A maximum pseudo-likelihood approach for estimating species trees under the coalescent model.

ABSTRACT:

Background

Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE) of the species tree (topology, branch lengths, and population sizes) from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units.

Results

We show that the MPE of the species

SUBMITTER: Liu L 

PROVIDER: S-EPMC2976751 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature