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diversity currently known for the species; intragenic recombination between the RATs originally present in one allele can generate size polymorphisms in the resulting alleles. The process of bottleneck reduction, ensued by generation of new variations through intragenic recombination, may have occurred numerous times in the evolution of the species, and may continue to do so, given the nature of the parasite lifestyle and its propensity for being confronted by population bottlenecks, for example, upon colonization of new geographic regions or during seasonal epidemic relapses.

We have proposed that most of the variation in antigenic genes is attributable to duplication and/or deletion of the repeated segments within the genes, which is simply an instance of the general slipped-strand process for generating length variation in repetitive DNA regions (Fig. 2). This process occurs by several mechanisms, each of which is well understood at the molecular level and may involve either intrahelical or

FIGURE 2. A model of RAT evolution. Black boxes represent flanking singlecopy regions; gray and white boxes represent different RATs. (A) A single slippage event yields a duplication of two gray RATs. (B) Six new alleles, derived from a single ancestor (indicated by *) after several cell generations. Slippage produces deletions as well as duplications. Karats at the bottom mark artifactual substitutions appearing when the alleles are aligned. Reprinted with permission from Ayala et al. (1999).



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