. "9 Population Structure and Recent Evolution of Plasmodium falciparum." Variation and Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years after Stebbins. Washington, DC: The National Academies Press, 2000.
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Variation and Evolution in Plants and Microorganisms: TOWARD A NEW SYNTHESIS 50 YEARS AFTER STEBBINS
TABLE 7. Nucleotide diversity (π) within and between group I and II alleles of the P. falciparum Msp-1 genes
Synonymous
Nonsynonymous
Block
Length, codons
Group I
Group II
Group I + group II
Group I
Group II
Group 1 + group II
1
55
0.019
0.021
0.017
0.017
0.010
0.013
2
55
0.106
0.185
0.150
0.449
0.497
0.553
3
202
0.038
0.006
0.042
0.018
0.000
0.023
4
31
0.031
0.000
0.020
0.307
0.000
0.215
5
35
0.000
0.000
0.070
0.000
0.000
0.026
6
227
0.000
0.000
0.282
0.004
0.001
0.300
7
73
0.000
0.000
0.361
0.003
0.000
0.072
8
95
0.000
0.000
0.338
0.000
0.003
0.711
9
107
0.000
0.023
0.409
0.005
0.043
0.126
10
126
0.008
0.000
0.448
0.011
0.000
0.394
11
35
0.000
0.000
0.128
0.000
0.000
0.068
12
79
0.000
0.000
0.000
0.000
0.000
0.000
13
84
0.000
0.042
0.040
0.005
0.007
0.052
14
60
0.000
0.018
0.212
0.002
0.005
0.371
15
89
0.000
0.000
0.216
0.001
0.003
0.089
16
217
0.002
0.032
0.277
0.027
0.027
0.185
17
99
0.002
0.019
0.007
0.010
0.027
0.016
Blocks are as defined by Tanabe et al. (1987). Some block lengths vary between group I and II alleles; thevalue given is the average length of group I and II alleles.
for generating polymorphism (in block 4 there is considerable nonsynonymous polymorphism among group I alleles). Table 7 gives the nucleotide diversity (π) for synonymous and nonsynonymous substitutions for each of the 17 blocks, both within and between groups (see Fig. 3). The most extensive amino acid polymorphism between the two allele groups occurs in block 8, which has been assumed to have no simple repeats, but that we will show below to be composed of tandem and proximal repeats (see Fig. 4).
The dimorphism observed among group I and II alleles within block 2 has been shown to result by processes analogous to those within the Csp central repeat region (Frontali and Pizzi, 1991; Frontali, 1994). The occurrence of repetitive DNA within other blocks has not been described to date. However, we have identified repeats within several of the most polymorphic Msp-1 blocks; in particular, blocks 4, 8, and 14, which heretofore were assumed to be NR. We focus on the repeats detected within block 8, identified by Tanabe et al. (1987) as showing the lowest amino acid similarity between groups (10%; π = 0.711 in Table 7). We have identified three group-specific repeats within this block, two in group I alleles (R1a and R1b), and one in group II alleles (R2a). R2a is a 9-bp repeat
