The seven deadly sins of comparative analysis
Open accessAbstract
Phylogenetic comparative methods are extremely commonly used in evolutionary biology. In this paper, I highlight some of the problems that are frequently encountered in comparative analyses and review how they can be fixed. In broad terms, the problems boil down to a lack of appreciation of the underlying assumptions of comparative methods, as well as problems with implementing methods in a manner akin to more familiar statistical approaches. I highlight that the advent of more flexible computing environments should improve matters and allow researchers greater scope to explore methods and data.
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.
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
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
APE: Analyses of Phylogenetics and Evolution in R language
Paradis, E., Claude, J., & Strimmer, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg412 · Cited by 12,037 · see citing works
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793 · see citing works
Model Selection and Multimodel Inference
(2003) · Technometrics · doi:10.1198/tech.2003.s146 · Cited by 5,505 · see citing works
Inferring the historical patterns of biological evolution
Pagel, M. (1999) · Nature · doi:10.1038/44766 · Cited by 5,200 · see citing works
The comparative method in evolutionary biology
Harvey, P., & Pagel, M. (1991) · Choice Reviews Online · doi:10.5860/choice.29-5104 · Cited by 4,778 · see citing works
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 · see citing works
The Comparative Method in Evolutionary Biology
Harvey, P. H., & Pagel, M. D. (1991) · doi:10.1093/oso/9780198546412.001.0001 · Cited by 4,337 · see citing works
Effect size, confidence interval and statistical significance: a practical guide for biologists
Nakagawa, S., & Cuthill, I. C. (2007) · Biological Reviews · doi:10.1111/j.1469-185x.2007.00027.x · Cited by 3,835 · see citing works
Behavioural Ecology: An Evolutionary Approach
Ormond, R., Krebs, J. R., & Davies, N. (1983) · Journal of Animal Ecology · doi:10.2307/4581 · Cited by 2,907 · see citing works
Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence
Freckleton, R. P., Harvey, P. H., & Pagel, M. (2002) · The American Naturalist · doi:10.1086/343873 · Cited by 2,604 · see citing works
Self-citationProcedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts
Garland, T., Harvey, P. H., & Ives, A. R. (1992) · Systematic Biology · doi:10.1093/sysbio/41.1.18 · Cited by 2,151 · see citing works
Grafen, A. (1989) · Philosophical Transactions of the Royal Society of London. B, Biological Sciences · doi:10.1098/rstb.1989.0106 · Cited by 2,142 · see citing works
The ecological detective: confronting models with data
(1997) · Choice Reviews Online · doi:10.5860/choice.35-1501 · Cited by 1,726 · see citing works
Martins, E. P., & Hansen, T. F. (1997) · The American Naturalist · doi:10.1086/286013 · Cited by 1,718 · see citing works
Data Mining: Concepts, Models, Methods, and Algorithms
(2003) · Technometrics · doi:10.1198/tech.2003.s785 · Cited by 1,369 · see citing works
Stabilizing selection and the comparative analysis of adaptation
Hansen, T. F. (1997) · Evolution · doi:10.1111/j.1558-5646.1997.tb01457.x · Cited by 1,361 · see citing works
Body mass in comparative primatology
Smith, R. J., & Jungers, W. L. (1997) · Journal of Human Evolution · doi:10.1006/jhev.1996.0122 · Cited by 1,307 · see citing works
Optimization Theory in Evolution
Smith, J. M. (1978) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.09.110178.000335 · Cited by 1,139 · see citing works
Purvis, A., & Rambaut, A. (1995) · Computer applications in the biosciences · doi:10.1093/bioinformatics/11.3.247 · Cited by 1,126 · see citing works
Inferring evolutionary processes from phylogenies
PAGEL, M. (1997) · Zoologica Scripta · doi:10.1111/j.1463-6409.1997.tb00423.x · Cited by 1,106 · see citing works
Pennycuick, C. J. (1975) · Avian Biology · doi:10.1016/b978-0-12-249405-5.50009-4 · Cited by 1,072 · see citing works
PHYLOGENIES AND QUANTITATIVE CHARACTERS
Felsenstein, J. (1988) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.19.110188.002305 · Cited by 831 · see citing works
Garland, T., & Ives, A. R. (2000) · The American Naturalist · doi:10.1086/303327 · Cited by 824 · see citing works
Tempo and Mode of Evolutionary Radiation in Iguanian Lizards
Harmon, L. J., Schulte, J. A., Larson, A., & Losos, J. B. (2003) · Science · doi:10.1126/science.1084786 · Cited by 727 · see citing works
Analysis of Phylogenetics and Evolution with R
Paradis, E. (2011) · Springer eBooks · doi:10.1007/978-1-4614-1743-9 · Cited by 713 · see citing works
PHYLOGENETIC ANALYSES OF THE CORRELATED EVOLUTION OF CONTINUOUS CHARACTERS: A SIMULATION STUDY
Martins, E. P., & Garland, T. (1991) · Evolution · doi:10.1111/j.1558-5646.1991.tb04328.x · Cited by 635 · see citing works
Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence
Freckleton, Harvey, & Pagel (2002) · The American Naturalist · doi:10.2307/3078855 · Cited by 631 · see citing works
(2002) · Cited by 603 · see citing works
Garland, T., Midford, P. E., & Ives, A. R. (1999) · American Zoologist · doi:10.1093/icb/39.2.374 · Cited by 568 · see citing works
Modern Statistics for the Life Sciences
Sissons, S. (2003) · Journal of the Royal Statistical Society Series D (The Statistician) · doi:10.1111/1467-9884.00369_10 · Cited by 565 · see citing works
How much variance can be explained by ecologists and evolutionary biologists?
Møller, A., & Jennions, M. D. (2002) · Oecologia · doi:10.1007/s00442-002-0952-2 · Cited by 553 · see citing works
On the misuse of residuals in ecology: testing regression residuals vs. the analysis of covariance
García‐Berthou, E. (2001) · Journal of Animal Ecology · doi:10.1046/j.1365-2656.2001.00524.x · Cited by 511 · see citing works
Limiting Resources and Territoriality in Microtine Rodents
Ostfeld, R. S. (1985) · The American Naturalist · doi:10.1086/284391 · Cited by 506 · see citing works
Hilborn, R., & Mangel, M. (2013) · Princeton University Press eBooks · doi:10.1515/9781400847310 · Cited by 490 · see citing works
Within-Species Variation and Measurement Error in Phylogenetic Comparative Methods
Ives, A. R., Midford, P. E., & Garland, T. (2007) · Systematic Biology · doi:10.1080/10635150701313830 · Cited by 487 · see citing works
On the misuse of residuals in ecology: regression of residuals vs. multiple regression
Freckleton, R. P. (2002) · Journal of Animal Ecology · doi:10.1046/j.1365-2656.2002.00618.x · Cited by 480 · see citing works
Self-citationMETHODS FOR THE ANALYSIS OF COMPARATIVE DATA IN EVOLUTIONARY BIOLOGY
Lynch, M. (1991) · Evolution · doi:10.1111/j.1558-5646.1991.tb04375.x · Cited by 436 · see citing works
Missing inaction: the dangers of ignoring missing data
Nakagawa, S., & Freckleton, R. P. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.06.014 · Cited by 414 · see citing works
Self-citationOn Misinterpreting the `Phylogenetic Correction'
Westoby, M., Leishman, M. R., & Lord, J. M. (1995) · Journal of Ecology · doi:10.2307/2261605 · Cited by 413 · see citing works
MODEL WEIGHTS AND THE FOUNDATIONS OF MULTIMODEL INFERENCE
Link, W. A., & Barker, R. (2006) · Ecology · doi:10.1890/0012-9658(2006)87[2626:mwatfo]2.0.co;2 · Cited by 400 · see citing works
Comparative methods for explaining adaptations
Harvey, P. H., & Purvis, A. (1991) · Nature · doi:10.1038/351619a0 · Cited by 383 · see citing works
Information theory and hypothesis testing: a call for pluralism
Stephens, P. A., Buskirk, S. W., Hayward, G. D., & del Rio, C. M. (2005) · Journal of Applied Ecology · doi:10.1111/j.1365-2664.2005.01002.x · Cited by 361 · see citing works
Accommodating Phylogenetic Uncertainty in Evolutionary Studies
Huelsenbeck, J. P., Rannala, B. H., & Masly, J. P. (2000) · Science · doi:10.1126/science.288.5475.2349 · Cited by 352 · see citing works
Correlated evolution and independent contrasts
Price, T. D. (1997) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1997.0036 · Cited by 342 · see citing works
A COMPARATIVE METHOD FOR STUDYING ADAPTATION TO A RANDOMLY EVOLVING ENVIRONMENT
Hansen, T. F., Pienaar, J., & Orzack, S. H. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00412.x · Cited by 336 · see citing works
LIKELIHOOD METHODS FOR DETECTING TEMPORAL SHIFTS IN DIVERSIFICATION RATES
Rabosky, D. L. (2006) · Evolution · doi:10.1111/j.0014-3820.2006.tb01194.x · Cited by 325 · see citing works
Extrinsic versus intrinsic factors in the decline and extinction of Australian marsupials
Fisher, D. O., Blomberg, S. P., & Owens, I. P. F. (2003) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2003.2447 · Cited by 308 · see citing works
Housworth, E. A., Martins, E. P., & Lynch, M. (2004) · The American Naturalist · doi:10.1086/380570 · Cited by 294 · see citing works
Clark, J. S. (2007) · Princeton University Press eBooks · doi:10.1515/9780691220123 · Cited by 279 · see citing works
A survey of the statistical power of research in behavioral ecology and animal behavior
Jennions, M. D. (2003) · Behavioral Ecology · doi:10.1093/beheco/14.3.438 · Cited by 278 · see citing works
Harvey, P., Colwell, R. K., SILVERTOWN, J. W., & May, R. M. (1983) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.14.110183.001201 · Cited by 275 · see citing works
Smith, R. J. (1980) · Journal of Theoretical Biology · doi:10.1016/0022-5193(80)90222-2 · Cited by 254 · see citing works
Harvey, P., & Nee, S. (1993) · European Review · doi:10.1017/s106279870000034x · Cited by 248 · see citing works
Felsenstein, J. (2008) · The American Naturalist · doi:10.1086/587525 · Cited by 243 · see citing works
Analysis of Phylogenetics and Evolution with R
Paradis, E. (2006) · Springer eBooks · doi:10.1007/978-0-387-35100-1 · Cited by 233 · see citing works
Garland, & Ives (2000) · The American Naturalist · doi:10.2307/3078871 · Cited by 228 · see citing works
Why Ecologists Need to be Phylogenetically Challenged
Harvey, P., Read, A. F., & Nee, S. (1995) · Journal of Ecology · doi:10.2307/2261606 · Cited by 223 · see citing works
Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data
Freckleton, R. P., & Jetz, W. (2008) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2008.0905 · Cited by 205 · see citing works
Self-citationCONFOUNDING ASYMMETRIES IN EVOLUTIONARY DIVERSIFICATION AND CHARACTER CHANGE
Maddison, W. P. (2006) · Evolution · doi:10.1111/j.0014-3820.2006.tb00517.x · Cited by 195 · see citing works
Detecting Non-Brownian Trait Evolution in Adaptive Radiations
Freckleton, R. P., & Harvey, P. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040373 · Cited by 193 · see citing works
Self-citationPhenotypic plasticity in the scaling of avian basal metabolic rate
McKechnie, A. E., Freckleton, R. P., & Jetz, W. (2006) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2005.3415 · Cited by 183 · see citing works
Self-citationSeeking the Evolutionary Regression Coefficient: An Analysis of What Comparative Methods Measure
Pagel, M. D. (1993) · Journal of Theoretical Biology · doi:10.1006/jtbi.1993.1148 · Cited by 176 · see citing works
PHYLOGENETIC ANALYSIS OF THE EVOLUTIONARY CORRELATION USING LIKELIHOOD
Revell, L. J., & Collar, D. C. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00616.x · Cited by 160 · see citing works
Thomas, G. H., Freckleton, R. P., & Székely, T. (2006) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2006.3488 · Cited by 150 · see citing works
Self-citationComparative analyses for adaptive radiations
Harvey, P., & Rambaut, A. (2000) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2000.0721 · Cited by 144 · see citing works
The Illusion of Invariant Quantities in Life Histories
Nee, S., Colegrave, N., West, S. A., & Grafen, A. (2005) · Science · doi:10.1126/science.1114488 · Cited by 127 · see citing works
Phylogenetic tests of ecological and evolutionary hypotheses: checking for phylogenetic independence
Freckleton, R. P. (2000) · Functional Ecology · doi:10.1046/j.1365-2435.2000.00400.x · Cited by 119 · see citing works
Self-citation(1996) · doi:10.1093/oso/9780198549857.001.0001 · Cited by 119 · see citing works
Bokma, F. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00492.x · Cited by 115 · see citing works
STATISTICAL ANALYSIS OF DIVERSIFICATION WITH SPECIES TRAITS
Paradis, E. (2005) · Evolution · doi:10.1111/j.0014-3820.2005.tb00889.x · Cited by 92 · see citing works
Olson, V., Liker, A., Freckleton, R. P., & Székely, T. (2007) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2007.1395 · Cited by 91 · see citing works
Self-citationRelating Traits to Diversification: A Simple Test
Freckleton, R. P., Phillimore, A. B., & Pagel, M. D. (2008) · The American Naturalist · doi:10.1086/588076 · Cited by 79 · see citing works
Self-citationKantardzic, M. M. (2009) · Institute of Electrical and Electronics Engineers eBooks · doi:10.1109/9780470544341 · Cited by 46 · see citing works
Ridley, J., Kolm, N., FRECKELTON, R. P., & Gage, M. J. G. (2007) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2006.01291.x · Cited by 34 · see citing works
Further Remarks on the Role of Phylogeny in Comparative Ecology
Harvey, P., Read, A. F., & Nee, S. (1995) · Journal of Ecology · doi:10.2307/2261643 · Cited by 31 · see citing works
ASYMMETRIES IN PHYLOGENETIC DIVERSIFICATION AND CHARACTER CHANGE CAN BE UNTANGLED
Paradis, E. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00252.x · Cited by 26 · see citing works
Recent advances in comparative methods
Freckleton, R. P., & Pagel, M. D. (2010) · Cambridge University Press eBooks · doi:10.1017/cbo9780511781360.011 · Cited by 7 · see citing works
Self-citationExplaining a little is often a lot
Roslin, T. V. (2002) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(02)02610-1 · Cited by 2 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- J O U R N A L C O M P I L A T I O N ª 2 0 0 9 E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y 14209101, 2009, 7, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2009.01757.x by Readcube (Labtiva Inc.), Wiley Online Library on [20/11/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License · DOI
Cited by
Sorted by citations
Global analysis of thermal tolerance and latitude in ectotherms
Sunday, J. M., Bates, A. E., & Dulvy, N. K. (2011) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2010.1295 · Cited by 1,300 · see citing works
Metabolic rate and body size are linked with perception of temporal information
Healy, K., McNally, L., Ruxton, G. D., Cooper, N., & Jackson, A. L. (2013) · Animal Behaviour · doi:10.1016/j.anbehav.2013.06.018 · Cited by 202 · see citing works
THE EVOLUTIONARY HISTORY OF CETACEAN BRAIN AND BODY SIZE: CETACEAN BRAIN EVOLUTION
Montgomery, S. H., Geisler, J. H., McGowen, M. R., Fox, C., Marino, L., & Gatesy, J. (2013) · Evolution · doi:10.1111/evo.12197 · Cited by 106 · see citing works
Mammalian intestinal allometry, phylogeny, trophic level and climate
Duque-Correa, M. J., Codron, D., Meloro, C., McGrosky, A., Schiffmann, C., Edwards, M. S., & Clauss, M. (2021) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2020.2888 · Cited by 40 · see citing works
A Guided Tour of Phylogenetic Comparative Methods for Studying Trait Evolution
Cornwallis, C. K., & Griffin, A. S. (2024) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-102221-050754 · Cited by 37 · see citing works
- Authors
- FRECKLETON, R. P.
- Affiliations
- University of Sheffield (GB)
- Corresponding author
- FRECKLETON, R. P.
- ORCID
- FRECKLETON, R. P.
- Venue
- Journal of Evolutionary Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-06-22
- Volume
- 22
- Issue
- 7
- Pages
- 1367-1375
- ISSN
- 1010-061X (ISSN-L)
- 1420-9101
- OpenAlex
- W2102746773
- Cited by
- 339
- References
- 79
- Citations by year
- 2026: 7 · 2025: 14 · 2024: 13 · 2023: 19 · 2022: 14 · 2021: 19 · 2020: 13 · 2019: 15 · 2018: 12 · 2017: 14 · 2016: 16 · 2015: 46 · 2014: 33 · 2013: 29 · 2012: 22
- FWCI
- 2.57
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Evolutionary Biology (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 › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- phylogenetic comparative analysis, methodological assumptions
- MeSH terms
- Biological Evolution, Phylogeny, Models, Statistical
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