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Volumn 18, Issue 2, 2003, Pages 241-255

Bootstrapping Phylogenetic Trees: Theory and Methods

Author keywords

Bootstrap; Confidence regions; Nonpositive curvature; Phylogenetic trees

Indexed keywords


EID: 0346271739     PISSN: 08834237     EISSN: None     Source Type: Journal    
DOI: 10.1214/ss/1063994979     Document Type: Review
Times cited : (120)

References (61)
  • 1
    • 0002717710 scopus 로고    scopus 로고
    • Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today
    • ALDOUS, D. (2001). Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Statist. Sci. 16 23-34.
    • (2001) Statist. Sci. , vol.16 , pp. 23-34
    • Aldous, D.1
  • 2
    • 0034702213 scopus 로고    scopus 로고
    • Predicted decline of protected whales based on molecular genetic monitoring of Japanese and Korean markets
    • BAKER, C., LENTO, G., CIPRIANO, F. and PALUMBI, S. (2000). Predicted decline of protected whales based on molecular genetic monitoring of Japanese and Korean markets. Proc. Roy. Soc. London Ser. B 267 1191-1199.
    • (2000) Proc. Roy. Soc. London Ser. B , vol.267 , pp. 1191-1199
    • Baker, C.1    Lento, G.2    Cipriano, F.3    Palumbi, S.4
  • 3
    • 0028018156 scopus 로고
    • Which whales are hunted? A molecular genetic approach to monitoring whaling
    • BAKER, C. and PALUMBI, S. (1994). Which whales are hunted? A molecular genetic approach to monitoring whaling. Science 265 1538-1539.
    • (1994) Science , vol.265 , pp. 1538-1539
    • Baker, C.1    Palumbi, S.2
  • 4
    • 0029794480 scopus 로고    scopus 로고
    • On the interpretation of bootstrap trees: Appropriate threshold of clade selection and induced gain
    • BERRY, V. and GASCUEL, O. (1996). On the interpretation of bootstrap trees: Appropriate threshold of clade selection and induced gain. Molecular Biology and Evolution 13 999-1011.
    • (1996) Molecular Biology and Evolution , vol.13 , pp. 999-1011
    • Berry, V.1    Gascuel, O.2
  • 5
    • 0035520029 scopus 로고    scopus 로고
    • Geometry of the space of phylogenetic trees
    • BILLERA, L., HOLMES, S. and VOGTMANN, K. (2001). Geometry of the space of phylogenetic trees. Adv. in Appl. Math. 27 733-767.
    • (2001) Adv. in Appl. Math. , vol.27 , pp. 733-767
    • Billera, L.1    Holmes, S.2    Vogtmann, K.3
  • 6
    • 0030211964 scopus 로고    scopus 로고
    • Bagging predictors
    • BREIMAN, L. (1996). Bagging predictors. Machine Learning 24 123-140.
    • (1996) Machine Learning , vol.24 , pp. 123-140
    • Breiman, L.1
  • 7
    • 0000367652 scopus 로고
    • The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
    • BREMER, K. (1988). The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42 795-803.
    • (1988) Evolution , vol.42 , pp. 795-803
    • Bremer, K.1
  • 8
    • 0030621127 scopus 로고    scopus 로고
    • Mass survival of birds across the cretaceous-tertiary boundary: Molecular evidence
    • COOPER, A. and PENNY, D. (1997). Mass survival of birds across the cretaceous-tertiary boundary: Molecular evidence. Science 275 1109-1113.
    • (1997) Science , vol.275 , pp. 1109-1113
    • Cooper, A.1    Penny, D.2
  • 9
    • 0000813623 scopus 로고
    • A generalization of spectral analysis with application to ranked data
    • DIACONIS, P. (1989). A generalization of spectral analysis with application to ranked data. Ann. Statist. 17 949-979.
    • (1989) Ann. Statist. , vol.17 , pp. 949-979
    • Diaconis, P.1
  • 14
    • 0032264630 scopus 로고    scopus 로고
    • The problem of regions
    • EFRON, B. and TIBSHIRANI, R. (1998). The problem of regions. Ann. Statist. 26 1687-1718.
    • (1998) Ann. Statist. , vol.26 , pp. 1687-1718
    • Efron, B.1    Tibshirani, R.2
  • 15
    • 0030581603 scopus 로고    scopus 로고
    • Bootstrap confidence levels for phylogenetic trees
    • EFRON, B., HALLORAN, E. and HOLMES, S. (1996). Bootstrap confidence levels for phylogenetic trees. Proc. Nat. Acad. Sci. U.S.A. 93 13,429-13,434.
    • (1996) Proc. Nat. Acad. Sci. U.S.A. , vol.93 , pp. 13429-13434
    • Efron, B.1    Halloran, E.2    Holmes, S.3
  • 16
    • 0001027766 scopus 로고
    • Statistical inference of phylogenies
    • FELSENSTEIN, J. (1983). Statistical inference of phylogenies (with discussion). J. Roy. Statist. Soc. Ser. A 146 246-272.
    • (1983) J. Roy. Statist. Soc. Ser. A , vol.146 , pp. 246-272
    • Felsenstein, J.1
  • 18
    • 0030034795 scopus 로고    scopus 로고
    • A hidden Markov model approach to variation among sites in rate of evolution
    • FELSENSTEIN, J. and CHURCHILL, G. A. (1996). A hidden Markov model approach to variation among sites in rate of evolution. Molecular Biology and Evolution 13 93-104.
    • (1996) Molecular Biology and Evolution , vol.13 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 19
    • 0015076741 scopus 로고
    • The nonidentity of invariable positions in the cytochromes c of different species
    • FITCH, W. (1971a). The nonidentity of invariable positions in the cytochromes c of different species. Biochemical Genetics 5 231-241.
    • (1971) Biochemical Genetics , vol.5 , pp. 231-241
    • Fitch, W.1
  • 20
    • 0015162378 scopus 로고
    • Rate of change of concomitantly variable codons
    • FITCH, W. (1971b). Rate of change of concomitantly variable codons. Journal of Molecular Evolution 1 84-96.
    • (1971) Journal of Molecular Evolution , vol.1 , pp. 84-96
    • Fitch, W.1
  • 21
    • 0014860857 scopus 로고
    • An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
    • FITCH, W. M. and MARKOWITZ, E. (1970). An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochemical Genetics 4 579-593.
    • (1970) Biochemical Genetics , vol.4 , pp. 579-593
    • Fitch, W.M.1    Markowitz, E.2
  • 22
    • 84950447423 scopus 로고
    • Bootstrapping a regression equation; Some empirical results
    • FREEDMAN, D. A. and PETERS, S. C. (1984a). Bootstrapping a regression equation; Some empirical results. J. Amer. Statist. Assoc. 79 97-106.
    • (1984) J. Amer. Statist. Assoc. , vol.79 , pp. 97-106
    • Freedman, D.A.1    Peters, S.C.2
  • 23
    • 84924004198 scopus 로고
    • Bootstrapping an econometric model: Some empirical results
    • FREEDMAN, D. A. and PETERS, S. C. (1984b). Bootstrapping an econometric model: Some empirical results. J. Bus. Econom. Statist. 2 150-158.
    • (1984) J. Bus. Econom. Statist. , vol.2 , pp. 150-158
    • Freedman, D.A.1    Peters, S.C.2
  • 24
    • 0001552995 scopus 로고
    • Cross-validation, the jackknife, and the bootstrap: Excess error estimation in forward logistic regression
    • GONG, G. (1986). Cross-validation, the jackknife, and the bootstrap: Excess error estimation in forward logistic regression. J. Amer. Statist. Assoc. 81 108-113.
    • (1986) J. Amer. Statist. Assoc. , vol.81 , pp. 108-113
    • Gong, G.1
  • 25
    • 0002870642 scopus 로고
    • Peeling bivariate data
    • (V. Barnett, ed.) Wiley, New York
    • GREEN, P. J. (1981). Peeling bivariate data. In Interpreting Multi-variate Data (V. Barnett, ed.) 3-19. Wiley, New York.
    • (1981) Interpreting Multi-variate Data , pp. 3-19
    • Green, P.J.1
  • 26
    • 0010538970 scopus 로고
    • On the bootstrap and likelihood-based confidence regions
    • HALL, P. (1987). On the bootstrap and likelihood-based confidence regions. Biometrika 74 481-493.
    • (1987) Biometrika , vol.74 , pp. 481-493
    • Hall, P.1
  • 28
    • 0026562079 scopus 로고
    • The number of replications needed for accurate estimation of the bootstrap p-value in phylogenetic studies
    • HEDGES, S. B. (1992). The number of replications needed for accurate estimation of the bootstrap p-value in phylogenetic studies. Molecular Biology and Evolution 9 366-369.
    • (1992) Molecular Biology and Evolution , vol.9 , pp. 366-369
    • Hedges, S.B.1
  • 29
    • 21144475766 scopus 로고
    • Spectral analysis of phylogenetic data
    • HENDY, M. D. and PENNY, D. (1993). Spectral analysis of phylogenetic data. J. Classification 10 5-23.
    • (1993) J. Classification , vol.10 , pp. 5-23
    • Hendy, M.D.1    Penny, D.2
  • 30
    • 0028255876 scopus 로고
    • A discrete Fourier analysis for evolutionary trees
    • HENDY, M. D., PENNY, D. and STEEL, M. A. (1994). A discrete Fourier analysis for evolutionary trees. Proc. Nat. Acad. Sci. U.S.A. 91 3339-3343.
    • (1994) Proc. Nat. Acad. Sci. U.S.A. , vol.91 , pp. 3339-3343
    • Hendy, M.D.1    Penny, D.2    Steel, M.A.3
  • 31
    • 12044253190 scopus 로고
    • An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
    • HILLIS, D. M. and BULL, J. J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42 182-192.
    • (1993) Systematic Biology , vol.42 , pp. 182-192
    • Hillis, D.M.1    Bull, J.J.2
  • 32
    • 0008138483 scopus 로고    scopus 로고
    • Phylogenies: An overview
    • M. E. Halloran and S. Geisser, eds. Springer, New York
    • HOLMES, S. (1999). Phylogenies: An overview. In Statistics in Genetics (M. E. Halloran and S. Geisser, eds.) 81-119. Springer, New York.
    • (1999) Statistics in Genetics , pp. 81-119
    • Holmes, S.1
  • 34
    • 0000181737 scopus 로고
    • The jackknife and the bootstrap for general stationary observations
    • KÜNSCH, H. R. (1989). The jackknife and the bootstrap for general stationary observations. Ann. Statist. 17 1217-1241.
    • (1989) Ann. Statist. , vol.17 , pp. 1217-1241
    • Künsch, H.R.1
  • 35
    • 84855626830 scopus 로고    scopus 로고
    • LANL (2002). HIV database. Available at URL: http://hiv-web.lanl.gov/content/hiv-db/mainpage.html.
    • (2002) HIV Database
  • 36
    • 0002879917 scopus 로고
    • Extremal Families and Systems of Sufficient Statistics
    • Springer, Berlin
    • LAURITZEN, S. L. (1988). Extremal Families and Systems of Sufficient Statistics. Lecture Notes in Statist. 49. Springer, Berlin.
    • (1988) Lecture Notes in Statist. , vol.49
    • Lauritzen, S.L.1
  • 37
    • 25944433574 scopus 로고    scopus 로고
    • Taking stock of minke whale in the North Pacific: The origins of products for sale in Japan and Korea
    • Scientific Committee, International Whaling Commission
    • LENTO, G. M., CIPRIANO, F., PATENAUDE, N. J., PALUMBI, S. R. and BAKER, C. S. (1998). Taking stock of minke whale in the North Pacific: The origins of products for sale in Japan and Korea. Technical Report SC/50/RMP15, Scientific Committee, International Whaling Commission.
    • (1998) Technical Report , vol.SC-50-RMP15
    • Lento, G.M.1    Cipriano, F.2    Patenaude, N.J.3    Palumbi, S.R.4    Baker, C.S.5
  • 38
    • 1542532208 scopus 로고    scopus 로고
    • Phylogenetic tree construction using Markov chain Monte Carlo
    • LI, S., PEARL, D. K. and DOSS, H. (2000). Phylogenetic tree construction using Markov chain Monte Carlo. J. Amer. Statist. Assoc. 95 493-508.
    • (2000) J. Amer. Statist. Assoc. , vol.95 , pp. 493-508
    • Li, S.1    Pearl, D.K.2    Doss, H.3
  • 40
    • 11944272095 scopus 로고
    • Statistical tests of DNA phylogenies
    • LI, W. H. and ZHARKIKH, A. (1995). Statistical tests of DNA phylogenies. Systematic Biology 44 49-63.
    • (1995) Systematic Biology , vol.44 , pp. 49-63
    • Li, W.H.1    Zharkikh, A.2
  • 41
    • 0033147626 scopus 로고    scopus 로고
    • Multivariate analysis by data depth: Descriptive statistics, graphics and inference
    • LIU, R. Y., PARELIUS, J. M. and SINGH, K. (1999). Multivariate analysis by data depth: Descriptive statistics, graphics and inference (with discussion). Ann. Statist. 77 783-858.
    • (1999) Ann. Statist. , vol.77 , pp. 783-858
    • Liu, R.Y.1    Parelius, J.M.2    Singh, K.3
  • 42
    • 0029935637 scopus 로고    scopus 로고
    • Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis
    • LOCKHART, P. J., LARKUM, A. W. D., STEEL, M. A., WADDELL, P. J. and PENNY, D. (1996). Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis. Proc. Nat. Acad. Sci. U.S.A. 93 1930-1934.
    • (1996) Proc. Nat. Acad. Sci. U.S.A. , vol.93 , pp. 1930-1934
    • Lockhart, P.J.1    Larkum, A.W.D.2    Steel, M.A.3    Waddell, P.J.4    Penny, D.5
  • 43
    • 84960569058 scopus 로고
    • The discovery and importance of multiple islands of most parsimonious trees
    • MADDISON, D. (1991). The discovery and importance of multiple islands of most parsimonious trees. Systematic Zoology 40 315-328.
    • (1991) Systematic Zoology , vol.40 , pp. 315-328
    • Maddison, D.1
  • 44
    • 0032906031 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference via Markov chain Monte Carlo methods
    • MAU, B., NEWTON, M. A. and LARGET, B. (1999). Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55 1-12.
    • (1999) Biometrics , vol.55 , pp. 1-12
    • Mau, B.1    Newton, M.A.2    Larget, B.3
  • 45
    • 0032514671 scopus 로고    scopus 로고
    • The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small
    • NEI, M., KUMAR, S. and TAKAHASHI, K. (1998). The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc. Nat. Acad. Sci. U.S.A. 95 12,390-12,397.
    • (1998) Proc. Nat. Acad. Sci. U.S.A. , vol.95 , pp. 12390-12397
    • Nei, M.1    Kumar, S.2    Takahashi, K.3
  • 46
    • 33746439442 scopus 로고    scopus 로고
    • Bootstrapping phylogenies: Large deviations and dispersion effects
    • NEWTON, M. A. (1996). Bootstrapping phylogenies: Large deviations and dispersion effects. Biometrika 83 315-328.
    • (1996) Biometrika , vol.83 , pp. 315-328
    • Newton, M.A.1
  • 48
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • RAMBAUT, A. and GRASSLY, N. C. (1997). Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computational Applied Bioscience 13 235-238.
    • (1997) Computational Applied Bioscience , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 49
    • 0001184395 scopus 로고
    • Confidence regions for multidimensional scaling analysis
    • RAMSAY, J. O. (1978). Confidence regions for multidimensional scaling analysis. Psychometrika 43 145-160.
    • (1978) Psychometrika , vol.43 , pp. 145-160
    • Ramsay, J.O.1
  • 50
    • 0347124352 scopus 로고
    • An empirical Bayes estimation problem
    • ROBBINS, H. (1980). An empirical Bayes estimation problem. Proc. Nat. Acad. Sci. USA. 77 6,988-6,989.
    • (1980) Proc. Nat. Acad. Sci. USA. , vol.77 , pp. 6988-6989
    • Robbins, H.1
  • 51
    • 0000801059 scopus 로고
    • Some thoughts on empirical Bayes estimation
    • ROBBINS, H. (1983). Some thoughts on empirical Bayes estimation. Ann. Statist. 11 713-723.
    • (1983) Ann. Statist. , vol.11 , pp. 713-723
    • Robbins, H.1
  • 52
    • 0022036805 scopus 로고
    • Linear empirical Bayes estimation of means and variances
    • ROBBINS, H. (1985). Linear empirical Bayes estimation of means and variances. Proc. Nat. Acad. Sci. U.S.A. 82 1571-1574.
    • (1985) Proc. Nat. Acad. Sci. U.S.A. , vol.82 , pp. 1571-1574
    • Robbins, H.1
  • 54
    • 0029526909 scopus 로고
    • Objections to bootstrapping phylogenies: A critique
    • SANDERSON, M. J. (1995). Objections to bootstrapping phylogenies: A critique. Systematic Biology 44 299-320.
    • (1995) Systematic Biology , vol.44 , pp. 299-320
    • Sanderson, M.J.1
  • 56
    • 0032855533 scopus 로고    scopus 로고
    • Locating regions of differential variability in DNA and protein sequences
    • TANG, H. and LEWONTIN, R. (1999). Locating regions of differential variability in DNA and protein sequences. Genetics 153 485-495.
    • (1999) Genetics , vol.153 , pp. 485-495
    • Tang, H.1    Lewontin, R.2
  • 57
    • 0031986279 scopus 로고    scopus 로고
    • Modeling the covarion hypothesis of nucleotide substitution
    • TUFFLEY, C. and STEEL, M. (1998). Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147 63-91.
    • (1998) Math. Biosci. , vol.147 , pp. 63-91
    • Tuffley, C.1    Steel, M.2
  • 58
    • 0000640338 scopus 로고
    • Mathematics and the picturing of data
    • R. D. James, ed. Vancouver
    • TUKEY, J. (1975). Mathematics and the picturing of data. In Proc. International Congress of Mathematicians (R. D. James, ed.) 523-531. Vancouver.
    • (1975) Proc. International Congress of Mathematicians , pp. 523-531
    • Tukey, J.1
  • 59
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • YANG, Z. (1994). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Molecular Evolution 39 306-314.
    • (1994) J. Molecular Evolution , vol.39 , pp. 306-314
    • Yang, Z.1
  • 60
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
    • YANG, Z. and RANNALA, B. (1997). Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Molecular Biology and Evolution 14 717-724.
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 717-724
    • Yang, Z.1    Rannala, B.2
  • 61
    • 0029261787 scopus 로고
    • Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique
    • ZHARKIKH, A. and LI, W.-H. (1995). Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique. Molecular Phylogenetics and Evolution 4 44-63.
    • (1995) Molecular Phylogenetics and Evolution , vol.4 , pp. 44-63
    • Zharkikh, A.1    Li, W.-H.2


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