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

Qiqing Tao1,2, Sudip Sharma1,2, Koichiro Tamura3,4

  • 1Institute for Genomics and Evolutionary Medicine, Temple University.

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|February 20, 2025
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Summary
This summary is machine-generated.

The R3F R package implements the relative rate framework for accurate molecular dating and phylogenetic analyses. It aids in estimating divergence times, testing rate correlations, and building tree priors for evolutionary studies.

Keywords:
Bayesian priorRdivergence timesrelative rate framework

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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.