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

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...

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Bibliographic Details
Published in:Systematic biology 2010-05, Vol.59 (3), p.288-297
Main Authors: Grievink, Liat Shavit, Penny, David, Hendy, Michael D., Holland, Barbara R.
Format: Article
Language:English
Subjects:
Accuracy
Bayes Theorem
Bayesian analysis
Classification - methods
Data Interpretation, Statistical
Datasets
Effects
Evolution, Molecular
Inference
Markov analysis
Markov Chains
Modeling
Models, Genetic
Monte Carlo Method
Monte Carlo simulation
Parametric models
Phylogenetics
Phylogeny
Regular
Sample Size
Simulations
Steels
Taxa
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Summary: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.
ISSN:1063-5157
1076-836X
DOI:10.1093/sysbio/syq003