Apr 15, 2015

Capturing heterotachy through multi-gamma site models

BioRxiv : the Preprint Server for Biology
Remco Bouckaert, Peter Lockhart

Abstract

Most methods for performing a phylogenetic analysis based on sequence alignments of gene data assume that the mechanism of evolution is constant through time. It is recognised that some sites do evolve somewhat faster than others, and this can be captured using a (gamma) rate heterogeneity model. Further, some species have shorter replication times than others, and this results in faster rates of substitution in some lineages. This feature of lineage specific rate variation can be captured to some extent, by using relaxed clock models. However, it is also clear that there are additional poorly characterised features of sequence data that can sometimes lead to extreme differences in lineage specific rates. This variation is poorly captured by constant time reversible substitution models. The significance of extreme lineage specific rate differences is that they lead both to errors in reconstructing evolutionary relationships as well as biased estimates for the age of ancestral nodes. We propose a new model that allows gamma rate heterogeneity to change on branches, thus offering a more realistic model of sequence evolution. It adds negligible computational cost to likelihood calculations. We illustrate its effectiveness with an ...Continue Reading

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Mentioned in this Paper

Genes
Virus Replication
Phylogenetic Analysis
Site
Chlorophyta
Chemical Substitution
Species
Branching (Qualifier Value)
Biological Evolution
Anatomic Node

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