메뉴 건너뛰기




Volumn 5, Issue 11, 2014, Pages 1133-1146

Intrinsic inference difficulties for trait evolution with Ornstein-Uhlenbeck models

Author keywords

Change point model; Comparative method; Identifiability; Modified BIC; Selection regime

Indexed keywords


EID: 84913531711     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12285     Document Type: Article
Times cited : (137)

References (50)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike, H. (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19, 716-723.
    • (1974) IEEE Transactions on Automatic Control , vol.19 , pp. 716-723
    • Akaike, H.1
  • 2
    • 79957548902 scopus 로고    scopus 로고
    • Analysis of comparative data with hierarchical autocorrelation
    • Ané, C. (2008) Analysis of comparative data with hierarchical autocorrelation. Annals of Applied Statistics, 2, 1078-1102.
    • (2008) Annals of Applied Statistics , vol.2 , pp. 1078-1102
    • Ané, C.1
  • 4
    • 84864320749 scopus 로고    scopus 로고
    • Modeling stabilizing selection: expanding the Ornstein-Uhlenbeck model of adaptive evolution
    • Beaulieu, J.M., Jhwueng, D.-C., Boettiger, C. & O'Meara, B.C. (2012) Modeling stabilizing selection: expanding the Ornstein-Uhlenbeck model of adaptive evolution. Evolution, 66, 2369-2383.
    • (2012) Evolution , vol.66 , pp. 2369-2383
    • Beaulieu, J.M.1    Jhwueng, D.-C.2    Boettiger, C.3    O'Meara, B.C.4
  • 6
    • 84863435149 scopus 로고    scopus 로고
    • Is your phylogeny informative? Measuring the power of comparative methods
    • Boettiger, C., Coop, G. & Ralph, P. (2012). Is your phylogeny informative? Measuring the power of comparative methods. Evolution, 66, 2240-2251.
    • (2012) Evolution , vol.66 , pp. 2240-2251
    • Boettiger, C.1    Coop, G.2    Ralph, P.3
  • 8
    • 11944264347 scopus 로고    scopus 로고
    • Phylogenetic comparative analysis: a modeling approach for adaptive evolution
    • Butler, M.A. & King, A.A. (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist, 164, 683-695.
    • (2004) American Naturalist , vol.164 , pp. 683-695
    • Butler, M.A.1    King, A.A.2
  • 10
    • 82855161365 scopus 로고    scopus 로고
    • A novel comparative method for identifying shifts in the rate of character evolution on trees
    • Eastman, J.M., Alfaro, M.E., Joyce, P., Hipp, A.L. & Harmon, L.J. (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
  • 12
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • Felsenstein, J. (1985) Phylogenies and the comparative method. American Naturalist, 125, 1-15.
    • (1985) American Naturalist , vol.125 , pp. 1-15
    • Felsenstein, J.1
  • 13
    • 0036920097 scopus 로고    scopus 로고
    • Phylogenetic analysis and comparative data: a test and review of evidence
    • Freckleton, R.P., Harvey, P.H. & Pagel, M. (2002) Phylogenetic analysis and comparative data: a test and review of evidence. American Naturalist, 160, 712-726.
    • (2002) American Naturalist , vol.160 , pp. 712-726
    • Freckleton, R.P.1    Harvey, P.H.2    Pagel, M.3
  • 14
    • 0034001912 scopus 로고    scopus 로고
    • Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods
    • Garland Jr, T. & Ives, A.R. (2000) Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist, 155, 346-364.
    • (2000) American Naturalist , vol.155 , pp. 346-364
    • Garland, T.1    Ives, A.R.2
  • 15
    • 58849102142 scopus 로고    scopus 로고
    • Language phylogenies reveal expansion pulses and pauses in pacific settlement
    • Gray, R.D., Drummond, A.J. & Greenhill, S.J. (2009) Language phylogenies reveal expansion pulses and pauses in pacific settlement. Science, 323, 479-483.
    • (2009) Science , vol.323 , pp. 479-483
    • Gray, R.D.1    Drummond, A.J.2    Greenhill, S.J.3
  • 16
    • 0030772835 scopus 로고    scopus 로고
    • Stabilizing selection and the comparative analysis of adaptation
    • Hansen, T.F. (1997) Stabilizing selection and the comparative analysis of adaptation. Evolution, 51, 1341-1351.
    • (1997) Evolution , vol.51 , pp. 1341-1351
    • Hansen, T.F.1
  • 17
    • 27644562177 scopus 로고    scopus 로고
    • Assessing current adaptation and phylogenetic inertia as explanations of trait evolution: the need for controlled comparisons
    • Hansen, T.F. & Orzack, S.H. (2005). Assessing current adaptation and phylogenetic inertia as explanations of trait evolution: the need for controlled comparisons. Evolution, 59, 2063-2072.
    • (2005) Evolution , vol.59 , pp. 2063-2072
    • Hansen, T.F.1    Orzack, S.H.2
  • 18
    • 47749107969 scopus 로고    scopus 로고
    • A comparative method for studying adaptation to a randomly evolving environment
    • Hansen, T.F., Pienaar, J. & Orzack, S.H. (2008). A comparative method for studying adaptation to a randomly evolving environment. Evolution, 62, 1965-1977.
    • (2008) Evolution , vol.62 , pp. 1965-1977
    • Hansen, T.F.1    Pienaar, J.2    Orzack, S.H.3
  • 20
    • 84879163204 scopus 로고    scopus 로고
    • Asymptotic theory with hierarchical autocorrelation: Ornstein-Uhlenbeck tree models
    • Ho, L.S.T. & Ané, C. (2013) Asymptotic theory with hierarchical autocorrelation: Ornstein-Uhlenbeck tree models. Annals of Statistics, 41, 957-981.
    • (2013) Annals of Statistics , vol.41 , pp. 957-981
    • Ho, L.S.T.1    Ané, C.2
  • 21
    • 84898959182 scopus 로고    scopus 로고
    • A linear-time algorithm for Gaussian and non-Gaussian trait evolution models
    • Ho, L.S.T. & Ané, C. (2014) A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Systematic Biology, 63, 397-408.
    • (2014) Systematic Biology , vol.63 , pp. 397-408
    • Ho, L.S.T.1    Ané, C.2
  • 22
    • 40449103038 scopus 로고    scopus 로고
    • Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage
    • Hunt, G., Bell, M.A. & Travis, M.P. (2008) Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage. Evolution, 62, 700-710.
    • (2008) Evolution , vol.62 , pp. 700-710
    • Hunt, G.1    Bell, M.A.2    Travis, M.P.3
  • 23
    • 84877917356 scopus 로고    scopus 로고
    • Surface: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike information criterion
    • Ingram, T. & Mahler, D.L. (2013) Surface: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike information criterion. Methods in Ecology and Evolution, 4, 416-425.
    • (2013) Methods in Ecology and Evolution , vol.4 , pp. 416-425
    • Ingram, T.1    Mahler, D.L.2
  • 24
    • 84869088692 scopus 로고    scopus 로고
    • The global diversity of birds in space and time
    • Jetz, W., Thomas, G., Joy, J., Hartmann, K. & Mooers, A. (2012) The global diversity of birds in space and time. Nature, 491, 444-448.
    • (2012) Nature , vol.491 , pp. 444-448
    • Jetz, W.1    Thomas, G.2    Joy, J.3    Hartmann, K.4    Mooers, A.5
  • 25
    • 46149108174 scopus 로고    scopus 로고
    • Morphometrics of the avian small intestine compared with that of nonflying mammals: a phylogenetic approach
    • Lavin, S.R., Karasov, W.H., Ives, A.R., Middleton, K.M. & Garland Jr, T. (2008) Morphometrics of the avian small intestine compared with that of nonflying mammals: a phylogenetic approach. Physiological and Biochemical Zoology, 81, 526-550.
    • (2008) Physiological and Biochemical Zoology , vol.81 , pp. 526-550
    • Lavin, S.R.1    Karasov, W.H.2    Ives, A.R.3    Middleton, K.M.4    Garland, T.5
  • 26
    • 0034237772 scopus 로고    scopus 로고
    • Adaptation and the comparative method
    • Martins, E.P. (2000) Adaptation and the comparative method. Trends in Ecology and Evolution, 15, 296-299.
    • (2000) Trends in Ecology and Evolution , vol.15 , pp. 296-299
    • Martins, E.P.1
  • 27
    • 33645665925 scopus 로고    scopus 로고
    • Phylogeny of the ants: diversification in the age of angiosperms
    • Moreau, C.S., Bell, C.D., Vila, R., Archibald, S.B. & Pierce, N.E. (2006) Phylogeny of the ants: diversification in the age of angiosperms. Science, 312, 101-104.
    • (2006) Science , vol.312 , pp. 101-104
    • Moreau, C.S.1    Bell, C.D.2    Vila, R.3    Archibald, S.B.4    Pierce, N.E.5
  • 28
    • 33747056328 scopus 로고    scopus 로고
    • Testing for different rates of continuous trait evolution using likelihood
    • O'Meara, B.C., Ané, C., Sanderson, M.J. & Wainwright, P.C. (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
  • 29
    • 0034061046 scopus 로고    scopus 로고
    • Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny
    • Oakley, T.H. & Cunningham, C.W. (2000) Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution, 54, 397-405.
    • (2000) Evolution , vol.54 , pp. 397-405
    • Oakley, T.H.1    Cunningham, C.W.2
  • 30
    • 0036402267 scopus 로고    scopus 로고
    • Analysis of comparative data using generalized estimating equations
    • Paradis, E. & Claude, J. (2002) Analysis of comparative data using generalized estimating equations. Journal of Theoretical Biology, 218, 175-185.
    • (2002) Journal of Theoretical Biology , vol.218 , pp. 175-185
    • Paradis, E.1    Claude, J.2
  • 31
    • 84879308395 scopus 로고    scopus 로고
    • An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology
    • Pennell, M.W. & Harmon, L.J. (2013) An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Annals of the New York Academy of Sciences, 1289, 90-105.
    • (2013) Annals of the New York Academy of Sciences , vol.1289 , pp. 90-105
    • Pennell, M.W.1    Harmon, L.J.2
  • 32
    • 84896270571 scopus 로고    scopus 로고
    • Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees
    • Rabosky, D.L. (2014) Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE, 9, e89543.
    • (2014) PLoS ONE , vol.9 , pp. e89543
    • Rabosky, D.L.1
  • 33
    • 84859754173 scopus 로고    scopus 로고
    • Exact posterior distributions and model selection criteria for multiple change-point detection problems
    • Rigaill, G., Lebarbier, E. & Robin, S. (2012) Exact posterior distributions and model selection criteria for multiple change-point detection problems. Statistics and Computing, 22, 917-929.
    • (2012) Statistics and Computing , vol.22 , pp. 917-929
    • Rigaill, G.1    Lebarbier, E.2    Robin, S.3
  • 34
    • 84891786317 scopus 로고    scopus 로고
    • Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within species variation
    • Rohlfs, R.V., Harrigan, P. & Nielsen, R. (2014) Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within species variation. Molecular Biology and Evolution, 31, 201-211.
    • (2014) Molecular Biology and Evolution , vol.31 , pp. 201-211
    • Rohlfs, R.V.1    Harrigan, P.2    Nielsen, R.3
  • 35
    • 67650233960 scopus 로고    scopus 로고
    • Running for your life or running for your dinner: what drives fibertype evolution in lizard locomotor muscles
    • Scales, J.A., King, A.A. & Butler, M.A. (2009). Running for your life or running for your dinner: what drives fibertype evolution in lizard locomotor muscles? American Naturalist, 173, 543-553.
    • (2009) American Naturalist , vol.173 , pp. 543-553
    • Scales, J.A.1    King, A.A.2    Butler, M.A.3
  • 36
    • 0031417707 scopus 로고    scopus 로고
    • Likelihood of ancestor states in adaptive radiation
    • Schluter, D., Price, T., Mooers, A.O. & Ludwig, D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution, 51, 1699-1711.
    • (1997) Evolution , vol.51 , pp. 1699-1711
    • Schluter, D.1    Price, T.2    Mooers, A.O.3    Ludwig, D.4
  • 37
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • Schwarz, G. (1978) Estimating the dimension of a model. Annals of Statistics, 6, 461-464.
    • (1978) Annals of Statistics , vol.6 , pp. 461-464
    • Schwarz, G.1
  • 39
    • 84881606628 scopus 로고    scopus 로고
    • Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the cretaceous-palaeogene boundary
    • Slater, G.J. (2013) Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the cretaceous-palaeogene boundary. Methods in Ecology and Evolution, 4, 734-744.
    • (2013) Methods in Ecology and Evolution , vol.4 , pp. 734-744
    • Slater, G.J.1
  • 40
    • 84881605948 scopus 로고    scopus 로고
    • Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution
    • Slater, G.J. & Harmon, L.J. (2013). Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution. Methods in Ecology and Evolution, 4, 699-702.
    • (2013) Methods in Ecology and Evolution , vol.4 , pp. 699-702
    • Slater, G.J.1    Harmon, L.J.2
  • 41
    • 41749106913 scopus 로고    scopus 로고
    • The role of pollinator shifts in the floral diversification of iochroma (solanaceae)
    • Smith, S.D., Ané, C. & Baum, D.A. (2008) The role of pollinator shifts in the floral diversification of iochroma (solanaceae). Evolution, 62, 793-806.
    • (2008) Evolution , vol.62 , pp. 793-806
    • Smith, S.D.1    Ané, C.2    Baum, D.A.3
  • 44
    • 84913549686 scopus 로고    scopus 로고
    • A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data
    • Uyeda, J.C. & Harmon, L.J. (2014). A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data. Systematic Biology, 63, 902-918.
    • (2014) Systematic Biology , vol.63 , pp. 902-918
    • Uyeda, J.C.1    Harmon, L.J.2
  • 45
    • 84913568475 scopus 로고    scopus 로고
    • bayou: Bayesian fitting of Ornstein-Uhlenbeck models to phylogenies. R package version 1.0.1. URL .
    • Uyeda, J.C., Eastman, J. & Harmon, L. (2014) bayou: Bayesian fitting of Ornstein-Uhlenbeck models to phylogenies. R package version 1.0.1. URL http://CRAN.Rproject.org/package=bayou.
    • (2014)
    • Uyeda, J.C.1    Eastman, J.2    Harmon, L.3
  • 46
    • 81555202533 scopus 로고    scopus 로고
    • Multiple routes to mammalian diversity
    • Venditti, C., Meade, A. & Pagel, M. (2011) Multiple routes to mammalian diversity. Nature, 479, 393-396.
    • (2011) Nature , vol.479 , pp. 393-396
    • Venditti, C.1    Meade, A.2    Pagel, M.3
  • 47
    • 2142734871 scopus 로고    scopus 로고
    • Inconsistent estimation and asymptotically equal interpolations in model-based geostatistics
    • Zhang, H. (2004) Inconsistent estimation and asymptotically equal interpolations in model-based geostatistics. Journal of the American Statistical Association, 99, 250-261.
    • (2004) Journal of the American Statistical Association , vol.99 , pp. 250-261
    • Zhang, H.1
  • 48
    • 34247243220 scopus 로고    scopus 로고
    • A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data
    • Zhang, N.R. & Siegmund, D.O. (2007) A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data. Biometrics, 63, 22-32.
    • (2007) Biometrics , vol.63 , pp. 22-32
    • Zhang, N.R.1    Siegmund, D.O.2
  • 49
    • 84866842795 scopus 로고    scopus 로고
    • Model selection for high-dimensional, multi-sequence change point problems
    • Zhang, N.R. & Siegmund, D.O. (2012) Model selection for high-dimensional, multi-sequence change point problems. Statistica Sinica, 22, 1507.
    • (2012) Statistica Sinica , vol.22 , pp. 1507
    • Zhang, N.R.1    Siegmund, D.O.2
  • 50


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.