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FIGURE 3. Three possible models of the evolution of Msp-1 group I and group II alleles. (A) After an ancient bottleneck, only two alleles survive; these two alleles each give rise to new alleles over time. We expect the two allele groups to be very heterogeneous within groups, and more so between groups, with respect to both synonymous and nonsynonymous substitutions. (B) After a recent bottleneck, only two alleles survive, each of which give rise to new alleles. Alleles within a group are fairly similar to each other but alleles from different groups are very heterogeneous throughout the length of the gene, with respect to synonymous and nonsynonymous substitutions. (C) After a recent bottleneck, only one allele survives that gives rise to new alleles over time. Alleles within and between groups are similar, except for occasional (mostly synonymous) substitutions and for differences generated by intragenic recombination, evidenced by the presence of repeats. A and B are inconsistent with the data in Table 6.

tandemly replicated five times in all group II alleles (the five uppermost alleles in Fig. 3). R1a is a 7-bp repeat replicated five times, and R1b is a 6-bp repeat replicated four times in all group I alleles. The occurrence of repeats within this very short stretch of DNA is a highly significant departure from chance (Ayala et al., 1999). We have searched the recently completed genomic sequences of P. falciparum chromosomes 2 and 3. The nucleotide sequences of repeats R1a, R1b, and R2a appear 25, 116, and 11 times, respectively, within the 947 kb of chromosome 2. Within the 1,060 kb of chromosome 3, the R1a, R1b, and R2a are present 39, 52, and seven times, respectively. None of the three nucleotide repeats ever appears in tandem on either chromosome 2 or 3. The average distance between each occurrence on these chromosomes is >20 kb, corroborating that their repeated occurrence in the short 147-bp segment of Msp-1 block 8 is a strong departure from random expectation. The Msp-1 gene is located on chromosome 9, which has not yet been assembled as a complete nucleotide

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