Origin of Plasmodium falciparum malaria is traced by mitochondrial DNA

Abstract

The origin and geographical spread of Plasmodium falciparum is here determined by analysis of mitochondrial DNA sequence polymorphism and divergence from its most closely related species P. reichenowi (a rare parasite of chimpanzees). The complete 6 kb mitochondrial genome was sequenced from the single known isolate of P. reichenowi and from four different cultured isolates of P. falciparum, and aligned with the two previously derived P. falciparum sequences. The extremely low synonymous nucleotide polymorphism in P. falciparum (π=0.0004) contrasts with the divergence at such sites between the two species (K=0.1201), and supports a hypothesis that P. falciparum has recently emerged from a single ancestral population. To survey the geographical distribution of mitochondrial haplotypes in P. falciparum, 104 isolates from several endemic areas were typed for each of the identified single nucleotide polymorphisms. The haplotypes show a radiation out of Africa, with unique types in Southeast Asia and South America being related to African types by single nucleotide changes. This indicates that P. falciparum originated in Africa and colonised Southeast Asia and South America separately.

Introduction

The origins of major infectious diseases of humans are of relevance to understanding evolution of pathogen virulence and natural selection on the human genome [1]. The malaria parasite Plasmodium falciparum has had an unparalleled impact on human gene polymorphisms [2], and remains a major agent of human mortality [3]. Human sickle cell and α-thalassaemia alleles (which confer some protection from P. falciparum malaria) have multiple independent geographical origins in Africa and Asia, and no ancestral haplotype is very widespread, suggesting that selection by malaria has mainly occurred after human settlement of these regions [4].

Emergence of P. falciparum from a small founding population less than 50 000 years ago has been suggested from the very low level of synonymous single nucleotide polymorphism in some housekeeping genes [5]. However, rRNA gene sequence data indicate that it diverged from the most closely related extant species P. reichenowi at approximately the same time as chimpanzees and hominids (5–10 million years ago) [6], and some alleles of P. falciparum antigen genes may have even more ancient origins which would predate this split [7], [8], [9], [10].

The origin of a species, and its geographical spread, can sometimes be resolved by study of mitochondrial (mt) sequence divergence and variation [11]. Malaria parasites have a small (∼6 kb) tandemly repeated linear mt genome [12] which is uniparentally inherited [13]. Replication involves recombination within but probably not between mt lineages [14]. A broad phylogeny of distantly related Plasmodium species based on sequences of the mitochondrial cytochrome b gene [15] was consistent with that derived from rRNA gene sequences in chromosomal DNA [6]. Here, the complete mt genome sequence was derived from P. reichenowi and four cultured isolates of P. falciparum, and analysed together with two previously derived P. falciparum sequences. This identifies, and provides a quantitative survey of, intra- and inter-specific nucleotide differences. The single nucleotide polymorphisms (SNPs) and their composite haplotypes within P. falciparum were then determined from 104 field isolates, revealing a stark geographical radiation of mtDNA haplotypes.