Until recently, it has been common practice for a phylogenetic analysis to use a single gene
sequence from a single individual organism as a proxy for an entire species. With
technological advances, it is now becoming more common to collect data sets containing
multiple gene loci and multiple individuals per species. These data sets often reveal the
need to directly model intraspecies polymorphism and incomplete lineage sorting in
phylogenetic estimation procedures. For a single species, coalescent theory is widely used …

We describe a full Bayesian framework for species tree estimation. We have attempted to
combine the best aspects of previous methods to provide joint inference of a species tree
topology, divergence times, population sizes, and gene trees from multiple genes sampled
from multiple individuals across a set of closely related species. We have achieved this by
extending BEAST to* BEAST (pronounced” star beast”), which is published below: