Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

GOLOBOFF, PABLO A.; TORRES, AMBROSIO; ARIAS, J. SALVADOR

CLADISTICS (PRINT)

WILEY-BLACKWELL PUBLISHING, INC

Año: 2017

0748-3007

One of the lasting controversies in phylogenetic inference is the degree to which specific evolutionary models should influencethe choice of methods. Model-based approaches to phylogenetic inference (likelihood, Bayesian) are defended on the premisethat without explicit statistical models there is no science, and parsimony is defended on the grounds that it provides the bestrationalization of the data, while refraining from assigning specific probabilities to trees or character-state reconstructions.Authors who favour model-based approaches often focus on the statistical properties of the methods and models themselves,but this is of only limited use in deciding the best method for phylogenetic inference?such decision also requires consideringthe conditions of evolution that prevail in nature. Another approach is to compare the performance of parsimony and modelbased methods in simulations, which traditionally have been used to defend the use of models of evolution for DNA sequences.Some recent papers, however, have promoted the use of model-based approaches to phylogenetic inference for discrete morphological data as well. These papers simulated data under models already known to be unfavourable to parsimony, and modelledmorphological evolution as if it evolved just like DNA, with probabilities of change for all characters changing in concert alongtree branches. The present paper discusses these issues, showing that under reasonable and less restrictive models of evolutionfor discrete characters, equally weighted parsimony performs as well or better than model-based methods, and that parsimonyunder implied weights clearly outperforms all other methods.