Sudan’s complex genetic admixture history drives adaptation to malaria in Sudanese Copts
Vilà-Valls et al. · doi:10.1073/pnas.2516263123
What the study found
Sudan lies at the crossroads of Africa and the Middle East. Researchers sequenced the whole genomes of 125 people at high coverage, about 30 reads per position, from five ethnolinguistic groups spanning three language families. The genomes show deep population structure, built from four ancestral components: Nilo-Saharan, West Eurasian, Northern African and Western African, along with signatures of the Arab expansion.
The study reports over one million variants not previously catalogued, including deleterious alleles specific to these populations. The authors use this to argue that African genomes are still too thinly represented in reference datasets.
Working out where each stretch of a genome came from, the researchers found a strong signal of adaptive admixture on chromosome 1 in Sudanese Copts. A peak of Nilo-Saharan ancestry there was introduced by admixture 1,000 to 1,500 years ago. At that spot sits rs2814778, a variant in the ACKR1 gene that produces the Duffy-null blood group and gives resistance to Plasmodium vivax malaria. The estimated selection coefficient, 0.0996, is described by the authors as remarkably strong.
Key points
High-coverage whole genomes from 125 people in five Sudanese ethnolinguistic groups, spanning three language families.
Four ancestral components appear: Nilo-Saharan, West Eurasian, Northern African and Western African, plus signatures of the Arab expansion.
Over one million novel variants were reported, including population-specific deleterious alleles the authors say show how thinly African genomes are represented.
In Sudanese Copts, Nilo-Saharan ancestry brought in 1,000 to 1,500 years ago carries rs2814778, the Duffy-null variant that resists Plasmodium vivax malaria.
Relevance to this lineage
Sudan is a long way from the Souss-Massa, and this paper does not touch the Chtouka family line. It names no E-PF2546, no H1-T16189C! and no Amazigh (Berber) population.
Where it fits the story told here is the most recent layer, Arabization. The other sources on this site place Arab genetic input into North Africa in the medieval and later period; this study finds signatures of the same Arab expansion at the eastern end of the corridor, alongside a Northern African ancestry component inside Sudanese groups. It is a useful reminder that North African ancestry is itself a component that turns up elsewhere in Africa, and that the north-east of the continent was a crossroads on its own schedule, separate from the Maghreb.
This is a summary, not the paper
Written here as an aid to reading, from the paper’s published abstract. Where this page and the study disagree, the study is right — read it. Full citation: Vilà-Valls, L. et al. (2026). Proceedings of the National Academy of Sciences, 123, e2516263123. All fifteen summaries are listed on the research page.
Last updated: 16 September 2026