# Modeling trait-dependent evolution on a random species tree

## TL;DR

This paper introduces a probabilistic framework for modeling the evolution of binary traits on species trees, linking mating systems to molecular evolution rates and applying it to plant families to analyze evolutionary dynamics.

## Contribution

It develops a novel Markov process-based model for trait-dependent species evolution and provides a method to estimate parameters from phylogenetic data.

## Key findings

- Differences in mutation rates between outcrossing and selfing species.
- Variation in selection intensity linked to mating systems.
- Model successfully applied to Geraniaceae and Solanaceae data.

## Abstract

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.