Data from: A covarion model for phylogenetic estimation using discrete morphological datasets

The rate of evolution of a single morphological character is not
homogeneous across the phylogeny, and this rate heterogeneity varies
between morphological characters. However, traditional models of
morphological character evolution often assume that all characters evolve
according to a time-homogeneous Markov process, which applies uniformly
across the entire phylogeny. While models incorporating among-character
rate variation alleviate the assumption of the same rate for all
characters, they still fail to address lineage-specific rate variation for
individual characters. The covarion model, originally developed for
molecular data to model the invariability of some sites for parts of the
phylogeny, provides a promising framework for addressing this issue in
morphological phylogenetics. In this study, we extend the covarion model
in RevBayes to morphological character evolution, which we call the
covariomorph model, and apply it to a diverse range of morphological
datasets. Our covariomorph model utilizes multiple rate categories derived
from a discretized probability distribution, which scales rate matrices
accordingly. Characters are allowed to evolve within any of these rate
categories, with the possibility of switching between rate categories
during the evolutionary process. We verified our implementation of the
covariomorph model with the help of simulations. Additionally, we examined
164 empirical datasets, finding covarion-like rate variation in
approximately half of them. Upon further examination of two focal datasets
that exhibited covarion-like rate variation, we found that the
covariomorph model provides a more nuanced approach to incorporate rate
variation across lineages, significantly affecting the resulting tree
topology and branch lengths compared to traditional models. The observed
sensitivity of branch lengths to model choice underscores potential
implications of this approach for divergence time estimation and
evolutionary rate calculations. By accounting for lineage- and character-
specific rate shifts, the covariomorph model offers a robust framework to
improve the accuracy of morphological phylogenetic inference.