PROBABILITY-DISTRIBUTION OF MOLECULAR EVOLUTIONARY TREES - A NEW METHOD OF PHYLOGENETIC INFERENCE

A new method is presented for inferring evolutionary trees using nucle otide sequence data. The birth-death process is used as a model of spe ciation and extinction to specify the prior distribution of phylogenie s and branching times. Nucleotide substitution is modeled by a continu ous-time Markov process. Parameters of the branching model and the sub stitution model are estimated by maximum likelihood. The posterior pro babilities of different phylogenies are calculated and the phylogeny w ith the highest posterior probability is chosen as the best estimate o f the evolutionary relationship among species. We refer to this as the maximum posterior probability (MAP) tree, The posterior probability p rovides a natural measure of the reliability of the estimated phylogen y. Two example data sets are analyzed to infer the phylogenetic relati onship of human, chimpanzee, gorilla, and orangutan, The best trees es timated by the new method are the same as those from the maximum likel ihood analysis of separate topologies, but the posterior probabilities are quite different from the bootstrap proportions. The results of th e method are found to be insensitive to changes in the rate parameter of the branching process.