A survey of the monotonicity and non-contradiction of consensus methods and supertree methods

TL;DR

This survey investigates the properties of consensus and supertree methods in phylogenetics, focusing on their monotonicity and consistency when new data or insights are introduced, and identifies both limitations and positive results for common methods.

Contribution

The paper analyzes monotonicity and non-contradiction properties of consensus and supertree methods, providing new insights into their robustness and identifying classes of methods with desirable properties.

Findings

Majority rule and strict consensus methods are monotonic.

Some consensus methods are inherently non-monotonic, leading to potential conflicts.

Infinitely many consensus methods possess monotonicity and other favorable properties.

Abstract

In a recent study, Bryant, Francis and Steel investigated the concept of \enquote{future-proofing} consensus methods in phylogenetics. That is, they investigated if such methods can be robust against the introduction of additional data like added trees or new species. In the present manuscript, we analyze consensus methods under a different aspect of introducing new data, namely concerning the discovery of new clades. In evolutionary biology, often formerly unresolved clades get resolved by refined reconstruction methods or new genetic data analyses. In our manuscript we investigate which properties of consensus methods can guarantee that such new insights do not disagree with previously found consensus trees, but merely refine them, a property termed \emph{monotonicity}. Along the lines of analyzing monotonicity, we also study two {established} supertree methods, namely Matrix Representation with Parsimony (MRP) and Matrix Representation with Compatibility (MRC), which have also been suggested as consensus methods in the literature. While we (just like Bryant, Francis and Steel in their recent study) unfortunately have to conclude some negative answers concerning general consensus methods, we also state some relevant and positive results concerning the majority rule ($\mathtt{MR}$) and strict consensus methods, which are amongst the most frequently used consensus methods. Moreover, we show that there exist infinitely many consensus methods which are monotonic and have some other desirable properties. \textbf{Keywords:} consensus tree, phylogenetics, majority rule, tree refinement, matrix representation with parsimony \textbf{MSC:} C92B05, 05C05