Comparing evolutionary rates between trees, clades and traits

L.J. Revell, L.E. González-Valenzuela, A. Alfonso, L.A. Castellanos-García, C.E. Guarnizo, A.J. Crawford

Resultado de la investigación: Contribución a RevistaArtículo

5 Citas (Scopus)

Resumen

The tempo of evolutionary change through time is among the most heavily studied dimensions of macroevolution using phylogenies. Here, we present a simple, likelihood-based method for comparing the rate of phenotypic evolution for continuous characters between trees. Our method is derived from a previous approach published by Brian O'Meara and colleagues in 2006. We examine the statistical performance of the method and find that it suffers from the typical downward bias expected for maximum likelihood estimates of the variance, but only for very small trees. We find that evolutionary rates are estimated with minimal bias for trees of even relatively modest size. We also find that type I error rates based on a likelihood-ratio test are minimally elevated above the nominal level, even for small phylogenies. The type I error rate can be reduced to a level at or below its nominal value by substituting a test-statistic distribution obtained via simulation under the null hypothesis of no difference in evolutionary rate among trees. We discuss the consequences of failing to account for uncertainty in the estimation of species means or in the phylogeny, and describe strategies for taking this uncertainty into consideration during estimation. We also identify how our approach is related to previous methods for comparing the rate of evolution among different clades of a single tree or between different phenotypic traits. Finally, we describe how the method can be applied to different evolutionary models and to discrete characters—options that are already implemented in software. Evolutionary biologists continue to be intrigued by changes in the tempo of phenotypic evolution across the tree of life. The method described herein should be useful for contexts in which changes in the evolutionary rate or process between two or more clades of distant or unknown relationship are of interest. © 2018 The Authors. Methods in Ecology and Evolution © 2018 British Ecological Society
Idioma originalEnglish (US)
Páginas (desde-hasta)994-1005
Número de páginas12
PublicaciónMethods in Ecology and Evolution
Volumen9
N.º4
DOI
EstadoPublished - 2018

Huella dactilar

phylogeny
methodology
uncertainty
rate
method
biologists
statistics
testing
ecology
software
simulation
test
distribution

Citar esto

Revell, L. J., González-Valenzuela, L. E., Alfonso, A., Castellanos-García, L. A., Guarnizo, C. E., & Crawford, A. J. (2018). Comparing evolutionary rates between trees, clades and traits. Methods in Ecology and Evolution, 9(4), 994-1005. https://doi.org/10.1111/2041-210X.12977
Revell, L.J. ; González-Valenzuela, L.E. ; Alfonso, A. ; Castellanos-García, L.A. ; Guarnizo, C.E. ; Crawford, A.J. / Comparing evolutionary rates between trees, clades and traits. En: Methods in Ecology and Evolution. 2018 ; Vol. 9, N.º 4. pp. 994-1005.
@article{be94be49cb6449e5aada37f20a033bc0,
title = "Comparing evolutionary rates between trees, clades and traits",
abstract = "The tempo of evolutionary change through time is among the most heavily studied dimensions of macroevolution using phylogenies. Here, we present a simple, likelihood-based method for comparing the rate of phenotypic evolution for continuous characters between trees. Our method is derived from a previous approach published by Brian O'Meara and colleagues in 2006. We examine the statistical performance of the method and find that it suffers from the typical downward bias expected for maximum likelihood estimates of the variance, but only for very small trees. We find that evolutionary rates are estimated with minimal bias for trees of even relatively modest size. We also find that type I error rates based on a likelihood-ratio test are minimally elevated above the nominal level, even for small phylogenies. The type I error rate can be reduced to a level at or below its nominal value by substituting a test-statistic distribution obtained via simulation under the null hypothesis of no difference in evolutionary rate among trees. We discuss the consequences of failing to account for uncertainty in the estimation of species means or in the phylogeny, and describe strategies for taking this uncertainty into consideration during estimation. We also identify how our approach is related to previous methods for comparing the rate of evolution among different clades of a single tree or between different phenotypic traits. Finally, we describe how the method can be applied to different evolutionary models and to discrete characters—options that are already implemented in software. Evolutionary biologists continue to be intrigued by changes in the tempo of phenotypic evolution across the tree of life. The method described herein should be useful for contexts in which changes in the evolutionary rate or process between two or more clades of distant or unknown relationship are of interest. {\circledC} 2018 The Authors. Methods in Ecology and Evolution {\circledC} 2018 British Ecological Society",
author = "L.J. Revell and L.E. Gonz{\'a}lez-Valenzuela and A. Alfonso and L.A. Castellanos-Garc{\'i}a and C.E. Guarnizo and A.J. Crawford",
note = "Export Date: 17 April 2018 Correspondence Address: Revell, L.J.; Programa de Biolog{\'i}a, Facultad de Ciencias Naturales y Matem{\'a}ticas, Universidad del RosarioColombia; email: liam.revell@phytools.org Funding details: 120456934310, COLCIENCIAS, Departamento Administrativo de Ciencia, Tecnolog{\'i}a e Innovaci{\'o}n Funding details: BSF, United States-Israel Binational Science Foundation Funding details: 1350474, DEB, Division of Environmental Biology Funding details: DEB 1350474, BSF, United States-Israel Binational Science Foundation Funding text: Departamento Administrativo de Ciencia, Tecnolog{\'i}a e Innovaci{\'o}n, Grant/Award Number: 120456934310; United States National Science Foundation, Division of Environmental Biology, Grant/Award Number: 1350474 Funding text: The authors thank the United States National Science Foundation (DEB 1350474 to L.J.R.) and Colombia’s Departamento Administrativo de Ciencia, Tecnolog{\'i}a e Innovaci{\'o}n (Colciencias), Programa Nacional en Ciencias B{\'a}sicas (award number 120456934310 to A.J.C.) for supporting portions of this research. The majority of this research was undertaken by L.J.R. during a sabbatical at the Universidad de los Andes in Bogot{\'a}, Colombia. References: Adams, D.C., Comparing evolutionary rates for different phenotypic traits on a phylogeny using likelihood (2013) Systematic Biology, 62, pp. 181-192. , https://doi.org/10.1093/sysbio/sys083; Akaike, H., A new look at the statistical model identification (1974) IEEE Transactions on Automatic Control, 19, pp. 716-723. , https://doi.org/10.1109/TAC.1974.1100705; Azzalini, A., Genz, A., (2016) The r package “mnormt”: The multivariate normal and ‘t’ distributions (version 1.5-5), , http://azzalini.stat.unipd.it/SW/Pkg-mnormt; Becker, R.A., Wilks, A.R., Brownrigg, R., Minka, T.P., Deckmyn, A., (2016) maps: Draw geographical maps, , https://CRAN.R-project.org/package=maps, package version 3.1.1; Blomberg, S.P., Garland, T., Jr., Ives, A.R., Testing for phylogenetic signal in comparative data: Behavioral traits are more labile (2003) Evolution, 57, pp. 717-745. , https://doi.org/10.1111/j.0014-3820.2003.tb00285.x; Brunet, F.G., Crollius, H.R., Paris, M., Aury, J.-M., Gilbert, P., Jaillon, O., Robinson-Rechavi, M., Gene loss and evolutionary rates following whole-genome duplication in teleost fishes (2006) Molecular Biology and Evolution, 23, pp. 1808-1816. , https://doi.org/10.1093/molbev/msl049; Butler, M.A., King, A.A., Phylogenetic comparative analysis: A modeling approach for adaptive evolution (2004) The American Naturalist, 164, pp. 683-695. , https://doi.org/10.1086/426002; Chasalow, S., (2012) combinat: Combinatorics utilities, , https://CRAN.R-project.org/package=combinat, package version 0.0-8; Collar, D.C., Near, T.J., Wainwright, P.C., Comparative analysis of morphological diversity: Does disparity accumulate at the same rate in two lineages of centrarchid fishes? (2005) Evolution, 59, pp. 1783-1794. , https://doi.org/10.1111/j.0014-3820.2005.tb01826.x; Collar, D.C., O'Meara, B.C., Wainwright, P.C., Near, T.J., Piscivory limits diversification of feeding morphology in centrarchid fishes (2009) Evolution, 63, pp. 1557-1573. , https://doi.org/10.1111/j.1558-5646.2009.00626.x; Edwards, E.J., Smith, S.A., Phylogenetic analyses reveal the shady history of C4 grasses (2010) Proceedings of the National Academy of Sciences of the United States of America, 107, pp. 2532-2537. , https://doi.org/10.1073/pnas.0909672107; Ehrlich, P.R., Raven, P.H., Butterflies and plants: A study in coevolution (1964) Evolution, 18, pp. 586-608. , https://doi.org/10.1111/j.1558-5646.1964.tb01674.x; Evans, M.E.K., Smith, S.A., Flynn, R.S., Donoghue, M.J., Climate, niche evolution, and diversification of the “bird-cage” evening primroses (Oenothera, sections Anogra and Kleinia) (2009) The American Naturalist, 173, pp. 225-240. , https://doi.org/10.1086/595757; Felsenstein, J., Maximum likelihood estimation of evolutionary trees from continuous characters (1973) American Journal of Human Genetics, 25, pp. 471-492; Felsenstein, J., Phylogenies and the comparative method (1985) The American Naturalist, 125, pp. 1-15. , https://doi.org/10.1086/284325; Felsenstein, J., Comparative methods with sampling error and within-species variation: Contrasts revisited and revised (2008) The American Naturalist, 171, pp. 713-725. , https://doi.org/10.1086/587525; Garland, T.G., Jr., Rate tests for phenotypic evolution using phylogenetically independent contrasts (1992) The American Naturalist, 140, pp. 509-519. , https://doi.org/10.1086/285424; Gavrilets, S., Losos, J.B., Adaptive radiation: Contrasting theory with data (2009) Science, 323, pp. 732-737. , https://doi.org/10.1126/science.1157966; Gilbert, P., Varadhan, R., (2016) numDeriv: Accurate numerical derivatives, , https://CRAN.R-project.org/package=numDeriv, package version 2016.8-1; Hansen, T.F., Stabilizing selection and the comparative analysis of adaptation (1997) Evolution, 51, pp. 1341-1351. , https://doi.org/10.1111/j.1558-5646.1997.tb01457.x; Hansen, T.F., The evolution of genetic architecture (2006) Annual Review of Ecology, Evolution, and Systematics, 37, pp. 123-157. , https://doi.org/10.1146/annurev.ecolsys.37.091305.110224; Harmon, L.J., Losos, J.B., Davies, J., Gillespie, R.G., Gittleman, J.L., Jennings, W.B., Mooers, A.{\O}., Early bursts of body size and shape evolution are rare in comparative data (2010) Evolution, 64, pp. 2385-2396. , https://doi.org/10.1111/j.1558-5646.2010.01025.x; Harmon, L.J., Losos, J.B., Davies, J., Gillespie, R.G., Gittleman, J.L., Jennings, W.B., Mooers, A.{\O}., Data from: Early bursts of body size and shape evolution are rare in comparative data (2010) Dryad Digital Repository, , https://doi.org/10.5061/dryad.f660p; Harmon, L.J., Schulte, J.A., II, Larson, A., Losos, J.B., Tempo and mode of evolutionary radiation in iguanian lizards (2003) Science, 301, pp. 961-964. , https://doi.org/10.1126/science.1084786; Harmon, L.J., Weir, J.T., Brock, C.D., Glor, R.E., Challenger, W., GEIGER: Investigating evolutionary radiations (2008) Bioinformatics, 24, pp. 129-131. , https://doi.org/10.1093/bioinformatics/btm538; Hunter, J.P., Jernvall, J., The hypocone as a key innovation in mammalian evolution (1995) Proceedings of the National Academy of Sciences of the United States of America, 92, pp. 10718-10722; Ives, A.R., Midford, P.E., Garland, T., Jr., Within-species variation and measurement error in phylogenetic comparative methods (2007) Systematic Biology, 56, pp. 252-270. , https://doi.org/10.1080/10635150701313830; Jackson, C.H., Multi-state models for panel data: The msm package for r (2011) Journal of Statistical Software, 38, pp. 1-29. , https://doi.org/10.18637/jss.v038.i08; Kozak, K.H., Wiens, J.J., Accelerated rates of climatic-niche evolution underlie rapid species diversification (2010) Ecology Letters, 13, pp. 1378-1389. , https://doi.org/10.1111/j.1461-0248.2010.01530.x; Lemon, J., plotrix: A package in the red light district of r (2006) R-News, 6, pp. 8-12; Lewis, P.O., A likelihood approach to estimating phylogeny from discrete morphological character data (2001) Systematic Biology, 50, pp. 913-925. , https://doi.org/10.1080/106351501753462876; Liem, K.F., Evolutionary strategies and morphological innovations: Cichlid pharyngeal jaws (1973) Systematic Zoology, 22, pp. 425-441. , https://doi.org/10.2307/2412950; Ligges, U., M{\"a}chler, M., Scatterplot3d – An r package for visualizing multivariate data (2003) Journal of Statistical Software, 8, pp. 1-20. , https://doi.org/10.18637/jss.v008.i11; Mahler, D.L., Revell, L.J., Glor, R.E., Losos, J.B., Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles (2010) Evolution, 64, pp. 2731-2745. , https://doi.org/10.1111/j.1558-5646.2010.01026.x; O'Meara, B.C., An{\'e}, C., Sanderson, M.J., Wainwright, P.C., Testing for different rates of continuous trait evolution using likelihood (2006) Evolution, 60, pp. 922-933. , https://doi.org/10.1111/j.0014-3820.2006.tb01171.x; Pagel, M., Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters (1994) Proceedings of the Royal Society London B, 255, pp. 37-45. , https://doi.org/10.1098/rspb.1994.0006; Paradis, E., Claude, J., Strimmer, K., ape: Analyses of phylogenetics and evolution in R language (2004) Bioinformatics, 20, pp. 289-290. , https://doi.org/10.1093/bioinformatics/btg412; Pinheiro, J., Bates, D., DebRoy, S., Sarkar, D., (2017) nlme: Linear and nonlinear mixed effects models, , https://CRAN.R-project.org/package=nlme, #x0026;, package version 3.1-131; Plummer, M., Best, N., Cowles, K., Vines, K., CODA: Convergence diagnosis and output analysis for MCMC (2006) R-News, 6, pp. 7-11; Price, S.A., Holzman, R., Near, T.J., Wainwright, P.C., Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes (2011) Ecology Letters, 14, pp. 462-469. , https://doi.org/10.1111/j.1461-0248.2011.01607.x; Qiu, W., Joe, H., (2015) clusterGeneration: Random cluster generation (with specified degree of separation), , https://CRAN.R-project.org/package=clusterGeneration, package version 1.3.4; (2017) R: A language and environment for statistical computing, , https://www.R-project.org/, Vienna, Austria, R Foundation for Statistical Computing; Rabosky, D.L., No substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses (2015) Evolution, 69, pp. 3207-3216. , https://doi.org/10.1111/evo.12817; Revell, L.J., On the analysis of evolutionary change along single branches in a phylogeny (2008) The American Naturalist, 172, pp. 140-147. , https://doi.org/10.1086/588078; Revell, L.J., Size-correction and principal components for interspecific comparative studies (2009) Evolution, 63, pp. 3258-3268. , https://doi.org/10.1111/j.1558-5646.2009.00804.x; Revell, L.J., phytools: An r package for phylogenetic comparative biology (and other things) (2012) Methods in Ecology and Evolution, 3, pp. 217-223. , https://doi.org/10.1111/j.2041-210X.2011.00169.x; Revell, L.J., Graphical methods for visualizing comparative data on phylogenies (2014) Modern phylogenetic comparative methods and their application in evolutionary biology: Concepts and practice, pp. 77-103. , In, L. Z. Garamszegi, (Ed.),, Berlin, Heidelberg, Springer-Verlag; Revell, L.J., Gonz{\'a}lez-Valenzuela, L.E., Alfonso, A., Castellanos-Garc{\'i}a, L.A., Guarnizo, C.E., Crawford, A.J., Data from: Comparing evolutionary rates between trees, clades and traits (2018) Dryad Digital Repository, , https://doi.org/10.5061/dryad.5st8m; Revell, L.J., Harmon, L.J., Collar, D.C., Phylogenetic signal, evolutionary process, and rate (2008) Systematic Biology, 57, pp. 591-601. , https://doi.org/10.1080/10635150802302427; Schliep, K.P., phangorn: Phylogenetic analysis in r (2011) Bioinformatics, 27, pp. 592-593. , https://doi.org/10.1093/bioinformatics/btq706; Schluter, D., (2000) The ecology of adaptive radiation, , Oxford, UK, Oxford University Press; Simpson, G.G., (1944) Tempo and mode in evolution, , New York, NY, Columbia University Press; Thomas, G.H., Freckleton, R.P., Sz{\'e}kely, T., Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds (2006) Proceedings of the Royal Society B, 273, pp. 1619-1624. , https://doi.org/10.1098/rspb.2006.3488; Van Valen, L., Adaptive zones and the orders of mammals (1971) Evolution, 25, pp. 420-428. , https://doi.org/10.2307/2406935; Venables, W.N., Ripley, B.D., (2002) Modern applied statistics with S, , https://doi.org/10.1007/978-0-387-21706-2, 4th ed., New York, NY, Springer; Xie, Y., animation: An r package for creating animations and demonstrating statistical methods (2013) Journal of Statistical Software, 53, pp. 1-27. , https://doi.org/10.18637/jss.v053.i01; Yoder, J.B., Clancey, E., Des Roches, S., Eastman, J.M., Gentry, L., Godsoe, W., Harmon, L.J., Ecological opportunity and the origin of adaptive radiations (2010) Journal of Evolutionary Biology, 23, pp. 1581-1596. , https://doi.org/10.1111/j.1420-9101.2010.02029.x",
year = "2018",
doi = "10.1111/2041-210X.12977",
language = "English (US)",
volume = "9",
pages = "994--1005",
journal = "Methods in Ecology and Evolution",
issn = "2041-210X",
publisher = "British Ecological Society",
number = "4",

}

Revell, LJ, González-Valenzuela, LE, Alfonso, A, Castellanos-García, LA, Guarnizo, CE & Crawford, AJ 2018, 'Comparing evolutionary rates between trees, clades and traits', Methods in Ecology and Evolution, vol. 9, n.º 4, pp. 994-1005. https://doi.org/10.1111/2041-210X.12977

Comparing evolutionary rates between trees, clades and traits. / Revell, L.J.; González-Valenzuela, L.E.; Alfonso, A.; Castellanos-García, L.A.; Guarnizo, C.E.; Crawford, A.J.

En: Methods in Ecology and Evolution, Vol. 9, N.º 4, 2018, p. 994-1005.

Resultado de la investigación: Contribución a RevistaArtículo

TY - JOUR

T1 - Comparing evolutionary rates between trees, clades and traits

AU - Revell, L.J.

AU - González-Valenzuela, L.E.

AU - Alfonso, A.

AU - Castellanos-García, L.A.

AU - Guarnizo, C.E.

AU - Crawford, A.J.

N1 - Export Date: 17 April 2018 Correspondence Address: Revell, L.J.; Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del RosarioColombia; email: liam.revell@phytools.org Funding details: 120456934310, COLCIENCIAS, Departamento Administrativo de Ciencia, Tecnología e Innovación Funding details: BSF, United States-Israel Binational Science Foundation Funding details: 1350474, DEB, Division of Environmental Biology Funding details: DEB 1350474, BSF, United States-Israel Binational Science Foundation Funding text: Departamento Administrativo de Ciencia, Tecnología e Innovación, Grant/Award Number: 120456934310; United States National Science Foundation, Division of Environmental Biology, Grant/Award Number: 1350474 Funding text: The authors thank the United States National Science Foundation (DEB 1350474 to L.J.R.) and Colombia’s Departamento Administrativo de Ciencia, Tecnología e Innovación (Colciencias), Programa Nacional en Ciencias Básicas (award number 120456934310 to A.J.C.) for supporting portions of this research. The majority of this research was undertaken by L.J.R. during a sabbatical at the Universidad de los Andes in Bogotá, Colombia. References: Adams, D.C., Comparing evolutionary rates for different phenotypic traits on a phylogeny using likelihood (2013) Systematic Biology, 62, pp. 181-192. , https://doi.org/10.1093/sysbio/sys083; Akaike, H., A new look at the statistical model identification (1974) IEEE Transactions on Automatic Control, 19, pp. 716-723. , https://doi.org/10.1109/TAC.1974.1100705; Azzalini, A., Genz, A., (2016) The r package “mnormt”: The multivariate normal and ‘t’ distributions (version 1.5-5), , http://azzalini.stat.unipd.it/SW/Pkg-mnormt; Becker, R.A., Wilks, A.R., Brownrigg, R., Minka, T.P., Deckmyn, A., (2016) maps: Draw geographical maps, , https://CRAN.R-project.org/package=maps, package version 3.1.1; Blomberg, S.P., Garland, T., Jr., Ives, A.R., Testing for phylogenetic signal in comparative data: Behavioral traits are more labile (2003) Evolution, 57, pp. 717-745. , https://doi.org/10.1111/j.0014-3820.2003.tb00285.x; Brunet, F.G., Crollius, H.R., Paris, M., Aury, J.-M., Gilbert, P., Jaillon, O., Robinson-Rechavi, M., Gene loss and evolutionary rates following whole-genome duplication in teleost fishes (2006) Molecular Biology and Evolution, 23, pp. 1808-1816. , https://doi.org/10.1093/molbev/msl049; Butler, M.A., King, A.A., Phylogenetic comparative analysis: A modeling approach for adaptive evolution (2004) The American Naturalist, 164, pp. 683-695. , https://doi.org/10.1086/426002; Chasalow, S., (2012) combinat: Combinatorics utilities, , https://CRAN.R-project.org/package=combinat, package version 0.0-8; Collar, D.C., Near, T.J., Wainwright, P.C., Comparative analysis of morphological diversity: Does disparity accumulate at the same rate in two lineages of centrarchid fishes? (2005) Evolution, 59, pp. 1783-1794. , https://doi.org/10.1111/j.0014-3820.2005.tb01826.x; Collar, D.C., O'Meara, B.C., Wainwright, P.C., Near, T.J., Piscivory limits diversification of feeding morphology in centrarchid fishes (2009) Evolution, 63, pp. 1557-1573. , https://doi.org/10.1111/j.1558-5646.2009.00626.x; Edwards, E.J., Smith, S.A., Phylogenetic analyses reveal the shady history of C4 grasses (2010) Proceedings of the National Academy of Sciences of the United States of America, 107, pp. 2532-2537. , https://doi.org/10.1073/pnas.0909672107; Ehrlich, P.R., Raven, P.H., Butterflies and plants: A study in coevolution (1964) Evolution, 18, pp. 586-608. , https://doi.org/10.1111/j.1558-5646.1964.tb01674.x; Evans, M.E.K., Smith, S.A., Flynn, R.S., Donoghue, M.J., Climate, niche evolution, and diversification of the “bird-cage” evening primroses (Oenothera, sections Anogra and Kleinia) (2009) The American Naturalist, 173, pp. 225-240. , https://doi.org/10.1086/595757; Felsenstein, J., Maximum likelihood estimation of evolutionary trees from continuous characters (1973) American Journal of Human Genetics, 25, pp. 471-492; Felsenstein, J., Phylogenies and the comparative method (1985) The American Naturalist, 125, pp. 1-15. , https://doi.org/10.1086/284325; Felsenstein, J., Comparative methods with sampling error and within-species variation: Contrasts revisited and revised (2008) The American Naturalist, 171, pp. 713-725. , https://doi.org/10.1086/587525; Garland, T.G., Jr., Rate tests for phenotypic evolution using phylogenetically independent contrasts (1992) The American Naturalist, 140, pp. 509-519. , https://doi.org/10.1086/285424; Gavrilets, S., Losos, J.B., Adaptive radiation: Contrasting theory with data (2009) Science, 323, pp. 732-737. , https://doi.org/10.1126/science.1157966; Gilbert, P., Varadhan, R., (2016) numDeriv: Accurate numerical derivatives, , https://CRAN.R-project.org/package=numDeriv, package version 2016.8-1; Hansen, T.F., Stabilizing selection and the comparative analysis of adaptation (1997) Evolution, 51, pp. 1341-1351. , https://doi.org/10.1111/j.1558-5646.1997.tb01457.x; Hansen, T.F., The evolution of genetic architecture (2006) Annual Review of Ecology, Evolution, and Systematics, 37, pp. 123-157. , https://doi.org/10.1146/annurev.ecolsys.37.091305.110224; Harmon, L.J., Losos, J.B., Davies, J., Gillespie, R.G., Gittleman, J.L., Jennings, W.B., Mooers, A.Ø., Early bursts of body size and shape evolution are rare in comparative data (2010) Evolution, 64, pp. 2385-2396. , https://doi.org/10.1111/j.1558-5646.2010.01025.x; Harmon, L.J., Losos, J.B., Davies, J., Gillespie, R.G., Gittleman, J.L., Jennings, W.B., Mooers, A.Ø., Data from: Early bursts of body size and shape evolution are rare in comparative data (2010) Dryad Digital Repository, , https://doi.org/10.5061/dryad.f660p; Harmon, L.J., Schulte, J.A., II, Larson, A., Losos, J.B., Tempo and mode of evolutionary radiation in iguanian lizards (2003) Science, 301, pp. 961-964. , https://doi.org/10.1126/science.1084786; Harmon, L.J., Weir, J.T., Brock, C.D., Glor, R.E., Challenger, W., GEIGER: Investigating evolutionary radiations (2008) Bioinformatics, 24, pp. 129-131. , https://doi.org/10.1093/bioinformatics/btm538; Hunter, J.P., Jernvall, J., The hypocone as a key innovation in mammalian evolution (1995) Proceedings of the National Academy of Sciences of the United States of America, 92, pp. 10718-10722; Ives, A.R., Midford, P.E., Garland, T., Jr., Within-species variation and measurement error in phylogenetic comparative methods (2007) Systematic Biology, 56, pp. 252-270. , https://doi.org/10.1080/10635150701313830; Jackson, C.H., Multi-state models for panel data: The msm package for r (2011) Journal of Statistical Software, 38, pp. 1-29. , https://doi.org/10.18637/jss.v038.i08; Kozak, K.H., Wiens, J.J., Accelerated rates of climatic-niche evolution underlie rapid species diversification (2010) Ecology Letters, 13, pp. 1378-1389. , https://doi.org/10.1111/j.1461-0248.2010.01530.x; Lemon, J., plotrix: A package in the red light district of r (2006) R-News, 6, pp. 8-12; Lewis, P.O., A likelihood approach to estimating phylogeny from discrete morphological character data (2001) Systematic Biology, 50, pp. 913-925. , https://doi.org/10.1080/106351501753462876; Liem, K.F., Evolutionary strategies and morphological innovations: Cichlid pharyngeal jaws (1973) Systematic Zoology, 22, pp. 425-441. , https://doi.org/10.2307/2412950; Ligges, U., Mächler, M., Scatterplot3d – An r package for visualizing multivariate data (2003) Journal of Statistical Software, 8, pp. 1-20. , https://doi.org/10.18637/jss.v008.i11; Mahler, D.L., Revell, L.J., Glor, R.E., Losos, J.B., Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles (2010) Evolution, 64, pp. 2731-2745. , https://doi.org/10.1111/j.1558-5646.2010.01026.x; O'Meara, B.C., Ané, C., Sanderson, M.J., Wainwright, P.C., Testing for different rates of continuous trait evolution using likelihood (2006) Evolution, 60, pp. 922-933. , https://doi.org/10.1111/j.0014-3820.2006.tb01171.x; Pagel, M., Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters (1994) Proceedings of the Royal Society London B, 255, pp. 37-45. , https://doi.org/10.1098/rspb.1994.0006; Paradis, E., Claude, J., Strimmer, K., ape: Analyses of phylogenetics and evolution in R language (2004) Bioinformatics, 20, pp. 289-290. , https://doi.org/10.1093/bioinformatics/btg412; Pinheiro, J., Bates, D., DebRoy, S., Sarkar, D., (2017) nlme: Linear and nonlinear mixed effects models, , https://CRAN.R-project.org/package=nlme, #x0026;, package version 3.1-131; Plummer, M., Best, N., Cowles, K., Vines, K., CODA: Convergence diagnosis and output analysis for MCMC (2006) R-News, 6, pp. 7-11; Price, S.A., Holzman, R., Near, T.J., Wainwright, P.C., Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes (2011) Ecology Letters, 14, pp. 462-469. , https://doi.org/10.1111/j.1461-0248.2011.01607.x; Qiu, W., Joe, H., (2015) clusterGeneration: Random cluster generation (with specified degree of separation), , https://CRAN.R-project.org/package=clusterGeneration, package version 1.3.4; (2017) R: A language and environment for statistical computing, , https://www.R-project.org/, Vienna, Austria, R Foundation for Statistical Computing; Rabosky, D.L., No substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses (2015) Evolution, 69, pp. 3207-3216. , https://doi.org/10.1111/evo.12817; Revell, L.J., On the analysis of evolutionary change along single branches in a phylogeny (2008) The American Naturalist, 172, pp. 140-147. , https://doi.org/10.1086/588078; Revell, L.J., Size-correction and principal components for interspecific comparative studies (2009) Evolution, 63, pp. 3258-3268. , https://doi.org/10.1111/j.1558-5646.2009.00804.x; Revell, L.J., phytools: An r package for phylogenetic comparative biology (and other things) (2012) Methods in Ecology and Evolution, 3, pp. 217-223. , https://doi.org/10.1111/j.2041-210X.2011.00169.x; Revell, L.J., Graphical methods for visualizing comparative data on phylogenies (2014) Modern phylogenetic comparative methods and their application in evolutionary biology: Concepts and practice, pp. 77-103. , In, L. Z. Garamszegi, (Ed.),, Berlin, Heidelberg, Springer-Verlag; Revell, L.J., González-Valenzuela, L.E., Alfonso, A., Castellanos-García, L.A., Guarnizo, C.E., Crawford, A.J., Data from: Comparing evolutionary rates between trees, clades and traits (2018) Dryad Digital Repository, , https://doi.org/10.5061/dryad.5st8m; Revell, L.J., Harmon, L.J., Collar, D.C., Phylogenetic signal, evolutionary process, and rate (2008) Systematic Biology, 57, pp. 591-601. , https://doi.org/10.1080/10635150802302427; Schliep, K.P., phangorn: Phylogenetic analysis in r (2011) Bioinformatics, 27, pp. 592-593. , https://doi.org/10.1093/bioinformatics/btq706; Schluter, D., (2000) The ecology of adaptive radiation, , Oxford, UK, Oxford University Press; Simpson, G.G., (1944) Tempo and mode in evolution, , New York, NY, Columbia University Press; Thomas, G.H., Freckleton, R.P., Székely, T., Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds (2006) Proceedings of the Royal Society B, 273, pp. 1619-1624. , https://doi.org/10.1098/rspb.2006.3488; Van Valen, L., Adaptive zones and the orders of mammals (1971) Evolution, 25, pp. 420-428. , https://doi.org/10.2307/2406935; Venables, W.N., Ripley, B.D., (2002) Modern applied statistics with S, , https://doi.org/10.1007/978-0-387-21706-2, 4th ed., New York, NY, Springer; Xie, Y., animation: An r package for creating animations and demonstrating statistical methods (2013) Journal of Statistical Software, 53, pp. 1-27. , https://doi.org/10.18637/jss.v053.i01; Yoder, J.B., Clancey, E., Des Roches, S., Eastman, J.M., Gentry, L., Godsoe, W., Harmon, L.J., Ecological opportunity and the origin of adaptive radiations (2010) Journal of Evolutionary Biology, 23, pp. 1581-1596. , https://doi.org/10.1111/j.1420-9101.2010.02029.x

PY - 2018

Y1 - 2018

N2 - The tempo of evolutionary change through time is among the most heavily studied dimensions of macroevolution using phylogenies. Here, we present a simple, likelihood-based method for comparing the rate of phenotypic evolution for continuous characters between trees. Our method is derived from a previous approach published by Brian O'Meara and colleagues in 2006. We examine the statistical performance of the method and find that it suffers from the typical downward bias expected for maximum likelihood estimates of the variance, but only for very small trees. We find that evolutionary rates are estimated with minimal bias for trees of even relatively modest size. We also find that type I error rates based on a likelihood-ratio test are minimally elevated above the nominal level, even for small phylogenies. The type I error rate can be reduced to a level at or below its nominal value by substituting a test-statistic distribution obtained via simulation under the null hypothesis of no difference in evolutionary rate among trees. We discuss the consequences of failing to account for uncertainty in the estimation of species means or in the phylogeny, and describe strategies for taking this uncertainty into consideration during estimation. We also identify how our approach is related to previous methods for comparing the rate of evolution among different clades of a single tree or between different phenotypic traits. Finally, we describe how the method can be applied to different evolutionary models and to discrete characters—options that are already implemented in software. Evolutionary biologists continue to be intrigued by changes in the tempo of phenotypic evolution across the tree of life. The method described herein should be useful for contexts in which changes in the evolutionary rate or process between two or more clades of distant or unknown relationship are of interest. © 2018 The Authors. Methods in Ecology and Evolution © 2018 British Ecological Society

AB - The tempo of evolutionary change through time is among the most heavily studied dimensions of macroevolution using phylogenies. Here, we present a simple, likelihood-based method for comparing the rate of phenotypic evolution for continuous characters between trees. Our method is derived from a previous approach published by Brian O'Meara and colleagues in 2006. We examine the statistical performance of the method and find that it suffers from the typical downward bias expected for maximum likelihood estimates of the variance, but only for very small trees. We find that evolutionary rates are estimated with minimal bias for trees of even relatively modest size. We also find that type I error rates based on a likelihood-ratio test are minimally elevated above the nominal level, even for small phylogenies. The type I error rate can be reduced to a level at or below its nominal value by substituting a test-statistic distribution obtained via simulation under the null hypothesis of no difference in evolutionary rate among trees. We discuss the consequences of failing to account for uncertainty in the estimation of species means or in the phylogeny, and describe strategies for taking this uncertainty into consideration during estimation. We also identify how our approach is related to previous methods for comparing the rate of evolution among different clades of a single tree or between different phenotypic traits. Finally, we describe how the method can be applied to different evolutionary models and to discrete characters—options that are already implemented in software. Evolutionary biologists continue to be intrigued by changes in the tempo of phenotypic evolution across the tree of life. The method described herein should be useful for contexts in which changes in the evolutionary rate or process between two or more clades of distant or unknown relationship are of interest. © 2018 The Authors. Methods in Ecology and Evolution © 2018 British Ecological Society

U2 - 10.1111/2041-210X.12977

DO - 10.1111/2041-210X.12977

M3 - Article

VL - 9

SP - 994

EP - 1005

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

SN - 2041-210X

IS - 4

ER -

Revell LJ, González-Valenzuela LE, Alfonso A, Castellanos-García LA, Guarnizo CE, Crawford AJ. Comparing evolutionary rates between trees, clades and traits. Methods in Ecology and Evolution. 2018;9(4):994-1005. https://doi.org/10.1111/2041-210X.12977