Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin

Abstract

The geographical distribution of single nucleotide polymorphism (SNP) in the mitochondrial genome of the human malaria parasite Plasmodium falciparum was investigated. We identified 88 SNPs in 516 isolates from seven parasite populations in Africa, Southeast Asia and Oceania. Analysis of the SNPs postulated a sub-Saharan African origin and recovered a strong negative correlation between within-population SNP diversity and geographic distance from the putative African origin over Southeast Asia and Oceania. These results are consistent with those previously obtained for nuclear genome-encoded housekeeping genes, indicating that the pattern of inheritance does not substantially affect the geographical distribution of SNPs.

Keywords: ATQ; F(ST); Genetic diversity; MAF; Malaria; Mitochondrial genome; Mitochondrion; Plasmodium falciparum; Polymorphism; SNP; adenylosuccinate lyase gene; adsl; atovaquone; cob; cox1; cox3; cytochrome b gene; cytochrome c oxidase subunit I gene; cytochrome c oxidase subunit III gene; dN; dS; minor allele frequency; mitochondria; mt; sarcoplasmic/endoplasmic reticulum Ca(2+)-transporting ATPase gene; serca; single nucleotide polymorphism; the Wright's fixation index of inter-population variance in allele frequencies; the average number of pair-wise nucleotide differences; the mean number of non-synonymous substitutions per non-synonymous site; the mean number of synonymous substitutions per synonymous site; the standardized number of polymorphic sites per site; θ(S); θ(π).