EvoPhylo: an R package for pre-and postprocessing of morphological data from relaxed clock Bayesian phylogenetics

Publication information:

Simões, TR, Greifer N, Barido-Sottani J, and Pierce SE. “EvoPhylo: An R Package for Pre-and Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics”. Methods in Ecology and Evolution 14, no. 1981–1993 (2023).

Abstract

  1. Relaxed clock Bayesian evolutionary inference (BEI) enables the co-estimation of phylogenetic trees and evolutionary parameters associated with models of character and lineage evolution. Fast advances in new model developments over the past decade have boosted BEI as a major macroevolutionary analytical framework using morphological and/or molecular data across vastly different study systems. However, there is limited availability of bioinformatic tools to pre- and postprocess data from BEI, such as identifying morphological data partitions, or statistically testing and creating publication quality plots of evolutionary hypotheses.
  2. Here, we introduce EvoPhylo, an r package to perform automated morphological character partitioning and analyse macroevolutionary parameter from relaxed clock (time-calibrated) BEI outputted by the programs Mr.Bayes and BEAST2. These include rates of evolution and mode of selection for each character partition, diversification rate parameters, and handling fossil-only posterior trees.
  3. We present the theoretical background behind EvoPhylo's functions and analytical tools for evolutionary hypothesis testing, its potential uses, and interpretation of its results with a series of vignettes and links to a step-by-step tutorial using examples from two empirical datasets.
  4. EvoPhylo will facilitate the use of Bayesian relaxed clocks as a tool for macroevolutionary inference across a wide range of users and fields of research, especially those that make usage of morphological datasets, from paleontological to total evidence dating analyses.
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