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A Practical Guide to Phylogenetics for Nonexperts
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Why the phylogenetic regression appears robust to tree misspecification.

Eric A Stone1

  • 1Department of Genetics, North Carolina State University, Raleigh, NC 27695-8203, USA. eric stone@ncsu.edu

Systematic Biology
|February 18, 2011
PubMed
Summary

Phylogenetic comparative methods analyze trait evolution using estimated evolutionary trees. This study shows how errors in these trees, particularly branch lengths, impact analyses, but finds phylogenetic regression is generally robust.

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Area of Science:

  • Evolutionary Biology
  • Comparative Genomics
  • Phylogenetics

Background:

  • Phylogenetic comparative methods model interspecific data covariance using evolutionary relationships.
  • Accounting for common ancestry prevents confounding similarities due to descent.
  • Estimates of evolutionary trees introduce quantifiable error into analyses.

Purpose of the Study:

  • Elucidate how tree misspecification propagates through comparative analyses.
  • Focus on phylogenetic regression under a Brownian motion model.
  • Quantify the impact of local phylogenetic perturbations on regression fit.

Main Methods:

  • Derived a matrix square root of the phylogenetic covariance matrix.
  • Transformed the perturbed phylogenetic regression model into an ordinary linear regression.
  • Analyzed the effect of branch length misspecification and soft polytomies.

Main Results:

  • Branch length misspecification can be explained by reweighting contrast scores.
  • Phylogenetic regression generally demonstrates robustness to tree misspecification.
  • Identified conditions under which regression results may not be robust.

Conclusions:

  • Soft polytomies do not typically meet problematic conditions for regression fit.
  • Unresolved bifurcations in phylogenies have modest effects on regression.
  • The developed formulation disentangles data and phylogeny contributions in misspecification studies.