Evaluating strategies of phylogenetic analyses by the coherence of their results

TL;DR

This paper introduces a method to evaluate phylogenetic analysis strategies by measuring the consistency of their results across independent data, aiming to identify the most accurate approaches.

Contribution

It proposes a coherence-based evaluation method for phylogenetic strategies, linking result reproducibility to historical signal extraction.

Findings

More coherent results tend to indicate better analytical strategies

Robinson-Foulds distances effectively measure tree similarity

Risks of false positives and negatives are acknowledged

Abstract

I propose an approach to identify, among several strategies of phylogenetic analysis, those producing the most accurate results. This approach is based on the hypothesis that the more a result is reproduced from independent data, the more it reflects the historical signal common to the analysed data. Under this hypothesis, the capacity of an analytical strategy to extract historical signal should correlate positively with the coherence of the obtained results. I apply this approach to a series of analyses on empirical data, basing the coherence measure on the Robinson-Foulds distances between the obtained trees. At first approximation, the analytical strategies most suitable for the data produce the most coherent results. However, risks of false positives and false negatives are identified, which are difficult to rule out.