Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax

Abstract

Examination of nucleotide diversity in 106 mitochondrial genomes of the most geographically widespread human malaria parasite, Plasmodium vivax, revealed a level of diversity similar to, but slightly higher than, that seen in the virulent human malaria parasite Plasmodium falciparum. The pairwise distribution of nucleotide differences among mitochondrial genome sequences supported the hypothesis that both these parasites underwent ancient population expansions. We estimated the age of the most recent common ancestor (MRCA) of the mitochondrial genomes of both P. vivax and P. falciparum at around 200,000-300,000 years ago. This is close to the previous estimates of the time of the human mitochondrial MRCA and the origin of modern Homo sapiens, consistent with the hypothesis that both these Plasmodium species were parasites of the hominid lineage before the origin of modern H. sapiens and that their population expansion coincided with the population expansion of their host.

Figure 1

Neighbor-joining tree based on Kimura 2-prameter distance at 2617 aligned nucleotide sites in non-coding portions of the mitochondrial genome of Plasmodium vivax and related species. Numbers on the branches represent the percent of 1000 boostrap pseudo-samples supporting the branch; only values ≥ 95% are shown.

Figure 2

Mismatch distributions for mitochondrial genome sequences of (A) P. vivax and (B) P. falciparum. Observed distributions (clear bars) were compared with that expected under constant population size (shaded bars). In both species, the observed and expected patterns were significantly different. For P. vivax, χ² = 2076.8, 10 d.f., P < 0.001; for P. falciparum, χ² = 3129.3, 5 d.f., P < 0.001.