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

Abstract

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.

The genetic variation of lactase persistence alleles in northeast Africa

“…(Table 2) is in agreement with frequencies found in a study identifying lactose digesters through the hydrogen breath test (Bayoumi et al, 1981). been noted (Tishko↵ et al, 2007), and is in agreement with a previous study, that found the South Sudanese Nilotes to have remained largely isolated (Hollfelder et al, 2017). The lack of LP-associated alleles in the agro-pastoralist Nilotic populations has been observed before (Hassan et al, 2016;Tishko↵ et al, 2007) et al, 2004).…”

“…In an early study of lactose digesters in Sudan (Bayoumi et al, 1981) the Nuba and the Messiria also showed higher LP-phenotypes than predicted in this study. These populations are genetically close to the Nilotic populations (Hollfelder et al, 2017) and LP might be driven by the same unknown mechanism/mutations as in the Nilotes.…”

“…The sequencing results were added to 323,726 additional SNPs from chromosome 2, obtained from a filtered dataset of 3.9 million SNPs, typed on an Illumina HumanOmni5M Exome SNP array in a previous study (Hollfelder et al, 2017). This combined dataset was imputed and phased using "output" -2020/4/23 -10:39 -page 12 -#12 shown that F ST estimates on this diploid data set correlate strongly with a randomly haploidized version of the data set, therefore, measures such as LSBL can be used safely on the fully diploid data set (Hollfelder et al, 2017, SI).…”

“…To deepen our understanding of LP in Northeast Africa and the associated variants, we sequenced a 316bp region spanning all known SNPs associated with LP, in 221 individuals from 18 Sudanese and South Sudanese (SASS) populations. Combining this data with previously published high-density genome-wide genotyping data of the same individuals (Hollfelder et al, 2017), we were able to investigate the allele frequencies of the LPassociated SNPs, their haplotype backgrounds and to scan for signals of selection.…”

“…Even though this study investigated a range of Nilotic populations, no LP-associated SNPs were detected in these agropastoralist populations, that have been shown to be able to digest milk in hydrogen breath tests (Bayoumi et al, 1981(Bayoumi et al, , 1982Tishko↵ et al, 2007). Further studies on Nilotic populations will reveal more about the substructure in northeast Africa (Hollfelder et al, 2017) and can be informative about the underlying biology of LP in Nilotic populations.…”