 1600 Amphitheatre Parkway, Mountain View, CA 94043, USA
2 Department of Statistics, University of California, Berkeley, 367 Evans Hall #429, Berkeley, CA 94720-3860, USA
3 Institut für Integrative Biologie, ETH Zentrum/CHN K 12.2, Universitätstrasse 16, 8092 Zürich, Switzerland

* Correspondence to be sent to: Department of Statistics, University of California, Berkeley, 367 Evans Hall #429, Berkeley, CA 94720-3860, USA; E-mail: matsen{at}berkeley.edu.


  Abstract

In this paper, we present a new way to describe the timing of branching events in phylogenetic trees. Our description is in terms of the relative timing of diversification events between sister clades; as such it is complementary to existing methods using lineages-through-time plots which consider diversification in aggregate. The method can be applied to look for evidence of diversification happening in lineage-specific "bursts", or the opposite, where diversification between 2 clades happens in an unusually regular fashion. In order to be able to distinguish interesting events from stochasticity, we discuss 2 classes of neutral models on trees with relative timing information and develop a statistical framework for testing these models. These model classes include both the coalescent with ancestral population size variation and global rate speciation–extinction models. We end the paper with 2 example applications: first, we show that the evolution of the hepatitis C virus deviates from the coalescent with arbitrary population size. Second, we analyze a large tree of ants, demonstrating that a period of elevated diversification rates does not appear to have occurred in a bursting manner.

Keywords: Branch length; key innovation; neutral models; phylogenetics

Received March 14, 2008; Revised May 30, 2008; Accepted January 10, 2009

All authors contributed equally to this manuscript.

Associate Editor: Cécile Ané


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