Axiomatic opportunities and obstacles for inferring a species tree from gene trees

TL;DR

This paper explores the theoretical limitations and opportunities in inferring species trees from gene trees, especially under incomplete taxon coverage, and discusses a concordance-based consensus method.

Contribution

It identifies axiomatic constraints for species tree inference methods and analyzes their feasibility, introducing a concordance-based approach and extensions for supertrees.

Findings

Certain desirable properties cannot all be satisfied simultaneously in supertree settings.

It is possible to satisfy some properties when taxon coverage is complete.

Proposes a concordance-based consensus method and its extension to supertrees.

Abstract

The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all taxa are present in every gene tree. Here, we list four apparently desirable properties that a method for estimating a species tree from gene trees could have (the strongest property states that building a species tree from input gene trees and then pruning leaves gives a tree that is the same as, or more resolved than, the tree obtained by first removing the taxa from the input trees and then building the species tree). We show that while it is technically possible to simultaneously satisfy these properties when taxon coverage is complete, they cannot all be satisfied in the more general supertree setting. In part two, we discuss a concordance-based consensus method based on Baum's `plurality clusters', and an extension to concordance supertrees.