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

TL;DR

R3F is an R package that implements the relative rate framework for estimating divergence times, lineage rates, and priors in molecular phylogenies, facilitating more accurate evolutionary dating and analysis.

Contribution

It introduces a comprehensive R package that integrates multiple methods for divergence time estimation, rate testing, and prior selection based on the relative rate framework.

Findings

Enables divergence time estimation and lineage rate inference.

Provides tools for autocorrelation testing and prior selection.

Facilitates integration with visualization software.

Abstract

The relative rate framework (RRF) can estimate divergence times from branch lengths in a phylogeny, which is the theoretical basis of the RelTime method frequently applied, a relaxed clock approach for molecular dating that scales well for large phylogenies. The use of RRF has also enabled the development of computationally efficient and accurate methods for testing the autocorrelation of lineage rates in a phylogeny (CorrTest) and selecting data-driven parameters of the birth-death speciation model (ddBD), which can be used to specify priors in Bayesian molecular dating. We have developed R3F, an R package implementing RRF to estimate divergence times, infer lineage rates, conduct CorrTest, and build a ddBD tree prior for Bayesian dating in molecular phylogenies. Here, we describe R3F functionality and explain how to interpret and use its outputs in other visualization software and packages, such as MEGA, ggtree, and FigTree. Ultimately, R3F is intended to enable the dating of the Tree of Life with greater accuracy and precision, which would have important implications for studies of organism evolution, diversification dynamics, phylogeography, and biogeography. Availability and Implementation: The source codes and related instructions for installing and implementing R3F are available from GitHub (https://github.com/cathyqqtao/R3F).