Phylogenetic Signal, Evolutionary Process, and Rate
Open accessAbstract
A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement of "phylogenetic signal" in data sets composed of observations collected from species related by a phylogenetic tree. Phylogenetic signal is a measure of the statistical dependence among species' trait values due to their phylogenetic relationships. Although phylogenetic signal is a measure of pattern (statistical dependence), there has nonetheless been a widespread propensity in the literature to attribute this pattern to aspects of the evolutionary process or rate. This may be due, in part, to the perception that high evolutionary rate necessarily results in low phylogenetic signal; and, conversely, that low evolutionary rate or stabilizing selection results in high phylogenetic signal (due to the resulting high resemblance between related species). In this study, we use individual-based numerical simulations on stochastic phylogenetic trees to clarify the relationship between phylogenetic signal, rate, and evolutionary process. Under the simplest model for quantitative trait evolution, homogeneous rate genetic drift, there is no relation between evolutionary rate and phylogenetic signal. For other circumstances, such as functional constraint, fluctuating selection, niche conservatism, and evolutionary heterogeneity, the relationship between process, rate, and phylogenetic signal is complex. For these reasons, we recommend against interpretations of evolutionary process or rate based on estimates of phylogenetic signal.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
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 [56]
The section “Phylogenetic Signal and Evolutionary Rate” (page unavailable) reports that, under unconstrained genetic drift, evolutionary rate has no relationship with phylogenetic signal. This supports the point that rapidly evolving traits cannot simply be assumed independent. But the paper does not establish that non-independence persists for traits produced by very recent events; its discussion of changes concentrated near the tree tips says they can reduce phylogenetic signal, and its introductory passage cautions against assuming dependence without estimating it. (LLM, conf=0.83)
Experimental — accuracy not yet measuredA 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 [56]
The Abstract (page unavailable) treats phylogenetic signal as a measure of statistical dependence that can be weak, and the Conclusions (page unavailable) recommend fitting evolutionary models to the data and tree rather than inferring process from signal alone. These passages support treating signal as variable, but they do not explicitly say that a total lack of signal is one end of a spectrum or give a rule about whether to avoid phylogenetic comparative methods when signal is absent. The citing sentence also contains a double negative ('not a reason not to avoid'), so its intended methodological advice is unclear. (LLM, conf=0.78)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793 · see citing works
The Ecology of Adaptive Radiation
Schluter, D. (2000) · doi:10.1093/oso/9780198505235.001.0001 · Cited by 4,974 · see citing works
Determinants of rate variation in mammalian DNA sequence evolution.
Bromham, L., Rambaut, A., & Harvey, P. H. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02202109 · Cited by 291 · cited 2× · see citing works
“The rate of phenotypic evolution by genetic drift might be heterogeneous through time for any of a variety of biological reasons (such as higher solar radiation in tropical climes, concerted changes in the fidelity of DNA replication over time, trends in size or metabolic rate over time, and irreversible changes in pl…”
Flagged first, then by citations
Research works printed but not linked: 13
- Crow, J. F., and M. Kimura. 1964. The theory of genetic loads. Pages 495-505 in Proceedings of the XI International Congress of Genetics (S. J. Geerts, ed.). Pergamon, Oxford, UK.
- Falconer, D. S., and T. F. C. Mackay. 1996. Introduction to quantitative genetics. Prentice Hall, Essex, UK.
- Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic anal- ysis and comparative data: A test and review of evidence. Am. Nat. 160:712-726.
- Gittleman, J. L., C. G. Anderson, M. Kot, and H.-K. Luh. 1996. Compar- ative tests of evolutionary lability and rates using molecular phylo- genies. Pages 289-307 in New uses for new phylogenies (P. H. Har- vey, A. J. Leigh Brown, J. Maynard Smith, and S. Nee, eds.). Oxford University Press, Oxford, UK.
- Gould, S. J. 2002. The structure of evolutionary theory. Harvard Uni- versity Press, Cambridge, Massachusetts.
- Grafen, A. 1989. The phylogenetic regression. Philos. Trans. R. Soc. B 326:119-157.
- Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evo- lutionary biology. Oxford University Press, Oxford, UK.
- Harvey, P. H., and A. Rambaut. 2000. Comparative analyses for adap- tive radiations. Phil. Trans. R. Soc. Lond. B 355:1599-1605.
- Hein, J., M. H. Schierup, and C. Wiuf. 2005. Gene genealogies, varia- tion and evolution: A primer in coalescent theory. Oxford University Press, Oxford, UK.
- Price, T. 1997. Correlated evolution and independent contrasts. Phil. Trans. R. Soc. Lond. B 352:519-529.
- Rohde, K. 1978. Latitudinal gradients in species diversity and their causes. I. A review of the hypotheses explaining the gradients. Biol- ogisches Zentralblatt 97:393-403.
- Silvertown, J., K. McConway, D. Gowing, M. Dodd, M. F. Fay, J. A. Joseph, and K. Dolphin. 2006. Absence of phylogenetic signal in the niche structure of meadow plant communities. Proc. R. Soc. B 273:39- 44.
- Whitehead, A., and D. L. Crawford. 2006. Neutral and adaptive varia- tion in gene expression. Proc. Natl. Acad. Sci. USA 103:5425-5430.
Cited by
Sorted by citations
The merging of community ecology and phylogenetic biology
Cavender‐Bares, J., Kozak, K. H., Fine, P. V. A., & Kembel, S. W. (2009) · Ecology Letters · doi:10.1111/j.1461-0248.2009.01314.x · Cited by 2,321 · see citing works
Slater, G. J., Harmon, L. J., & Alfaro, M. E. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01723.x · Cited by 334 · see citing works
Self-citationEastman, J. M., Alfaro, M. E., Joyce, P., Hipp, A. L., & Harmon, L. J. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01401.x · Cited by 240 · see citing works
Self-citationHopkins, M. J., & Smith, A. B. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418153112 · Cited by 133 · see citing works
Brender, J. R., & Zhang, Y. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004494 · Cited by 140 · see citing works
Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa
Odom, K. J., Araya‐Salas, M., Morano, J. L., Ligon, R. A., Leighton, G. M., Taff, C. C., Dalziell, A. H., Billings, A. C., Germain, R. R., Pardo, M., et al. (2021) · Biological Reviews · doi:10.1111/brv.12695 · Cited by 81 · see citing works
A phylogenetic approach to comparative genomics
Dewar, A. E., Belcher, L. J., & West, S. A. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-024-00803-0 · Cited by 41 · see citing works
Muntané, G., Horvath, J. E., Hof, P. R., Ely, J. J., Hopkins, W. D., Raghanti, M. A., Lewandowski, A. H., Wray, G. A., & Sherwood, C. C. (2015) · Cerebral Cortex · doi:10.1093/cercor/bht354 · Cited by 36 · see citing works
Hartikainen, S. M., & Robson, T. M. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.1058162 · Cited by 10 · see citing works
- Authors
- Revell, L. J., Harmon, L. J., & Collar, D. C.
- Affiliations
- Harvard University (US)
- University of Idaho (US)
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-08-01
- Volume
- 57
- Issue
- 4
- Pages
- 591-601
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2162399971
- Cited by
- 879
- References
- 3
- Citations by year
- 2026: 40 · 2025: 65 · 2024: 57 · 2023: 53 · 2022: 61 · 2021: 62 · 2020: 65 · 2019: 57 · 2018: 61 · 2017: 51 · 2016: 57 · 2015: 57 · 2014: 43 · 2013: 34 · 2012: 38
- FWCI
- 17.84
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Systematic Biology (publishedVersion)
- PubMed (publishedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- Funders
- Harvard University
- 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
- phylogenetic signal, evolutionary rates, evolutionary processes, continuous traits, phylogenetic comparative analysis, genetic drift, functional constraints, fluctuating selection, niche conservatism, numerical simulation
- MeSH terms
- Computer Simulation, Models, Genetic, Mutation, Phylogeny, Evolution, Molecular, Genetic Drift
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
