Markov models provide many solutions for appropriate modeling of inapplicable morphological characters in phylogenetics

Abstract

AO_SCPLOWBSTRACTC_SCPLOWThis paper proposes new Markov models for phylogenetic inference with anatomically dependent (inapplicable) morphological characters. The proposed models can explicitly model an anatomical dependency in which one or several characters are allowed to evolve only within a specific state of the hierarchically upstream character. The new models come up in two main types depending on the type of character hierarchy. The functions for constructing custom character hierarchies are provided in the R package rphenoscate. The performance of the new models is assessed using theory and simulations. This paper provides practical recommendations for using the new models in Bayesian phylogenetic inference with RevBayes.