On the analysis of evolutionary change along single branches in a phylogeny

L.J. Revell

doi:10.1086/588078

On the analysis of evolutionary change along single branches in a phylogeny

L.J. Revell

Producción científica: Contribución a una revista › Artículo › revisión exhaustiva

46 Citas (Scopus)

Resumen

Comparative biologists are sometimes interested in estimating the evolutionary rate along single branches in a phylogeny. I evaluate two methods by which the evolutionary rate along single branches can be compared with the evolutionary rate throughout the rest of the tree. The first is McPeek's contrasts method, and the second is a likelihood method presented independently in two recently published studies. Although the latter method was developed primarily for the comparison of rates among clades, the approach is equally suited for the analysis of evolutionary rate along single or isolated branches. I find that Type I error is acceptable in both methods but that power and parameter estimation are relatively poor in McPeek's method as it is typically applied. © 2008 by The University of Chicago. All rights reserved.

Idioma original	Inglés estadounidense
Páginas (desde-hasta)	140-147
Número de páginas	8
Publicación	American Naturalist
Volumen	172
N.º	1
DOI	https://doi.org/10.1086/588078
Estado	Publicada - jul. 2008

Acceder al documento

10.1086/588078

https://www.scopus.com/inward/record.uri?eid=2-s2.0-46749098036&doi=10.1086%2f588078&partnerID=40&md5=54d23cd3865b442d87b716f344736ccb

Citar esto

@article{8502c5e0bcdf4ec2a77ed70d6f2e689f,

title = "On the analysis of evolutionary change along single branches in a phylogeny",

abstract = "Comparative biologists are sometimes interested in estimating the evolutionary rate along single branches in a phylogeny. I evaluate two methods by which the evolutionary rate along single branches can be compared with the evolutionary rate throughout the rest of the tree. The first is McPeek's contrasts method, and the second is a likelihood method presented independently in two recently published studies. Although the latter method was developed primarily for the comparison of rates among clades, the approach is equally suited for the analysis of evolutionary rate along single or isolated branches. I find that Type I error is acceptable in both methods but that power and parameter estimation are relatively poor in McPeek's method as it is typically applied. {\textcopyright} 2008 by The University of Chicago. All rights reserved.",

author = "L.J. Revell",

note = "Cited By :34 Export Date: 17 April 2018 CODEN: AMNTA Correspondence Address: Revell, L. J.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States; email: lrevell@fas.harvard.edu References: Butler, M.A., King, A.A., Phylogenetic comparative analysis: A modeling approach for adaptive evolution (2004) American Naturalist, 164, pp. 683-695; Cheverud, J.M., Dow, M.M., Leutenegger, W., The quantitative assessment of phylogenetic constraints in comparative analyses: Sexual dimorphism in body weight among primates (1985) Evolution, 39, pp. 1335-1351; Crespi, B., Worobey, M., Comparative analysis of gall morphology in Australian gall thrips: The evolution of extended phenotypes (1998) Evolution, 52, pp. 1686-1696; Crespi, B.J., Teo, R., Comparative phylogenetic analysis of the evolution of semelparity and life history in salmonid fishes (2002) Evolution, 56, pp. 1008-1020; Edwards, A.W.F., Cavalli-Sforza, L.L., Reconstruction of evolutionary trees (1964) Phenetic and phylogenetic classification, pp. 67-76. , V. H. Heywood and J. McNeill, eds, Systematics Association, London; Felsenstein, J., Phylogenies and the comparative method (1985) American Naturalist, 125, pp. 1-15; Felsenstein, J., Phylogenies and quantitative characters (1988) Annual Review of Ecology and Systematics, 19, pp. 445-471; Felsenstein, J., (2004) Inferring phylogenies, , Sinauer, Sunderland, MA; Garland Jr., T., Rate tests for phenotypic evolution using phylogenetically independent contrasts (1992) American Naturalist, 140, pp. 509-519; Garland Jr., T., Ives, A.R., Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods (2000) American Naturalist, 155, pp. 346-364; Garland Jr., T., Harvey, P.H., Ives, A.R., Procedures for the analysis of comparative data using phylogenetically independent contrasts (1992) Systematic Biology, 41, pp. 18-32; Garland Jr., T., Dickerman, A.W., Janis, C.M., Jones, J.A., Phylogenetic analysis of covariance by computer simulation (1993) Systematic Biology, 42, pp. 265-292; Garland Jr., T., Midford, P.E., Ives, A.R., An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values (1999) American Zoologist, 39, pp. 374-388; Grafen, A., The phylogenetic regression (1989) Philosophical Transactions of the Royal Society B: Biological Sciences, 326, pp. 119-157; Hansen, T.F., Stabilizing selection and the comparative analysis of adaptation (1997) Evolution, 51, pp. 1341-1351; Hansen, T.F., Martins, E.P., Translating between microevolutionary process and macroevolutionary patterns: The correlation structure of interspecific data (1996) Evolution, 50, pp. 1404-1417; Harrison, M.K., Crespi, B.J., A phylogenetic test of ecomorphological adaptation in Cancer crabs (1999) Evolution, 53, pp. 961-965; Harvey, P.H., Pagel, M.D., (1991) The comparative method in evolutionary biology, , Oxford University Press, Oxford; Harvey, P.H., Purvis, A., Comparative methods for explaining adaptations (1991) Nature, 351, pp. 619-624; Hendry, A.P., Kinnison, M.T., The pace of modern life: Measuring rates of contemporary microevolution (1999) Evolution, 53, pp. 1637-1653; Klingenberg, C.P., Ekau, W., A combined morphometric and phylogenetic analysis of an ecomorphological trend: Pelagization of Antarctic fishes (Perciformes: Nototheniidae) (1996) Biological Journal of the Linnean Society, 59, pp. 143-177; Larson, A., Losos, J.B., Phylogenetic systematics of adaptation (1996) Adaptation, pp. 187-220. , M. R. Rose and G. V. Lauder, eds, Academic Press, San Diego, CA; McPeek, M.A., Testing hypotheses about evolutionary change on single branches of a phylogeny using evolutionary contrasts (1995) American Naturalist, 145, pp. 686-703; McPeek, M.A., Biochemical evolution associated with antipredator adaptation in damselflies (1999) Evolution, 53, pp. 1835-1845; McPeek, M.A., Brown, J.M., Building a regional species pool: Diversification of the Enallagma damselflies in eastern North America (2000) Ecology, 81, pp. 904-920; McPeek, M.A., Schrot, A.K., Brown, J.M., Adaptation to predators in a new community: Swimming performance and predator avoidance in damselflies (1996) Ecology, 77, pp. 617-629; 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; Revell, L.J., Testing the genetic constraint hypothesis in a phylogenetic context: A simulation study (2007) Evolution, 61, pp. 2720-2727; Revell, L.J., Harmon, L.J., Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters (2008) Evolutionary Ecology Research, 10, pp. 311-331; Revell, L.J., Harmon, L.J., Langerhans, R.B., Kolbe, J.J., A phylogenetic approach to determining the importance of constraint on phenotypic evolution in the Neotropical lizard Anolis cristatellus (2007) Evolutionary Ecology Research, 9, pp. 261-282; Revell, L.J., Johnson, M.A., Schulte II, J.A., Kolbe, J.J., Losos, J.B., A phylogenetic test for adaptive convergence in rock-dwelling lizards (2007) Evolution, 61, pp. 2898-2912; Ridley, M., (1983) The explanation of organic diversity: The comparative method and adaptations for mating, , Oxford University Press, Oxford; Rohlf, F.J., Comparative methods for the analysis of continuous variables: Geometric interpretations (2001) Evolution, 55, pp. 2143-2160; Schluter, D., Price, T., Mooers, A., Ludwig, D., Likelihood of ancestor states in adaptive radiation (1997) Evolution, 51, pp. 1699-1711; Stoks, R., McPeek, M.A., A tale of two diversifications: Reciprocal habitat shifts to fill ecological space along the pond permanence gradient (2006) American Naturalist, 168 (SUPPL.), pp. S50-S72; Stoks, R., McPeek, M.A., Mitchell, J.L., Evolution of prey behavior in response to changes in predation regime: Damselflies in fish and dragonfly lakes (2003) Evolution, 57, pp. 574-585; Thomas, G.H., Freckleton, R.P., Sz{\'e}kely, T., Comparative analysis of the influence of developmental mode on phenotypic diversification rates in shorebirds (2006) Proceedings of the Royal Society B: Biological Sciences, 273, pp. 1619-1624; Wiens, J.J., Parra-Olea, G., Garc{\'i}a-Par{\'i}s, M., Wake, D.B., Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders (2007) Proceedings of the Royal Society B: Biological Sciences, 274, pp. 919-928",

year = "2008",

month = jul,

doi = "10.1086/588078",

language = "English (US)",

volume = "172",

pages = "140--147",

journal = "American Naturalist",

issn = "0003-0147",

publisher = "University of Chicago",

number = "1",

}

TY - JOUR

T1 - On the analysis of evolutionary change along single branches in a phylogeny

AU - Revell, L.J.

N1 - Cited By :34 Export Date: 17 April 2018 CODEN: AMNTA Correspondence Address: Revell, L. J.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States; email: lrevell@fas.harvard.edu References: Butler, M.A., King, A.A., Phylogenetic comparative analysis: A modeling approach for adaptive evolution (2004) American Naturalist, 164, pp. 683-695; Cheverud, J.M., Dow, M.M., Leutenegger, W., The quantitative assessment of phylogenetic constraints in comparative analyses: Sexual dimorphism in body weight among primates (1985) Evolution, 39, pp. 1335-1351; Crespi, B., Worobey, M., Comparative analysis of gall morphology in Australian gall thrips: The evolution of extended phenotypes (1998) Evolution, 52, pp. 1686-1696; Crespi, B.J., Teo, R., Comparative phylogenetic analysis of the evolution of semelparity and life history in salmonid fishes (2002) Evolution, 56, pp. 1008-1020; Edwards, A.W.F., Cavalli-Sforza, L.L., Reconstruction of evolutionary trees (1964) Phenetic and phylogenetic classification, pp. 67-76. , V. H. Heywood and J. McNeill, eds, Systematics Association, London; Felsenstein, J., Phylogenies and the comparative method (1985) American Naturalist, 125, pp. 1-15; Felsenstein, J., Phylogenies and quantitative characters (1988) Annual Review of Ecology and Systematics, 19, pp. 445-471; Felsenstein, J., (2004) Inferring phylogenies, , Sinauer, Sunderland, MA; Garland Jr., T., Rate tests for phenotypic evolution using phylogenetically independent contrasts (1992) American Naturalist, 140, pp. 509-519; Garland Jr., T., Ives, A.R., Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods (2000) American Naturalist, 155, pp. 346-364; Garland Jr., T., Harvey, P.H., Ives, A.R., Procedures for the analysis of comparative data using phylogenetically independent contrasts (1992) Systematic Biology, 41, pp. 18-32; Garland Jr., T., Dickerman, A.W., Janis, C.M., Jones, J.A., Phylogenetic analysis of covariance by computer simulation (1993) Systematic Biology, 42, pp. 265-292; Garland Jr., T., Midford, P.E., Ives, A.R., An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values (1999) American Zoologist, 39, pp. 374-388; Grafen, A., The phylogenetic regression (1989) Philosophical Transactions of the Royal Society B: Biological Sciences, 326, pp. 119-157; Hansen, T.F., Stabilizing selection and the comparative analysis of adaptation (1997) Evolution, 51, pp. 1341-1351; Hansen, T.F., Martins, E.P., Translating between microevolutionary process and macroevolutionary patterns: The correlation structure of interspecific data (1996) Evolution, 50, pp. 1404-1417; Harrison, M.K., Crespi, B.J., A phylogenetic test of ecomorphological adaptation in Cancer crabs (1999) Evolution, 53, pp. 961-965; Harvey, P.H., Pagel, M.D., (1991) The comparative method in evolutionary biology, , Oxford University Press, Oxford; Harvey, P.H., Purvis, A., Comparative methods for explaining adaptations (1991) Nature, 351, pp. 619-624; Hendry, A.P., Kinnison, M.T., The pace of modern life: Measuring rates of contemporary microevolution (1999) Evolution, 53, pp. 1637-1653; Klingenberg, C.P., Ekau, W., A combined morphometric and phylogenetic analysis of an ecomorphological trend: Pelagization of Antarctic fishes (Perciformes: Nototheniidae) (1996) Biological Journal of the Linnean Society, 59, pp. 143-177; Larson, A., Losos, J.B., Phylogenetic systematics of adaptation (1996) Adaptation, pp. 187-220. , M. R. Rose and G. V. Lauder, eds, Academic Press, San Diego, CA; McPeek, M.A., Testing hypotheses about evolutionary change on single branches of a phylogeny using evolutionary contrasts (1995) American Naturalist, 145, pp. 686-703; McPeek, M.A., Biochemical evolution associated with antipredator adaptation in damselflies (1999) Evolution, 53, pp. 1835-1845; McPeek, M.A., Brown, J.M., Building a regional species pool: Diversification of the Enallagma damselflies in eastern North America (2000) Ecology, 81, pp. 904-920; McPeek, M.A., Schrot, A.K., Brown, J.M., Adaptation to predators in a new community: Swimming performance and predator avoidance in damselflies (1996) Ecology, 77, pp. 617-629; 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; Revell, L.J., Testing the genetic constraint hypothesis in a phylogenetic context: A simulation study (2007) Evolution, 61, pp. 2720-2727; Revell, L.J., Harmon, L.J., Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters (2008) Evolutionary Ecology Research, 10, pp. 311-331; Revell, L.J., Harmon, L.J., Langerhans, R.B., Kolbe, J.J., A phylogenetic approach to determining the importance of constraint on phenotypic evolution in the Neotropical lizard Anolis cristatellus (2007) Evolutionary Ecology Research, 9, pp. 261-282; Revell, L.J., Johnson, M.A., Schulte II, J.A., Kolbe, J.J., Losos, J.B., A phylogenetic test for adaptive convergence in rock-dwelling lizards (2007) Evolution, 61, pp. 2898-2912; Ridley, M., (1983) The explanation of organic diversity: The comparative method and adaptations for mating, , Oxford University Press, Oxford; Rohlf, F.J., Comparative methods for the analysis of continuous variables: Geometric interpretations (2001) Evolution, 55, pp. 2143-2160; Schluter, D., Price, T., Mooers, A., Ludwig, D., Likelihood of ancestor states in adaptive radiation (1997) Evolution, 51, pp. 1699-1711; Stoks, R., McPeek, M.A., A tale of two diversifications: Reciprocal habitat shifts to fill ecological space along the pond permanence gradient (2006) American Naturalist, 168 (SUPPL.), pp. S50-S72; Stoks, R., McPeek, M.A., Mitchell, J.L., Evolution of prey behavior in response to changes in predation regime: Damselflies in fish and dragonfly lakes (2003) Evolution, 57, pp. 574-585; Thomas, G.H., Freckleton, R.P., Székely, T., Comparative analysis of the influence of developmental mode on phenotypic diversification rates in shorebirds (2006) Proceedings of the Royal Society B: Biological Sciences, 273, pp. 1619-1624; Wiens, J.J., Parra-Olea, G., García-París, M., Wake, D.B., Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders (2007) Proceedings of the Royal Society B: Biological Sciences, 274, pp. 919-928

PY - 2008/7

Y1 - 2008/7

N2 - Comparative biologists are sometimes interested in estimating the evolutionary rate along single branches in a phylogeny. I evaluate two methods by which the evolutionary rate along single branches can be compared with the evolutionary rate throughout the rest of the tree. The first is McPeek's contrasts method, and the second is a likelihood method presented independently in two recently published studies. Although the latter method was developed primarily for the comparison of rates among clades, the approach is equally suited for the analysis of evolutionary rate along single or isolated branches. I find that Type I error is acceptable in both methods but that power and parameter estimation are relatively poor in McPeek's method as it is typically applied. © 2008 by The University of Chicago. All rights reserved.

AB - Comparative biologists are sometimes interested in estimating the evolutionary rate along single branches in a phylogeny. I evaluate two methods by which the evolutionary rate along single branches can be compared with the evolutionary rate throughout the rest of the tree. The first is McPeek's contrasts method, and the second is a likelihood method presented independently in two recently published studies. Although the latter method was developed primarily for the comparison of rates among clades, the approach is equally suited for the analysis of evolutionary rate along single or isolated branches. I find that Type I error is acceptable in both methods but that power and parameter estimation are relatively poor in McPeek's method as it is typically applied. © 2008 by The University of Chicago. All rights reserved.

U2 - 10.1086/588078

DO - 10.1086/588078

M3 - Article

SN - 0003-0147

VL - 172

SP - 140

EP - 147

JO - American Naturalist

JF - American Naturalist

IS - 1

ER -

On the analysis of evolutionary change along single branches in a phylogeny

Resumen

Acceder al documento

Huella

Citar esto