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Cited by 2,151Evolution and Paleontology StudiesMorphological variations and asymmetryAnimal Behavior and Reproduction

Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts

Garland, T., Harvey, P. H., Ives, A. R.·1992·Systematic Biology
DOI 10.1093/sysbio/41.1.18
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Abstract

We discuss and clarify several aspects of applying Felsenstein's (1985, Am. Nat. 125: 1–15) procedures to test for correlated evolution of continuous traits. This is one of several available comparative methods that maps data for phenotypic traits onto an existing phylogenetic tree (derived from independent information). Application of Felsenstein's method does not require an entirely dichotomous topology. It also does not require an assumption of gradual, clocklike character evolution, as might be modeled by Brownian motion. Almost any available information can be used to estimate branch lengths (e.g., genetic distances, divergence times estimated from the fossil record or from molecular clocks, numbers of character changes from a cladistic analysis). However, the adequacy for statistical purposes of any proposed branch lengths must be verified empirically for each phytogeny and for each character. We suggest a simple way of doing this, based on graphical analysis of plots of standardized independent contrasts versus their standard deviations (i.e., the square roots of the sums of their branch lengths). In some cases, the branch lengths and/or the values of traits being studied will require transformation. An example involving the scaling of mammalian home range area is presented. Once adequately standardized, sets of independent contrasts can be analyzed using either linear or nonlinear (multiple) regression. In all cases, however, regressions (or correlations) must be computed through the origin. We also discuss ways of correcting for body size effects and how this relates to making graphical representations of relationships of standardized independent contrasts. We close with a consideration of the types of traits that can be analyzed with independent contrasts procedures and conclude that any (continuous) trait that is inherited from ancestors is appropriate for analysis, regardless of the mechanism of inheritance (e.g., genetic or cultural).

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  • Because of shared phylogenetic descent, species data are likely not to represent statistically independent points, resulting in overestimation of degrees of freedom and increased Type I error rate.

    “Firstly, because of shared phylogenetic descent, species data are likely not to represent statistically independent points.This results in overestimation of degrees of freedom and an increased Type I error rate.”

    From Allometric scaling of mammalian metabolism (2005) · cites this paper as Garland et al., 1992

  • Rigorous examination of goodness-of-fit and model adequacy following any comparative analysis is critical for finding unforeseen singular events driving signal in the data set.

    “Furthermore, we also think that rigorous examination of goodness-of-fit and model adequacy following any comparative analysis is critical for finding unforeseen singular events driving signal in the data set (Garland et al. 1992;Boettiger et al. 2012;Slater and Pennell 2013;Pennell et al. 2015).”

    From Rethinking phylogenetic comparative methods (2018) · cites this paper as Garland et al. 1992

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Authors
Garland, T., Harvey, P. H., & Ives, A. R.
Affiliations
  • University of Wisconsin–Madison (US)
  • University of Oxford (GB)
ORCID
Venue
Systematic Biology
Publisher
Oxford University Press (OUP)
Published
1992-03-01
Volume
41
Issue
1
Pages
18-32
ISSN
  • 1063-5157 (ISSN-L)
  • 1076-836X
DOI
10.1093/sysbio/41.1.18
OpenAlex
W2081555343
Cited by
2,151
References
0
Citations by year
2026: 12 · 2025: 14 · 2024: 30 · 2023: 19 · 2022: 24 · 2021: 30 · 2020: 28 · 2019: 42 · 2018: 53 · 2017: 31 · 2016: 54 · 2015: 57 · 2014: 69 · 2013: 87 · 2012: 85
FWCI
39.79
Type
journal article
Language
en
Open access
closed
Locations
Systematic Biology (publishedVersion)
Funders
National Science Foundation
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
phylogenetically independent contrasts, comparative analysis, branch length estimation, regression through the origin, body size correction, cultural transmission, character evolution

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