General heterotachy and distance method adjustments.
Heterotachy is a general term to describe positions in a sequence that evolve at different rates in different lineages. Kolaczkowski and Thornton (2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.) recently described an intriguing heterotachy model that leads to topological bias for likelihood-based methods and parsimony methods. In this article, we show that heterotachy can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each site. Motivated by this idea, we propose a pairwise alpha heterotachy adjustment model, which gives us much improved topological estimation in the settings by Kolaczkowski and Thornton (2004).
Wu
Jihua
J
Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada. jihuaw@mathstat.dal.ca
Susko
Edward
E
D001483:Base Sequence; D002736:Chloroplasts / Q000235:genetics; D003198:Computer Simulation; D019143:Evolution, Molecular; D016013:Likelihood Functions; D008957:Models, Genetic; D015999:Multivariate Analysis; D010802:Phylogeny