Mathematical Framework for Phylogenetic Birth-And-Death Models

TL;DR

This paper develops a rigorous mathematical framework for phylogenetic birth-and-death models, enabling more precise analysis of gene family evolution and related bioinformatics applications.

Contribution

It introduces a formal mathematical structure for phylogenetic birth-and-death models and provides an algorithm for likelihood computation in gain-loss-duplication scenarios.

Findings

Formal mathematical framework established

Algorithm for likelihood computation developed

Enhances analysis of genome evolution processes

Abstract

A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in bioinformatics analyses for the inference of evolutionary trees, and of functional associations between gene families, as well as for the quantification of various processes guiding genome evolution. Here we describe the mathematical formalism for phylogenetic birth-and-death models. We also present an algorithm for computing the likelihood in a gain-loss-duplication model.