A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES: IDENTIFYING RATE HETEROGENEITY IN CHARACTER EVOLUTION

Eastman, Jonathan M.; Alfaro, Michael E.; Joyce, Paul; Hipp, Andrew L.; Harmon, Luke J.

doi:10.1111/j.1558-5646.2011.01401.x

Cited by 240Evolution and Paleontology StudiesMorphological variations and asymmetryEvolution and Genetic Dynamics

A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES: IDENTIFYING RATE HETEROGENEITY IN CHARACTER EVOLUTION

Eastman, Jonathan M., Alfaro, Michael E., Joyce, Paul, Hipp, Andrew L., Harmon, Luke J.·2011·Evolution

DOI 10.1111/j.1558-5646.2011.01401.x

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Abstract

Evolutionary biologists since Darwin have been fascinated by differences in the rate of trait-evolutionary change across lineages. Despite this continued interest, we still lack methods for identifying shifts in evolutionary rates on the growing tree of life while accommodating uncertainty in the evolutionary process. Here we introduce a Bayesian approach for identifying complex patterns in the evolution of continuous traits. The method (auteur) uses reversible-jump Markov chain Monte Carlo sampling to more fully characterize the complexity of trait evolution, considering models that range in complexity from those with a single global rate to potentially ones in which each branch in the tree has its own independent rate. This newly introduced approach performs well in recovering simulated rate shifts and simulated rates for datasets nearing the size typical for comparative phylogenetic study (i.e., ≥64 tips). Analysis of two large empirical datasets of vertebrate body size reveal overwhelming support for multiple-rate models of evolution, and we observe exceptionally high rates of body-size evolution in a group of emydid turtles relative to their evolutionary background. auteur will facilitate identification of exceptional evolutionary dynamics, essential to the study of both adaptive radiation and stasis.

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The problem of non-independence is not solved by alternative methods such as grouping data by a higher taxonomic rank or by downsampling.
“The problem of non-independence is not solved by alternative methods such as grouping data by a higher taxonomic rank (for example, genera or family), or by sampling the same number of genomes from taxonomic groups to minimize oversampling (‘downsampling’)102,103.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [102]

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A NEW PHYLOGENETIC METHOD FOR IDENTIFYING EXCEPTIONAL PHENOTYPIC DIVERSIFICATION
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Authors: Eastman, J. M., Alfaro, M. E., Joyce, P., Hipp, A. L., & Harmon, L. J.
Affiliations: University of Idaho (US)
University of California, Los Angeles (US)
Morton Arboretum (US)
ORCID: Alfaro, Michael E.
Hipp, Andrew L.
Harmon, Luke J.
Venue: Evolution
Publisher: Oxford University Press (OUP)
Published: 2011-08-24
Volume: 65
Issue: 12
Pages: 3578-3589
ISSN: 0014-3820 (ISSN-L)
DOI: 10.1111/j.1558-5646.2011.01401.x
OpenAlex: W2124424299
Cited by: 240
References: 52
Citations by year: 2026: 4 · 2025: 5 · 2024: 4 · 2023: 14 · 2022: 11 · 2021: 11 · 2020: 13 · 2019: 24 · 2018: 22 · 2017: 17 · 2016: 19 · 2015: 23 · 2014: 25 · 2013: 24 · 2012: 22
FWCI: 16.17
Type: journal article
Language: en
Open access: closed
Licence: doi.wiley.com/10.1002/tdm_license_1.1 (tdm, 1469 d)
Locations: Evolution (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 › Genetics › Evolution and Genetic Dynamics
Keywords: rate shifts, character evolution, continuous traits, reversible jump MCMC, emydid turtles, adaptive radiation, Stasi
MeSH terms: Animals, Bayes Theorem, Markov Chains, Models, Biological, Monte Carlo Method, Phylogeny, Time Factors, Vertebrates, Body Size

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A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES: IDENTIFYING RATE HETEROGENEITY IN CHARACTER EVOLUTION

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