An analytical comparison of coalescent-based multilocus methods: The three-taxon case

TL;DR

This paper provides a mathematical analysis of coalescent-based methods for inferring species trees from multilocus data, focusing on the three-taxon case and assuming accurate gene tree reconstruction.

Contribution

It offers an analytical comparison of various coalescent-based methods specifically for three-taxon species trees, highlighting their properties under ideal conditions.

Findings

Identifies differences in method performance for three-taxon cases.

Provides insights into the conditions under which methods agree or differ.

Lays groundwork for understanding method behavior in more complex scenarios.

Abstract

Incomplete lineage sorting (ILS) is a common source of gene tree incongruence in multilocus analyses. A large number of methods have been developed to infer species trees in the presence of ILS. Here we provide a mathematical analysis of several coalescent-based methods. Our analysis is performed on a three-taxon species tree and assumes that the gene trees are correctly reconstructed along with their branch lengths.