Inferring the root of a phylogenetic tree Journal Article


Author(s): Huelsenbeck, John P; Bollback, Jonathan P; Levine, Amy M
Article Title: Inferring the root of a phylogenetic tree
Affiliation
Abstract: Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.
Keywords: Models, Genetic; Computer Simulation; Phylogeny; Bayes Theorem; DNA/genetics; Databases, Nucleic Acid; Markov Chains
Journal Title: Systematic Biology
Volume: 51
Issue 1
ISSN: 1063-5157
Publisher: Oxford University Press  
Publication Place: England
Date Published: 2002-02-01
Start Page: 32
End Page: 43
Language: eng
DOI: 10.1080/106351502753475862
Open access: no