High recombination rate in natural populations of Plasmodium falciparum

Abstract

Malaria parasites are sexually reproducing protozoa, although the extent of effective meiotic recombination in natural populations has been debated. If meiotic recombination occurs frequently, compared with point mutation and mitotic rearrangement, linkage disequilibrium between polymorphic sites is expected to decline with increasing distance along a chromosome. The rate of this decline should be proportional to the effective meiotic recombination rate in the population. Multiple polymorphic sites covering a 5-kb region of chromosome 9 (the msp1 gene) have been typed in 547 isolates from six populations in Africa to test for such a decline and estimate its rate in populations of Plasmodium falciparum. The magnitude of two-site linkage disequilibrium declines markedly with increasing molecular map distance between the sites, reaching nonsignificant levels within a map range of 0.3-1.0 kb in five of the populations and over a larger map distance in the population with lowest malaria endemicity. The rate of decline in linkage disequilibrium over molecular map distance is at least as rapid as that observed in most chromosomal regions of other sexually reproducing eukaryotes, such as humans and Drosophila. These results are consistent with the effective recombination rate expected in natural populations of P. falciparum, predicted on the basis of the underlying molecular rate of meiotic crossover and the coefficient of inbreeding caused by self-fertilization events. This is conclusive evidence to reject any hypothesis of clonality or low rate of meiotic recombination in P. falciparum populations. Moreover, the data have major implications for the design and interpretation of population genetic studies of selection on P. falciparum genes.

Figure 1

Scheme of the P. falciparum msp1 gene with positions of the 10 polymorphic sites studied. The coding sequence of the gene covers 5.1 kb, and there are no introns. 5′- and 3′ ends of the gene are marked by the corresponding N and C termini of the protein. The 17 block scheme of Tanabe et al. (17) is shown above, indicating the amount of sequence polymorphism in different parts of the gene. The positions of the 10 sequence sites typed in this study are marked at the bottom (sequences of allelic oligonucleotide probes are given in Table 1). Dashed lines under blocks 6–16 indicate that this whole region exists as either one of two highly divergent dimorphic sequence types, between which no recombinants have been detected (18, 19); therefore, typing of a sequence at only one representative dimorphic site (in block 14) was performed.

Figure 2

Proportions of significant linkage disequilibrium tests between pairs of loci within the msp1 gene in each of six countries, according to molecular distance between the loci. Overall proportions are shown above the histogram, illustrating a highly significant decline with increasing molecular distance (P < 10⁻⁷, see text).

Figure 3

Decline in linkage disequilibrium (D′) with increasing nucleotide distance between pairs of sites in the msp1 gene, in three countries. The magnitude of D′ is considered, irrespective of sign (positive or negative, which is reversible if an alternative allele is considered). Squares indicate the points that are significantly different from 0, and triangles indicate those not significantly different from 0. Only the distance range of <1.0 kb is plotted, because almost all tests for linkage disequilibrium over a larger nucleotide distance were nonsignificant (Fig. 2). The exponential decay curves (1 − e^−xn) were fitted by using glim statistical software, with n = nucleotide distance in kilobases between sites (exponential function x = 3.97 in The Gambia, 2.80 in Gabon, and 0.50 in Sudan). Note the slower rate of decline in Sudan compared with the other countries. Rates of decline in Nigeria, Tanzania, and South Africa were similar to that in Gabon (see text).