Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool
Open accessAbstract
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 the dataset of Pagani et al. (2012), different Eastern African populations have Levantine ancestry, with the remainder of their ancestry forming a clade with Mota, a ~4,500 year old sample from Ethiopia.
“(b) Levantine ancestry in different Eastern African population in the dataset of Pagani et al. (2012); the remainder of the ancestry is a clade with Mota, a ~4,500 year old sample from Ethiopia50.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as Pagani et al. (2012)
The Results (page unavailable) find that the non-African component of Semitic and Cushitic Ethiopian populations is closer to populations inhabiting the Levant than to Yemen, supporting the Levantine-affinity part of the claim. The paper distinguishes an African component but does not mention Mota or establish that this component forms a clade with a ~4,500-year-old Ethiopian sample. (LLM, conf=0.89)
Experimental — accuracy not yet measuredThe hypothesis that European farmers stem directly from a population related to the ancient farmers of the southern Levant can be ruled out, since European early farmers share more alleles with Anatolian Neolithic farmers than with Levantine farmers: f4(Europe_EN, Chimp; Anatolia_N, Levant_N) is positive (Z=15).
“We can rule out the hypothesis that European farmers stem directly from a population related to the ancient farmers of the southern Levant29,30, however, since they share more allele with Anatolian Neolithic farmers than with Levantine farmers as attested by the positive statistic f4(Europe_EN, Chimp; Anatolia_N, Levant_N) (Z=15).”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [30]
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- Authors
- Pagani, L., Kivisild, T., Tarekegn, A., Ekong, R., Plaster, C., Gallego Romero, I., Ayub, Q., Mehdi, S. Q., Thomas, M. G., Luiselli, D., Bekele, E., Bradman, N., Balding, D. J., & Tyler-Smith, C.
- Affiliations
- University of Cambridge (GB)
- Addis Ababa University (ET)
- University College London (GB)
- Wellcome Sanger Institute (GB)
- Sindh Institute of Urology and Transplantation (PK)
- University of Bologna (IT)
- Corresponding author
- Pagani, Luca
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2012-07
- Volume
- 91
- Issue
- 1
- Pages
- 83-96
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC3397267
- OpenAlex
- W2089722101
- Cited by
- 230
- References
- 55
- Citations by year
- 2026: 7 · 2025: 49 · 2024: 1 · 2023: 17 · 2022: 16 · 2021: 11 · 2020: 14 · 2019: 20 · 2018: 18 · 2017: 12 · 2016: 14 · 2015: 23 · 2014: 19 · 2013: 6 · 2012: 3
- FWCI
- 9.83
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion)
- Funders
- Wellcome Trust (098051)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Keywords
- Ethiopian population, genetic diversity, linguistic stratification, SLC24A5, out-of-Africa migration, Levant, linkage disequilibrium decay, human origins, Somali
- MeSH terms
- Emigration and Immigration, Ethiopia, Gene Pool, Genotype, Haplotypes, Humans, Language, Phylogeny, Genetic Variation, Linkage Disequilibrium, Black People, Phylogeography
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