This paper describes the updated features and functionalities of the 'phytools' R package, a widely used tool for phylogenetic comparative methods. It provides multiple example workflows illustrating the use of 'phytools' for analyzing discrete and continuous character evolution, diversification rates, and visualizing phylogenetic data, including stochastic character mapping, ancestral state reconstruction, and lineage-through-time plots.

The author is the developer and maintainer of the 'phytools' package, which could create a potential bias in the presentation and evaluation of its features. However, this is transparently disclosed and is inherent in software-focused publications.

The paper provides a comprehensive overview of 'phytools' functionality and workflows, which is useful for users of the package. However, the lack of novel scientific findings and the heavy reliance on examples limits its broader scientific impact. The author's conflict of interest as the package developer is noted, but does not significantly detract from the paper's value as a software description.