A Guided Tour of Phylogenetic Comparative Methods for Studying Trait Evolution

Cornwallis, Charlie K.; Griffin, Ashleigh S.

doi:10.1146/annurev-ecolsys-102221-050754

Cited by 37Evolution and Paleontology StudiesMorphological variations and asymmetryAnimal Behavior and Reproduction

A Guided Tour of Phylogenetic Comparative Methods for Studying Trait Evolution

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Cornwallis, Charlie K., Griffin, Ashleigh S.·2024·Annual Review of Ecology, Evolution, and Systematics

DOI 10.1146/annurev-ecolsys-102221-050754

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Abstract

Phylogenetic comparative methods are important tools in biology, providing insights into the way traits evolve. There are many technical resources describing how these methods work. Our aim here is to complement these with an overview of the types of biological questions that can be addressed by different methods and to outline potential pitfalls and considerations when embarking on comparative studies. First, we introduce what comparative methods are and why they are important. Second, we outline how they can be used to understand when, where, and how frequently traits evolve. Third, we examine how the coevolution of traits within and between species can be studied, along with patterns of causality. Finally, we discuss how to approach comparative analyses and the ways in which different types of data, such as published relationships, omic, and remote sensing data, can be integrated.

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Phylogenetic methods can be used to also address other questions, such as how features of the genome influence diversification.
“Of note, phylogenetic methods can be used to also address other questions, such as how features of the genome influence diversification41–43.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [42]
More recently developed methods allow analyses to go further and test competing causal hypotheses.
“More recently developed methods allow analyses to go further and test competing causal hypotheses42,84.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [42]
Testing whether an ancestral change in one trait consistently leads to the same change in the other trait would suggest the co-evolution is due to a causal link.
“To distinguish which scenario is more likely, we could test whether an ancestral change in one trait consistently leads to the same change in the other trait, which would suggest the co-evolution is due to a causal link42,43,51,85–87 (Fig. 3).”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [42]
Controlling for phylogeny can reduce the chance of detecting a significant result that is not real (Type II error or 'false positive').
“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 [42]
Correlational results from observational data do not prove causation, but correlations can be used within comparative analyses to test causal hypotheses and examine evidence for causality.
“A general point here is that correlational results from observational data do not prove causation, but correlations can be used within comparative analyses to test causal hypotheses and examine evidence for causality42,90.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [42]

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A phylogenetic approach to comparative genomics
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“Communication systems could now be compared across species and clades with statistical precision, laying the groundwork for phylogenetically informed studies of communication evolution (Cornwallis and Griffin 2024 ; Jorgewich-Cohen et al. 2022; Pika et al. 2018).”

Authors: Cornwallis, C. K., & Griffin, A. S.
Affiliations: Lund University (SE)
University of Oxford (GB)
ORCID: Cornwallis, Charlie K.
Griffin, Ashleigh S.
Venue: Annual Review of Ecology, Evolution, and Systematics
Publisher: Annual Reviews
Published: 2024-11-04
Volume: 55
Issue: 1
Pages: 181-204
ISSN: 1543-592X (ISSN-L)
1545-2069
DOI: 10.1146/annurev-ecolsys-102221-050754
OpenAlex: W4401406493
Cited by: 37
References: 107
Citations by year: 2026: 18 · 2025: 19
FWCI: 3.14
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: Annual Review of Ecology Evolution and Systematics (publishedVersion, cc-by)
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 comparative analysis, character evolution, coevolution, evolutionary rates, phylogenetic signal, multi-omics integration, remote sensing data

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A Guided Tour of Phylogenetic Comparative Methods for Studying Trait Evolution

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