Effects of natural selection and gene conversion on the evolution of human glycophorins coding for MNS blood polymorphisms in malaria-endemic African populations

Abstract

Malaria has been a very strong selection pressure in recent human evolution, particularly in Africa. Of the one million deaths per year due to malaria, more than 90% are in sub-Saharan Africa, a region with high levels of genetic variation and population substructure. However, there have been few studies of nucleotide variation at genetic loci that are relevant to malaria susceptibility across geographically and genetically diverse ethnic groups in Africa. Invasion of erythrocytes by Plasmodium falciparum parasites is central to the pathology of malaria. Glycophorin A (GYPA) and B (GYPB), which determine MN and Ss blood types, are two major receptors that are expressed on erythrocyte surfaces and interact with parasite ligands. We analyzed nucleotide diversity of the glycophorin gene family in 15 African populations with different levels of malaria exposure. High levels of nucleotide diversity and gene conversion were found at these genes. We observed divergent patterns of genetic variation between these duplicated genes and between different extracellular domains of GYPA. Specifically, we identified fixed adaptive changes at exons 3-4 of GYPA. By contrast, we observed an allele frequency spectrum skewed toward a significant excess of intermediate-frequency alleles at GYPA exon 2 in many populations; the degree of spectrum distortion is correlated with malaria exposure, possibly because of the joint effects of gene conversion and balancing selection. We also identified a haplotype causing three amino acid changes in the extracellular domain of glycophorin B. This haplotype might have evolved adaptively in five populations with high exposure to malaria.

Figure 1

Spatial Distribution of SNPs and Genetic Difference between Glycophorins (A) Gene structures of human glycophorin A (GYPA), B (GYPB), and E (GYPE) are marked by SNPs that are classified into “gene-specific” SNPs (black lines) or “shared” SNPs between these three paralogs (orange lines). Each nonsynonymous SNP is labeled by an inverted triangle. The exonic regions that code for the extracellular domains are colored in blue. For GYPB and GYPE, the region homologous to exon 3 or 4 of GYPA is colored in red if it is an unexpressed pseudoexon (φ). The exonic regions that code for the 3′ UTR in GYPA and GYPE are not shown. The three homologs are tandemly arrayed on the long arm of human chromosome 4 (cytogenetic map: 4q28.2-31.3). (B) We used Nei's D_xy to estimate pairwise genetic differentiation between paralogs at different genetic regions. Nei's D_xy calculates the average number of “fixed” differences (per site) between any two paralogs. D_xy estimates of pairwise difference for the GYPA-GYPB, GYPA-GYPE, and GYPB-GYPE pairs are labeled as D_AB, D_AE, and D_BE, respectively. “int” is used as an abbreviation for intron.

Figure 2

Geographic Distribution of Malarial Endemicity and Sampled Populations in Africa The map of spatial limits and endemic levels of malaria in Africa was kindly provided by Drs. Robert W. Snow and Carlos Guerra from the Malaria Atlas Project published in Snow et al. and was reprinted with permission from the Nature Publishing Group and Macmillan Publishers Ltd. The following endemicity classes are shown: dark green, hyperendemic and holoendemic (area in which childhood infection prevalence is ≥ 50%); medium green, mesoendemic (area with infection prevalence between 11%–50%); and light green, hypoendemic (area with infection prevalence ≤ 10%). The spatial limit for malaria transmission in 1946 is also shown. The value in parentheses indicates Tajima's D statistics for exon 2 of GYPA. Significance was calculated by coalescence simulations with no recombination for a given observed number of segregating sites (S) and number of chromosomes sampled in a population. ^∗p < 0.05, ^∗∗p < 0.01.

Figure 3

Phylogeny of Glycophorins in Great Apes A maximum likelihood tree of glycophorin homologous genes in human, chimpanzee, and orangutan was reconstructed by maximizing the parameters that account for the nucleotide substitution assuming the HKY85 model, substitution-rate variation among sites assuming a gamma distribution, and branch lengths. Numbers on each internal node (from left to right) indicate scores of bootstrap resampling (1000 replicates) for maximum likelihood (ML), neighbor-joining (NJ), and maximum parsimony (MP) methods, respectively. The total length of sequence alignment is 5618 bp. The name of each chimpanzee homolog is based on its most closely related gene in humans. A number is also given if more than one chimpanzee gene is assigned to the same human ortholog.

Figure 4

Structural Models of Glycophorins A and B (A) Extracellular domain of GYPA. O- and N-glycosylated amino acid residues are labeled in magenta and green, respectively. Amino acid residues where polymorphic (poly) or fixed (fix) changes occurred are colored in red. Amino acid abbreviations at these sites are given in parentheses and the ancestral residue is shown at left and the derived one at right for a fixed change. The two images are rotated by 180 degrees with respect to each other. (B) 3D structure of the transmembrane domain of GYPA (PDB code: 1AFO). The two fixed mutations occur at the extracellular peptide residues (in red) adjacent to the helical region. (C) Extracellular domain of GYPB. Amino acid residues that are both glycosylated (O-linked) and variable are colored in pink. The MN and Ss blood groups are determined by amino acid variants at GYPA and GYPB, respectively. The M and N antigens are determined by two genetically linked amino acid variants of GYPA where M blood type is determined by Ser and Gly at position 1 and 5, respectively, and N blood type is determined by Leu and Glu (introduced by gene conversion from GYPB) at these two sites. The S and s are determined by Met and Thr, respectively, at position 29 of the polypeptide chain of GYPB.