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PCCA: a program for phylogenetic canonical correlation analysis.

Liam J Revell1, Alexis S Harrison

  • 1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. lrevell@fas.harvard.edu

Bioinformatics (Oxford, England)
|February 23, 2008
PubMed
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Phylogenetic Canonical Correlation Analysis (PCCA) is a new program that analyzes correlations between biological traits while accounting for evolutionary relationships. This tool helps researchers understand trait evolution across species.

Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Comparative genomics

Background:

  • Canonical correlation analysis (CCA) is a statistical method for analyzing relationships between sets of variables.
  • Phylogenetic history can introduce non-independence in species data, complicating traditional CCA.
  • Existing methods may not adequately address phylogenetic effects in multivariate trait analysis.

Purpose of the Study:

  • Introduce Phylogenetic Canonical Correlation Analysis (PCCA), a novel program for analyzing multivariate biological data.
  • Address the challenge of species non-independence due to phylogenetic history in correlation analyses.
  • Provide a tool for calculating and testing correlations between character sets in an evolutionary context.

Main Methods:

  • PCCA implements canonical correlation analysis for multivariate, continuous data from biological species.

Related Experiment Videos

  • The program explicitly controls for species non-independence arising from phylogenetic history.
  • It computes canonical coefficients, correlations, scores, and performs hypothesis tests on canonical correlations.

    • Main Results:

    • PCCA enables robust correlation analysis between sets of biological traits, accounting for phylogeny.
    • The software facilitates the calculation of a multivariate version of Pagel's lambda for phylogenetic transformation.
    • Provides essential statistical outputs for understanding trait correlations in an evolutionary framework.

    Conclusions:

    • PCCA is a valuable tool for researchers studying trait evolution and covariation across species.
    • The program enhances the accuracy of correlation analyses by incorporating phylogenetic information.
    • Facilitates deeper insights into the evolutionary processes shaping biological diversity.