In both humans and a bacterial pathogen, Helicobacter pylori, it has been reported that levels of genetic diversity decrease with distance from the area of origin of modern humans in East Africa. In an analysis of the genetic diversity using two housekeeping genes from 519 samples, Tanabe et al. (2010), found that the genetic diversity of P. falciparum also decreased with distance from the eastern part of Central Africa. They interpreted this as evidence that P. falciparum emerged from Africa at the same time as humans, around 60,000 years ago.
Now, thousands of P. falciparum whole genome sequences are available. This study aims to determine the geographical distribution of genome-wide genetic diversity and its implications for the origin of P. falciparum. Genome-wide genetic diversity was calculated for a total of 10, 333 sequences from 88 study sites in 33 countries. As expected, it was found that the genome-wide nucleotide diversity was higher in African sites (0.050%) as compared to other regions of the world (0.038% in Oceania, 0.035% in Asia, 0.031% in S America).
For the 46 study sites across Africa, the ‘least-cost’ geographical distance from each of 2,000 uniformly spaced potential sites of origin was calculated, and the Spearman correlation between genome-wide genetic diversity and least-cost geographical distance was calculated. The highest negative correlation was obtained for locations in the Western part of central Africa, close to the range of Western lowland gorillas (Gorilla gorilla) that harbour P. praefalciparum, i.e., the genetic diversity of P. falciparum declines with distance from where western gorillas are found. Since this correlation is expected to be disrupted by demographic factors over time, this finding is consistent with a very recent origin of P. falciparum.
