High recombination rate in natural populations of Plasmodium falciparum

Malaria parasites are sexually reproducing protozoa, although the extent of effective meiotic recombination in natural populations has been debated. I f 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 recombinati on rate in the population. Multiple polymorphic sites covering a 5-kb regio n 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 p opulations of Plasmodium falciparum, The magnitude of two-site linkage dise quilibrium 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 populatio n with lowest malaria endemicity, The rate of decline in linkage disequilib rium over molecular map distance is at least as rapid as that observed in m ost chromosomal regions of other sexually reproducing eukaryotes, such as h umans and Drosophila, These results are consistent with the effective recom bination rate expected in natural populations of P, falciparum, predicted o n the basis of the underlying molecular rate of meiotic crossover and the c oefficient of inbreeding caused by self-fertilization events. This is concl usive evidence to reject any hypothesis of clonality or low rate of meiotic recombination in P, falciparam populations. Moreover, the data have major implications for the design and interpretation of population genetic studie s of selection on P, falciparum genes.