Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans

Abstract

The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of positive selection in humans. Despite this, details of the timing and mode of selection at DARC remain poorly understood. Here, we use sequencing data from over 1,000 individuals in twenty-one human populations, as well as ancient human genomes, to perform a fine-scale investigation of the evolutionary history of DARC. We estimate the time to most recent common ancestor (TMRCA) of the most common FY*O haplotype to be 42 kya (95% CI: 34-49 kya). We infer the FY*O null mutation swept to fixation in Africa from standing variation with very low initial frequency (0.1%) and a selection coefficient of 0.043 (95% CI:0.011-0.18), which is among the strongest estimated in the human genome. We estimate the TMRCA of the FY*A mutation in non-Africans to be 57 kya (95% CI: 48-65 kya) and infer that, prior to the sweep of FY*O, all three alleles were segregating in Africa, as highly diverged populations from Asia and ≠Khomani San hunter-gatherers share the same FY*A haplotypes. We test multiple models of admixture that may account for this observation and reject recent Asian or European admixture as the cause.

Fig 1. Geographical distribution of allelic classes in samples.

*The FY*O/FY*A haplotype is a very rare haplotype that includes both the FY*A and FY*O mutations and is present only in the Zulu samples.

Fig 2. Haplotype networks.

Median joining networks of three subsets of haplotypes in the 5kb region centered on the FY*O mutation. The FY*A mutation is located 671 bps downstream from the FY*O mutation. Arrows indicates ancestral sequence. A) All haplotypes observed at least four times B) All FY*O haplotypes observed at least twice. (Note that none of the FY*O haplotypes in this network also carry the FY*A mutation.) C) All FY*A haplotypes observed at least twice. (Note that none of the FY*A hapotypes in this network also include the FY*O mutation.)

Fig 3. FY*O selection coefficient results.

Prior and posterior distributions of FY*O selection coefficient.