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Cited by 2,604Evolution and Paleontology StudiesMorphological variations and asymmetryAnimal Behavior and Reproduction

Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence

Freckleton, R. P., Harvey, P. H., Pagel, M.·2002·The American Naturalist
DOI 10.1086/343873
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Abstract

The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.

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  • The pGLS approach takes the phylogenetic relatedness of the species as given by the phylogenetic tree into account.

    “This approach takes the phylogenetic relatedness of the species as given by the phylogenetic tree into account.”

    From A genomics approach reveals insights into the importance of gene losses for mammalian adaptations (2018) · cites this paper as [45]

  • Estimating a transformation for the errors will not rescue the analysis; the estimated value lies between 0 and 1, and both OLS and IC are susceptible.

    “We also note that estimating a transformation for the errors (Pagel 1999;Freckleton et al. 2002) will not rescue the analysis; the estimated value of will lie between 0 and 1 and we have found both these more extreme cases (OLS and IC, respectively) to be susceptible.”

    From Rethinking phylogenetic comparative methods (2018) · cites this paper as Freckleton et al. 2002

  • Many methods to detect phylogenetic signal perform poorly with datasets of less than 20 species.

    “Indeed, many methods to detect phylogenetic signal perform poorly with datasets of less than 20 species (Freckleton et al. 2002).”

    From How does cognition evolve? Phylogenetic comparative psychology (2012) · cites this paper as Freckleton et al. 2002

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Authors
Freckleton, R. P., Harvey, P. H., & Pagel, M.
Affiliations
University of Oxford (GB)
ORCID
Venue
The American Naturalist
Publisher
University of Chicago Press
Published
2002-12
Volume
160
Issue
6
Pages
712-726
ISSN
  • 0003-0147 (ISSN-L)
  • 1537-5323
DOI
10.1086/343873
OpenAlex
W2180478016
Cited by
2,604
References
66
Citations by year
2026: 77 · 2025: 121 · 2024: 117 · 2023: 123 · 2022: 129 · 2021: 150 · 2020: 127 · 2019: 137 · 2018: 148 · 2017: 141 · 2016: 149 · 2015: 152 · 2014: 165 · 2013: 156 · 2012: 133
FWCI
30.11
Type
journal article
Language
en
Open access
closed
Locations
  • The American Naturalist (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Physical Sciences › Mathematics › Geometry and Topology › Morphological variations and asymmetry
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Animal Behavior and Reproduction
Keywords
phylogenetic correlation, Lambda, phylogenetic correction, comparative analysis, type I error, statistical power, trait covariation

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