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

2024/01/05 by Liam J. Revell · 89 citations
Earth and Planetary Sciences · Environmental Science · #Ecology and Vegetation Dynamics Studies #Evolution and Paleontology Studies #Species Distribution and Climate Change

paper · doi:10.7717/peerj.16505

openalex publication_date 2024/01/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30

Abstract

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 has grown to become an important research tool 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.

Citations

• ECOLOGICAL OPPORTUNITY AND THE RATE OF MORPHOLOGICAL EVOLUTION IN THE DIVERSIFICATION OF GREATER ANTILLEAN ANOLES
• TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
• Mapping Mutations on Phylogenies
• SIZE-CORRECTION AND PRINCIPAL COMPONENTS FOR INTERSPECIFIC COMPARATIVE STUDIES
• Stochastic Mapping of Morphological Characters
• A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence
• TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD

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