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0030023247
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In recent investigations of the age of the MRCA from protein data sets, estimates varied from 2000 to 6000 million years, exclusively depending on the assumed amino acid substitution model [R. F. Doolittle, D. F. Feng, S. Tsang, G. Cho, E. Little, Science 271, 470 (1996); M. Hasegawa and W. M. Fitch, ibid. 274, 1750 (1996); J. P. Gogarten, L. Olendzenski, E. Hilario, C. Simon, K. E. Holzinger, ibid., p. 1750; X. Gu, Mol. Biol. Evol. 14, 861 (1997)].
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In recent investigations of the age of the MRCA from protein data sets, estimates varied from 2000 to 6000 million years, exclusively depending on the assumed amino acid substitution model [R. F. Doolittle, D. F. Feng, S. Tsang, G. Cho, E. Little, Science 271, 470 (1996); M. Hasegawa and W. M. Fitch, ibid. 274, 1750 (1996); J. P. Gogarten, L. Olendzenski, E. Hilario, C. Simon, K. E. Holzinger, ibid., p. 1750; X. Gu, Mol. Biol. Evol. 14, 861 (1997)].
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0030023247
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In recent investigations of the age of the MRCA from protein data sets, estimates varied from 2000 to 6000 million years, exclusively depending on the assumed amino acid substitution model [R. F. Doolittle, D. F. Feng, S. Tsang, G. Cho, E. Little, Science 271, 470 (1996); M. Hasegawa and W. M. Fitch, ibid. 274, 1750 (1996); J. P. Gogarten, L. Olendzenski, E. Hilario, C. Simon, K. E. Holzinger, ibid., p. 1750; X. Gu, Mol. Biol. Evol. 14, 861 (1997)].
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Gogarten, J.P.1
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5
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In recent investigations of the age of the MRCA from protein data sets, estimates varied from 2000 to 6000 million years, exclusively depending on the assumed amino acid substitution model [R. F. Doolittle, D. F. Feng, S. Tsang, G. Cho, E. Little, Science 271, 470 (1996); M. Hasegawa and W. M. Fitch, ibid. 274, 1750 (1996); J. P. Gogarten, L. Olendzenski, E. Hilario, C. Simon, K. E. Holzinger, ibid., p. 1750; X. Gu, Mol. Biol. Evol. 14, 861 (1997)].
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Z. Yang, J. Mol. Evol. 39, 306 (1994). Eight equally probable classes of rates were used to approach the gamma distribution. All parameters were numerically estimated using the Newton-Raphson method. First and second derivatives of the likelihood function with respect to each parameter were analytically derived, excepting the shape parameter of the gamma distribution, whose derivatives were computed numerically.
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0345162916
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note
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Eighty data sets were generated by simulating the evolution of a randomly drawn DNA sequence along the tree of Fig. 1 using the maximally likely values of the parameters of the model. Ancestral G + C content was estimated for each data set. The highest two and lowest two values were removed. The remaining 76 ancestral G + C content values define a 95% confidence interval.
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17
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0344732617
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note
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Two hundred data sets, each with 36 species, were built by randomly drawing representatives of the main eukaryotic, bacterial, and archaeal phyla among 167 available LSU rRNA sequences (16). For each data set, a neighbor-joining tree was reconstructed and ancestral G + C content estimated.
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19
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0025901140
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N. R. Pace, Cell 65, 531 (1991); S. M. Barns, C. F. Delwiche, J. D. Palmer, N. R. Pace, Proc. Natl. Acad. Sci. U.S.A. 93, 9188 (1996).
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Pace, N.R.1
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N. R. Pace, Cell 65, 531 (1991); S. M. Barns, C. F. Delwiche, J. D. Palmer, N. R. Pace, Proc. Natl. Acad. Sci. U.S.A. 93, 9188 (1996).
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Barns, S.M.1
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P. Forterre, Cell 85, 789 (1996); Curr. Opin. Genet. Dev. 7, 764 (1997).
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P. Forterre, Cell 85, 789 (1996); Curr. Opin. Genet. Dev. 7, 764 (1997).
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24
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0344300401
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Data sets are available at http://pbil.univ-lyon1.fr/ datasets/gcanc/.
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