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Cited by 2,142Evolution and Paleontology StudiesMorphological variations and asymmetryGenomics and Phylogenetic Studies

The phylogenetic regression

Grafen, Alan·1989·Philosophical Transactions of the Royal Society of London. B, Biological Sciences
DOI 10.1098/rstb.1989.0106
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Abstract

A new statistical method called the phylogenetic regression is proposed that applies multiple regression techniques to cross-species data. It allows continuous and categorical variables to be tested for and controlled for. The new method is valid despite the problem that phylogenetically close species tend to be similar, and is designed to be used when information about the phylogeny is incomplete. Information about the phylogeny of the species is assumed to be available in the form of a working phylogeny, which contains multiple nodes representing ignorance about the order of splitting of taxa. The non-independence between species is divided into that due to recognized phylogeny, that is, to phylogenetic associations represented in the working phylogeny; and that due to unrecognized phylogeny. The new method uses one linear contrast for each higher node in the working phylogeny, thus applying the ‘radiation principle’. For binary phylogenies the method is similar to an existing method. A criterion is suggested in the form of a simulation test for deciding on the acceptability of proposed statistical methods for analysing cross-species data with a continuous y-variable. This criterion is applied to the phylogenetic regression and to some other methods. The phylogenetic regression passes this test; the other methods tested fail it. Arbitrary choices have to be made about the covariance structure of the error in order to implement the method. It is argued that error results from omitted but relevant variables, and the implications for those arbitrary choices are discussed. One conclusion is that the dates of splits between taxa, even supplemented by rates of neutral gene evolution, do not provide the ‘ true ’ covariance structure. A pragmatic approach is adopted. Several analytical results about the phylogenetic regression are given, without proof, in a mathematical appendix. A computer program has been written in GLIM to implement the phylogenetic regression, and readers are informed how to obtain a copy.

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  • This led to the development of numerous methods that take phylogeny into account and control for the non-independence of species.

    “This led to the development of numerous methods that take phylogeny into account and control for the non-independence of species16,18,19,33.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [19]

  • Closely related species tend to be similar because they share genes by common descent.

    “Closely related species tend to be similar because they share genes by common descent, which must be accounted for in analyses.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [19]

  • The problem of species not being independent can be exacerbated by additional levels of non-independence, including genes within genomes and genomes of the same or closely related species.

    “In genomic datasets, data points can correspond to genomes or even individual genes, meaning the problem of species not being independent can be exacerbated by additional levels of non-independence, including genes within genomes, such as those carried on the same replicon, and genomes of the same or closely related species16,19,21–26.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [19]

  • The problem of non-independence can be exacerbated when examining genomes or genes.

    “This problem of non-independence can be exacerbated when examining genomes or genes.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [19]

  • Species, genomes, and genes cannot be considered independent data points within statistical tests.

    “However, species, genomes and genes cannot be considered as independent data points within statistical tests.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [19]

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Authors
Grafen, A.
Affiliations
University of Oxford (GB)
Corresponding author
Grafen, Alan
ORCID
Grafen, Alan
Venue
Philosophical Transactions of the Royal Society of London. B, Biological Sciences
Publisher
The Royal Society
Published
1989-12-21
Volume
326
Issue
1233
Pages
119-157
ISSN
  • 0080-4622 (ISSN-L)
  • 2054-0280
DOI
10.1098/rstb.1989.0106
OpenAlex
W2117066938
Cited by
2,142
References
0
Citations by year
2026: 54 · 2025: 68 · 2024: 91 · 2023: 77 · 2022: 119 · 2021: 124 · 2020: 83 · 2019: 87 · 2018: 95 · 2017: 90 · 2016: 99 · 2015: 100 · 2014: 111 · 2013: 84 · 2012: 69
FWCI
17.56
Type
journal article
Language
en
Open access
closed
Licence
royalsociety.org/journals/ethics-policies/data-sharing-mining/ (tdm)
Locations
  • Philosophical transactions of the Royal Society of London. Series B, Biological sciences (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 › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
phylogenetic regression, phylogenetic non-independence, linear contrasts, simulation-based testing, covariance structure, omitted variable bias
MeSH terms
Animals, Models, Biological, Phylogeny, Random Allocation, Regression Analysis, Models, Statistical

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