phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

By Liam J. Revell. bioRxiv, 2023

718 citations recorded by the source corpus.

Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package (Revell 2012) has grown to become an important research tools for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.

Subfields: Genetics, Nature and Landscape Conservation, Paleontology

View Paper: https://www.semanticscholar.org/paper/90b3081c3d451e205329a01f3d443916d4a79fd1

Citations in the corpus

• Collective behavior drives diversification across the tree of ray-finned fishes (2026, unknown): “While an Mk model can be fit to our data, we found that trait evolution simulations under the best-fit model ('fitMk' in phytools [ 85 ]) on our phylogenetic tree did not recreate the distribution of isolation values present in the observed data (compare Fig.”