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Multi-response phylogenetic mixed models: concepts and application.

Ben Halliwell1,2, Barbara R Holland1,2, Luke A Yates1,2

  • 1School of Natural Sciences, Private Bag 55, University of Tasmania, Hobart, Tasmania, Australia.

Biological Reviews of the Cambridge Philosophical Society
|April 7, 2025
PubMed
Summary
This summary is machine-generated.

Multi-response phylogenetic mixed models (MR-PMMs) enable complex trait evolution analyses. This guide makes these powerful statistical tools accessible for ecologists and evolutionary biologists studying trait coevolution.

Keywords:
evolutionary ecologygeneralised linear mixed modelsmultivariate statisticsphylogenetic comparative methodstrait evolutionvariance partitioning

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Area of Science:

  • Comparative biology
  • Evolutionary biology
  • Ecology

Background:

  • Increasing scale of trait databases and molecular phylogenies.
  • Need for advanced statistical tools to address open questions in comparative biology.
  • Limited accessibility of current multivariate phylogenetic mixed models (PMMs) for researchers.

Purpose of the Study:

  • Provide a practical guide to multi-response PMMs (MR-PMMs) for trait evolution analysis.
  • Demonstrate the utility of MR-PMMs for understanding trait coevolution and covariances.
  • Lower barriers to using advanced statistical methods in ecology and evolution.

Main Methods:

  • Review of single-response PMMs to establish foundational concepts.
  • Detailed explanation of MR-PMMs for multivariate trait analyses.
  • Discussion of multilevel models, non-Gaussian traits, causal inference, and model validation techniques.

Main Results:

  • MR-PMMs offer superior decomposition of trait covariances compared to single-response models.
  • Demonstrated practical application of MR-PMMs using simulated and real-world plant trait data.
  • Implementation examples provided in popular R packages (MCMCglmm and brms).

Conclusions:

  • MR-PMMs are a powerful and accessible approach for complex trait evolution studies.
  • The guide and tutorials aim to facilitate wider adoption of MR-PMMs in ecological and evolutionary research.
  • Highlights the potential for a synthesis of comparative techniques through MR-PMMs.