New Phylogenetic Markov Models for Inapplicable Morphological Characters

This article 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 article provides practical recommendations for using the new models in Bayesian phylogenetic inference with RevBayes. [Bayesian; inapplicable characters; likelihood; Markov models; morphology; parsimony; RevBayes.]