Limitations, controversies, and recommendations in phylogenetic analyses: a guide for evolutionary inferences

Abstract

Phylogenetic reconstructions are essential for understanding the evolution of organisms and classifying them according to their ancestry-descent relationships. Comparative biology studies are increasingly incorporating phylogenetic information to explain how living organisms have evolved. Advances in molecular techniques and bioinformatics have facilitated phylogenetic analysis, which has generated controversy among evolutionary biologists, as some new methods are seen as neglecting basic principles. This essay shows that maximum likelihood and Bayesian inference approaches provides evidence for the monophyly of the study groups. The article addresses common issues in the interpretation of phylogenetic trees, such as the confusion between “basal” and “derived” nodes and the inappropriate use of bootstrap values. Character-based methods –such as parsimony, maximum likelihood and Bayesian inference– are compared with distance-based approaches, such as Neighbor-Joining. This study offers practical recommendations to improve the robustness of phylogenetic inferences, emphasizing the importance of integrating multiple methods and critically evaluating supporting indicators to achieve more reliable evolutionary interpretations.