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A community divided? Revealing the community genome(s) of Medieval Kulubnarti using next- generation sequencing

The Nubian site of Kulubnarti is home to two contemporaneous and geographically proximate cemeteries that appear to reflect the existence of two socioeconomically disparate communities living side-by-side during the Early Christian era (AD 550-800). While anthropological analyses suggest substantial inequality between the island and the mainland communities, biologicalrelationships within and between these two groups have only been explored using morphology. Because of its location along the Nile migration corridor, Kulubnarti represents an ideal site to explore a connection between biological and social relationships. However, the genetic analysis of ancient sub-Saharan African populations presents exceptional challenges due to the thermal degradation of DNA. Here we demonstrate that ancient DNA analysis of African samples is now possible when optimized methodologies for DNA preparation and next-generation sequencing technologies are used. Thirty-two samples have been analyzed so far and have yielded endogenous human DNA contents ranging from 0.15-33.8%. Preliminary results, including mitochondrial haplogroup analysis, suggests there may be substantial differences in the genomic composition between the two Kulubnarti communities, with 70% of individuals from the island cemetery demonstrating African-based haplogroups (L2, L1, and L5), compared to only 36.4% of mainlanders, who instead show an increased prevalence of European and Near Eastern haplogroups (including K1, H, I5, and U1). Low-density principal component analysis suggests genetic affinities that include both African and Near Eastern input. Continuing work that includes deeper sequencing of Kulubnarti samples will provide even more informative genetic data from the Kulubnarti Nubians going forward.

Nubia; ancient DNA; next-generation sequencing

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