Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

Division of Biological Anthropology, University of Cambridge, UK.
The American Journal of Human Genetics (Impact Factor: 10.93). 06/2012; 91(1):83-96. DOI: 10.1016/j.ajhg.2012.05.015
Source: PubMed


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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    • " in Uganda has a likely European source , for example , resulting from the heavy European colonial involvement since the 1870s ( Maxon 2009 ) . One possibility is a Bronze - Age dispersal from the Near East accompanying the spread of Semitic languages ( Kitchen et al . 2009 ) , consistent with an inferred Levantine ( rather than Arabian ) source ( Pagani et al . 2012 ) . However , the T1a lineage is a possible candidate , and it is also possible that the Arabian lineages in Uganda , such as HV1b1 , might only have arrived very recently in the Great Lakes region . We therefore used 46 autosomal AIMs to explore further the ancestry of the individuals carrying HV1b1 and T1a , to test whether or not the"
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    ABSTRACT: The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.
    Human Genetics 07/2015; 134(9). DOI:10.1007/s00439-015-1583-0 · 4.82 Impact Factor
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    • "Finally, we note that the sampling scheme used here is geographically uneven, and is constrained by current knowledge on the distribution of extremely rare deep lineages (Supplemental Table S7). This calls for a more even sampling coverage of MSY diversity in Africa, which should be also compared with the conclusions of recent autosomal genetic and craniometric data (Ramachandran et al. 2005; Manica et al. 2007; Tishkoff et al. 2009; Pagani et al. 2012; Schlebusch et al. 2012). "
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    ABSTRACT: The phylogeography of the paternally-inherited MSY has been the subject of intense research. However, sequence diversity and the ages of the deepest nodes of the phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next generation sequencing, including 18 deep-rooting ones, and identified 2,386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY a large proportion of newly arisen alleles have survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our MSY tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: 1) patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; 2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; 3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e. a period of our evolution which had been previously considered to be poorly accessible with paternally-inherited markers.
    Genome Research 01/2014; 24(3). DOI:10.1101/gr.160788.113 · 14.63 Impact Factor
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    • "the latter of which will also include data pertaining to Gambian (The Gambia), Mende (Sierra Leone) and Esan (Nigeria) populations. The Human Genetic Diversity Project (HGDP) provides genotyping information for populations residing in the Central African Republic, the Democratic Republic of Congo and Senegal [3], whilst independent assessments of Malawian and Ethiopian genetic structure are also available [4,5]. "
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    ABSTRACT: Due to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap and 1000 Genomes Projects. Notably excluded, however, is the southern Africa region, which is inhabited predominantly by southeastern Bantu-speakers, currently suffering under the dual burden of infectious and non-communicable diseases. Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure. Here, we present the most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg). Participants were typed for ~4.3 million SNPs using the Illumina Omni5 beadchip. PCA and ADMIXTURE plots were used to compare the observed variation with that seen in selected populations worldwide. Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources. To assess the suitability of our sample as representative of Sowetans, we compared our results to participants in a larger rheumatoid arthritis case--control study. The control group showed good clustering with our sample, but among the cases were individuals who demonstrated notable admixture. Sowetan population structure appears unique compared to other black Africans, and may have clinical implications. Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme.
    BMC Genomics 09/2013; 14(1):644. DOI:10.1186/1471-2164-14-644 · 3.99 Impact Factor
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