When two trees go to war

TL;DR

This paper demonstrates that for data from two binary trees, various phylogenetic network models require the same minimum number of reticulations, unifying their complexity and resolving longstanding open questions.

Contribution

It proves the equivalence of different models' reticulation counts for two binary trees and addresses related complexity issues in phylogenetic network construction.

Findings

Minimum reticulations are equal across models for two binary trees.

Results hold when minimizing network level instead of reticulations.

Models diverge when data from three or more trees are used.

Abstract

Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate how they are related. In general, the model chosen influences the minimum number of reticulation events required. However, when one obtains the input data from two binary trees, we show that the minimum number of reticulations is independent of the model. The number of reticulations necessary to represent the trees, triplets, clusters (in the softwired sense) and characters (with unrestricted multiple crossover recombination) are all equal. Furthermore, we show that these results also hold when not the number of reticulations but the level of the constructed network is minimised. We use these unification results to settle several complexity questions that have been open in the field for some time. We also give explicit examples to show that already for data obtained from three binary trees the models begin to diverge.