Populations of the Middle Nile: Using Bioarchaeological and Paleogenetic Analyses to Understand Nubian Ancestry

Abstract

This work investigated a new means to explore Nubian ancestry using ancient DNA retrieved from archaeological skeletal material and marrying this perspective with bioarchaeological and other data sources. The focus of this project is centered on sites within the Middle Nile region of Sudan dated to before the Islamic conquest, where no paleogenomic work has recently taken place, but there is a wealth of bioarchaeological research. To begin, a sample population of 27 individuals was excavated from a cemetery, El-Kurru, northern Sudan, (near the 4th Cataract). Burial traditions and body treatment identify these individuals as Christian and their remains were bioarchaeologically analyzed for demographics (estimations of sex and age) and physiological markers of stress and disease (orbital lesions and cranial lesions, dental hypoplasias, non-specific lesions, trauma). The cemetery was contextually dated to post-14th century CE, meaning these people were living on the brink of a cultural transition, from Christian to Islamic dominance in the Upper Nubian region. Their remains showed high frequencies of dental hypoplasias and non-specific lesions, especially in subadults, indicating a heavy disease load and other stressors before adulthood; however, many adults lived to an older age with little signs of trauma. The frequencies of stress signals were interpreted within the context of Nubian contemporaneous populations and found to be consistent with other reported ranges. Christian burial treatments and “normal” stress markers of this population indicated the cultural transition had likely not arrived or did not have adverse consequences on this Medieval community along the Nile. To explore the genetic structure of Nubian ancestry in the Middle Nile region, a new dataset needed to be built from archaeological materials and new protocols were trialed to establish the most successful method to extract ancient DNA from human bone and tooth samples. Trials included the use of bleach and/or a predigestion treatment prior to extraction to increase the endogenous genetic content, leading to higher numbers of ancient sequence reads without compromising the uniqueness of reads obtained. Next-generation sequencing techniques were used to sequence these samples with a 40 percent success rate. Various burial contexts, states of preservation, and tissue types used were compared across the skeletal sample collection. These trials established that aDNA can be retrieved from material from the Middle Nile region of Sudan with extensive pretreatments of the tissue prior to extraction of the DNA. Mitochondrial genomes of six ancient Nubians were constructed using a hybridization enrichment method, which was vital to obtain sufficient 10X coverage of the genome. As a uniparental marker, mitochondrial DNA can reconstruct maternal heritage of individuals through common ancestors with genetic similarities. Two individuals showed African lineage, while the other four showed non-African ancestry. While limited, these results showed Nubians had a strong African component with evidence of gene flow from Eurasia dating back to at least Meroitic (4th century BCE) through Christian times. Through two dimension-reduction analyses, ancient Nubians show most genetic affinity with modern Egyptians, Middle Easterners, and East Africans, while less so to modern Sudanese. Although these individuals encompass varying archaeological contexts and span well over one thousand years, these initial results hint at a complexity of the genetic makeup and begin to reconstruct the impact of human migrations from outside Africa. This would be expected given the dynamic history of this powerful kingdom centered in the Middle Nile Valley.