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Unformatted text preview: mpanzees, but the value for the comparison of Cl and C3 is as high as 0.153. For human sequences, the d value is given only for the deepest root of the sequences. That is, figure 1 shows that the human sequences can be divided into NUCleOtide Substitution in mtDNA 521 Table 4 Estimates of the Number of Nucleotide Substitutions d, Transition/Transversion Ratio i/8, and Their SEs d+SE f//8 + SE Ew. (20) and (2 1) 9.4 16.7 16.9 15.2 14.6 4.7 5.2 7.7 14.3 10.4 14.1 + f + + f GROUPS COMPARED~ H-Cl .................. H-C2 .................. H-C3 .................. . . H-P1 . . Average Cl-C2 Cl-C3 Cl-PI C2-C3 c2-P 1 c3-Pl Within humansc Eq. (15) 0.586 0.706 0.840 0.874 0.752 0.118 0.153 0.317 0.072 0.265 0.349 f 0.161 + 0.213 + 0.264 +- 0.246 + 0.224 + + f + k f 0.024 0.072 0.073 0.016 0.060 0.094 0.141 0.144 0.154 0.162 0.150 0.066 0.077 0.111 0.046 0.100 0.107 K2b f + -t + f 0.013 0.013 0.013 0.014 0.013 K2b 2.7 3.8 3.6 3.3 3.4 2.8 2.8 3.0 9.2 4.2 4.6 + 0.5 + 0.8 Z!I0.7 + 0.6 + 0.7 I+ 0.8 +- 0.7 + 0.7 + 4.4 + 1.0 + 1.1 3.0 5.8 6.1 4.9 5.1 f 0.008 + 0.009 * 0.011 f 0.007 k 0.016 Zk0.011 + 1.4 + 1.5 f 2.2 + 6.8 f. 3.2 I!I 4.8 .. 0.024 + 0.006 0.020 + 0.004 15.7 I!I 3.5d ’ Cl-3 = common chimpanzees; PI = pygmy chimpanzee; and H = humans. Data from Kocher and Wilson (199 1) and Vigilant et al. (199 1) were used. b Estimates obtained by Kimura’s ( 1980) two-parameter ’ Divergence for the deepest root. d Estimated by Nei’s ( 1992) method. method. two major groups, i.e., the !Kung cluster, including a few pygmies and an AfricanAmerican, and the rest of the sequences. The first group includes 2 complete sequences (sequences 3 and 13), whereas the second group has 18 sequences. The d for the deepest human mtDNA root is obtained by computing the average distance between the sequences belonging to the two groups. It becomes 0.024. This value is substantially smaller than the d values between common chimpanzee sequences. In this case, Kimura’ two-parameter s method gives an estimate of a similar to that obtained by equation ( 15), because the number of nucleotide differences per site is very small. Table 4 includes the ratio of transitional (g) and transversional(6) substitutions estimated by using equations ( 20) and (2 1) for various sequence comparisons. In the case of human and chimpanzee comparisons, the average ratio is 14.6, which is very close to the empirical s^/8 ratio ( 15.7) obtained by parsimony analysis of human sequences. In the case of chimpanzee sequence comparisons, however, the ratio tends to be smaller than that for human sequences. In particular, all comparisons involving sequence C 1 show a low s”/ 5 ratio. Nevertheless, it is not clear whether this tendency is real, because the number of sequences used is small and the sampling errors of the s^/5 ratio are very large. Kimura’ s method consistently gives underestimates of the ratio. Rate of Nucleotide mtDNA Substitution and the Age of the Common Ancestral Conducting a phylogenetic analysis of human mtDNA sequences, Vigilant et al. ( 199 1) concluded that the age of the common ancestral mtDNA is 166,000-249,000 years. Nei ( 1992) reanalyzed their data and reached the conclusion that the age is 522 I‘ amura and Nel - 1 lO,OOO-504,000 years when the 95% confidence examine this problem, using our new mathematical interval is considered. method. Let us now To estimate the age of the common ancestral mtDNA, it is necessary to know the average rate of nucleotide substitution for the control region. This rate can be obtained by assuming that humans and chimpanzees diverged 4-6 Mya (Vigilant et al. 199 1) . Since the mean h value * standard error (SE) between humans and chimpanzees is 0.752 * 0.224, the 95% confiden...
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This note was uploaded on 01/06/2010 for the course NS 2750 taught by Professor Haas&gu during the Spring '08 term at Cornell University (Engineering School).

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