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Volumn 66, Issue 9, 2012, Pages 2697-2707

A new bayesian method for fitting evolutionary models to comparative data with intraspecific variation

Author keywords

Comparative method; Interspecific data; Phylogenetic tree

Indexed keywords

BAYESIAN ANALYSIS; BROWNIAN MOTION; COMPARATIVE STUDY; EMPIRICAL ANALYSIS; INTRASPECIFIC VARIATION; PHENOTYPE; PHYLOGENETICS; PHYLOGENY; PROBABILITY;

EID: 84865709842     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2012.01645.x     Document Type: Article
Times cited : (50)

References (46)
  • 1
    • 34548388929 scopus 로고    scopus 로고
    • Bayesian predictive information criterion for the evaluation of hierarchical Bayesian and empirical Bayes models
    • Ando, T. 2007. Bayesian predictive information criterion for the evaluation of hierarchical Bayesian and empirical Bayes models. Biometrika 94:443-458.
    • (2007) Biometrika , vol.94 , pp. 443-458
    • Ando, T.1
  • 2
    • 0038325772 scopus 로고    scopus 로고
    • Testing for phylogenetic signal in comparative data: Behavioral traits are more labile
    • Blomberg, S. P., T. Garland, Jr., and A. R. Ives 2003. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 57:717-745.
    • (2003) Evolution , vol.57 , pp. 717-745
    • Blomberg, S.P.1    Garland Jr, T.2    Ives, A.R.3
  • 3
    • 0036846704 scopus 로고    scopus 로고
    • Detection of punctuated equilibrium from molecular phylogenies
    • Bokma, F. 2002. Detection of punctuated equilibrium from molecular phylogenies. J. Evol. Biol. 15:1048-1056.
    • (2002) J. Evol. Biol. , vol.15 , pp. 1048-1056
    • Bokma, F.1
  • 4
    • 54849411673 scopus 로고    scopus 로고
    • Detection of "punctuated equilibrium" by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny
    • ---. 2008. Detection of "punctuated equilibrium" by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny. Evolution 62:2718-2726.
    • (2008) Evolution , vol.62 , pp. 2718-2726
  • 5
    • 0024936691 scopus 로고
    • How much heritable variation can be maintained in a finite population by mutation-selection balance
    • Bürger, R., G. P. Wagner, and F. Stettinger 1989. How much heritable variation can be maintained in a finite population by mutation-selection balance. Evolution 43:1748-1766.
    • (1989) Evolution , vol.43 , pp. 1748-1766
    • Bürger, R.1    Wagner, G.P.2    Stettinger, F.3
  • 6
    • 11944264347 scopus 로고    scopus 로고
    • Phylogenetic comparative analysis: a modeling approach for adaptive evolution
    • Butler, M. A., and A. A. King 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164:683-695.
    • (2004) Am. Nat. , vol.164 , pp. 683-695
    • Butler, M.A.1    King, A.A.2
  • 7
    • 0014082615 scopus 로고
    • Phylogenetic analysis: models and estimation procedures
    • Cavalli-Sforza, L. L., and A. W. F. Edwards 1967. Phylogenetic analysis: models and estimation procedures. Am. J. Hum. Genet. 19:233-257.
    • (1967) Am. J. Hum. Genet. , vol.19 , pp. 233-257
    • Cavalli-Sforza, L.L.1    Edwards, A.W.F.2
  • 8
    • 82855161365 scopus 로고    scopus 로고
    • A novel comparative method for identifying shifts in the rate of character evolution on trees
    • Eastman, J. M., M. E. Alfaro, P. Joyce, A. L. Hipp, and L. J. Harmon 2011. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65:3578-3589.
    • (2011) Evolution , vol.65 , pp. 3578-3589
    • Eastman, J.M.1    Alfaro, M.E.2    Joyce, P.3    Hipp, A.L.4    Harmon, L.J.5
  • 10
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
    • (1985) Am. Nat. , vol.125 , pp. 1-15
    • Felsenstein, J.1
  • 11
    • 43949115169 scopus 로고    scopus 로고
    • Comparative methods with sampling error and within-species variation: contrasts revisited and revised
    • ---. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am. Nat. 171:713-725.
    • (2008) Am. Nat. , vol.171 , pp. 713-725
  • 12
    • 30344477632 scopus 로고    scopus 로고
    • The effect of intraspecific sample size on type I and type II error rates in comparative studies
    • Harmon, L. J., and J. B. Losos 2005. The effect of intraspecific sample size on type I and type II error rates in comparative studies. Evolution 59:2705-2710.
    • (2005) Evolution , vol.59 , pp. 2705-2710
    • Harmon, L.J.1    Losos, J.B.2
  • 14
    • 0020850136 scopus 로고
    • Simulation run length control in the presence of an initial transient
    • Heidelberger, P., and P. D. Welch 1983. Simulation run length control in the presence of an initial transient. Oper. Res. 31:1109-1144.
    • (1983) Oper. Res. , vol.31 , pp. 1109-1144
    • Heidelberger, P.1    Welch, P.D.2
  • 15
    • 0035527347 scopus 로고    scopus 로고
    • Empirical and hierarchical Bayesian estimation of ancestral states
    • Huelsenbeck, J. P., and J. P. Bollback 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50:351-366.
    • (2001) Syst. Biol. , vol.50 , pp. 351-366
    • Huelsenbeck, J.P.1    Bollback, J.P.2
  • 16
    • 79954588303 scopus 로고    scopus 로고
    • Do constructional constraints influence cyprinid (Cyprinidae: Leuciscinae) craniofacial coevolution?
    • Hulsey, C. D., and P. J. Hollingsworth Jr. 2011. Do constructional constraints influence cyprinid (Cyprinidae: Leuciscinae) craniofacial coevolution? Biol. J. Linn. Soc. 103:136-146.
    • (2011) Biol. J. Linn. Soc. , vol.103 , pp. 136-146
    • Hulsey, C.D.1    Hollingsworth Jr, P.J.2
  • 17
    • 34447280382 scopus 로고    scopus 로고
    • Within-species variation and measurement error in phylogenetic comparative methods
    • Ives, A. R., P. E. Midford, and T. Garland Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Syst. Biol. 56:252-270.
    • (2007) Syst. Biol. , vol.56 , pp. 252-270
    • Ives, A.R.1    Midford, P.E.2    Garland Jr, T.3
  • 19
    • 0043286742 scopus 로고    scopus 로고
    • Stability of the G-matrix in a population experiencing pleiotropic mutation, stabilizing selection, and genetic drift
    • Jones, A. G., S. J. Arnold, and R. Bürger 2003. Stability of the G-matrix in a population experiencing pleiotropic mutation, stabilizing selection, and genetic drift. Evolution 57:1747-1760.
    • (2003) Evolution , vol.57 , pp. 1747-1760
    • Jones, A.G.1    Arnold, S.J.2    Bürger, R.3
  • 21
    • 84865705686 scopus 로고    scopus 로고
    • MathWorks. The MathWorks, Inc., Natick, MA
    • MathWorks. 2011. MATLAB 7.13 R2011b. The MathWorks, Inc., Natick, MA
    • (2011) MATLAB 7.13 R2011b
  • 22
    • 63849162423 scopus 로고    scopus 로고
    • Craniodental indicators of prey size preference in the Felidae
    • Meachen-Samuels, J., and B. Van Valkenburgh 2009. Craniodental indicators of prey size preference in the Felidae. Biol. J. Linn. Soc. 96:784-799.
    • (2009) Biol. J. Linn. Soc. , vol.96 , pp. 784-799
    • Meachen-Samuels, J.1    Van Valkenburgh, B.2
  • 24
    • 33747056328 scopus 로고    scopus 로고
    • Testing for different rates of continuous trait evolution using likelihood
    • O'Meara, B. C., C. Ané, M. J. Sanderson, and P. C. Wainwright 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933.
    • (2006) Evolution , vol.60 , pp. 922-933
    • O'Meara, B.C.1    Ané, C.2    Sanderson, M.J.3    Wainwright, P.C.4
  • 25
    • 0033613376 scopus 로고    scopus 로고
    • Inferring the historical patterns of biological evolution
    • Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
    • (1999) Nature , vol.401 , pp. 877-884
    • Pagel, M.1
  • 26
    • 1042304216 scopus 로고    scopus 로고
    • APE: analyses of phylogenetics and evolution in R language
    • Paradis, E., J. Claude, and K. Strimmer 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290.
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 27
    • 41149087694 scopus 로고    scopus 로고
    • CODA: convergence diagnostics and output analysis for MCMC
    • Plummer, M., N. Best, K. Cowles, and K. Vines 2006. CODA: convergence diagnostics and output analysis for MCMC. R. News 6:7-11.
    • (2006) R. News , vol.6 , pp. 7-11
    • Plummer, M.1    Best, N.2    Cowles, K.3    Vines, K.4
  • 28
    • 33747828694 scopus 로고    scopus 로고
    • ModelTest Server: A web-based tool for the statistical selection of models of nucleotide substitution online
    • Posada, D. 2006. ModelTest Server: A web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Research 34:W700-W703.
    • (2006) Nucleic Acids Research , vol.34
    • Posada, D.1
  • 29
    • 0031589930 scopus 로고    scopus 로고
    • Correlated evolution and independent contrasts
    • Price, T. 1997. Correlated evolution and independent contrasts. Philos. Trans. R. Soc. Lond. Ser. B 352:519-529.
    • (1997) Philos. Trans. R. Soc. Lond. Ser. B , vol.352 , pp. 519-529
    • Price, T.1
  • 30
    • 84908418476 scopus 로고    scopus 로고
    • R: a language and environment for statistical computing
    • R Development Core Team. ., Vienna, Austria
    • R Development Core Team. 2011 R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria
    • (2011) R foundation for statistical computing
  • 31
    • 35748932658 scopus 로고    scopus 로고
    • Testing the genetic constraint hypothesis in a phylogenetic context: a simulation study
    • Revell, L. J. 2007. Testing the genetic constraint hypothesis in a phylogenetic context: a simulation study. Evolution 61:2720-2727.
    • (2007) Evolution , vol.61 , pp. 2720-2727
    • Revell, L.J.1
  • 32
    • 46749098036 scopus 로고    scopus 로고
    • On the analysis of evolutionary change along single branches in a phylogeny
    • ---. 2008. On the analysis of evolutionary change along single branches in a phylogeny. Am. Nat. 172:140-147.
    • (2008) Am. Nat. , vol.172 , pp. 140-147
  • 33
    • 84867364321 scopus 로고    scopus 로고
    • Phytools: An R package for phylogenetic comparative biology (and other things)
    • ---. 2012. Phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3:217-223.
    • (2012) Methods in Ecology and Evolution , vol.3 , pp. 217-223
  • 34
    • 62949120782 scopus 로고    scopus 로고
    • Phylogenetic analysis of the evolutionary correlation using likelihood
    • Revell, L. J., and D. C. Collar 2009. Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution 63:1090-1100.
    • (2009) Evolution , vol.63 , pp. 1090-1100
    • Revell, L.J.1    Collar, D.C.2
  • 35
    • 66249102409 scopus 로고    scopus 로고
    • Phylogenetic signal, evolutionary process, and rate
    • Revell, L. J., L. J. Harmon, and D. C., Collar 2008. Phylogenetic signal, evolutionary process, and rate. Syst. Biol. 57:591-601.
    • (2008) Syst. Biol. , vol.57 , pp. 591-601
    • Revell, L.J.1    Harmon, L.J.2    Collar, D.C.3
  • 36
    • 84855283706 scopus 로고    scopus 로고
    • A new phylogenetic method for identifying exceptional phenotypic diversification
    • Revell, L. J., D. L. Mahler, P. R. Peres-Neto, and B. D. Redelings 2012. A new phylogenetic method for identifying exceptional phenotypic diversification. Evolution 66:135-146.
    • (2012) Evolution , vol.66 , pp. 135-146
    • Revell, L.J.1    Mahler, D.L.2    Peres-Neto, P.R.3    Redelings, B.D.4
  • 37
    • 0035685482 scopus 로고    scopus 로고
    • Comparative methods for the analysis of continuous variables: geometric interpretations
    • Rohlf, F. J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55:2143-2160.
    • (2001) Evolution , vol.55 , pp. 2143-2160
    • Rohlf, F.J.1
  • 38
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist, F., and J. P. Huelsenbeck 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 39
    • 0036135468 scopus 로고    scopus 로고
    • Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach
    • Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 101-109
    • Sanderson, M.J.1
  • 40
    • 84857692151 scopus 로고    scopus 로고
    • Fitting models of continuous trait evolution to incompletely sampled comparative data using Approximate Bayesian Computation
    • Slater, G. J., L. J. Harmon, D. Wegmann, P. Joyce, L. J. Revell, and M. E. Alfaro 2012. Fitting models of continuous trait evolution to incompletely sampled comparative data using Approximate Bayesian Computation. Evolution 66:752-762.
    • (2012) Evolution , vol.66 , pp. 752-762
    • Slater, G.J.1    Harmon, L.J.2    Wegmann, D.3    Joyce, P.4    Revell, L.J.5    Alfaro, M.E.6
  • 42
    • 84862247666 scopus 로고    scopus 로고
    • MOTMOT: models of trait macroevolution on trees
    • Thomas, G. H., and R. P. Freckleton 2012. MOTMOT: models of trait macroevolution on trees. Methods Ecol. Evol. 3:145-151.
    • (2012) Methods Ecol. Evol. , vol.3 , pp. 145-151
    • Thomas, G.H.1    Freckleton, R.P.2
  • 43
    • 33747174297 scopus 로고    scopus 로고
    • Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds
    • Thomas, G. H., R. P. Freckleton, and T. Székely 2006. Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proc. R. Soc. B 273:1619-1624.
    • (2006) Proc. R. Soc. B , vol.273 , pp. 1619-1624
    • Thomas, G.H.1    Freckleton, R.P.2    Székely, T.3
  • 44
    • 0002894886 scopus 로고
    • Cranial and dental adaptations to predation in Canids
    • Van Valkenburgh, B., and K. P. Koepfli 1993. Cranial and dental adaptations to predation in Canids. Symp. Zool. Soc. Lond. 65:15-37.
    • (1993) Symp. Zool. Soc. Lond. , vol.65 , pp. 15-37
    • Van Valkenburgh, B.1    Koepfli, K.P.2
  • 46
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method
    • Yang, Z., and B. Rannala 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 717-724
    • Yang, Z.1    Rannala, B.2


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