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iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees.

James A Fordyce1, Premal Shah2, Benjamin M Fitzpatrick1

  • 1Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA. ; National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA.

Evolutionary Bioinformatics Online
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PubMed
Summary

This study introduces iteRates, an R package for phylogenetic comparative methods. It helps analyze diversification rate variation across evolutionary trees using parametric rate comparison (PRC).

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chronogramdiversification-ratephylogenyrate-variation

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Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Computational Biology

Background:

  • Diversification rate variation in phylogenetic trees offers insights into evolutionary processes.
  • Parametric rate comparison (PRC) is a statistical method to detect such variations.
  • Existing methods may lack comprehensive tools for analyzing these rates.

Purpose of the Study:

  • Introduce iteRates, a novel R package for phylogenetic analysis.
  • Provide functions for subtree identification and tree manipulation.
  • Implement PRC and K-clades PRC analyses for detecting diversification rate variation.

Main Methods:

  • Utilizes the R statistical computing environment.
  • Models branch lengths as random variables from statistical distributions.
  • Includes functions for subtree identification, tree manipulation, and randomization tests.

Main Results:

  • iteRates offers a suite of functions for robust phylogenetic comparative analysis.
  • The package facilitates the application of PRC and K-clades PRC methods.
  • A whole-tree randomization test is included for statistical validation.

Conclusions:

  • iteRates provides a valuable computational tool for evolutionary biologists.
  • The package enhances the ability to infer historical and ecological processes from phylogenetic data.
  • Facilitates advanced analyses of diversification rate heterogeneity in phylogenetic trees.