Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 25, Issue 6, Pages 1054-1066Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msn042
Keywords
heterotachy; covarion; phylogenetics; maximum likelihood; mixed model; evolutionary heterogeneity; mixed branch length
Funding
- NIGMS NIH HHS [R01 GM062351, GM62351] Funding Source: Medline
Ask authors/readers for more resources
Evolutionary relationships are typically inferred from molecular sequence data using a statistical model of the evolutionary process. When the model accurately reflects the underlying process, probabilistic phylogenetic methods recover the correct relationships with high accuracy. There is ample evidence, however, that models commonly used today do not adequately reflect real-world evolutionary dynamics. Virtually all contemporary models assume that relatively fast-evolving sites are fast across the entire tree, whereas slower sites always evolve at relatively slower rates. Many molecular sequences, however, exhibit site-specific changes in evolutionary rates, called heterotachy. Here we examine the accuracy of 2 phylogenetic methods for incorporating heterotachy, the mixed branch length model-which incorporates site-specific rate changes by summing likelihoods over multiple sets of branch lengths on the same tree-and the covarion model, which uses a hidden Markov process to allow sites to switch between variable and invariable as they evolve. Under a variety of simple heterogeneous simulation conditions, the mixed model was dramatically more accurate than homotachous models, which were subject to topological biases as well as biases in branch length estimates. When data were simulated with strong versions of the types of heterotachy observed in real molecular sequences, the mixed branch length model was more accurate than homotachous techniques. Analyses of empirical data sets confirmed that the mixed branch length model can improve phylogenetic accuracy under conditions that cause homotachous models to fail. In contrast, the covarion model did not improve phylogenetic accuracy compared with homotachous models and was sometimes substantially less accurate. We conclude that a mixed branch length approach, although not the solution to all phylogenetic errors, is a valuable strategy for improving the accuracy of inferred trees.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available