Comparing the topology of phylogenetic network generators

TL;DR

This paper compares various stochastic phylogenetic network generators by analyzing their topological features, highlighting differences in the structures they produce and aiding in their selection for evolutionary studies.

Contribution

It provides a systematic comparison of multiple phylogenetic network generators based on topological summary statistics, addressing a gap in the evaluation of these tools.

Findings

Different generators produce distinct topological profiles.

Reticulation number influences network topology.

Insights aid in selecting appropriate network generators.

Abstract

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive representation of evolutionary history compared to phylogenetic trees. Stochastic processes for generating random trees or networks are important tools in evolutionary analysis, especially in phylogeny reconstruction where they can be utilized for validation or serve as priors for Bayesian methods. However, as more network generators are developed, there is a lack of discussion or comparison for different generators. To bridge this gap, we compare a set of phylogenetic network generators by profiling topological summary statistics of the generated networks over the number of reticulations and comparing the topological profiles.