Mean genetic ancestry proportions determined via ancestry informative markers and HLA haplotype origin frequencies for subpopulations defined by reported race/ethnicity or geographic ancestry.

<p>* All individuals have two HLA haplotypes. Multi-origin haplotype classification indicates that one of the individual’s haplotypes is closely associated with one continental origin while the other haplotype is associated with a different continental origin.</p><p>Mean genetic ancestry proportions determined via ancestry informative markers and HLA haplotype origin frequencies for subpopulations defined by reported race/ethnicity or geographic ancestry.</p

African and Amerindian genetic ancestry proportions (a,c) and HLA origin frequencies (b,d) are correlated with the number of grandparents with reported African and Latin American ancestry, respectively.

<p>Genetic ancestry proportions were estimated from AIMs data using Structure and the HGDP reference set. For this analysis, k = 4, reflecting broad continental ancestry. For each subpopulation defined by the number of respondents’ grandparents with Sub-Saharan African/African American or Latin American ancestry, the percentage of individuals with zero, one or two African or Amerindian HLA haplotypes, respectively, was calculated. Individuals reporting one, two, three or four African-ancestry grandparents: n = 4; 4; 2; 21, respectively. Individuals reporting one, two, three or four Latin American-ancestry grandparents: n = 16; 21; 7; 38, respectively.</p

KIR polymorphism modulates the avidity and specificity for HLA-C, as well as KIR abundance at the cell surface.

<p>(A) Binding of KIR2DL1-Fc fusion proteins to C2-bearing HLA-C allotypes. For each C2-bearing HLA-C allotype, the KIR2DL1 binding is the mean of the values obtained with 11 different KIR2DL1-Fc (2DL1*001, *003, *004, *007, *008, *012, *020, *021, *023 *024, *025). Each individual binding value was normalized to the binding of the W6/32 antibody before calculating the average. (B) Binding of KIR2DL1*022-Fc and KIR2DL2/3-Fc fusion proteins to C1-bearing HLA-B and -C allotypes. For each C1-bearing HLA-B and HLA-C allotype, the KIR2DL2/3 binding is the mean of the values obtained with 16 KIR2DL-Fc fusion proteins (2DL1*022; 2DL2*001,*003, *004, *006, 009 *011; and 2DL3*001, *005, *008, *009, *011, *013, *015, *016, *018). The proteins were tested against microbeads coated with one of nine C1 HLA-C or two C1 HLA-B allotypes. Each individual binding value was normalized to the binding to that of the W6/32 antibody before calculating the average. (C) Variable cell-surface expression of KIR2DL1. FLAG-tagged KIR2DL1 allotypes were transfected into HeLa cells. Cell-surface expression was detected using FLAG-specific antibody and analysis by flow cytometry. MFI = median fluorescence intensity. The experiment was performed in triplicate, error bars give the standard deviation. The difference between 2DL1*012 and 2DL1*026 is statistically significant as assessed by a two-tailed t-test.</p

<i>KIR2DL1*022</i> and <i>2DL1*026</i> are of recent origin compared to other KhoeSan <i>KIR2DL1</i> alleles.

<p>(A) For each KhoeSan <i>KIR2DL1</i> allele, the number of centromeric <i>KIR</i> haplotypes on which the allele is present in the KhoeSan (number observed) is plotted against the number of different (distinct) haplotypes on which the allele is present. In total, 110 haplotypes were analyzed. Haplotypes that lack <i>KIR2DL1</i> are denoted ‘blank’. The r² was calculated from Pearson correlation of the alleles shown in blue. This analysis excluded <i>2DL1*022</i> and <i>*026</i> (shown in red). (B) Shows the allele content of centromeric <i>KIR</i> haplotypes containing either <i>2DL1*022</i> (purple) or <i>2DL1*026</i> (yellow). The observed number of each haplotype is given on the left. Also shown (in white) are the KhoeSan haplotypes that are the putative parents (Par?) of the derived <i>2DL*022-</i>containing and <i>2DL1*026</i>-containing haplotypes. The putative parents are the haplotypes that differ from the derived haplotypes by the least number of nucleotide substitutions. (C) Plot of haplotype frequency against linkage disequilibrium (LD). The analysis was conditioned so that <i>2DL2*003</i>-bearing haplotypes were analyzed. The figure illustrates the high level of linkage disequilibrium observed for haplotypes containing <i>2DL1*022</i> and <i>2DL1*026</i> suggesting they appeared more recently in the KhoeSan population than other <i>KIR2DL1</i> alleles.</p

A variant of KIR2DL1 originating in the KhoeSan is a C1-specific receptor and not a C2-specific receptor like other KIR2DL1.

<p>(A) This alignment of KIR2DL1 sequence differences shows the sites of polymorphism in the D1 domain (D1), the D2 domain (D2) and the transmembrane region (Tm). Dashes denote identity with the KIR2DL1*003 sequence, an asterisk denotes a termination codon. Sequences of the KhoeSan KIR2DL1 allotypes are highlighted in yellow. The names of allotypes with D1, D2 and Tm identical to an aligned sequence are listed in the column at the right. (B) Binding of KIR2DL1-Fc fusion proteins to microbeads coated with C1-bearing and seven C2-bearing HLA-C allotypes. Each binding value was normalized to that of the W6/32 antibody and these normalized values were averaged for the C1 (N = 9) and C2 (N = 7) allotype groups. The names of allotypes present in the KhoeSan are boldened. A dagger following the listed allotype indicates that the allotype represents a group of two or more alleles that encode identical ligand binding domains (see Panel A). (C) This alignment of KIR2DL2/3 sequence differences shows the sites of polymorphism in the D1 and D2 domains. Dashes denote identity with the KIR2DL2*001 sequence Sequences of the KhoeSan KIR2DL2/3 allotypes are highlighted in yellow. The names of allotypes with D1 and D2 identical to an aligned sequence are listed in the column at the right. (D) Binding of KIR2DL2/3-Fc fusion proteins to microbeads coated with C1-bearing and C2-bearing HLA-C allotypes. Each binding value was normalized to that of the W6/32 antibody and these normalized values were averaged for the C1 (N = 9) and C2 (N = 7) groups. The names of allotypes present in the KhoeSan are boldened. Groups of allotypes with identical D1 and D2 domains, and which are represented by a single KIR2DL2/3-Fc, are as shown in the column on the right of Panel A. A dagger following the listed allotype indicates that the allotype represents a group of two or more alleles that encode identical ligand binding domains (see Panel A).</p

The C2 frequency in the KhoeSan is unusually high.

<p>Each of the seven blue-shaded vertical bars gives the number of populations, of 140 considered [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005439#pgen.1005439.ref034" target="_blank">34</a>], that have a C2 frequency within the range covered by the bar, given on the horizontal axis. The frequency data are not significantly different from a normal distribution (grey line). The black-shaded dots on the curve give the frequencies for the KhoeSan and the four other populations for which <i>KIR2DL1</i> allele frequencies are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005439#pgen.1005439.g003" target="_blank">Fig 3</a>.</p

The KhoeSan have high <i>KIR2DL1</i> diversity compared to other human populations.

<p>(A and B) The pie charts show the number and relative frequencies of <i>KIR2DL1</i> alleles in the KhoeSan of Southern Africa (A), and four other populations representing four continents (B): the Ga-Adangbe from Ghana in Western Africa [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005439#pgen.1005439.ref014" target="_blank">14</a>], Northern Ireland Caucasians from Europe [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005439#pgen.1005439.ref021" target="_blank">21</a>], Japanese from East Asia [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005439#pgen.1005439.ref024" target="_blank">24</a>] and Yucpa Amerindians from South America [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005439#pgen.1005439.ref020" target="_blank">20</a>]. The 'blank' is the frequency of <i>KIR</i> haplotypes that lack the <i>KIR2DL1</i> gene. (C) Also compared in the five populations are the frequencies of strong KIR2DL1, weak KIR2DL1, KIR2DL1 that are not inhibitory C2 receptors (inactive) and the absence of KIR2DL1 (blank). The definition and designation of these KIR2DL1 categories are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005439#pgen.1005439.s004" target="_blank">S4 Fig</a>.</p

Robust footprint of balancing selection characterizes HLA-class I alleles in Ghana.

<p>A. Shown are values for Tajima's D generated from the nucleotide sequences of the <i>HLA-A</i>, <i>-B</i> and <i>-C</i> alleles present in the Ga-Adangbe. Significance values are from a two-tailed test comparing observed values to those obtained from 10,000 coalescent simulations, under a range of demographic models (p<0.001 for all models). B. The binding sites for lymphocyte receptors (in blue) on a 3D structure of HLA class I (PDB ref. 3SKO). For the peptide binding motifs, the residues that form the B and F anchor pockets (P2P9) are shown in a lighter blue. The LILRB1 binding domain is ringed. Relative orientation of the three domains is shown at the right. C. Shown are the normalized deviate values of Ewens-Watterson's F test (F_nd<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003938#pgen.1003938-Salamon1" target="_blank">[63]</a>) for motifs of HLA-class I that interact with immune accessory molecules. ‘All’ - complete polypeptide sequence. For peptide-binding, TCR, KIR, LILR and CD8, only the residues exclusive to their respective motifs were included. (-) indicates motif is monomorphic. The KIR3DL2 binding sites of HLA-A are unknown. p values were calculated using the exact test described by Slatkin <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003938#pgen.1003938-Tajima1" target="_blank">[98]</a>. D. Shown are the F_nd values for accessory molecule-interacting motifs of HLA-B in West African and other populations chosen to represent major worldwide groups.</p

Low diversity in the telomeric region of Ga-Adangbe <i>KIR</i> haplotypes.

<p>A. Shown are the 19 <i>KIR</i> gene-content haplotypes detected in the Ga-Adangbe study population (2N = 366) and their frequencies (right column). Presence of a gene is indicated with a black box. ‘Cen’ and ‘Tel’ in the left columns denote the component haplotype motifs in the centromeric and telomeric regions of the <i>KIR</i> locus. † indicates eight <i>KIR</i> haplotypes that have not been identified in other populations. The <i>tB04</i> motif is unique to Africa and harbors the <i>KIR3DL1/2v</i> fusion gene, a recombinant of <i>KIR3DL1</i> and <i>KIR3DL2 </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003938#pgen.1003938-Norman3" target="_blank">[57]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003938#pgen.1003938-Shilling1" target="_blank">[112]</a>. B. Shown are the heterozygosity values (H_e = 1-SSF) of 72 populations who were genotyped for <i>KIR</i> gene-content only (reference <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003938#pgen.1003938-GonzalezGalarza1" target="_blank">[74]</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003938#s4" target="_blank">Materials and Methods</a>). The genotypes were split into centromeric (left) and telomeric regions (right: p<0.001 for SSA vs. each other population group by T-test). EA East Asia (11 populations: mean N = 106), EUR Europe (15∶161), ME Middle East (12∶121), OCE Oceania (9∶47), SA South Asia (8∶82), SAM South America (12∶66), SSA sub-Saharan Africa (5∶58).</p

Co-evolution of Human Leukocyte Antigen (HLA) Class I Ligands with Killer-Cell Immunoglobulin-Like Receptors (KIR) in a Genetically Diverse Population of Sub-Saharan Africans

<div><p>Interactions between HLA class I molecules and killer-cell immunoglobulin-like receptors (KIR) control natural killer cell (NK) functions in immunity and reproduction. Encoded by genes on different chromosomes, these polymorphic ligands and receptors correlate highly with disease resistance and susceptibility. Although studied at low-resolution in many populations, high-resolution analysis of combinatorial diversity of <i>HLA class I</i> and <i>KIR</i> is limited to Asian and Amerindian populations with low genetic diversity. At the other end of the spectrum is the West African population investigated here: we studied 235 individuals, including 104 mother-child pairs, from the Ga-Adangbe of Ghana. This population has a rich diversity of 175 <i>KIR</i> variants forming 208 <i>KIR</i> haplotypes, and 81 <i>HLA-A</i>, <i>-B</i> and <i>-C</i> variants forming 190 <i>HLA class I</i> haplotypes. Each individual we studied has a unique compound genotype of <i>HLA class I</i> and <i>KIR</i>, forming 1–14 functional ligand-receptor interactions. Maintaining this exceptionally high polymorphism is balancing selection. The centromeric region of the <i>KIR</i> locus, encoding HLA-C receptors, is highly diverse whereas the telomeric region encoding Bw4-specific KIR3DL1, lacks diversity in Africans. Present in the Ga-Adangbe are high frequencies of Bw4-bearing HLA-B*53:01 and Bw4-lacking HLA-B*35:01, which otherwise are identical. Balancing selection at key residues maintains numerous HLA-B allotypes having and lacking Bw4, and also those of stronger and weaker interaction with LILRB1, a KIR-related receptor. Correspondingly, there is a balance at key residues of KIR3DL1 that modulate its level of cell-surface expression. Thus, capacity to interact with NK cells synergizes with peptide binding diversity to drive HLA-B allele frequency distribution. These features of KIR and HLA are consistent with ongoing co-evolution and selection imposed by a pathogen endemic to West Africa. Because of the prevalence of malaria in the Ga-Adangbe and previous associations of cerebral malaria with HLA-B*53:01 and KIR, <i>Plasmodium falciparum</i> is a candidate pathogen.</p></div