A General Method for Simultaneously Accounting for Phylogenetic and Species Sampling Uncertainty via Rubin’s Rules in Comparative Analysis

Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species’ trait evolution. These methods, however, usually assume that phylogenetic trees are known without error or uncertainty, but this assumption is most likely incorrect. So far, Markov chain Monte Carlo (MCMC)-based Bayesian methods have mainly been deployed to account for such “phylogenetic uncertainty” in PCMs....