title: Reconstructing reticulate evolution in species-theory and practice.
abstract: We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of Wayne Maddison's approach in his seminal 1997 paper. Our first method is a polynomial time algorithm for constructing phylogenetic networks from two gene trees contained inside the network. We allow the network to have an arbitrary number of reticulations, but we limit the reticulation in the network so that the cycles in the network are node-disjoint ("galled"). Our second method is a polynomial time algorithm for constructing networks with one reticulation, where we allow for errors in the estimated gene trees. Using simulations, we demonstrate improved performance of this method over both NeighborNet and Maddison's method.
authors.affiliation: Department of Computer Science, Rice University, 6100 Main Street, MS 132, Houston, TX 77005, USA. nakhleh@cs.rice.edu
authors.forename: Luay
authors.initials: L
authors.lastname: Nakhleh
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
authors.forename: C Randal
authors.initials: CR
authors.lastname: Linder
authors.forename: Katherine
authors.initials: K
authors.lastname: St John
mesh_terms: D003198:Computer Simulation; D019143:Evolution, Molecular; D005787:Gene Frequency; D014644:Genetic Variation; D008957:Models, Genetic; D015233:Models, Statistical; D009154:Mutation; D010802:Phylogeny; D012641:Selection, Genetic