Inferring Species Trees

Species trees are a basic and common type of phylogenetic tree whose tips are species, population and lineages. Inferring species trees is a growing area of research that uses many classical methods of phylogenetic inference, such as Bayesian or maximum likelihood methods, but differs from traditional phylogenetic analysis by explicitly modeling the stochastic evolution of gene trees, which in turn produce the directly observable DNA sequence data. Models for inference of species trees facilitate the analysis of, but do not require, data sets in which there is heterogeneity in the topologies and branch lengths of the underlying gene trees.