The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
Phylogenies and the Comparative Method
Abstract
Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause overstatement of the significance in hypothesis tests. Some illustrative examples of these phenomena have been given, and limitations of previous proposals of ways to correct for the nonindependence have been discussed. A method of correcting for the phylogeny has been proposed. It requires that we know both the tree topology and the branch lengths, and that we be willing to allow the characters to be modeled by Brownian motion on a linear scale. Given these conditions, the phylogeny specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. The considerable barriers to making practical use of this technique have been discussed.
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In the citing paper
“We calculated standardized independent contrasts (FIC: Felsenstein 1985) for each of the above factors (territoriality, shoulder height, body mass, habitat openness and group size) using the PDTREE module (Midford et al. 2005) in Mesquite 2.5 (Maddison & Maddison 2008) to account for shared ancestry.”
From Evolution of weaponry in female bovids (2009) · cites this paper as Felsenstein 1985
In the citing paper
“To test the effects of shared ancestry on trait correlations, we also carried out EMMLi analysis on the phylogenetic independent contrasts (45) of the landmark configurations. This analysis supported the same most likely model and relative strength of correlations within and among modules as the analysis of the raw data did.”
From Developmental origins of mosaic evolution in the avian cranium (2018) · cites this paper as [45]
In the citing paper
“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 Felsenstein, 1985
In the citing paper
“Felsenstein also noted that the problem of nonindependence does not occur if”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Felsenstein 1985
In the citing paper
“He then evolved traits according to a BM process along the phylogeny; he recovered a significant regression slope using Ordinary Least Squares (OLS) despite there being no evolutionary covariance between the traits.”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Felsenstein 1985
In the citing paper
“As stated above, the IC method is based on the BM model of trait evolution.”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Felsenstein 1985
In the citing paper
“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 [18]
In the citing paper
“The fact that species cannot be considered independent data points was first recognized in the 1970s by evolutionary biologists studying the evolution of life history traits such as sexual dimorphism and home range in primates16,18,30–32.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
In the citing paper
“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 [18]
In the citing paper
“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 [18]
In the citing paper
“There is no simple and robust alternative to controlling for phylogeny, and consequently, the best effort possible must be made to take phylogeny into account, to be able to detect real effects and avoid false positives.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
In the citing paper
“Collecting many more data points from the same phylogenetic cluster could increase any bias due to phylogenetic non-independence (Fig. 1)16,18,20.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
In the citing paper
“Instead, controlling for phylogeny can reduce the chance of detecting a significant result that is not real (Type II error or ‘false positive’)18,42.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
In the citing paper
“Controlling for confounding variables such as phylogeny does not reduce statistical power, because such variables should be accounted for before making any estimates of power18,114,115.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
In the citing paper
“Phylogenetic independent contrasts were also calculated from the data to examine scaling relationships while controlling for the effects of phylogenetic relatedness in the data set (59).”
From Evolution of increased glia–neuron ratios in the human frontal cortex (2006) · cites this paper as [59]
In the citing paper
“With a phylogeny, it becomes possible to examine correlated evolutionary change directly along the branches of the tree, for example with the method of independent contrasts (Felsenstein 1985; Garland et al. 1992; Nunn and Barton 2001). Alternatively, one can use the phylogeny to statistically control for nonindependence in the underlying data, for example by using phylogenetic generalized least”
From How does cognition evolve? Phylogenetic comparative psychology (2012) · cites this paper as Felsenstein 1985
Citations
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Self-citationCases in which Parsimony or Compatibility Methods Will be Positively Misleading
Felsenstein, J. (1978) · Systematic Biology · doi:10.1093/sysbio/27.4.401 · Cited by 3,261
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Self-citationFelsenstein, J. (1981) · Evolution · doi:10.1111/j.1558-5646.1981.tb04991.x · Cited by 456
Self-citationPilbeam, D., & Gould, S. J. (1974) · Science · doi:10.1126/science.186.4167.892 · Cited by 416
Parsimony in Systematics: Biological and Statistical Issues
Felsenstein, J. (1983) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.14.110183.001525 · Cited by 352
Self-citationRelative Brain Size and Metabolism in Mammals
Armstrong, E. (1983) · Science · doi:10.1126/science.6407108 · Cited by 252
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Metadata
- Authors
- Felsenstein, J.
- Affiliations
- University of Washington (US)
- Corresponding author
- Felsenstein, Joseph
- Venue
- The American Naturalist
- Publisher
- University of Chicago Press
- Published
- 1985-01
- Volume
- 125
- Issue
- 1
- Pages
- 1-15
- ISSN
- 0003-0147 (ISSN-L)
- 1537-5323
- OpenAlex
- W2013410948
- Cited by
- 9,793
- References
- 13
- Citations by year
- 2026: 242 · 2025: 311 · 2024: 287 · 2023: 361 · 2022: 335 · 2021: 391 · 2020: 332 · 2019: 465 · 2018: 375 · 2017: 374 · 2016: 374 · 2015: 399 · 2014: 436 · 2013: 342 · 2012: 343
- FWCI
- 40.48
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The American Naturalist (publishedVersion)
- Funders
- U.S. Department of Energy
- University of Washington
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Morphological variations and asymmetry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- phylogenetic comparative analysis, Brownian motion model, branch length, tree topology, contingency tables, character evolution
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