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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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phylopath: Easy phylogenetic path analysis in R.

Wouter van der Bijl1

  • 1Department of Zoology, Stockholm University, Stockholm, Sweden.

Peerj
|May 2, 2018
PubMed
Summary

This study introduces phylopath, an R package simplifying phylogenetic path analysis (PPA) for comparative biologists. It enables easier causal modeling with observational data, including binary variables, for macro-evolutionary research.

Keywords:
Comparative methodsEvolutionPath analysisPhylogenetic path analysisR package

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Area of Science:

  • Evolutionary biology
  • Comparative biology
  • Bioinformatics

Background:

  • Confirmatory path analysis (CPA) is valuable for evaluating causal models with observational data in comparative biology.
  • Macro-evolutionary hypotheses often lack experimental data, making CPA essential.
  • Current CPA methods can be cumbersome and error-prone.

Purpose of the Study:

  • To introduce an R package, 'phylopath', for phylogenetic path analysis (PPA).
  • To simplify the implementation of PPA for researchers.
  • To extend PPA to include binary variables.

Main Methods:

  • The study implements phylogenetic path analysis (PPA) using the 'phylopath' R package.
  • The package supports the inclusion of binary variables in PPA models.
  • The method is illustrated by analyzing the relationship between brain size and extinction vulnerability.

Main Results:

  • The 'phylopath' package provides a more straightforward approach to PPA.
  • Convenience functions and plotting methods are included to facilitate analysis.
  • The package aims to increase the adoption of PPA in macro-evolutionary studies.

Conclusions:

  • The 'phylopath' R package democratizes phylogenetic path analysis for evolutionary research.
  • It offers a user-friendly tool for causal modeling with observational and binary data.
  • The package is expected to promote wider use of PPA in comparative biology.