To study the relative frequencies of substitutions

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Unformatted text preview: To study the relative frequencies of substitutions between different nucleotides, we used Gojobori et al.‘ ( 1982) method. In this method the nucleotide sequences of s ancestral mtDNA are inferred by using the principle of maximum parsimony, and the directional changes of nucleotides are determined by comparing a sequence with its immediate ancestral sequence. When the nucleotide at a site of an ancestral sequence was ambiguous and two nucleotides were possible at the site, each of the nucleotides was considered as the ancestral nucleotide with a probability of I/2. When three or more nucleotides were possible, the site was discarded from the analysis. In the present case, all nucleotide sequences were so closely related to each other that almost all nucleotide substitutions were probably detected by the parsimony method. To apply the above method, it is necessary to have the phylogenetic tree for all the sequences used. This tree was inferred by using Saitou and Nei’ ( 1987) neighbors joining method, which is known generally to produce the minimum-evolution tree (Saitou and Imanishi 1989; Rzhetsky and Nei 1992). The root of the tree was determined by using the chimpanzee sequence C3 of Kocher and Wilson ( 199 1) as an outgroup (fig. 1). According to the bootstrap test, the location of the root was not stable (see Hedges et al. 1992; Templeton 1992)) and the root was sometimes located to the cluster of !Kungs, pygmies, or some other non-African groups. However, this change in root, as well as other changes in the tree topology, had little effect on the relative frequencies of nucleotide substitutions estimated. The numbers of directional nucleotide changes observed were as follows: A-T = 2; A-C = 5; A-+G = 64.5; T-A = 1; T-C = 112; T-G = 1; C-A = 5; C-T = 115; C-G = 3; G-+A = 37.5; G-T = 2; and G-C = 2. To obtain the relative frequency of a class of nucleotide substitution, we must divide the above value by the frequency of the original nucleotide, for each substitution class. For example, the relative frequency of substitution A-T is obtained by dividing 2 by 0.321, which is the frequency of nucleotide A. In practice, however, it is more convenient to express the relative substitution frequencies (J$; change from nucleotide i toj), so as to make the total sum ofJj’ s equal to 100%. The Jj’ in table 1 are obtained in this way. In s this computation we used the average nucleotide frequencies of A, T, C, and G, over all sequences compared. The average frequencies of A, T, C, and G are 0.32 1,0.233, 0.3 14, and 0.132, respectively. Table 1 shows that the rate of transitional nucleotide substitution is much higher than that of transversional substitution. The transition / transversion ratio is usually defined as the ratio of the observed number of transitions to that of transversions. This was 329/2 1 = 15.7 in the present case. This ratio is close to the value ( 15.0) observed by Vigilant et al. ( 199 1). It is interesting that the transitional rate between pyrimidines (T*C) is higher than that between purines ( A+G). A similar purinepyrimidine bias in the transitional substitutions has been observed in Drosophila EuropeanClll) Asian(112) -European(99) Yoruban(57); 1 11AEuroDean(lO4) . Asian(58) I' New Guinean(81) New Guinean(79) New Guinean(80) Australian(49)" E. pYgmy(32) Afr. American(35)* Afr. American(36)* w. PYgmy(37) ,(I) Amer ican(3)* II Lnimpanzee ^. I 0.01 I FIG. 1.-Phylogenetic tree for 95 human and one chimpanzee sequences of the mtDNA control region. This tree was constructed by the neighbor-joining method (Saitou and Nei 1987)) from the distance matrix of the proportion of different nucleoti...
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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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