Likelihood analysis of phylogenetic networks using directed graphical models

Strimmer, Korbinian and Moulton, Vincent ORCID: (2000) Likelihood analysis of phylogenetic networks using directed graphical models. Molecular Biology and Evolution, 17 (6). pp. 875-881. ISSN 1537-1719

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A method for computing the likelihood of a set of sequences assuming a phylogenetic network as an evolutionary hypothesis is presented. The approach applies directed graphical models to sequence evolution on networks and is a natural generalization of earlier work by Felsenstein on evolutionary trees, including it as a special case. The likelihood computation involves several steps. First, the phylogenetic network is rooted to form a directed acyclic graph (DAG). Then, applying standard models for nucleotide/amino acid substitution, the DAG is converted into a Bayesian network from which the joint probability distribution involving all nodes of the network can be directly read. The joint probability is explicitly dependent on branch lengths and on recombination parameters (prior probability of a parent sequence). The likelihood of the data assuming no knowledge of hidden nodes is obtained by marginalization, i.e., by summing over all combinations of unknown states. As the number of terms increases exponentially with the number of hidden nodes, a Markov chain Monte Carlo procedure (Gibbs sampling) is used to accurately approximate the likelihood by summing over the most important states only. Investigating a human T-cell lymphotropic virus (HTLV) data set and optimizing both branch lengths and recombination parameters, we find that the likelihood of a corresponding phylogenetic network outperforms a set of competing evolutionary trees. In general, except for the case of a tree, the likelihood of a network will be dependent on the choice of the root, even if a reversible model of substitution is applied. Thus, the method also provides a way in which to root a phylogenetic network by choosing a node that produces a most likely network.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Depositing User: EPrints Services
Date Deposited: 01 Oct 2010 13:42
Last Modified: 15 Dec 2022 01:57
DOI: 10.1093/oxfordjournals.molbev.a026367

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