A Corrected Parsimony Criterion for Reconstructing Phylogenies

TL;DR

This paper introduces a corrected parsimony criterion for phylogenetic reconstruction that emphasizes characters as fundamental units, aiming to improve the accuracy of morphological data analysis.

Contribution

It proposes a new criterion that prioritizes character-based signals over step counts, addressing biases caused by previous methods.

Findings

Character-based weighting improves phylogenetic accuracy.

Retention index effectively quantifies character contribution.

Method reduces bias in morphological phylogenetic analysis.

Abstract

In phylogenetic analysis, for non-molecular data, particularly morphology, parsimony optimization is the most commonly employed approach. In the past and present application of the parsimony principle, extra step numbers have been added across different characters without proper justification. This practice, however, has caused the impacts of characters to be inflated or deflated without a valid reason. To resolve this methodological deficiency, here I present a corrected parsimony criterion for reconstructing phylogenies. In essence, character rather than step is the most fundamental unit. Accordingly, the most parsimonious tree should maximize the sum or average of the phylogenetic signals, quantified by retention index, contributed by each character. Assigning proper weights to characters is a separate task that requires information other than the intra-character step number changing range.