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

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Tiago R. Simões , Noah Greifer , Joëlle Barido‐Sottani , Stephanie E. Pierce ·

YOU? · · 2023 · Open Access · · DOI: https://doi.org/10.1111/2041-210x.14128

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.

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Bayesian probability Phylogenetic tree Inference Molecular clock Bayes' theorem Phylogenetics Computer science Character evolution Range (aeronautics) Character (mathematics) Lineage (genetic) Bayesian inference Biology Evolutionary biology Macroevolution R package Artificial intelligence Clade Mathematics Genetics Materials science Gene Geometry Computational science Composite material

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Type: article
Language: en
Landing Page: https://doi.org/10.1111/2041-210x.14128
PDF: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/2041-210X.14128
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Cited By: 11
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DOI: https://doi.org/10.1111/2041-210x.14128

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

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Language: en

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Publication year: 2023

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Publication date: 2023-05-17

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Authors: Tiago R. Simões, Noah Greifer, Joëlle Barido‐Sottani, Stephanie E. Pierce

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Landing page: https://doi.org/10.1111/2041-210x.14128

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Concepts: Bayesian probability, Phylogenetic tree, Inference, Molecular clock, Bayes' theorem, Phylogenetics, Computer science, Character evolution, Range (aeronautics), Character (mathematics), Lineage (genetic), Bayesian inference, Biology, Evolutionary biology, Macroevolution, R package, Artificial intelligence, Clade, Mathematics, Genetics, Materials science, Gene, Geometry, Computational science, Composite material

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Cited by: 11

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