Phylogenetic networks: modeling, reconstructibility, and accuracy

Abstract

Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.

Reconstruction of certain phylogenetic networks from the genomes at their leaves

“…The network is normal if from every vertex that is not in X there is a directed path to a vertex in X such that no vertex after the initial vertex is a hybrid vertex. This property is similar to the defining property in ''tree-child networks'' (Cardona et al, 2007) or the assumption about ''tree nodes'' in ''model phylogenetic networks'' (Moret et al, 2004).…”

“…Basic models of recombination were suggested by Hein (1990Hein ( , 1993. General frameworks are discussed in Bandelt and Dress (1992), Baroni et al (2004), Moret et al (2004), and Nakhleh et al (2005).…”

“…One commonly assumed property is that they be rooted acyclic ARTICLE IN PRESS www.elsevier.com/locate/yjtbi 0022-5193/$ -see front matter r 2008 Elsevier Ltd. All rights reserved. doi: 10.1016/j.jtbi.2008.02.015 digraphs (Strimmer and Moulton, 2000;Moret et al, 2004;Nakhleh et al, 2005). Another is a kind of time consistency at hybridization events, roughly that the parents of a hybrid be possibly contemporaneous (''temporal representation'' for , ''coexistence in time'' for Moret et al, 2004).…”

“…doi: 10.1016/j.jtbi.2008.02.015 digraphs (Strimmer and Moulton, 2000;Moret et al, 2004;Nakhleh et al, 2005). Another is a kind of time consistency at hybridization events, roughly that the parents of a hybrid be possibly contemporaneous (''temporal representation'' for , ''coexistence in time'' for Moret et al, 2004). Another is a condition called ''regularity'' in Baroni et al (2004) in which, among other properties, no two vertices have the same set of leaves as descendents.…”

Analyzing and reconstructing reticulation networks under timing constraints

“…By allowing for additional taxa that for instance correspond to unsampled or extinct taxa one can always transform a non-temporal reticulation network into a temporal one without introducing any new reticulation events (Baroni et al 2006;Moret et al 2004). For example, consider the reticulation network shown in Fig.…”