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Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference (1996)
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| Venue: | J. Mol. Evol |
| Citations: | 243 - 12 self |
BibTeX
@ARTICLE{Rannala96probabilitydistribution,
author = {Bruce Rannala and Ziheng Yang},
title = {Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference},
journal = {J. Mol. Evol},
year = {1996},
volume = {43},
pages = {304--311}
}
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Abstract
. A new method is presented for inferring evolutionary trees using nucleotide sequence data. The birth--death process is used as a model of speciation and extinction to specify the prior distribution of phylogenies and branching times. Nucleotide substitution is modeled by a continuous-time Markov process. Parameters of the branching model and the substitution model are estimated by maximum likelihood. The posterior probabilities of different phylogenies are calculated and the phylogeny with the highest posterior probability is chosen as the best estimate of the evolutionary relationship among species. We refer to this as the maximum posterior probability (MAP) tree. The posterior probability provides a natural measure of the reliability of the estimated phylogeny. Two example data sets are analyzed to infer the phylogenetic relationship of human, chimpanzee, gorilla, and orangutan. The best trees estimated by the new method are the same as those from the maximum likelihood analysis of...
Keyphrases
new method molecular evolutionary tree phylogenetic inference probability distribution posterior probability substitution model natural measure maximum posterior probability evolutionary relationship nucleotide substitution different phylogeny nucleotide sequence data prior distribution example data set evolutionary tree birth death process branching model maximum likelihood maximum likelihood analysis continuous-time markov process phylogenetic relationship
