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Cited by 656Evolution and Paleontology StudiesMorphological variations and asymmetryGenomics and Phylogenetic Studies

Comparative methods for the analysis of continuous variables: geometric interpretations

Rohlf, F. James·2001·Evolution
DOI 10.1111/j.0014-3820.2001.tb00731.x
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Abstract

This study is concerned with statistical methods used for the analysis of comparative data (in which observations are not expected to be independent because they are sampled across phylogenetically related species). The phylogenetically independent contrasts (PIC), phylogenetic generalized least-squares (PGLS), and phylogenetic autocorrelation (PA) methods are compared. Although the independent contrasts are not orthogonal, they are independent if the data conform to the Brownian motion model of evolution on which they are based. It is shown that uncentered correlations and regressions through the origin using the PIC method are identical to those obtained using PGLS with an intercept included in the model. The PIC method is a special case of PGLS. Corrected standard errors are given for estimates of the ancestral states based on the PGLS approach. The treatment of trees with hard polytomies is discussed and is shown to be an algorithmic rather than a statistical problem. Some of the relationships among the methods are shown graphically using the multivariate space in which variables are represented as vectors with respect to OTUs used as coordinate axes. The maximum-likelihood estimate of the autoregressive parameter, p, has not been computed correctly in previous studies (an appendix with MATLAB code provides a corrected algorithm). The importance of the eigenvalues and eigenvectors of the connection matrix, W, for the distribution of p is discussed. The PA method is shown…

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  • If all phylogenetic signal in a data set is present in the predictor trait and the errors are i.i.d., then no phylogenetic correction is needed.

    “if all of the phylogenetic signal in a data set is present in the predictor trait and the errors are i.i.d., then there is no need for any phylogenetic correction”

    From Rethinking phylogenetic comparative methods (2018) · cites this paper as Rohlf 2001

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Authors
Rohlf, F. J.
Affiliations
State University of New York (US)
Corresponding author
Rohlf, F. James
ORCID
Rohlf, F. James
Venue
Evolution
Publisher
Oxford University Press (OUP)
Published
2001-11
Volume
55
Issue
11
Pages
2143-2160
ISSN
  • 0014-3820 (ISSN-L)
  • 1558-5646
DOI
10.1111/j.0014-3820.2001.tb00731.x
OpenAlex
W2196722132
Cited by
656
References
1
Citations by year
2026: 15 · 2025: 15 · 2024: 12 · 2023: 18 · 2022: 23 · 2021: 29 · 2020: 17 · 2019: 21 · 2018: 22 · 2017: 28 · 2016: 28 · 2015: 59 · 2014: 40 · 2013: 38 · 2012: 47
FWCI
12.71
Type
journal article
Language
en
Open access
closed
Licence
doi.wiley.com/10.1002/tdm_license_1.1 (tdm, 5052 d)
Locations
  • Evolution (publishedVersion)
  • PubMed (publishedVersion)
  • BioOne Complete (BioOne) (submittedVersion)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Physical Sciences › Mathematics › Geometry and Topology › Morphological variations and asymmetry
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
phylogenetically independent contrasts, phylogenetic generalized least squares, phylogenetic autocorrelation, comparative analysis, Brownian motion model, ancestral state estimation, polytomies, autoregressive parameter estimation, regression through the origin
MeSH terms
Mathematics, Models, Biological, Molecular Biology, Phylogeny, Likelihood Functions, Evolution, Molecular

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