Modelling phylogenetic relationships using reticulated networks

Abstract

Makarenkov, V., Legendre, P. & Desdevises, Y. (2004). Modelling phylogenetic relationships using reticulated networks. — Zoologica Scripta, 33, 89–96.Most traditional methods of phylogenetic analysis assume that species evolution can be represented by means of a bifurcating tree model. In many phylogenetic situations, however, some of the evolutionary links between species are due to reticulate evolution. For instance, reticulate models can adequately describe such complicated mechanisms as lateral gene transfer in bacteria or species hybridization. The theoretical concepts of reticulate evolution developed in the 1980s and 1990s need to be supported by appropriate analytical tools and software. In this paper, we present the main features of a new distance‐based method for modelling phylogenetic relationships among species by means of reticulated networks (RNs). The method uses the least‐squares model to build a RN by gradually improving upon the solution provided by a phylogenetic tree. A computer program facilitating the reconstruction and visualization of reticulate phylogenies is made available to researchers. In the application section, we illustrate the usefulness of the method by studying the evolution of honeybees (genus Apis). The method for reconstructing RNs has been included in the T‐Rex (Tree and Reticulogram Reconstruction) package recently developed by the first‐named author.