  Understanding the evolution of binary traits, which affects the birth and
survival of species and also the rate of molecular evolution, remains
challenging. A typical example is the evolution of mating systems in plant
species. In this work, we present a probabilistic modeling framework for binary
trait, random species trees, in which the number of species and their traits
are represented by a two-type, continuous time Markov branching process. We
develop our model by considering the impact of mating systems on dN/dS, the
ratio of nonsynonymous to synonymous substitutions. A methodology is introduced
which enables us to match model parameters with parameter estimates from
phylogenetic tree data. The properties obtained from the model are applied to
outcrossing and selfing species trees in the Geraniaceae and Solanaceae family.
This allows us to investigate not only the branching tree rates, but also the
mutation rates and the intensity of selection.
