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Molecular Biology and Evolution 18:97-99 (2001)
© 2001 Society for Molecular Biology and Evolution

LETTER

Recombination Analysis Using Directed Graphical Models

Korbinian Strimmer*, Carsten Wiuf{dagger} and Vincent Moulton{ddagger}

*Department of Zoology and
{dagger}Department of Statistics, University of Oxford, Oxford, England; and
{ddagger}FMI, Physics and Mathematics Department, Mid Sweden University, Sundsvall, Sweden

In Strimmer and Moulton (2000)Citation , we described a method for computing the likelihood of a set of sequences assuming a phylogenetic network as an evolutionary hypothesis. That approach relied on converting a given graph into a directed graphical model or stochastic network from which all desired probability distributions could be derived. In particular, we investigated how to compute likelihoods using split-graphs (Huson 1998Citation ). However, in the presence of recombination, split-graphs may not provide an appropriate choice of the underlying graph. In this letter, we propose basing the stochastic network on an ancestral recombination graph (ARG) (Hudson 1983Citation ; Griffiths and Marjoram 1996, 1997Citation ). We show that our approach using directed graphical models extends in a straightforward fashion to ARGs, and we outline the computation of their likelihoods. In particular, we provide an example of an ARG whose likelihood is greater than that of a competing nonnested tree, . . . [Full Text of this Article]

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