An algorithm for constructing local regions in a phylogenetic network

The groupings of taxa in a phylogenetic tree cannot represent all the confl icting signals that usually occur among site patterns in aligned homologous genetic sequences. Hence a tree-building program must compromise by report ing a subset of the patterns, using some discriminatory criterion. Thus, in the worst case, out of possibly a large number of equally good trees, only an arbitrarily chosen tree might be reported by the tree-building program as "The Tree." This tree might then be used as a basis for phylogenetic con clusions. One strategy to represent conflicting patterns in the data is to construct a network. The Buneman graph is a theoretically very attractive e xample of such a network. In particular, a characterization for when this n etwork will be a tree is known. Also the Buneman graph contains each of the most parsimonious trees indicated by the data. In this paper we describe a new method for constructing the Buneman graph that can be used for a gener alization of Hadamard conjugation to networks. This new method differs from previous methods by allowing us to focus on local regions of the graph wit hout having to first construct the full graph. The construction is illustra ted by an example. (C) 2001 Academic Press.