Data from: Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations

Northeast Africa has a long history of human habitation, with fossil-finds
from the earliest anatomically modern humans, and housing ancient
civilizations. The region is also the gate-way out of Africa, as well as a
portal for migration into Africa from Eurasia via the Middle East and the
Arabian Peninsula. We investigate the population history of northeast
Africa by genotyping ~3.9 million SNPs in 221 individuals from 18
populations sampled in Sudan and South Sudan and combine this data with
published genome-wide data from surrounding areas. We find a strong
genetic divide between the populations from the northeastern parts of the
region (Nubians, central Arab populations, and the Beja) and populations
towards the west and south (Nilotes, Darfur and Kordofan populations).
This differentiation is mainly caused by a large Eurasian ancestry
component of the northeast populations likely driven by migration of
Middle Eastern groups followed by admixture that affected the local
populations in a north-to-south succession of events. Genetic evidence
points to an early admixture event in the Nubians, concurrent with
historical contact between North Sudanese and Arab groups. We estimate the
admixture in current-day Sudanese Arab populations to about 700 years ago,
coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture
that reached the Darfurian/Kordofanian populations some 400-200 years ago.
In contrast to the northeastern populations, the current-day Nilotic
populations from the south of the region display little or no admixture
from Eurasian groups indicating long-term isolation and population
continuity in these areas of northeast Africa.