The DOI matches its Crossref record; 48 of the 52 references it cites were found in a registry or an index.
A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES: IDENTIFYING RATE HETEROGENEITY IN CHARACTER EVOLUTION
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.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
Citations
Cites
Equation of State Calculations by Fast Computing Machines
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller, E. (1953) · The Journal of Chemical Physics · doi:10.1063/1.1699114 · Cited by 37,192
MRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck, J. P., & Ronquist, F. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.8.754 · Cited by 21,937
Monte Carlo sampling methods using Markov chains and their applications.
Hastings, W. K. (1970) · Biometrika · doi:10.1093/biomet/57.1.97 · Cited by 15,195
Reversible Jump Markov Chain Monte Carlo Computation and Bayesian Model Determination
Green, P. J. (1995) · Biometrika · doi:10.1093/biomet/82.4.711 · Cited by 5,941
MRBAYES: Bayesian inference of phylogeny
Huelsenbeck, J. P., & Ronquist, F. (2001) · Bioinformatics · Cited by 4,892
TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
Blomberg, S. P., Garland, T., & Ives, A. R. (2003) · Evolution · doi:10.1111/j.0014-3820.2003.tb00285.x · Cited by 4,678
GEIGER: investigating evolutionary radiations
Harmon, L. J., Weir, J. T., Brock, C. D., Glor, R. E., & Challenger, W. O. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm538 · Cited by 2,508
Self-citationKass, R. E., & Raftery, A. E. (1995) · Journal of the American Statistical Association · doi:10.2307/2291091 · Cited by 2,359
The Major Features of Evolution
Simpson, G. G. (1953) · Columbia University Press eBooks · doi:10.7312/simp93764 · Cited by 2,091
THE MAJOR FEATURES OF EVOLUTION
Olson, E. C., & Simpson, G. G. (1954) · Evolution · doi:10.2307/2405671 · Cited by 2,029
Research works printed but not linked: 3
- 1984, Living fossils
- Stadler, 2010, TreeSim: simulating trees under the birth-death model
- Vos, 2006, A new dated supertree of the Primates. Chapter 5
Cited by
Sorted by citations
Items 201–236 of 236
(2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/033647 · Cited by 5
Elliot, M. G. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.09.033 · Cited by 3
Using ChromEvol to Determine the Mode of Chromosomal Evolution
Escudero, M., Maguilla, E., Márquez‐Corro, J. I., Martín‐Bravo, S., Mayrose, I., Shafir, A., Tan, L., Tribble, C. M., & Zenil‐Ferguson, R. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3226-0_32 · Cited by 3
Raia, P., Ferranti, L., Castiglione, S., Melchionna, M., Saggese, F., Raimondi, R., Serio, C., Carotenuto, F., Passaro, F., & Antonioli, F. (2016) · The Holocene · doi:10.1177/0959683616660169 · Cited by 3
Ancestral Reconstruction: Theory and Practice
Groussin, M., Daubin, V., Gouy, M., & Tannier, É. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-800049-6.00166-9 · Cited by 3
How to make any method "fail": BAMM at the kangaroo court of false equivalencyPreprint
Rabosky, D. L. (2017) · arXiv (Cornell University) · doi:10.48550/arxiv.1711.03253 · Cited by 4
Predicting evolutionary targets and parameters of gene deletion from expression data
dos Santos, A. L. C., DeGiorgio, M., & Assis, R. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae002 · Cited by 2
The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method
Griffin, R. H., & Yapuncich, G. (2015) · PLoS ONE · doi:10.1371/journal.pone.0144147 · Cited by 2
Sağlam, İ. K., Miller, M. R., O'Rourke, S., & Çağlar, S. S. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106597 · Cited by 2
Ecological and Evolutionary Morphology
Zelditch, M. L., Swiderski, D. L., & Sheets, H. D. (2012) · Elsevier eBooks · doi:10.1016/b978-0-12-386903-6.00010-1 · Cited by 2
Gründler, M. C., Rabosky, D. L., & Zapata, F. (2022) · Systematic Biology · doi:10.1093/sysbio/syac035 · Cited by 2
The Laplace Motion in Phylogenetic Comparative MethodsPreprint
Bartoszek, K. (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1403.1562 · Cited by 2
Rabosky, D. L., & Slater, G. J. (2014) · Oxford University Press eBooks · doi:10.1093/obo/9780199941728-0009 · Cited by 3
Yu, M., & Hahn, M. W. (2026) · Evolutionary Journal of the Linnean Society · doi:10.1093/evolinnean/kzag004 · Cited by 1
Are Historical Biogeographical Events Able to Promote Biological Diversification?
Velasco, J. A. (2018) · InTech eBooks · doi:10.5772/intechopen.69516 · Cited by 1
Parsimonious identification of evolutionary shifts for quantitative charactersPreprint
Chabrol, O., & Didier, G. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/184663 · Cited by 1
Phylogenetic Comparative Methods and Tests of Macroevolutionary Questions
Martins, E. P., & Fuentes-González, J. A. (2018) · Oxford University Press eBooks · doi:10.1093/obo/9780199941728-0099
Detecting mosaic patterns in macroevolutionary disparityPreprint
Parins-Fukuchi, C. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/423228
Sağlam, İ. K., Miller, M. R., O’Rourke, S., & Çağlar, S. S. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/610857
Probabilistic Models on Fibre Bundles
Shan, S. (2019)
Developments for the Next Generation of Evolutionary Paleobiology
Parins‐Fukuchi, C. (2019) · Deep Blue (University of Michigan)
(2012) · Elsevier eBooks · doi:10.1016/b978-0-12-386903-6.00024-1
Modèles d’évolution de caractères continus
Bastide, P., Mariadassou, M., & Robin, S. S. (2022) · doi:10.51926/iste.9069.ch3
Diniz‐Filho, J. A. F. (2023) · Springer eBooks · doi:10.1007/978-3-031-44611-5_8
Begum, T., Duchen, P., Bucao, C. F., & Robinson‐Rechavi, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.29.571877
Evolutionary Models of Continuous Traits
Bastide, P., Mariadassou, M., & Robin, S. S. (2024) · Wiley eBooks · doi:10.1002/9781394284252.ch3
Disparity over time, space, and evolving lineages
Zelditch, M. L., Swiderski, D. L., & Sheets, H. D. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-28965-1.00008-7
Multifaceted impacts of an innovation on dental diversity in an adaptive radiation of cichlid fishes
Peoples, N., & Wainwright, P. C. (2025) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2025.2208
Discriminating models of trait evolution
Lozano, J. R., Jangra, S., DeGiorgio, M., Assis, R., & Adams, R. (2026) · Evolution · doi:10.1093/evolut/qpag021
Modèles et algorithmes pour l'évolution biologique
Chabrol, O. (2017) · theses.fr (ABES) · doi:10.70675/23889726zfc97z4d77zbbb6z436783a7cb06
Phylograms better fit neutrally evolving traits than chronograms
Latrille, T., Gaboriau, T., & Salamin, N. (2026) · Evolution Letters · doi:10.1093/evlett/qrag015
Rates of passerine body plan evolution in time and space
Berv, J. S., Probst, C. M., Claramunt, S., Shipley, J. R., Friedman, M., Smith, S. A., Fouhey, D. F., & Weeks, B. C. (2026) · Nature Ecology & Evolution · doi:10.1038/s41559-026-03110-5
Metadata
- 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)
- Venue
- Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-08-24
- Volume
- 65
- Issue
- 12
- Pages
- 3578-3589
- ISSN
- 0014-3820 (ISSN-L)
- 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
- Locations
- Evolution (publishedVersion)
- PubMed (publishedVersion)
- 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 › 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
