EvoPhylo: An r package for pre‐ and postprocessing of morphological data from relaxed clock Bayesian phylogenetics

2023/05/17 by Tiago R. Simões, Noah Greifer, Joëlle Barido‐Sottani +1 · 1 voice · 4 citations
Earth and Planetary Sciences · Environmental Science · Mathematics · #Ecology and Vegetation Dynamics Studies #Evolution and Paleontology Studies #Morphological variations and asymmetry

paper · pdf · doi:10.1111/2041-210x.14128

openalex publication_date 2023/05/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22

Abstract

Abstract 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. Here, we introduce E voPhylo, 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. 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. 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.

Citations

• Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
• A General Coefficient of Similarity and Some of Its Properties
• MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
• Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions
• RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
• Biases with the Generalized Euclidean Distance measure in disparity analyses with high levels of missing data
• Selecting and averaging relaxed clock models in Bayesian tip dating of Mesozoic birds

Cited by

• Articulated specimens provide new insights into the iconic Mesozoic shark genus Sphenodus
• But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating
• A new Maastrichtian hyposaurine dyrosaurid (Crocodylomorpha) from Namibe province, Angola
• tbea : tools for pre- and post-processing in Bayesian evolutionary analyses

Discussions

• Don't forget to cite it if you use it!;) Simões, T. R., Greifer, N., Barido-Sottani, J., & Pierce, S. E. (2023). EvoPhylo: an R package for pre- and postprocessing of morphological data from relaxed [bsky, 1 points, 0 comments]

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