Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Open accessAbstract
North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from "back-to-Africa" gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.
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ALDER estimated a putative pulse-like admixture event at 24 generations ago (700 years ago), consistent with previous results from Henn and colleagues.
“We then used ALDER40 to estimate the time of a putative pulse-like admixture event, which was estimated to have occurred 24 generations ago (700 years ago), consistent with previous results from Henn and colleagues16.”
From Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods (2017) · cites this paper as [16]
By comparing ancient individuals from Abusir el-Meleq with modern Egyptian reference populations, the study found an influx of sub-Saharan African ancestry after the Roman Period, corroborating Henn and colleagues.
“By comparing ancient individuals from Abusir el-Meleq with modern Egyptian reference populations, we found an influx of sub-Saharan African ancestry after the Roman Period, which corroborates the findings by Henn and colleagues16.”
From Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods (2017) · cites this paper as [16]
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- Authors
- Henn, B. M., Botigué, L. R., Gravel, S., Wang, W., Brisbin, A., Byrnes, J. K., Fadhlaoui-Zid, K., Zalloua, P. A., Moreno-Estrada, A., Bertranpetit, J., Bustamante, C. D., & Comas, D.
- Affiliations
- Stanford University (US)
- Consejo Superior de Investigaciones Científicas (ES)
- Cornell University (US)
- Lebanese American University (LB)
- Corresponding author
- Bustamante, Carlos D.
- Comas, David
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-01-12
- Volume
- 8
- Issue
- 1
- Pages
- e1002397
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3257290
- OpenAlex
- W2059277852
- Cited by
- 331
- References
- 46
- Citations by year
- 2026: 11 · 2025: 25 · 2024: 16 · 2023: 26 · 2022: 11 · 2021: 29 · 2020: 16 · 2019: 28 · 2018: 29 · 2017: 27 · 2016: 29 · 2015: 22 · 2014: 26 · 2013: 23 · 2012: 13
- FWCI
- 16.19
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, other-oa)
- Greater South Information System
- Funders
- Generalitat de Catalunya (2009SGR1101)
- National Institutes of Health
- National Human Genome Research Institute (R01HG003229)
- National Institute of General Medical Sciences (R01GM083606)
- 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
- Berber populations, migration timing, local ancestry, Morocco
- MeSH terms
- Egypt, Ancient, Africa, Northern, DNA, Mitochondrial, Emigration and Immigration, Europe, Gene Pool, Genotype, Haplotypes, Humans, Middle East, Morocco, Population, Population Dynamics, Genetic Variation, Africa South of the Sahara, Polymorphism, Single Nucleotide, Genomics, Black People, White People, History, Ancient, Gene Flow
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