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. 2012 Jul 13;91(1):83-96.
doi: 10.1016/j.ajhg.2012.05.015. Epub 2012 Jun 21.

Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool

Luca Pagani  1 , Toomas Kivisild, Ayele Tarekegn, Rosemary Ekong, Chris Plaster, Irene Gallego Romero, Qasim Ayub, S Qasim Mehdi, Mark G Thomas, Donata Luiselli, Endashaw Bekele, Neil Bradman, David J Balding, Chris Tyler-Smith
Affiliations

Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool

Luca Pagani et al. Am J Hum Genet. .

Abstract

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ~3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ~60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.

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Figures

Figure 1
Figure 1
Principal Components and STRUCTURE-like Analyses of the Full African Data Set The first three PCs are represented in bidimensional plots (first versus second in A and first versus third in B). The samples genotyped in this study are represented in yellow (Semitic), orange (Cushitic), red (Omotic), or blue (Nilotic); the rest of the African samples are shown with the use of a gray scale. The proportion of explained variance is reported next to each axis. (C) displays the best fit (K = 7) ADMIXTURE result, including all the African samples and with the addition of French as a non-African population. The colors in (C) do not match those in (A) and (B). (D) shows the sampling locations in Ethiopia. Each population is colored according to the linguistic family to which it belongs. (E) Correlation between the proportion of “non-African” admixture (x axis, blue component from C) and the first three PCs for the Semitic, Cushitic, Omotic, and Egyptian samples. (F) Correlation between the proportion of Nigerian-Congolese admixture (x axis, red component from C) and the first three PCs for the Anuak, Gumuz, and South Sudanese samples.
Figure 2
Figure 2
Pairwise FST and SNP Heterozygosity in a Set of Worldwide Populations FST was calculated with the use of ten individuals from each worldwide population and Egyptians (A), Yoruba (B), and Semitic-Cushitic (C) and Nilotic-Omotic Ethiopians (D), and is displayed as a heat surface, produced with the Surfer software. Values in (C) and (D) are the averages for all the Semitic-Cushitic or Nilotic-Omotic populations. (E) shows the average genomic heterozygosity calculated for the same samples with the use of the available SNPs. The bottom-right section of each panel includes a scatter plot displaying the actual values of either Fst or heterozigosity over the geographic distance (in km) from Addis Ababa (negative for sub-Saharan populations). Filled and empty circles represent non-African populations along the putative northern or southern routes, respectively. Triangles represent sub-Saharan populations.
Figure 3
Figure 3
Pairwise FST between Semitic-Cushitic Ethiopians and Surrounding Populations Contour plots derived from FST were calculated with (A) ten haploid genomes from the Semitic-Cushitic Ethiopians, showing that modern Yemeni, Egyptians, and Moroccans are closest to the Ethiopians, and (B) ten haploid non-African genomes from the same groups, showing instead a prevalence of Egyptian and Middle Eastern contributions to the non-African Ethiopian gene pool.
Figure 4
Figure 4
ROLLOFF Plots Three populations from each of the four historical periods of admixture (A: 1500 CE) are plotted to show their LD decay (represented by a weighted correlation coefficient as previously described39) with genetic distance. The legend reports the name of each population, with the estimated date of admixture in brackets. Notably, all three Nilotic populations (Gumuz, South Sudanese, and Anuak) have very flat decay curves compared to those of the other populations in the same plot.
Figure 5
Figure 5
LD Decay over Distance Analyses were performed with the use of 12 individuals from a set of African populations (A), including Ethiopians (red-yellow scale), west-central Africans (gray scale), and click speakers (blue scale). A modified version of the same analyses (B) was performed with the use of only ten haploid African-genome equivalents. In both cases, the Ethiopian samples show less-rapid LD decay than the other African populations in the figure.
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