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Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating.

Jose Barba-Montoya1,2, Qiqing Tao1,2, Sudhir Kumar1,2,3

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

Genome Biology and Evolution
|November 9, 2021
PubMed
Summary
This summary is machine-generated.

RelTime is a more accurate method for estimating divergence times in large phylogenies compared to treePL and least-squares dating. It provides reliable confidence intervals, unlike other methods that tend to be too narrow.

Keywords:
least-squarespenalized likelihoodphylogenomicsrelative rate frameworkrelaxed molecular clock dating

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Area of Science:

  • Computational phylogenetics
  • Molecular evolution

Background:

  • Rapid relaxed-clock dating methods are crucial for analyzing large phylogenomic datasets due to their speed and accuracy.
  • The comparative performance of these rapid dating methods, however, remains unclear, limiting informed selection.

Purpose of the Study:

  • To compare the accuracy, bias, and coverage probabilities of three rapid dating methods: RelTime, treePL, and least-squares dating.
  • To evaluate method performance under varying evolutionary rates in computer-simulated phylogenies.

Main Methods:

  • Application of RelTime, treePL, and least-squares dating to simulated phylogenomic datasets.
  • Analysis of datasets with extensive and autocorrelated variations in evolutionary rates among lineages.

Main Results:

  • RelTime consistently yielded more accurate divergence time estimates than treePL and least-squares dating.
  • RelTime demonstrated superior performance, especially when evolutionary rates were autocorrelated or showed convergent shifts.
  • RelTime's confidence intervals exhibited appropriate coverage probabilities, unlike the overly narrow intervals of other methods.

Conclusions:

  • RelTime is a more efficient and accurate method for estimating divergence times in large phylogenies.
  • The choice of dating method significantly impacts the reliability of divergence time estimates, particularly with complex rate variations.