Phylogenies and the Comparative Method
Abstract
Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause overstatement of the significance in hypothesis tests. Some illustrative examples of these phenomena have been given, and limitations of previous proposals of ways to correct for the nonindependence have been discussed. A method of correcting for the phylogeny has been proposed. It requires that we know both the tree topology and the branch lengths, and that we be willing to allow the characters to be modeled by Brownian motion on a linear scale. Given these conditions, the phylogeny specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. The considerable barriers to making practical use of this technique have been discussed.
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Standardized independent contrasts were calculated for each factor to account for shared ancestry.
“We calculated standardized independent contrasts (FIC: Felsenstein 1985) for each of the above factors (territoriality, shoulder height, body mass, habitat openness and group size) using the PDTREE module (Midford et al. 2005) in Mesquite 2.5 (Maddison & Maddison 2008) to account for shared ancestry.”
From Evolution of weaponry in female bovids (2009) · cites this paper as Felsenstein 1985
EMMLi analysis on phylogenetic independent contrasts supported the same most likely model and relative strength of correlations within and among modules as the analysis of raw data.
“To test the effects of shared ancestry on trait correlations, we also carried out EMMLi analysis on the phylogenetic independent contrasts (45) of the landmark configurations. This analysis supported the same most likely model and relative strength of correlations within and among modules as the analysis of the raw data did.”
From Developmental origins of mosaic evolution in the avian cranium (2018) · cites this paper as [45]
Because of shared phylogenetic descent, species data are likely not to represent statistically independent points, resulting in overestimation of degrees of freedom and increased Type I error rate.
“Firstly, because of shared phylogenetic descent, species data are likely not to represent statistically independent points.This results in overestimation of degrees of freedom and an increased Type I error rate.”
From Allometric scaling of mammalian metabolism (2005) · cites this paper as Felsenstein, 1985
The problem of nonindependence does not occur if characters respond essentially instantaneously to natural selection in the current environment, so that phylogenetic inertia is essentially absent.
“Felsenstein also noted that the problem of nonindependence does not occur if”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Felsenstein 1985
Felsenstein recovered a significant regression slope using Ordinary Least Squares despite there being no evolutionary covariance between the traits.
“He then evolved traits according to a BM process along the phylogeny; he recovered a significant regression slope using Ordinary Least Squares (OLS) despite there being no evolutionary covariance between the traits.”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Felsenstein 1985
The IC method is based on the Brownian motion model of trait evolution.
“As stated above, the IC method is based on the BM model of trait evolution.”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Felsenstein 1985
This led to the development of numerous methods that take phylogeny into account and control for the non-independence of species.
“This led to the development of numerous methods that take phylogeny into account and control for the non-independence of species16,18,19,33.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
The fact that species cannot be considered independent data points was first recognized in the 1970s by evolutionary biologists studying the evolution of life history traits such as sexual dimorphism and home range in primates.
“The fact that species cannot be considered independent data points was first recognized in the 1970s by evolutionary biologists studying the evolution of life history traits such as sexual dimorphism and home range in primates16,18,30–32.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
Species, genomes, and genes cannot be considered independent data points within statistical tests.
“However, species, genomes and genes cannot be considered as independent data points within statistical tests.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
Closely related species tend to be similar because they share genes by common descent.
“Closely related species tend to be similar because they share genes by common descent, which must be accounted for in analyses.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
There is no simple and robust alternative to controlling for phylogeny.
“There is no simple and robust alternative to controlling for phylogeny, and consequently, the best effort possible must be made to take phylogeny into account, to be able to detect real effects and avoid false positives.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
Collecting many more data points from the same phylogenetic cluster could increase any bias due to phylogenetic non-independence.
“Collecting many more data points from the same phylogenetic cluster could increase any bias due to phylogenetic non-independence (Fig. 1)16,18,20.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
Controlling for phylogeny can reduce the chance of detecting a significant result that is not real (Type II error or 'false positive').
“Instead, controlling for phylogeny can reduce the chance of detecting a significant result that is not real (Type II error or ‘false positive’)18,42.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
Controlling for confounding variables such as phylogeny does not reduce statistical power.
“Controlling for confounding variables such as phylogeny does not reduce statistical power, because such variables should be accounted for before making any estimates of power18,114,115.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [18]
Phylogenetic independent contrasts were calculated to examine scaling relationships while controlling for the effects of phylogenetic relatedness in the data set.
“Phylogenetic independent contrasts were also calculated from the data to examine scaling relationships while controlling for the effects of phylogenetic relatedness in the data set (59).”
From Evolution of increased glia–neuron ratios in the human frontal cortex (2006) · cites this paper as [59]
With a phylogeny, it becomes possible to examine correlated evolutionary change directly along the branches of the tree, for example with the method of independent contrasts, or to statistically control for nonindependence in the underlying data, for example by using phylogenetic generalized least squares (PGLS).
“With a phylogeny, it becomes possible to examine correlated evolutionary change directly along the branches of the tree, for example with the method of independent contrasts (Felsenstein 1985; Garland et al. 1992; Nunn and Barton 2001). Alternatively, one can use the phylogeny to statistically control for nonindependence in the underlying data, for example by using phylogenetic generalized least”
From How does cognition evolve? Phylogenetic comparative psychology (2012) · cites this paper as Felsenstein 1985
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works
Self-citationCases in which Parsimony or Compatibility Methods Will be Positively Misleading
Felsenstein, J. (1978) · Systematic Biology · doi:10.1093/sysbio/27.4.401 · Cited by 3,221 · see citing works
Self-citationPopulation density and body size in mammals
Damuth, J. D. (1981) · Nature · doi:10.1038/290699a0 · Cited by 1,249 · see citing works
Primate Ecology and Social Organization
Richard, A. F. (1982) · Cited by 838 · see citing works
Relative brain size and basal metabolic rate in terrestrial vertebrates
Martin, R. D. (1981) · Nature · doi:10.1038/293057a0 · Cited by 711 · see citing works
Maximum-likelihood estimation of evolutionary trees from continuous characters.
(1973) · Europe PMC (PubMed Central) · Cited by 700 · see citing works
Self-citationFelsenstein, J. (1981) · Evolution · doi:10.1111/j.1558-5646.1981.tb04991.x · Cited by 433 · see citing works
Self-citationPilbeam, D., & Gould, S. J. (1974) · Science · doi:10.1126/science.186.4167.892 · Cited by 416 · see citing works
Parsimony in Systematics: Biological and Statistical Issues
Felsenstein, J. (1983) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.14.110183.001525 · Cited by 352 · see citing works
Self-citationRelative Brain Size and Metabolism in Mammals
Armstrong, E. (1983) · Science · doi:10.1126/science.6407108 · Cited by 252 · see citing works
Outcrossing Versus Ecological Constraints in the Evolution of Dioecy
Givnish, T. J. (1982) · The American Naturalist · doi:10.1086/283959 · Cited by 102 · see citing works
The phylogeny of parental care in fishes
Gittleman, J. L. (1981) · Animal Behaviour · doi:10.1016/s0003-3472(81)80031-0 · Cited by 101 · see citing works
Insect Chromosome Numbers and Eusociality
Sherman, P. W. (1979) · The American Naturalist · doi:10.1086/283445 · Cited by 56 · see citing works
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Cited by
Sorted by citations
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
phytools: an R package for phylogenetic comparative biology (and other things)
Revell, L. J. (2011) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00169.x · Cited by 9,143 · 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
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
Phylogenies and Community Ecology
Webb, C. O., Ackerly, D. D., McPeek, M. A., & Donoghue, M. J. (2002) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.33.010802.150448 · Cited by 4,559 · see citing works
Morpho J: an integrated software package for geometric morphometrics
Klingenberg, C. P. (2010) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2010.02924.x · Cited by 3,784 · see citing works
Cross‐validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure
Roberts, D. R., Bahn, V., Ciuti, S., Boyce, M. S., Elith, J., Guillera‐Arroita, G., Hauenstein, S., Lahoz‐Monfort, J. J., Schröder, B., Thuiller, W., et al. (2017) · Ecography · doi:10.1111/ecog.02881 · Cited by 3,689 · see citing works
Integrating animal temperament within ecology and evolution
Réale, D. J. F., Reader, S. M., Sol, D., McDougall, P. T., & Dingemanse, N. J. (2007) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2007.00010.x · Cited by 3,587 · see citing works
Plant Ecological Strategies: Some Leading Dimensions of Variation Between Species
Westoby, M., Falster, D. S., Moles, A. T., Vesk, P. A., & Wright, I. J. (2002) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.33.010802.150452 · Cited by 3,063 · see citing works
ENVIRONMENTAL NICHE EQUIVALENCY VERSUS CONSERVATISM: QUANTITATIVE APPROACHES TO NICHE EVOLUTION
Warren, D. L., Glor, R. E., & Turelli, M. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00482.x · Cited by 2,678 · 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
Coevolution of neocortical size, group size and language in humans
Dunbar, R. (1993) · Behavioral and Brain Sciences · doi:10.1017/s0140525x00032325 · Cited by 2,370 · see citing works
Bivariate line‐fitting methods for allometry
Warton, D. I., Wright, I. J., Falster, D. S., & Westoby, M. (2006) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1017/s1464793106007007 · Cited by 2,318 · see citing works
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901 · see citing works
A meta‐analysis of trait differences between invasive and non‐invasive plant species
van Kleunen, M., Weber, E., & Fischer, M. (2009) · Ecology Letters · doi:10.1111/j.1461-0248.2009.01418.x · Cited by 1,884 · see citing works
(1994) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.1994.0006 · Cited by 1,859 · see citing works
Efficient Control of Population Structure in Model Organism Association Mapping
Kang, H. M., Zaitlen, N., Wade, C. M., Kirby, A. W., Heckerman, D. E., Daly, M. J., & Eskin, E. (2008) · Genetics · doi:10.1534/genetics.107.080101 · Cited by 1,848 · see citing works
Phylocom: software for the analysis of phylogenetic community structure and trait evolution
Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn358 · Cited by 1,825 · see citing works
Predicting extinction risk in declining species
Purvis, A., Gittleman, J. L., Cowlishaw, G., & Mace, G. M. (2000) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.2000.1234 · Cited by 1,768 · see citing works
Edge effects and the extinction of populations inside protected areas
Woodroffe, R., & Ginsberg, J. (1998) · Science · doi:10.1126/science.280.5372.2126 · Cited by 1,818 · see citing works
Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity
Hortal, J., de Bello, F., Diniz-Filho, J. A. F., Lewinsohn, T. M., Lobo, J. M., & Ladle, R. J. (2015) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-112414-054400 · Cited by 1,743 · see citing works
Losos, J. B. (2008) · Ecology Letters · doi:10.1111/j.1461-0248.2008.01229.x · Cited by 1,735 · see citing works
smatr 3– an R package for estimation and inference about allometric lines
Warton, D., Duursma, R., Falster, D., & Taskinen, S. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00153.x · Cited by 1,530 · see citing works
Stevens, J. D. (2000) · ICES Journal of Marine Science · doi:10.1006/jmsc.2000.0724 · Cited by 1,725 · see citing works
Martins, E. P., & Hansen, T. F. (1997) · The American Naturalist · doi:10.1086/286013 · Cited by 1,718 · see citing works
Mouchet, M. A., Villéger, S., Mason, N. W. H., & Mouillot, D. (2010) · Functional Ecology · doi:10.1111/j.1365-2435.2010.01695.x · Cited by 1,646 · see citing works
Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees
Webb, C. O. (2000) · The American Naturalist · doi:10.1086/303378 · Cited by 1,630 · see citing works
Avian Life History Evolution in Relation to Nest Sites, Nest Predation, and Food
Martin, T. E. (1995) · Ecological Monographs · doi:10.2307/2937160 · Cited by 1,564 · see citing works
Phylogenetic comparative analysis: a modeling approach for adaptive evolution
Butler, M. A., & King, A. A. (2004) · The American Naturalist · doi:10.1086/426002 · Cited by 1,438 · 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
PATTERNS OF SPECIATION IN DROSOPHILA
Coyne, J. A., & Orr, H. A. (1989) · Evolution · doi:10.1111/j.1558-5646.1989.tb04233.x · Cited by 1,338 · see citing works
Trait-Based Community Ecology of Phytoplankton
Litchman, E., & Klausmeier, C. A. (2008) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.39.110707.173549 · Cited by 1,286 · see citing works
ADAPTIVE RADIATION ALONG GENETIC LINES OF LEAST RESISTANCE
Schluter, D. (1996) · Evolution · doi:10.1111/j.1558-5646.1996.tb03563.x · Cited by 1,269 · see citing works
Dispersal, Gene Flow, and Population Structure
Bohonak, A. J. (1999) · The Quarterly Review of Biology · doi:10.1086/392950 · Cited by 1,237 · see citing works
Phylogenetic Analysis of Covariance by Computer Simulation
Garland, T., Dickerman, A. W., Janis, C. M., & Jones, J. A. (1993) · Systematic Biology · doi:10.1093/sysbio/42.3.265 · Cited by 1,238 · see citing works
AVIAN LIFE HISTORY VARIATION AND CONTRIBUTION OF DEMOGRAPHIC TRAITS TO THE POPULATION GROWTH RATE
Sæther, B.-E., & Bakke, Ø. (2000) · Ecology · doi:10.1890/0012-9658(2000)081[0642:alhvac]2.0.co;2 · Cited by 1,233 · see citing works
Jones, R. T., Robeson, M. S., Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · The ISME Journal · doi:10.1038/ismej.2008.127 · Cited by 1,230 · see citing works
TOLERANCE TO SHADE, DROUGHT, AND WATERLOGGING OF TEMPERATE NORTHERN HEMISPHERE TREES AND SHRUBS
Niinemets, Ü., & Valladares, F. (2006) · Ecological Monographs · doi:10.1890/0012-9615(2006)076[0521:ttsdaw]2.0.co;2 · Cited by 1,228 · see citing works
EVOLUTION OF THE MAGNITUDE AND TIMING OF INBREEDING DEPRESSION IN PLANTS
Husband, B. C., & Schemske, D. W. (1996) · Evolution · doi:10.1111/j.1558-5646.1996.tb04472.x · Cited by 1,203 · see citing works
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
Touchon, M., Hoede, C., Tenaillon, O., Barbe, V., Baeriswyl, S., Bidet, P., Bingen, É., Bonacorsi, S., Bouchier, C., Bouvet, O. M. M., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000344 · Cited by 1,177 · see citing works
Computational Molecular Evolution
Yang, Z. (2006) · doi:10.1093/acprof:oso/9780198567028.001.0001 · Cited by 1,143 · see citing works
DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution
Xia, X. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst064 · Cited by 1,153 · see citing works
Pollen Limitation of Plant Reproduction: Pattern and Process
Knight, T. M., Steets, J. A., Vamosi, J. C., Mazer, S. J., Burd, M., Campbell, D. R., Dudash, M. R., Johnston, M. O., Mitchell, R. J., & Ashman, T. (2005) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.36.102403.115320 · Cited by 1,142 · see citing works
rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria
Klappenbach, J. A., Dunbar, J., & Schmidt, T. M. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.4.1328-1333.2000 · Cited by 1,140 · see citing works
Host and viral traits predict zoonotic spillover from mammals
Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., & Daszak, P. (2017) · Nature · doi:10.1038/nature22975 · Cited by 1,130 · see citing works
Plant-Pollinator Interactions over 120 Years: Loss of Species, Co-Occurrence, and Function
Burkle, L. A., Marlin, J. C., & Knight, T. M. (2013) · Science · doi:10.1126/science.1232728 · Cited by 1,118 · 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
STATISTICAL ISSUES IN ECOLOGICAL META-ANALYSES
Gurevitch, J., & Hedges, L. V. (1999) · Ecology · doi:10.1890/0012-9658(1999)080[1142:siiema]2.0.co;2 · Cited by 1,084 · see citing works
Shipley, B. (2000) · Cited by 1,094 · see citing works
Functional traits and the growth–mortality trade‐off in tropical trees
Wright, S. J., Kitajima, K., Kraft, N. J. B., Reich, P. B., Wright, I. J., Bunker, D. E., Condit, R., Dalling, J. W., Davies, S. J., Díaz, S. M., et al. (2010) · Ecology · doi:10.1890/09-2335.1 · Cited by 1,071 · see citing works
phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)
Revell, L. J. (2024) · PeerJ · doi:10.7717/peerj.16505 · Cited by 1,105 · see citing works
How to measure and test phylogenetic signal
Münkemüller, T., Lavergne, S., Bzeznik, B., Dray, S., Jombart, T., Schiffers, K. H., & Thuiller, W. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2012.00196.x · Cited by 1,064 · see citing works
Fritz, S. A., & Purvis, A. (2010) · Conservation Biology · doi:10.1111/j.1523-1739.2010.01455.x · Cited by 1,063 · 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
Hoffmann, A. A., Sørensen, J. G., & Loeschcke, V. (2003) · Journal of Thermal Biology · doi:10.1016/s0306-4565(02)00057-8 · Cited by 1,045 · see citing works
Fairbairn, D. J. (1997) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.28.1.659 · Cited by 1,043 · see citing works
Phylomatic: tree assembly for applied phylogenetics
Webb, C. O., & Donoghue, M. J. (2004) · Molecular Ecology Notes · doi:10.1111/j.1471-8286.2004.00829.x · Cited by 1,034 · see citing works
Methodological issues and advances in biological meta-analysis
Nakagawa, S., & Santos, E. S. A. (2012) · Evolutionary Ecology · doi:10.1007/s10682-012-9555-5 · Cited by 1,032 · see citing works
Elser, J. J., Fagan, W. F., Kerkhoff, A. J., Swenson, N. G., & Enquist, B. J. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03214.x · Cited by 1,024 · see citing works
CONVERGENCE, ADAPTATION, AND CONSTRAINT
Losos, J. B. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01289.x · Cited by 998 · see citing works
Venable, D. L., & Brown, J. S. (1988) · The American Naturalist · doi:10.1086/284795 · Cited by 995 · 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:10.1554/0014-3820(2003)057[0717:tfpsic]2.0.co;2 · Cited by 994 · see citing works
Rohlf, F. J. (2015) · Bollettino del CILEA (CILEA) · doi:10.4404/hystrix-26.1-11264 · Cited by 989 · see citing works
Diversitree: comparative phylogenetic analyses of diversification in R
FitzJohn, R. G. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2012.00234.x · Cited by 927 · see citing works
LIKELIHOOD OF ANCESTOR STATES IN ADAPTIVE RADIATION
Schluter, D., Price, T. D., Mooers, A. Ø., & Ludwig, D. (1997) · Evolution · doi:10.1111/j.1558-5646.1997.tb05095.x · Cited by 951 · see citing works
SIMMAP: Stochastic character mapping of discrete traits on phylogenies
Bollback, J. P. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-88 · Cited by 948 · see citing works
Phylogenetic signal and linear regression on species data: <i>Phylogenetic regression</i>
Revell, L. J. (2010) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2010.00044.x · Cited by 931 · see citing works
Phylogenetic Overdispersion in Floridian Oak Communities
Cavender-Bares, J. M., Ackerly, D. D., Baum, D., & Bazzaz, F. A. (2004) · The American Naturalist · doi:10.1086/386375 · Cited by 938 · see citing works
Stochastic Mapping of Morphological Characters
Huelsenbeck, J. P., Nielsen, R., & Bollback, J. P. (2003) · Systematic Biology · doi:10.1080/10635150390192780 · Cited by 930 · see citing works
The critical thermal maximum: history and critique
Lutterschmidt, W. I., & Hutchison, V. H. (1997) · Canadian Journal of Zoology · doi:10.1139/z97-783 · Cited by 919 · see citing works
Big brains, enhanced cognition, and response of birds to novel environments
Sol, D., Duncan, R. P., Blackburn, T. M., Cassey, P., & Lefebvre, L. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408145102 · Cited by 917 · see citing works
Ecological morphology: Integrative organismal biology
Sinervo, B. (1995) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)89062-x · Cited by 909 · see citing works
Phylogenetic Signal, Evolutionary Process, and Rate
Revell, L. J., Harmon, L. J., & Collar, D. C. (2008) · Systematic Biology · doi:10.1080/10635150802302427 · Cited by 879 · see citing works
Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods
Blomberg, S. P., & Garland, T. (2002) · Journal of Evolutionary Biology · doi:10.1046/j.1420-9101.2002.00472.x · Cited by 896 · see citing works
A Meta-Analysis of Competition in Field Experiments
Gurevitch, J., Morrow, L. L., Wallace, A., & Walsh, J. S. (1992) · The American Naturalist · doi:10.1086/285428 · Cited by 851 · see citing works
Are mountain passes higher in the tropics? janzen's hypothesis revisited
Ghalambor, C. K. (2006) · Integrative and Comparative Biology · doi:10.1093/icb/icj003 · Cited by 846 · see citing works
SIZE-CORRECTION AND PRINCIPAL COMPONENTS FOR INTERSPECIFIC COMPARATIVE STUDIES
Revell, L. J. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00804.x · Cited by 844 · see citing works
Taxonomic inflation: its influence on macroecology and conservation
Isaac, N. J. B. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.06.004 · Cited by 843 · 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
Self-citationHöhna, S., Landis, M. J., Heath, T. A., Boussau, B., Lartillot, N., Moore, B. R., Huelsenbeck, J. P., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syw021 · Cited by 829 · see citing works
Hadfield, J. D., & Nakagawa, S. (2010) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2009.01915.x · Cited by 813 · see citing works
Mosaic evolution of brain structure in mammals
Barton, R. A., & Harvey, P. H. (2000) · Nature · doi:10.1038/35016580 · Cited by 797 · see citing works
Garland, T., & Ives, A. R. (2000) · The American Naturalist · doi:10.1086/303327 · Cited by 824 · see citing works
ENERGETICS OF FREE-RANGING MAMMALS, REPTILES, AND BIRDS
Nagy, K. A., Girard, I. A., & Brown, T. K. (1999) · Annual Review of Nutrition · doi:10.1146/annurev.nutr.19.1.247 · Cited by 806 · see citing works
Starvation physiology: Reviewing the different strategies animals use to survive a common challenge
McCue, M. D. (2010) · Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology · doi:10.1016/j.cbpa.2010.01.002 · Cited by 799 · see citing works
Trait Evolution, Community Assembly, and the Phylogenetic Structure of Ecological Communities
Kraft, N. J. B., Cornwell, W. K., Webb, C. O., & Ackerly, D. D. (2007) · The American Naturalist · doi:10.1086/519400 · Cited by 793 · see citing works
Sympatric Speciation in Phytophagous Insects: Moving Beyond Controversy?
Berlocher, S. H., & Feder, J. L. (2002) · Annual Review of Entomology · doi:10.1146/annurev.ento.47.091201.145312 · Cited by 792 · see citing works
Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood
Huelsenbeck, J. P., & Crandall, K. A. (1997) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.28.1.437 · Cited by 1,018 · see citing works
Agrawal, A. A., & Fishbein, M. (2006) · Ecology · doi:10.1890/0012-9658(2006)87[132:pds]2.0.co;2 · Cited by 776 · see citing works
Møller, A. P., Rubolini, D., & Lehikoinen, E. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803825105 · Cited by 773 · see citing works
Genome-Based Taxonomic Classification of the Phylum Actinobacteria
Nouioui, I., Carro, L., García-López, M., Meier‐Kolthoff, J. P., Woyke, T., Kyrpides, N. C., Pukall, R., Klenk, H., Goodfellow, M., & Göker, M. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02007 · Cited by 771 · see citing works
Molecular phylogenetics: principles and practice
Yang, Z., & Rannala, B. H. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3186 · Cited by 758 · see citing works
Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
Louca, S., Doebeli, M., & Parfrey, L. W. (2018) · Microbiome · doi:10.1186/s40168-018-0420-9 · Cited by 755 · see citing works
Riley, R. W., Salamov, A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400592111 · Cited by 742 · see citing works
ADAPTIVE VARIATION IN THE VULNERABILITY OF WOODY PLANTS TO XYLEM CAVITATION
Maherali, H., Pockman, W. T., & Jackson, R. B. (2004) · Ecology · doi:10.1890/02-0538 · Cited by 748 · see citing works
PLANT FUNCTIONAL TRAITS IN RELATION TO FIRE IN CROWN-FIRE ECOSYSTEMS
Pausas, J. G., Bradstock, R. A., Keith, D. A., & Keeley, J. E. (2004) · Ecology · doi:10.1890/02-4094 · Cited by 747 · see citing works
A cladistic measure of gene flow inferred from the phylogenies of alleles.
Slatkin, M., & Maddison, W. P. (1989) · Genetics · doi:10.1093/genetics/123.3.603 · Cited by 733 · see citing works
Correlated evolution of morphology and vocal signal structure in Darwin's finches
Podos, J. (2001) · Nature · doi:10.1038/35051570 · Cited by 727 · see citing works
Cadotte, M. W., Cavender-Bares, J. M., Tilman, D. G., & Oakley, T. H. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005695 · Cited by 718 · see citing works
Abbott, D. H., Keverne, E. B., Bercovitch, F. B., Shively, C. A., Mendoza, S. P., Wendy Saltzman, A., Snowdon, C. T., Ziegler, T. E., Banjevic, M., Garland, T., et al. (2003) · Hormones and Behavior · doi:10.1016/s0018-506x(02)00037-5 · Cited by 726 · see citing works
- Authors
- Felsenstein, J.
- Affiliations
- University of Washington (US)
- Corresponding author
- Felsenstein, Joseph
- Venue
- The American Naturalist
- Publisher
- University of Chicago Press
- Published
- 1985-01
- Volume
- 125
- Issue
- 1
- Pages
- 1-15
- ISSN
- 0003-0147 (ISSN-L)
- 1537-5323
- OpenAlex
- W2013410948
- Cited by
- 9,793
- References
- 13
- Citations by year
- 2026: 242 · 2025: 311 · 2024: 287 · 2023: 361 · 2022: 335 · 2021: 391 · 2020: 332 · 2019: 465 · 2018: 375 · 2017: 374 · 2016: 374 · 2015: 399 · 2014: 436 · 2013: 342 · 2012: 343
- FWCI
- 40.48
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The American Naturalist (publishedVersion)
- Funders
- U.S. Department of Energy
- University of Washington
- 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, Brownian motion model, branch length, tree topology, contingency tables, character evolution
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