SURFACE : detecting convergent evolution from comparative data by fitting Ornstein‐Uhlenbeck models with stepwise Akaike Information Criterion
Open accessAbstract
Summary: We present a method, ‘ SURFACE ’, that uses the Ornstein‐Uhlenbeck stabilizing selection model to identify cases of convergent evolution using only continuous phenotypic characters and a phylogenetic tree. SURFACE uses stepwise Akaike Information Criterion first to locate regime shifts on a tree, then to identify whether shifts are towards convergent regimes. Simulations can be used to test the hypothesis that a clade contains more convergence than expected by chance. We demonstrate the method with an application to Hawaiian Tetragnatha spiders, and present numerical simulations showing that the method has desirable statistical properties given data for multiple traits. The r package surface is available as open source software from the Comprehensive R Archive Network.
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?
Tests of adaptive evolution come in two flavors: those with an a priori hypothesis about which lineages belong to which regimes, and those where the locations of regime changes are estimated along with the parameters of the OU process.
“Tests of adaptive evolution come in two flavors: those with an a priori hypothesis (or hypotheses) regarding which lineages belong to which distinct regimes based on ancestral state reconstruction of explanatory factors (Butler and King 2004;Beaulieu et al. 2012) and those where the locations of regime changes are themselves estimated along with the parameters of the OU process (Ingram and Mahler”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Ingram and Mahler 2013
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
Model selection and multimodel inference: a practical information-theoretic approach.
Guthery, F. S., Burnham, K. P., & Anderson, D. R. (2003) · The Journal of Wildlife Management · doi:10.2307/3802723 · Cited by 41,495 · 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
Eastman, 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
Flagged first, then by citations
Research works printed but not linked: 10
- Alfaro, M.E., Santini, F., Brock, C., Alamillo, H., Dornburg, A., Rabosky, D.L., Carnevale, G. & Harmon, L.J. (2009) Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences of the USA, 106, 13410-13414.
- Blackledge, T.A. & Gillespie, R.G. (2004) Convergent evolution of behavior in an adaptive radiation of Hawaiian web-building spiders. Proceedings of the National Academy of Sciences of the USA, 101, 16228-16233.
- Felsenstein, J. (1988) Phylogenies and quantitative characters. Annual Review of Ecology and Systematics, 19, 445-471.
- Gillespie, R.G., Croom, H.B. & Palumbi, S.R. (1994) Multiple origins of a spider radiation in Hawaii. Proceedings of the National Academy of Sciences of the USA, 91, 2290-2294.
- Hansen, T.F. (2012) Adaptive landscapes and macroevolutionary dynamics. The Adaptive Landscape in Evolutionary Biology (eds. E. Svensson & R. Calsbeek), pp. 205-226. Oxford University Press, Oxford, UK.
- Harvey, P.H. & Pagel, M.D. (1991) The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford, UK.
- Losos, J. (2009) Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles. University of California Press, Berkeley, CA.
- Moore, B.R. & Chan, K.M.A. (2004) Detecting diversification rate variation in supertrees. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (ed. O.R.P. Bininda-Emonds), pp. 487-533. Kluwer Academic, Dordr- echt, The Netherlands.
- Simpson, G.G. (1953) The Major Features of Evolution. Columbia University Press, New York, NY.
- Stayton, C.T. (2008) Is convergence surprising? An examination of the fre- quency of convergence in simulated datasets. Journal of Theoretical Biol- ogy, 252, 1-14.
Cited by
Sorted by citations
Rethinking phylogenetic comparative methods
Uyeda, J. C., Zenil-Ferguson, R., & Pennell, M. W. (2018) · Systematic Biology · doi:10.1093/sysbio/syy031 · Cited by 313 · see citing works
Grabowski, M., Voje, K. L., & Hansen, T. F. (2016) · Journal of Human Evolution · doi:10.1016/j.jhevol.2016.03.001 · Cited by 55 · see citing works
Balanoff, A. M., Smaers, J. B., & Turner, A. H. (2016) · Journal of Anatomy · doi:10.1111/joa.12403 · Cited by 46 · see citing works
- Authors
- Ingram, T., & Mahler, D. L.
- Affiliations
- Harvard University (US)
- University of California, Davis (US)
- Corresponding author
- Ingram, Travis
- Venue
- Methods in Ecology and Evolution
- Publisher
- Wiley
- Published
- 2013-03
- Volume
- 4
- Issue
- 5
- Pages
- 416-425
- ISSN
- 2041-210X (ISSN-L)
- OpenAlex
- W2103516605
- Cited by
- 300
- References
- 3
- Citations by year
- 2026: 13 · 2025: 18 · 2024: 12 · 2023: 18 · 2022: 14 · 2021: 22 · 2020: 17 · 2019: 43 · 2018: 29 · 2017: 35 · 2016: 28 · 2015: 28 · 2014: 20 · 2013: 3
- FWCI
- 17.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Methods in Ecology and Evolution (publishedVersion, cc-by)
- Funders
- Harvard University
- Natural Sciences and Engineering Research Council of Canada
- 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
- convergent evolution, Ornstein-Uhlenbeck process, stabilizing selection, tipping points, phylogenetic comparative analysis
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
