R3F: An R package for evolutionary dates, rates, and priors using the relative rate framework

Area of Science:

• Phylogenetics and evolutionary biology
• Computational biology
• Bioinformatics

Background:

• The relative rate framework (RRF) provides the theoretical foundation for the widely used RelTime method in molecular dating.
• RRF enables efficient methods for testing lineage rate autocorrelation (CorrTest) and data-driven birth-death speciation models (ddBD) for Bayesian dating priors.
• Accurate molecular dating is crucial for understanding organismal evolution, diversification, phylogeography, and biogeography.

Purpose of the Study:

• To introduce R3F, an R package designed to implement the relative rate framework (RRF).
• To provide tools for estimating divergence times, inferring lineage rates, conducting autocorrelation tests, and building tree priors for Bayesian molecular dating.
• To facilitate the accurate and precise dating of the Tree of Life and support evolutionary studies.

Main Methods:

• Implementation of the relative rate framework (RRF) within an R package (R3F).
• Development of functions for divergence time estimation, lineage rate inference, and CorrTest.
• Integration of ddBD model for constructing tree priors for Bayesian dating.

Main Results:

• R3F offers a comprehensive suite of tools for phylogenetic dating and analysis based on RRF.
• The package enables efficient computation and accurate estimation of evolutionary parameters.
• Outputs are compatible with common visualization tools like MEGA, ggtree, and FigTree.

Conclusions:

• R3F enhances the application of the relative rate framework in molecular phylogenetics.
• The package aims to improve the accuracy and precision of divergence time estimates.
• R3F supports a wide range of evolutionary studies, from organismal evolution to biogeography.