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Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree


Grievink, LS and Penny, D and Hendy, MD and Holland, BR, Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree, Systematic Biology, 59, (3) pp. 288-297. ISSN 1063-5157 (2010) [Refereed Article]


Copyright Statement

© The Author(s) 2010. Published by Oxford University Press on behalf of Society of Systematic Biologists.

DOI: doi:10.1093/sysbio/syq003


Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree with 4 lineages where 2 nonsister taxa undergo a change in the proportion of variable sites tree reconstruction under the best-fitting model, which is chosen using a relative test, often results in the wrong tree. In this case, we found that an absolute test of model fit is a better predictor of tree estimation accuracy. We also found further evidence that MP is not immune to heterotachy. In addition, we show that increased sampling of taxa that have undergone a change in proportion and positions of variable sites is critical for accurate tree reconstruction.

Item Details

Item Type:Refereed Article
Keywords:Covarion model; heterotachy; model fit; phylogenetics; simulation; taxon sampling
Research Division:Biological Sciences
Research Group:Evolutionary biology
Research Field:Phylogeny and comparative analysis
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the mathematical sciences
UTAS Author:Holland, BR (Professor Barbara Holland)
ID Code:63281
Year Published:2010
Web of Science® Times Cited:15
Deposited By:Mathematics
Deposited On:2010-04-27
Last Modified:2010-04-30
Downloads:397 View Download Statistics

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