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Volumn 280, Issue 5371, 1998, Pages 1868-1871

Limitations of a molecular clock applied to considerations of the origin of HIV-1

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS VACCINE; VIRUS ENVELOPE PROTEIN;

EID: 0032546809     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.280.5371.1868     Document Type: Short Survey
Times cited : (66)

References (78)
  • 1
    • 0028952146 scopus 로고
    • J. M. Coffin, Science 267, 483 (1995); B. D. Preston, B. J. Poiesz, L. A. Loeb, ibid. 242, 1168 (1988); K. Bebenek, J. Abbotts, S. H. Wilson, T. A. Kunkel, J. Biol. Chem. 268, 10324 (1993).
    • (1995) Science , vol.267 , pp. 483
    • Coffin, J.M.1
  • 2
    • 0024267430 scopus 로고
    • J. M. Coffin, Science 267, 483 (1995); B. D. Preston, B. J. Poiesz, L. A. Loeb, ibid. 242, 1168 (1988); K. Bebenek, J. Abbotts, S. H. Wilson, T. A. Kunkel, J. Biol. Chem. 268, 10324 (1993).
    • (1988) Science , vol.242 , pp. 1168
    • Preston, B.D.1    Poiesz, B.J.2    Loeb, L.A.3
  • 4
    • 0028100982 scopus 로고
    • E. C. Sabino et al., J. Virol. 68, 6340 (1994); D. L. Robertson, B. H. Hahn, P. M. Sharp, Mol. Evol. 40, 249 (1995); F. E. McCutchan, M. O. Salminen, J. K. Carr, D. S. Burke, AIDS 10, S13 (1996); M. Cornelissen et al., J. Virol. 70, 8209 (1996).
    • (1994) J. Virol. , vol.68 , pp. 6340
    • Sabino, E.C.1
  • 5
    • 0028969767 scopus 로고
    • E. C. Sabino et al., J. Virol. 68, 6340 (1994); D. L. Robertson, B. H. Hahn, P. M. Sharp, Mol. Evol. 40, 249 (1995); F. E. McCutchan, M. O. Salminen, J. K. Carr, D. S. Burke, AIDS 10, S13 (1996); M. Cornelissen et al., J. Virol. 70, 8209 (1996).
    • (1995) Mol. Evol. , vol.40 , pp. 249
    • Robertson, D.L.1    Hahn, B.H.2    Sharp, P.M.3
  • 6
    • 0029826598 scopus 로고    scopus 로고
    • E. C. Sabino et al., J. Virol. 68, 6340 (1994); D. L. Robertson, B. H. Hahn, P. M. Sharp, Mol. Evol. 40, 249 (1995); F. E. McCutchan, M. O. Salminen, J. K. Carr, D. S. Burke, AIDS 10, S13 (1996); M. Cornelissen et al., J. Virol. 70, 8209 (1996).
    • (1996) AIDS , vol.10
    • McCutchan, F.E.1    Salminen, M.O.2    Carr, J.K.3    Burke, D.S.4
  • 7
    • 0029795283 scopus 로고    scopus 로고
    • E. C. Sabino et al., J. Virol. 68, 6340 (1994); D. L. Robertson, B. H. Hahn, P. M. Sharp, Mol. Evol. 40, 249 (1995); F. E. McCutchan, M. O. Salminen, J. K. Carr, D. S. Burke, AIDS 10, S13 (1996); M. Cornelissen et al., J. Virol. 70, 8209 (1996).
    • (1996) J. Virol. , vol.70 , pp. 8209
    • Cornelissen, M.1
  • 8
    • 0002133523 scopus 로고    scopus 로고
    • B. Korber et al., Eds. Los Alamos National Laboratory, Los Alamos, NM
    • D. L. Robertson, F. Gao, B. H. Hahn, P. M. Sharp, in Human Retroviruses and AIDS, B. Korber et al., Eds. (Los Alamos National Laboratory, Los Alamos, NM, 1997), part III, pp. 25-30, http://hiv-web.lanl.gov/ HTML/reviews/hahn.html.
    • (1997) Human Retroviruses and AIDS , Issue.3 PART , pp. 25-30
    • Robertson, D.L.1    Gao, F.2    Hahn, B.H.3    Sharp, P.M.4
  • 9
    • 0026551082 scopus 로고
    • S. M. Wolinsky et al., Science 255, 1134 (1992); C. Wills, G. Myers, A. Farmer, AIDS Res. Hum. Retroviruses 12, 1383 (1996).
    • (1992) Science , vol.255 , pp. 1134
    • Wolinsky, S.M.1
  • 12
    • 0023026104 scopus 로고
    • F. Clavel et al., Nature 324, 691 (1986); M. Grez et al., J. Virol. 68, 2161 (1994); B. Korber, E. Allen, A. Farmer, G. Myers, AIDS 9 (suppl. A), S5 (1995); P. J. Kanki, M. Peeters, A. Gueye-Ndiaye, ibid. 11 (suppl. B), S33 (1997).
    • (1986) Nature , vol.324 , pp. 691
    • Clavel, F.1
  • 13
    • 0028346910 scopus 로고
    • F. Clavel et al., Nature 324, 691 (1986); M. Grez et al., J. Virol. 68, 2161 (1994); B. Korber, E. Allen, A. Farmer, G. Myers, AIDS 9 (suppl. A), S5 (1995); P. J. Kanki, M. Peeters, A. Gueye-Ndiaye, ibid. 11 (suppl. B), S33 (1997).
    • (1994) J. Virol. , vol.68 , pp. 2161
    • Grez, M.1
  • 14
    • 0013689795 scopus 로고
    • F. Clavel et al., Nature 324, 691 (1986); M. Grez et al., J. Virol. 68, 2161 (1994); B. Korber, E. Allen, A. Farmer, G. Myers, AIDS 9 (suppl. A), S5 (1995); P. J. Kanki, M. Peeters, A. Gueye-Ndiaye, ibid. 11 (suppl. B), S33 (1997).
    • (1995) AIDS , vol.9 , Issue.SUPPL. A
    • Korber, B.1    Allen, E.2    Farmer, A.3    Myers, G.4
  • 15
    • 0031299742 scopus 로고    scopus 로고
    • F. Clavel et al., Nature 324, 691 (1986); M. Grez et al., J. Virol. 68, 2161 (1994); B. Korber, E. Allen, A. Farmer, G. Myers, AIDS 9 (suppl. A), S5 (1995); P. J. Kanki, M. Peeters, A. Gueye-Ndiaye, ibid. 11 (suppl. B), S33 (1997).
    • (1997) AIDS , vol.11 , Issue.SUPPL. B
    • Kanki, P.J.1    Peeters, M.2    Gueye-Ndiaye, A.3
  • 16
    • 2642674154 scopus 로고
    • P. Chameau et al., Virology 205, 247 (1994); I. Loussert-Ajaka et al., J. Virol. 69, 5640 (1995).
    • (1994) Virology , vol.205 , pp. 247
    • Chameau, P.1
  • 17
    • 0029082118 scopus 로고
    • P. Chameau et al., Virology 205, 247 (1994); I. Loussert-Ajaka et al., J. Virol. 69, 5640 (1995).
    • (1995) J. Virol. , vol.69 , pp. 5640
    • Loussert-Ajaka, I.1
  • 18
    • 0025343127 scopus 로고
    • T. Huet et al., Nature 345, 356 (1990).
    • (1990) Nature , vol.345 , pp. 356
    • Huet, T.1
  • 19
    • 0001336205 scopus 로고    scopus 로고
    • D. M. Hillis, C. Moritz, B. K. Mable, Eds. Sinauer, Sunderland, MA, ed. 2
    • D. L. Swofford, G. J. Olsen, P. J. Waddell, D. M. Hillis, in Molecular Systematics, D. M. Hillis, C. Moritz, B. K. Mable, Eds. (Sinauer, Sunderland, MA, ed. 2, 1996), pp. 407-514.
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 20
    • 0027219687 scopus 로고    scopus 로고
    • J. Louwagie et al., AIDS 7, 769 (1993); Workshop Report from the European Commission (DG XII, INCO-DC) and the Joint United Nations Programme on HIV/AIDS, AIDS 11, 17 (1997).
    • (1993) AIDS , vol.7 , pp. 769
    • Louwagie, J.1
  • 21
    • 0027219687 scopus 로고    scopus 로고
    • Workshop Report from the European Commission (DG XII, INCO-DC) and the Joint United Nations Programme on HIV/AIDS
    • J. Louwagie et al., AIDS 7, 769 (1993); Workshop Report from the European Commission (DG XII, INCO-DC) and the Joint United Nations Programme on HIV/AIDS, AIDS 11, 17 (1997).
    • (1997) AIDS , vol.11 , pp. 17
  • 23
    • 2642712227 scopus 로고    scopus 로고
    • Santa Fe, NM, 18 to 20 April 1998, B. Korber, Ed. The Santa Fe Institute, Santa Fe, NM
    • F. E. McCutchan et al., in The Proceedings of the Fifth Annual HIV Dynamics and Evolution Meeting, Santa Fe, NM, 18 to 20 April 1998, B. Korber, Ed. (The Santa Fe Institute, Santa Fe, NM, 1998), vol. 5, p. 23, www.santafe.edu/hiv5/mccutchan.html; M. Peeters et al., ibid., p. 73, www.santafe.edu/hiv5/ peeters.html.
    • (1998) The Proceedings of the Fifth Annual HIV Dynamics and Evolution Meeting , vol.5 , pp. 23
    • McCutchan, F.E.1
  • 24
    • 2642672540 scopus 로고    scopus 로고
    • F. E. McCutchan et al., in The Proceedings of the Fifth Annual HIV Dynamics and Evolution Meeting, Santa Fe, NM, 18 to 20 April 1998, B. Korber, Ed. (The Santa Fe Institute, Santa Fe, NM, 1998), vol. 5, p. 23, www.santafe.edu/hiv5/mccutchan.html; M. Peeters et al., ibid., p. 73, www.santafe.edu/hiv5/ peeters.html.
    • The Proceedings of the Fifth Annual HIV Dynamics and Evolution Meeting , pp. 73
    • Peeters, M.1
  • 25
    • 0023740248 scopus 로고
    • W.-H. Li, M. Tanimura, P. M. Sharp, Mol. Biol. Evol. 5, 313 (1988); P. Sharp and W.-H. Li, Nature 333, 315 (1988); T. Gojobori, E. N. Moriyama, M. Kimura. Proc. Natl. Acad. Sci. U.S.A. 87, 10015 (1990).
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 313
    • Li, W.-H.1    Tanimura, M.2    Sharp, P.M.3
  • 26
    • 0024296033 scopus 로고
    • W.-H. Li, M. Tanimura, P. M. Sharp, Mol. Biol. Evol. 5, 313 (1988); P. Sharp and W.-H. Li, Nature 333, 315 (1988); T. Gojobori, E. N. Moriyama, M. Kimura. Proc. Natl. Acad. Sci. U.S.A. 87, 10015 (1990).
    • (1988) Nature , vol.333 , pp. 315
    • Sharp, P.1    Li, W.-H.2
  • 29
    • 2642680566 scopus 로고
    • Absolute, true, and mathematical time, of itself, and from its own nature, flows equably without relation to anything external
    • F. Cajori, transl. Univ. of California Press, Berkeley, CA
    • "Absolute, true, and mathematical time, of itself, and from its own nature, flows equably without relation to anything external." Isaac Newton, Principia (1687), F. Cajori, transl. (Univ. of California Press, Berkeley, CA, 1947), p. 6; "Wrongagain, Isaac," paraphrased by P. Ginsparg (personal communication), from Albert Einstein, Special Theory of Relativity (1905).
    • (1947) Principia , Issue.1687 , pp. 6
    • Newton, I.1
  • 30
    • 2642702304 scopus 로고
    • "Absolute, true, and mathematical time, of itself, and from its own nature, flows equably without relation to anything external." Isaac Newton, Principia (1687), F. Cajori, transl. (Univ. of California Press, Berkeley, CA, 1947), p. 6; "Wrongagain, Isaac," paraphrased by P. Ginsparg (personal communication), from Albert Einstein, Special Theory of Relativity (1905).
    • (1905) Special Theory of Relativity
    • Einstein, A.1
  • 31
    • 2642704779 scopus 로고
    • author's translation, Grove, New York
    • "One hand only. Finest of fine black darts. It advances by fits and starts. No tick. Leaps from dot to dot with so lightning a leap that but for its new position it had not stirred. Whole nights may pass as but a fraction of a second or any intermediate lapse of time soever before it flings itself from one degree to the next." Samuel Beckett, author's translation, III Seen, III Said (Grove, New York, 1981), p. 76.
    • (1981) III Seen, III Said , pp. 76
    • Beckett, S.1
  • 33
    • 0002967835 scopus 로고
    • The use of the distance to a common M group ancestral node to estimate the year of sampling of a sequence gives a root mean square error of 8.7 years. Given that the virus that causes AIDS was identified only 15 years ago, this is not much predictive power. This calculation was specifically based on a linear regression analysis of genetic distance : between contemporary sequences and the estimated ancestral origin of the HIV M group, shown in Fig. 1, plotted as a function of the year of sampling. The linear correlation coefficient (Pearson's r) is 0.282 for the full set of data in Fig. 1, with a Student's t probability of 0.002, that is, a highly significant but weak correlation. Using a regression analysis to estimate the rate of divergence and a bootstrap approach to . estimate the error (45), we calculated annual divergence rates of 0.00169 per year (95% confidence interval of 0.0011 to 0.0022). These rates are lower than numbers given in the past (approaching 1% per year) [C. Kuiken and B. Korber, AIDS 8, S73 (1994)], perhaps because these calculations were based on sequences of the full-length envelope protein gp160, including the conserved regions, and typically shorter variable domains of envelope have been studied.
    • (1994) AIDS , vol.8
    • Kuiken, C.1    Korber, B.2
  • 34
    • 0030891834 scopus 로고    scopus 로고
    • M. O. Salminen et al., J. Virol. 71, 2647 (1997); R. S. Diaz et al., ibid. 69, 3273 (1995).
    • (1997) J. Virol. , vol.71 , pp. 2647
    • Salminen, M.O.1
  • 35
    • 0029069857 scopus 로고
    • M. O. Salminen et al., J. Virol. 71, 2647 (1997); R. S. Diaz et al., ibid. 69, 3273 (1995).
    • (1995) J. Virol. , vol.69 , pp. 3273
    • Diaz, R.S.1
  • 36
    • 0032484908 scopus 로고    scopus 로고
    • T. Zhu et al., Nature 391, 594 (1998).
    • (1998) Nature , vol.391 , pp. 594
    • Zhu, T.1
  • 37
    • 2642706414 scopus 로고    scopus 로고
    • note
    • The branch location of the ZR.59 sample, between the B, D, and F clades, could have been the result of ZR.59 being a mosaic genome; however, the branch length was extremely short between the ancestral node of these clades and the ZR.59 sequence, indicating that it was simply close to the ancestral sequence. There was no evidence that the ZR.59 sequence was a mosaic when it was analyzed carefully for that possibility with a sliding window approach. However, evidence for a preclade recombination event emerged from the study. The B and D subtypes are generally the most closely associated subtypes throughout the genome. But in the fragments of the genome where sample ZR.59 was sequenced, B and F subtype sequences were most closely associated. [Additional evidence for early recombination events is that the subtypes cluster with different patterns of association in phylogenetic trees on the basis of different regions of the genome (11)].
  • 38
    • 15844385082 scopus 로고    scopus 로고
    • S. Wolinsky et al., Science 272, 537 (1996); S. Ganeshan, R. Dickover, B. Korber, Y. Bryson, S. Wolinsky, J. Virol. 71, 663 (1997); S.-L. Liu et al., ibid., p. 4284; E. Delwart et al., ibid., p. 7498; V. V. Lukashov et al., ibid. 69, 6911 (1995).
    • (1996) Science , vol.272 , pp. 537
    • Wolinsky, S.1
  • 39
    • 0031060165 scopus 로고    scopus 로고
    • S. Wolinsky et al., Science 272, 537 (1996); S. Ganeshan, R. Dickover, B. Korber, Y. Bryson, S. Wolinsky, J. Virol. 71, 663 (1997); S.-L. Liu et al., ibid., p. 4284; E. Delwart et al., ibid., p. 7498; V. V. Lukashov et al., ibid. 69, 6911 (1995).
    • (1997) J. Virol. , vol.71 , pp. 663
    • Ganeshan, S.1    Dickover, R.2    Korber, B.3    Bryson, Y.4    Wolinsky, S.5
  • 40
    • 15844385082 scopus 로고    scopus 로고
    • S. Wolinsky et al., Science 272, 537 (1996); S. Ganeshan, R. Dickover, B. Korber, Y. Bryson, S. Wolinsky, J. Virol. 71, 663 (1997); S.-L. Liu et al., ibid., p. 4284; E. Delwart et al., ibid., p. 7498; V. V. Lukashov et al., ibid. 69, 6911 (1995).
    • J. Virol. , pp. 4284
    • Liu, S.-L.1
  • 41
    • 15844385082 scopus 로고    scopus 로고
    • S. Wolinsky et al., Science 272, 537 (1996); S. Ganeshan, R. Dickover, B. Korber, Y. Bryson, S. Wolinsky, J. Virol. 71, 663 (1997); S.-L. Liu et al., ibid., p. 4284; E. Delwart et al., ibid., p. 7498; V. V. Lukashov et al., ibid. 69, 6911 (1995).
    • J. Virol. , pp. 7498
    • Delwart, E.1
  • 42
    • 0028826072 scopus 로고
    • S. Wolinsky et al., Science 272, 537 (1996); S. Ganeshan, R. Dickover, B. Korber, Y. Bryson, S. Wolinsky, J. Virol. 71, 663 (1997); S.-L. Liu et al., ibid., p. 4284; E. Delwart et al., ibid., p. 7498; V. V. Lukashov et al., ibid. 69, 6911 (1995).
    • (1995) J. Virol. , vol.69 , pp. 6911
    • Lukashov, V.V.1
  • 43
    • 0029052478 scopus 로고
    • M. A. Nowak et al., Nature 375, 606 (1995).
    • (1995) Nature , vol.375 , pp. 606
    • Nowak, M.A.1
  • 46
    • 16944365445 scopus 로고    scopus 로고
    • P. Borrow et al., Nature Med. 3, 205 (1997); D. A. Price et al., Proc. Natl. Acad. Sci. U.S.A. 94, 1890 (1997).
    • (1997) Nature Med. , vol.3 , pp. 205
    • Borrow, P.1
  • 48
    • 2642704250 scopus 로고    scopus 로고
    • H. F. Gunthard et al., J. Virol. 72, 2422 (1998); J. Hammond, B. A. Larder, R. F. Schinazi, J. W. Mellors, in (3), pp. 206-249.
    • (1998) J. Virol. , vol.72 , pp. 2422
    • Gunthard, H.F.1
  • 52
    • 0027980445 scopus 로고
    • B. T. M. Korber, K. MacInnes, R. Smith, G. Myers, J. Virol. 68, 6730 (1994); C. L. Kuiken, B. T. Foley, E. Guzman, B. T. M. Korber, in Molecular Evolution of HIV, K. Crandall, Ed. (Johns Hopkins Univ. Press, Baltimore, MD, in press).
    • (1994) J. Virol. , vol.68 , pp. 6730
    • Korber, B.T.M.1    MacInnes, K.2    Smith, R.3    Myers, G.4
  • 53
    • 2142704059 scopus 로고    scopus 로고
    • K. Crandall, Ed. (Johns Hopkins Univ. Press, Baltimore, MD, in press)
    • B. T. M. Korber, K. MacInnes, R. Smith, G. Myers, J. Virol. 68, 6730 (1994); C. L. Kuiken, B. T. Foley, E. Guzman, B. T. M. Korber, in Molecular Evolution of HIV, K. Crandall, Ed. (Johns Hopkins Univ. Press, Baltimore, MD, in press).
    • Molecular Evolution of HIV
    • Kuiken, C.L.1    Foley, B.T.2    Guzman, E.3    Korber, B.T.M.4
  • 54
    • 0030846020 scopus 로고    scopus 로고
    • H. Cao et al., J. Virol. 71, 8615 (1997); G. Ferrari, et al., Proc. Natl. Acad. Sci. U.S.A. 94, 1396 (1997).
    • (1997) J. Virol. , vol.71 , pp. 8615
    • Cao, H.1
  • 56
    • 0004161838 scopus 로고
    • Cambridge Univ. Press, Cambridge, ed. 2, section 15.3
    • Using a method that determines the best fit line for given data points including error estimates in both dimensions, one can determine how different assumptions of error influence the slope of a line [W. H. Press, S. A. Teukolsky, W. T. Vetterling, B. P. Flannery, Numerical Recipes in C: The Art of Scientific Computing (Cambridge Univ. Press, Cambridge, ed. 2, 1992), section 15.3, p. 666]. Use of the Poisson error as the fixed error for the distance and variation of the time error yields a range of quite different slopes (and as a consequence, the estimated year of origin of the M group) for the data shown in Fig. 1. This ranges from the extreme estimates of 1917 (no error in the time axis) to 1972 (at the limit of large error in the time axis, the equivalent to a fit with no error in the distance axis). If one assumes that the year of sampling could be confounded by a small pool of latently infected cells, carrying virus that originated some years before sampling, the predicted year of origin is intermediate. For example, if one assumes a 6-year error in the time axis, the estimated year of an ancestral sequence of the M group is 1942 (44).
    • (1992) Numerical Recipes in C: The Art of Scientific Computing , pp. 666
    • Press, W.H.1    Teukolsky, S.A.2    Vetterling, W.T.3    Flannery, B.P.4
  • 57
    • 0005000433 scopus 로고
    • J. P. Moore and D. D. Ho, AIDS 9 (suppl. A), S117 (1995); M. P. D'Souza, D. Livnat, J. A. Bradac, S. H. Bridges, Infect. Dis. 175, 1056 (1997); S. Beddows et al., J. Gen. Virol. 79, 77 (1998).
    • (1995) AIDS , vol.9 , Issue.SUPPL. A
    • Moore, J.P.1    Ho, D.D.2
  • 59
    • 0031964880 scopus 로고    scopus 로고
    • J. P. Moore and D. D. Ho, AIDS 9 (suppl. A), S117 (1995); M. P. D'Souza, D. Livnat, J. A. Bradac, S. H. Bridges, Infect. Dis. 175, 1056 (1997); S. Beddows et al., J. Gen. Virol. 79, 77 (1998).
    • (1998) J. Gen. Virol. , vol.79 , pp. 77
    • Beddows, S.1
  • 60
    • 0026647845 scopus 로고    scopus 로고
    • P. Berman et al., J. Virol. 66, 4464 (1992); P. Berman et al., J. Infect Dis. 176, 384 (1997); "FDA authorizes first full testing for HIV vaccine," New York Times, 4 June 1998, p. A1.
    • (1992) J. Virol. , vol.66 , pp. 4464
    • Berman, P.1
  • 61
    • 0030877108 scopus 로고    scopus 로고
    • P. Berman et al., J. Virol. 66, 4464 (1992); P. Berman et al., J. Infect Dis. 176, 384 (1997); "FDA authorizes first full testing for HIV vaccine," New York Times, 4 June 1998, p. A1.
    • (1997) J. Infect Dis. , vol.176 , pp. 384
    • Berman, P.1
  • 62
    • 0026647845 scopus 로고    scopus 로고
    • FDA authorizes first full testing for HIV vaccine
    • 4 June
    • P. Berman et al., J. Virol. 66, 4464 (1992); P. Berman et al., J. Infect Dis. 176, 384 (1997); "FDA authorizes first full testing for HIV vaccine," New York Times, 4 June 1998, p. A1.
    • (1998) New York Times
  • 63
    • 0026707516 scopus 로고
    • B. Korber et al., AIDS Res. Hum. Retroviruses 8, 1461 (1992); S. D. Rencher, T. D. Lockey, K. S. Slobod, J. L. Hurwitz, ibid. 13, 527 (1997).
    • (1992) AIDS Res. Hum. Retroviruses , vol.8 , pp. 1461
    • Korber, B.1
  • 66
    • 2642713073 scopus 로고    scopus 로고
    • Los Alamos National Laboratory
    • Los Alamos, NM (1997). Theoretical Biology and Biophysics, Los Alamos National Laboratory, http:// hiv-web.lanl.gov/HTML/ENV-index.html.
    • (1997) Theoretical Biology and Biophysics
  • 67
    • 0029840629 scopus 로고    scopus 로고
    • J. K. Carr et al., J. Virol. 70, 5935 (1996); F. Gao et al., ibid., p. 7013.
    • (1996) J. Virol. , vol.70 , pp. 5935
    • Carr, J.K.1
  • 68
    • 0029840629 scopus 로고    scopus 로고
    • J. K. Carr et al., J. Virol. 70, 5935 (1996); F. Gao et al., ibid., p. 7013.
    • J. Virol. , pp. 7013
    • Gao, F.1
  • 69
    • 0030018993 scopus 로고    scopus 로고
    • F. Gao et al., ibid. 70, 1651 (1996); F. McCutchan et al., AIDS Res. Hum. Retroviruses 14, 329 (1998).
    • (1996) J. Virol. , vol.70 , pp. 1651
    • Gao, F.1
  • 71
    • 2642609219 scopus 로고    scopus 로고
    • note
    • Two-letter country codes indicating the origins of the viruses included in the envelope tree in Fig. 1 are as follows: Malawi (MW), Burundi (BU), Ethiopia (ET), Brazil (BR), Central African Republic (CF), Thailand (TH), Uganda (UG), Kenya (KE), Rwanda (RW), Zaire (ZR), United States (US), Australia (AU), France (FR), and Haiti (HT).
  • 73
    • 2642648395 scopus 로고    scopus 로고
    • FastDNAml and DNArates were written by Gary Olsen and colleagues at the Ribosomal Database Project (RDP) at the University of Illinois at Urbana-Champaign
    • FastDNAml and DNArates were written by Gary Olsen and colleagues at the Ribosomal Database Project (RDP) at the University of Illinois at Urbana-Champaign, available by anonymous ftp from ftp:// rdp.life.uiuc.edu/.
  • 74
    • 2642615116 scopus 로고    scopus 로고
    • note
    • To create this tree, we generated a preliminary maximum likelihood tree which was then used as input for the DNArates program (47) that produced the maximum likelihood estimate of the rate of nucleotide substitution at every position in the alignment, allowing nine categories of rates. The preliminary tree and rates and categories were used to create a new tree, allowing global rearrangements and adjusting of branch lengths. Maximum likelihood was used to generate the tree to get the most accurate branch lengths possible (9, 11). It took 3 weeks of computer time on a SPARC workstation to generate this tree, so bootstrap analysis was done by using the neighbor joining package of Phylip with the maximum likelihood model to calculate the genetic distances (43).
  • 75
    • 0000461280 scopus 로고
    • J. Felsenstein, Evolution 39, 783 (1985); Cladistics 5, 164 (1989).
    • (1985) Evolution , vol.39 , pp. 783
    • Felsenstein, J.1
  • 76
    • 0000122573 scopus 로고
    • J. Felsenstein, Evolution 39, 783 (1985); Cladistics 5, 164 (1989).
    • (1989) Cladistics , vol.5 , pp. 164
  • 77
    • 2642680565 scopus 로고    scopus 로고
    • unpublished observations
    • B. Korber and J. Theiler, unpublished observations.
    • Korber, B.1    Theiler, J.2
  • 78
    • 2642681375 scopus 로고    scopus 로고
    • note
    • We thank C. Kuiken, T. Leitner, K. Rock, and B. Foley for helpful discussions, R. Thakallapally and A. Ploss for their help with the preparation of this manuscript, and P. Ginsparg for suggestions concerning the text. B.K. was supported by interagency agreements between the U.S. Department of Energy (DOE) and NIH, 3-Y01-AI-70001-13 and Y1-A1-4058-03; J.T. by the DOE; and S.M.W. by grants RO1 -HD-31756 and PO1 -AI-42454 from NIH, and a gift from an anonymous foundation.


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