Genomic variation in seven Khoe-San groups reveals adaptation and complex African history - PubMed
- ️Sun Jan 01 2012
. 2012 Oct 19;338(6105):374-9.
doi: 10.1126/science.1227721. Epub 2012 Sep 20.
Pontus Skoglund, Per Sjödin, Lucie M Gattepaille, Dena Hernandez, Flora Jay, Sen Li, Michael De Jongh, Andrew Singleton, Michael G B Blum, Himla Soodyall, Mattias Jakobsson
Affiliations
- PMID: 22997136
- PMCID: PMC8978294
- DOI: 10.1126/science.1227721
Genomic variation in seven Khoe-San groups reveals adaptation and complex African history
Carina M Schlebusch et al. Science. 2012.
Abstract
The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ~2.3 million single-nucleotide polymorphisms in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but population structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response; potential adaptive introgression of protection from ultraviolet light; and selection predating modern human diversification, involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history.
Figures

(A) Sampling locations. (B) PCA of African individuals showing PC1 and PC2 rotated to fit geography. (C) PCA for Khoe-San populations (~2.3 million SNPs). (D) Pairwise FST for sub-Saharan populations (excluding the Hadza; see fig. S24 for comparison). (E) Prediction of the genetic components from geographic, linguistic, and subsistence covariates. The predictive error relative to geography is given for each combination of covariates (values <1 show improved predictive capacity as compared to that of geography).

(A) Rooted population topology from a concordance-test approach (14). Nodes with boot-strap support <50% are collapsed (dashed lines); all other nodes have boot-strap support >85%. (B) Clustering of 403 sub-Saharan African individuals (~270,000 SNPs), assuming 2 to 11 clusters. (C) Clustering of 118 southern African individuals (~2.3 million SNPs), assuming 2 to 8 clusters. Compare with fig. S16, which includes recently admixed individuals.

(A) Expected heterozygosity of 5 SNP haplotypes as a function of haplotype length. (B) Haplotype richness for 5 SNP haplotypes as a function of haplotype length. (C) LD, represented as r2, as a function of distance. (D) Cumulative RoHs for each population (0.5- to 1-Mb runs and averaged across individuals). (E to H) Heat maps of the summary statistics indicated in (A) to (D). (E) and (F) show the results at 50-kb windows; (G) shows ρ = 4 Ne × c, where ρ is estimated from fitting r2-decay curves to simulated data from a constant-size model (14) and c is the unscaled recombination rate; and (H) shows the population cRoHs (0.5- to 1-Mb class) averaged across 50 replicates of subsampling. For (A) to (C), the colors of the African populations are as in Fig. 1, and gray lines represent various non-African groups. For (A) to (H), all populations were randomly downsampled to seven individuals (without replacement), and SNPs with minor allele frequency < 10% were excluded.

(A) iHS values for each SNP on chromosome 10 in Ju/’hoansi, surrounding the muscle gene MYPN, and (B) on chromosome 6 in #Khomani, surrounding the immune system genes PRSS16 and POM121L2. The empirical P values (14) for 200-kb regions centered on the peak are given for each population. Locations of genes are shown by blue rectangles. (C) The greatest FST values for particular SNPs and pairwise population comparisons versus genome-wide FST estimates for the same population comparison. The top pairwise comparisons involving the Nama and another Khoe-San population (yellow) are found in the same region, separated by less than 4000 bp. (D) Proportion of genome-local ancestry (14, 24) for chromosome 16 in the Nama assigned to Khoe-San, Herero, or Bantu-speakers (South Africa). The population-specific chromosome-wide means are shown as dashed horizontal lines. The 99 percentile for Bantu-speakers (South Africa) ancestry, and the 1 percentile for the Khoe-San ancestry are shown as dotted horizontal lines. The two top SNP FST values are highlighted in yellow in (C) and (D). (E) Illustration of the aPBS approach for detecting selective sweeps in early modern humans. AMH, anatomically modern humans. (F) Stretches of consecutive positive aPBS values, with the top aPBS value plotted against the size of the stretch.
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