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Cited by 4,678Evolution and Paleontology StudiesMorphological variations and asymmetryAnimal Behavior and Reproduction

TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE

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Blomberg, Simon P., Garland, Theodore, Ives, Anthony R.·2003·Evolution
DOI 10.1111/j.0014-3820.2003.tb00285.x
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Abstract

The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal alpha = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25% of traits) and/or ACDC (40%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses.

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  • The tracing of female horn evolution on the composite tree has strong phylogenetic signal (p < 0.001).

    “We determined that the tracing of female horn evolution on this composite tree has strong phylogenetic signal (Blomberg et al. 2003; p < 0.001) using PDAP 6.0 software (Garland et al. 1993); therefore, related species tend to resemble each other in their tendency for females to have horns.”

    From Evolution of weaponry in female bovids (2009) · cites this paper as Blomberg et al. 2003

  • Phylogenetic signal for genome size and body size was quantified using Pagel's λ and Blomberg's K before formal comparative tests.

    “Before conducting formal comparative tests, we quantified phylogenetic signal for both genome size and body size to assess the degree to which trait variation reflects shared evolutionary history. Two complementary metrics were calculated using the phylosig function in phytools: Pagel’s λ (83) and Blomberg’s K (84).”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [84]

  • Most continuous trait models are Gaussian and do not accommodate abrupt, discontinuous shifts in phenotypes.

    “While today we have a much wider range of comparative models to choose from including some that allow for adaptive shifts, most continuous trait models are Gaussian (e.g., Pagel 1999;Blomberg et al. 2003;Butler and King 2004;O'Meara et al. 2006;Eastman et al. 2011;Beaulieu et al. 2012;Uyeda and Harmon 2014) and do not accommodate abrupt, discontinuous shifts in phenotypes.”

    From Rethinking phylogenetic comparative methods (2018) · cites this paper as Blomberg et al. 2003

  • The problem of species non-independence still arises when examining evolutionary labile traits that evolve very fast or are the product of very recent events.

    “The problem of species non-independence still arises when examining evolutionary labile traits that evolve very fast or are the product of very recent events.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [55]

  • A total lack of phylogenetic signal is at one end of a spectrum and not a reason not to avoid phylogenetic comparative methods.

    “A total lack of phylogenetic signal is at one end of a spectrum and not a reason not to avoid phylogenetic comparative methods44,54–56.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [55]

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Authors
Blomberg, S. P., Garland, T., & Ives, A. R.
Affiliations
  • University of California, Riverside (US)
  • University of Wisconsin–Madison (US)
Corresponding author
  • Garland, Theodore
  • Ives, Anthony R.
ORCID
Venue
Evolution
Publisher
Oxford University Press (OUP)
Published
2003-04
Volume
57
Issue
4
Pages
717-745
ISSN
  • 0014-3820 (ISSN-L)
  • 1558-5646
DOI
10.1111/j.0014-3820.2003.tb00285.x
OpenAlex
W1990221500
Cited by
4,678
References
2
Citations by year
2026: 242 · 2025: 280 · 2024: 309 · 2023: 294 · 2022: 289 · 2021: 373 · 2020: 321 · 2019: 313 · 2018: 288 · 2017: 268 · 2016: 241 · 2015: 231 · 2014: 233 · 2013: 184 · 2012: 199
FWCI
32.93
Type
journal article
Language
en
Open access
Licence
doi.wiley.com/10.1002/tdm_license_1.1 (tdm, 4536 d)
Locations
  • Evolution (publishedVersion)
  • PubMed (publishedVersion)
  • Zenodo (CERN European Organization for Nuclear Research)
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 signal, comparative analysis, permutation tests, phylogenetically independent contrasts, Ornstein-Uhlenbeck process, k-statistics, Brownian motion model, measurement error, behavioral characteristics, trait evolution rates, adaptive radiation, evolutionary lability, type I error rate, power
MeSH terms
Animals, Behavior, Animal, Body Constitution, Models, Genetic, Models, Theoretical, Phylogeny, Research Design, Likelihood Functions

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