Phylogenetic networks, trees, and clusters

Abstract

Phylogenetic networks model evolutionary histories in the presence of non-treelike events such as hybrid speciation and horizontal gene transfer. In spite of their widely acknowledged importance, very little is known about phylogenetic networks, which have so far been studied mostly for specific datasets. Even when the evolutionary history of a set of species is non-treelike, individual genes in these species usually evolve in a treelike fashion. An important question, then, is whether a gene tree is "contained" inside a species network. This information is used to detect the presence of events such as horizontal gene transfer and hybrid speciation. Another question of interest for biologists is whether a group of taxa forms a clade based on a given phylogeny. This can be efficiently answered when the phylogeny is a tree simply by inspecting the edges of the tree, whereas no efficient solution currently exists for the problem when the phylogeny is a network. In this paper, we give polynomial-time algorithms for answering the above two questions. © Springer-Verlag Berlin Heidelberg 2005.