A Beta-splitting model for evolutionary trees

TL;DR

This paper introduces a generalized Beta-splitting model for evolutionary trees that incorporates asymmetry and extinction, providing a flexible framework for modeling speciation and extinction processes with detailed probabilistic descriptions.

Contribution

It extends the Beta-splitting model to include asymmetric diversification and extinction, with a detailed probabilistic framework and algorithms for tree construction.

Findings

Provides probability formulas for various tree resolutions

Includes a continuous-time model with branch lengths

Offers code implementations in SageMath/python

Abstract

In this article, we construct a generalization of the Blum-Fran\c{c}ois Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric shares of diversification rates (or diversification `potential') between two sister species in an evolutionarily interpretable manner, as well as the addition of extinction to the model in a natural way. We describe the incremental evolutionary construction of a tree with n leaves by splitting or freezing extant lineages through the Generating, Organizing and Deleting processes. We then give the probability of any (binary rooted) tree under this model with no extinction, at several resolutions: ranked planar trees giving asymmetric roles to the first and second offspring species of a given species and keeping track of the order of the speciation events occurring during the creation of the tree, unranked planar trees, ranked non-planar trees and finally (unranked non-planar) trees. We also describe a continuous-time equivalent of the Generating, Organizing and Deleting processes where tree topology and branch-lengths are jointly modeled and provide code in SageMath/python for these algorithms.