The algebraic $\alpha$-Ford tree under evolution

TL;DR

This paper models null phylogenetic trees as algebraic measure trees, analyzing their subtree structures and evolution using martingale methods to understand their statistical properties and similarities.

Contribution

It introduces an algebraic framework for phylogenetic trees and characterizes their evolution in the diffusion limit using martingale problem techniques.

Findings

Describes the law of subtree mass statistics for null models

Provides a diffusion limit characterization of evolving phylogenetic trees

Analyzes the similarity measures between real and simulated phylogenies

Abstract

Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic measure trees. This allows to describe the degree of similarity between actual and simulated phylogenies by focusing on the sample shape of subtrees and their subtree masses. We describe the annealed law of the statistics of subtree masses of null models, namely the branching tree, the coalescent tree, and the comb tree in more detail. Finally, we use methods from martingale problems to characterize evolving phylogenetic trees in the diffusion limit.