메뉴 건너뛰기




Volumn 28, Issue 1, 2011, Pages 729-744

A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters

Author keywords

Bayesian statistics; comparative method; independent contrasts; life history evolution; Markov chain Monte Carlo; molecular dating

Indexed keywords

CYTOCHROME B;

EID: 78650493648     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq244     Document Type: Article
Times cited : (174)

References (66)
  • 1
    • 33749595631 scopus 로고    scopus 로고
    • A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution
    • Blanquart S, Lartillot N. 2006. A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution. Mol Biol Evol. 23:2058-2071.
    • (2006) Mol Biol Evol , vol.23 , pp. 2058-2071
    • Blanquart, S.1    Lartillot, N.2
  • 2
    • 57749185463 scopus 로고    scopus 로고
    • Parallel adaptations to high temperatures in the Archaean eon
    • Boussau B, Blanquart S, Lartillot N, Gouy M. 2008. Parallel adaptations to high temperatures in the Archaean eon. Nature 456:942-945.
    • (2008) Nature , vol.456 , pp. 942-945
    • Boussau, B.1    Blanquart, S.2    Lartillot, N.3    Gouy, M.4
  • 3
    • 0030442757 scopus 로고    scopus 로고
    • Determinants of rate variation in mammalian DNA sequence evolution
    • Bromham L, Rambaut A, Harvey PH. 1996. Determinants of rate variation in mammalian DNA sequence evolution. J Mol Evol. 43:610-621.
    • (1996) J Mol Evol , vol.43 , pp. 610-621
    • Bromham, L.1    Rambaut, A.2    Harvey, P.H.3
  • 5
    • 11944264347 scopus 로고    scopus 로고
    • Phylogenetic comparative analysis: A modeling approach for adaptive evolution
    • Butler MA, King AA. 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
    • 0000685226 scopus 로고
    • The molecular clock and the relationship between population size and generation time
    • Chao L, Carr DE. 1993. The molecular clock and the relationship between population size and generation time. Evolution 47:688-690.
    • (1993) Evolution , vol.47 , pp. 688-690
    • Chao, L.1    Carr, D.E.2
  • 8
    • 77952037303 scopus 로고    scopus 로고
    • Body size evolution in mammals: Complexity in tempo and mode
    • Cooper N, Purvis A. 2010. Body size evolution in mammals: complexity in tempo and mode. Am Nat. 175:727-738.
    • (2010) Am Nat. , vol.175 , pp. 727-738
    • Cooper, N.1    Purvis, A.2
  • 9
    • 21344482755 scopus 로고
    • Hyper Markov laws in the statistical analysis of decomposable graphical models
    • Dawid AP, Lauritzen SL. 1993. Hyper Markov laws in the statistical analysis of decomposable graphical models. Ann Stat. 21:1272-1317.
    • (1993) Ann Stat , vol.21 , pp. 1272-1317
    • Dawid, A.P.1    Lauritzen, S.L.2
  • 10
    • 74549220350 scopus 로고    scopus 로고
    • Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories
    • de Koning AP, Gu W, Pollock D. 2010. Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Mol Biol Evol. 27:249-265.
    • (2010) Mol Biol Evol. , vol.27 , pp. 249-265
    • De Koning, A.P.1    Gu, W.2    Pollock, D.3
  • 11
    • 67650366969 scopus 로고    scopus 로고
    • A database of vertebrate longevity records and their relation to other life-history traits
    • de Magalhaes JP, Costa J. 2009. A database of vertebrate longevity records and their relation to other life-history traits. J Evol Biol. 22:1770-1774.
    • (2009) J Evol Biol , vol.22 , pp. 1770-1774
    • De Magalhaes, J.P.1    Costa, J.2
  • 12
    • 0001038826 scopus 로고
    • Covariance selection
    • Dempster AP. 1972. Covariance selection. Biometrics 28:157-175.
    • (1972) Biometrics , vol.28 , pp. 157-175
    • Dempster, A.P.1
  • 13
    • 0032226106 scopus 로고    scopus 로고
    • Effects of branch length errors on the performance of phylogenetically independent contrasts
    • Diaz-Uriarte R, Garland T Jr. 1998. Effects of branch length errors on the performance of phylogenetically independent contrasts. Syst Biol. 47:654-672.
    • (1998) Syst Biol , vol.47 , pp. 654-672
    • Diaz-Uriarte, R.1    Garland Jr., T.2
  • 16
    • 0019797407 scopus 로고
    • Evolutionary trees from dna sequences: A maximum likelihood approach
    • Felsenstein J. 1981. Evolutionary trees from dna sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 17
    • 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
  • 18
    • 43949115169 scopus 로고    scopus 로고
    • Comparative methods with sampling error and within-species variation: Contrasts revisited and revised
    • Felsenstein J. 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
    • Felsenstein, J.1
  • 19
    • 34447633026 scopus 로고    scopus 로고
    • The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla
    • Fontanillas E, Welch JJ, Thomas JA, Bromham L. 2007. The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla. BMC Evol Biol. 7:95.
    • (2007) BMC Evol Biol , vol.7 , pp. 95
    • Fontanillas, E.1    Welch, J.J.2    Thomas, J.A.3    Bromham, L.4
  • 20
    • 0033534584 scopus 로고    scopus 로고
    • A nonhyperthermophilic common ancestor to extant life forms
    • Galtier N, Tourasse N, Gouy M. 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283:220-221.
    • (1999) Science , vol.283 , pp. 220-221
    • Galtier, N.1    Tourasse, N.2    Gouy, M.3
  • 21
    • 24644494898 scopus 로고    scopus 로고
    • Phylogenetic approaches in comparative physiology
    • Garland TJ, Bennett AF, Rezende EL. 2005. Phylogenetic approaches in comparative physiology. J Exp Biol. 208:3015-3035.
    • (2005) J Exp Biol , vol.208 , pp. 3015-3035
    • Garland, T.J.1    Bennett, A.F.2    Rezende, E.L.3
  • 24
    • 11844288987 scopus 로고    scopus 로고
    • The rate of DNA evolution: Effects of body size and temperature on the molecular clock
    • Gillooly JF, Allen AP, West GB, Brown JH. 2005. The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc Natl Acad Sci USA. 102:140-145.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 140-145
    • Gillooly, J.F.1    Allen, A.P.2    West, G.B.3    Brown, J.H.4
  • 27
    • 0037965118 scopus 로고    scopus 로고
    • Detecting correlation between characters in a comparative analysis with uncertain phylogeny
    • Huelsenbeck JP, Rannala B. 2003. Detecting correlation between characters in a comparative analysis with uncertain phylogeny. Evolution 57:1237-1247.
    • (2003) Evolution , vol.57 , pp. 1237-1247
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 28
    • 11144277878 scopus 로고    scopus 로고
    • Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
    • Huelsenbeck JP, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol. 53:904-913.
    • (2004) Syst Biol , vol.53 , pp. 904-913
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 29
    • 0034733685 scopus 로고    scopus 로고
    • Accommodating phylogenetic uncertainty in evolutionary studies
    • Huelsenbeck JP, Rannala B, Masly JP. 2000. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288:2349-2350.
    • (2000) Science , vol.288 , pp. 2349-2350
    • Huelsenbeck, J.P.1    Rannala, B.2    Masly, J.P.3
  • 30
    • 72049121650 scopus 로고    scopus 로고
    • The impact of the representation of fossil calibration on Bayesin estimation of species divergence times
    • Inoue JG, Donogue PCJ, Yang Z. 2010. The impact of the representation of fossil calibration on Bayesin estimation of species divergence times. Syst Biol. 59:74-89.
    • (2010) Syst Biol. , vol.59 , pp. 74-89
    • Inoue, J.G.1    Pcj, D.2    Yang, Z.3
  • 32
    • 17744413756 scopus 로고
    • Model of effectively neutral mutations in which selective constraint is incorporated
    • Kimura M. 1979. Model of effectively neutral mutations in which selective constraint is incorporated. Proc Natl Acad Sci USA. 76: 3440-3444.
    • (1979) Proc Natl Acad Sci USA , vol.76 , pp. 3440-3444
    • Kimura, M.1
  • 34
    • 0035103260 scopus 로고    scopus 로고
    • Performance of a divergence time estimation method under a probabilistic model of rate evolution
    • Kishino H, Thorne JL, Bruno W. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol. 18:352-361.
    • (2001) Mol Biol Evol , vol.18 , pp. 352-361
    • Kishino, H.1    Thorne, J.L.2    Bruno, W.3
  • 36
    • 33846593309 scopus 로고    scopus 로고
    • Conjugate Gibbs sampling for Bayesian phylogenetic models
    • Lartillot N. 2006. Conjugate Gibbs sampling for Bayesian phylogenetic models. J Comput Biol. 13:1701-1722.
    • (2006) J Comput Biol , vol.13 , pp. 1701-1722
    • Lartillot, N.1
  • 37
    • 37549001784 scopus 로고    scopus 로고
    • A general comparison of relaxed molecular clock models
    • Lepage T, Bryant D, Philippe H, Lartillot N. 2007. A general comparison of relaxed molecular clock models. Mol Biol Evol. 24:2669-2680.
    • (2007) Mol Biol Evol , vol.24 , pp. 2669-2680
    • Lepage, T.1    Bryant, D.2    Philippe, H.3    Lartillot, N.4
  • 38
    • 44649147768 scopus 로고    scopus 로고
    • Wishart distributions for decomposable graphs
    • Letac G, Massam H. 2007. Wishart distributions for decomposable graphs. Ann Stat. 35:1278-1323.
    • (2007) Ann Stat , vol.35 , pp. 1278-1323
    • Letac, G.1    Massam, H.2
  • 39
    • 0030076124 scopus 로고    scopus 로고
    • Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis
    • Li W-H, Ellsworth DL, Krushkal J, Chang BH-J, Hewett-Emmett D. 1996. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol Phylogent Evol. 5:182-187.
    • (1996) Mol Phylogent Evol , vol.5 , pp. 182-187
    • Li, W.-H.1    Ellsworth, D.L.2    Krushkal, J.3    Bh-J, C.4    Hewett-Emmett, D.5
  • 40
    • 0023263979 scopus 로고
    • The molecular clock runs more slowly in man than in apes and monkeys
    • Li W-H, Tanimura M. 1987. The molecular clock runs more slowly in man than in apes and monkeys. Nature 326:93-96.
    • (1987) Nature , vol.326 , pp. 93-96
    • Li, W.-H.1    Tanimura, M.2
  • 42
    • 0027308854 scopus 로고
    • Body size, metabolic rate, generation time, and the molecular clock
    • Martins AP, Palumbi SR. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc Natl Acad Sci USA. 90:4087-4091.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 4087-4091
    • Martins, A.P.1    Palumbi, S.R.2
  • 43
    • 0002359941 scopus 로고    scopus 로고
    • The statistical analysis of interspecific data: A review and evaluation of phylogenetic comparative methods
    • Martins E, editor Oxford: Oxford University Press
    • Martins EP, Hansen TF. 1996. The statistical analysis of interspecific data: a review and evaluation of phylogenetic comparative methods. In: Martins E, editor. Phylogenies and the comparative method in animal behavior. Oxford: Oxford University Press. p. 22-75.
    • (1996) Phylogenies and the Comparative Method in Animal Behavior , pp. 22-75
    • Martins, E.P.1    Hansen, T.F.2
  • 44
    • 0030619995 scopus 로고    scopus 로고
    • Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into the analysis of interspecific data
    • Martins EP, Hansen TF. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am Nat. 149:646-667.
    • (1997) Am Nat , vol.149 , pp. 646-667
    • Martins, E.P.1    Hansen, T.F.2
  • 45
    • 33744982664 scopus 로고    scopus 로고
    • Inferring complex dna substitution processes on phylogenies using uniformization and data augmentation
    • Mateiu L, Rannala B. 2006. Inferring complex dna substitution processes on phylogenies using uniformization and data augmentation. Syst Biol. 55:259-269.
    • (2006) Syst Biol , vol.55 , pp. 259-269
    • Mateiu, L.1    Rannala, B.2
  • 46
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitutions, with applications to chloroplast genome
    • Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitutions, with applications to chloroplast genome. Mol Biol Evol. 11:715-724.
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 47
    • 38349192060 scopus 로고    scopus 로고
    • Strong variations of mitochon-drial mutation rate across mammals-the longevity hypothesis
    • Nabholz B, Glémin S, Galtier N. 2008. Strong variations of mitochon-drial mutation rate across mammals-the longevity hypothesis. Mol Biol Evol. 25:120-130.
    • (2008) Mol Biol Evol , vol.25 , pp. 120-130
    • Nabholz, B.1    Glémin, S.2    Galtier, N.3
  • 48
    • 0036804625 scopus 로고    scopus 로고
    • Mapping mutations on phylogenies
    • Nielsen R. 2002. Mapping mutations on phylogenies. Syst Biol. 51:729-739.
    • (2002) Syst Biol , vol.51 , pp. 729-739
    • Nielsen, R.1
  • 49
    • 78650452602 scopus 로고
    • Slightly deleterious mutant substitutions in evolution
    • Ohta T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 252:315-354.
    • (1973) Nature , vol.252 , pp. 315-354
    • Ohta, T.1
  • 50
    • 0016404732 scopus 로고
    • Mutational pressure as the main cause of molecular evolution and polymorphisms
    • Ohta T. 1974. Mutational pressure as the main cause of molecular evolution and polymorphisms. Nature 252:351-354.
    • (1974) Nature , vol.252 , pp. 351-354
    • Ohta, T.1
  • 51
    • 0027443866 scopus 로고
    • An examination of the generation-time effect on molecular evolution
    • Ohta T. 1993. An examination of the generation-time effect on molecular evolution. Proc Natl Acad Sci USA. 90:10676-10680.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 10676-10680
    • Ohta, T.1
  • 52
    • 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
  • 53
    • 34548082528 scopus 로고    scopus 로고
    • Accumulation of sightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals
    • Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K. 2007. Accumulation of sightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. Proc Natl Acad Sci USA. 104:13390-13395.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 13390-13395
    • Popadin, K.1    Polishchuk, L.V.2    Mamirova, L.3    Knorre, D.4    Gunbin, K.5
  • 54
    • 34548556039 scopus 로고    scopus 로고
    • Inferring speciation times under an episodic molecular clock
    • Rannala B, Yang Z. 2007. Inferring speciation times under an episodic molecular clock. Syst Biol. 56:453-466.
    • (2007) Syst Biol , vol.56 , pp. 453-466
    • Rannala, B.1    Yang, Z.2
  • 55
    • 37549005159 scopus 로고    scopus 로고
    • Uniformization for sampling realizations of Markov processes: Applications to Bayesian implementations of codon substitution models
    • Rodrigue N, Philippe H, Lartillot N. 2008. Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models. Bioinformatics 24:56-62.
    • (2008) Bioinformatics , vol.24 , pp. 56-62
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 56
    • 0035995077 scopus 로고    scopus 로고
    • Hyper inverse Wishart distribution for non-decomposable graphs and its application to Bayesian inference for Gaussian graphical models
    • Roverato A. 2002. Hyper inverse Wishart distribution for non-decomposable graphs and its application to Bayesian inference for Gaussian graphical models. Scand J Stat. 29:391-411.
    • (2002) Scand J Stat , vol.29 , pp. 391-411
    • Roverato, A.1
  • 57
    • 3042548848 scopus 로고    scopus 로고
    • Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences
    • Seo TK, Kishino H, Thorne JL. 2004. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol Biol Evol. 21:1201-1213.
    • (2004) Mol Biol Evol , vol.21 , pp. 1201-1213
    • Seo, T.K.1    Kishino, H.2    Thorne, J.L.3
  • 58
    • 24344480299 scopus 로고    scopus 로고
    • Correlations between physiology and lifespan- two widely ignored problems with comparative studies
    • Speakman JR. 2005. Correlations between physiology and lifespan- two widely ignored problems with comparative studies. Aging Cell 4:167-175.
    • (2005) Aging Cell , vol.4 , pp. 167-175
    • Speakman, J.R.1
  • 59
    • 33646591222 scopus 로고    scopus 로고
    • There is no universal molecular clock for invertebrates, but rate variation does not scale with body size
    • Thomas JA, Welch JJ, Woolfit M, Bromham L. 2006. There is no universal molecular clock for invertebrates, but rate variation does not scale with body size. Proc Natl Acad Sci USA. 103:7366-7371.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 7366-7371
    • Thomas, J.A.1    Welch, J.J.2    Woolfit, M.3    Bromham, L.4
  • 60
    • 0036803223 scopus 로고    scopus 로고
    • Divergence time and evolutionary rate estimation with multilocus data
    • Thorne JL, Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst Biol. 51:689-702.
    • (2002) Syst Biol , vol.51 , pp. 689-702
    • Thorne, J.L.1    Kishino, H.2
  • 61
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rate of evolution of the rate of molecular evolution
    • Thorne JL, Kishino H, Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol. 15:1647-1657.
    • (1998) Mol Biol Evol , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 62
    • 0035144026 scopus 로고    scopus 로고
    • The rates of molecular evolution in rodent and primate mitochondrial DNA
    • Weinreich DM. 2001. The rates of molecular evolution in rodent and primate mitochondrial DNA. J Mol Evol. 52:40-50.
    • (2001) J Mol Evol , vol.52 , pp. 40-50
    • Weinreich, D.M.1
  • 63
    • 41949132520 scopus 로고    scopus 로고
    • Correlates of substitution rate variation in mammalian protein-coding sequences
    • Welch JJ, Bininda-Edmonds ORP, Bromham L. 2008. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol Biol. 8:53.
    • (2008) BMC Evol Biol , vol.8 , pp. 53
    • Welch, J.J.1    Orp, B.2    Bromham, L.3
  • 64
    • 54349106869 scopus 로고    scopus 로고
    • Divergence and polymorphism under the nearly neutral theory of molecular evolution
    • Welch JJ, Eyre-Walker A, Waxman D. 2008. Divergence and polymorphism under the nearly neutral theory of molecular evolution. J Mol Evol. 67:418-426.
    • (2008) J Mol Evol , vol.67 , pp. 418-426
    • Welch, J.J.1    Eyre-Walker, A.2    Waxman, D.3
  • 65
    • 41049094758 scopus 로고    scopus 로고
    • Calculating independent contrasts for the comparative study of substitution rates
    • Welch JJ, Waxman D. 2008. Calculating independent contrasts for the comparative study of substitution rates. J Theor Biol. 251: 667-678.
    • (2008) J Theor Biol , vol.251 , pp. 667-678
    • Welch, J.J.1    Waxman, D.2
  • 66
    • 28944451210 scopus 로고    scopus 로고
    • Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
    • Yang Z, Rannala B. 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol Biol Evol. 23:212-226.
    • (2006) Mol Biol Evol , vol.23 , pp. 212-226
    • Yang, Z.1    Rannala, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.