Over the last decade, researchers had made advancements in unveiling some of the hidden secrets of the African continent with Ancient DNA. One region which have historically garnered attention was the lower Nile valley, North East Africa, home to who most refer to as Egyptians and Nubians. As of the 20th century, numerous archaeological expeditions contributed in rebuilding the lost legacies left by the societies of the region. And as of the last decade a handful of publications continued the tradition through the practice of Ancient genome analysis. Hundreds of individuals have been analyzed under this context, yet a decent resolution of who they were remain elusive, at least from an ethnogenic perspective. A few reasons for this is that 1. only a select few samples from pocketed regions were analyzed, 2. of them only a fraction had been subjected to Autosomal analysis and 3. of those individuals the oldest individual was only around 3,300 years before present.1 Now we might have a glimpse into what’s to come with a snapshot of possibly the oldest available aDNA sample from the Nile Valley.
Which sample(s) might we have?
It was a delight to be alerted of the possibility that new data especially on aDNA would be revealed soon. Though many strides have been made, Africa had still lagged behind many regions of the world when it came to aDNA recovery due to the warm climate harshly accelerating DNA degradation. Naturally as most would be, I was excited to learn that a 4,000 year old individual from the Upper Nile (Modern day Sudan) had been sequenced coming out of the Max Planck Institute. Along with the data availability, possible insight into how we can find more success in retrieving determinable genomic (specifically Autosomic) data might be discovered.
The sample was recovered from an archaeological site at Kadruka. From what could be interpreted, the DNA was highly degraded and was assembled by very short reads. The reads were processed form hair found at a funerary site after failed attempts at more conventional mummified tissue. And the findings were uploaded to a couple of gene-banks without or before any mainstream publication. This isn’t the first look or “rumor” of the advent of DNA extraction from samples at Kadruka nor is it the first time that discernible DNA of any kind had been reported. In 2020, it was acknowledged that the Laboratoire d’archéologie préhistorique et anthropologie, University of Geneva had sampled remains from Kadruka2. And over a decade prior Y. Hassan produced a thesis in which he’d report five individual’s Y-Chromosome Haplogroups from the site.3 The information presented on this page is merely the latest reported in hopes to make the information we have less fragmentary.
Which people occupied the neolithic site at Kadruka?
The peopling of Kadruka being close to the southern boarder of contemporary Egypt had been subjected to controversy related to identity. The site was associated with pastoralists from about 7,000 years ago (7Kya.)4,5 Analysis of physical remains there suggested that the area was peopled by a heterogeneous unit consisting of what some refer to as Biological North and Sub-Saharan Africans.6 On the other hand, there’s little archaeological evidence of high variance at the site, even when analyzing nearby contemporaneous cultural practices.7–9 The similarities stretched as far as Upper-Egypt where it had been noted at sites such as Gebel Ramlah (western desert)9. Funerary and dietary practices associated with pastoralism had been confirmed to link these various settlements near the Nile corridor.5,10 Uniparental Y-DNA analysis falls in-line with most findings but gives little resolution in addition. 60% of the samples at Kadruka identifiable as male carried haplogroups most frequent in South Sudan and the remaining individuals were shown to belong to the macro haplogroup E which is all encompassing of individuals of Africa and the Middle east at the time.11
This individual reported here (KDR001) shows notable differences with people of the region both Modern and Historic. Interestingly, the uploader(s) noted that the sample was indifferent from Pastoral populations of East Africa.
Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the site of Kadruka. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kilometres away. Our findings support established models for the southwards dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide the first direct evidence for a genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.
MPI-EVA (Max Planck Institute for Evolutionary Anthropology)
I took the initiative to further investigate how true the statement was with limited analysis via fstats testing for admixture (qpAdm12,13) and a Principal component analysis containing a large group of modern and ancient African Individuals.
The Principal Component Analysis (PCA)
An armchair analysis of the PCA chart suggests that the ancient individual closest to Kadruka was one discovered at the Molo caves, (GoJi3) Kenya.2 This individual had been linked to the Pastoral-Neolithic due to confirmed dietary practices such as milk consumption.14 Another notable aspect is how KDR001 treads further into the cline containing East African foragers. Other ancient individuals from Sudan as shown previously cluster intermediately between North Africans, Pastoral-Neolithic and Modern Sudanese populations like the Beja.
Admixture analysis
This is an admixture chart created with the sole purpose of displaying a parsimonious model of Ancestry in KDR001. Only the best 2-way model and overall p-value (0.8308) is published here for KDR001. Other related populations were investigated for a side by side comparison. With the exception of populations marked with an asterisk(*) all runs with a P-value <0.1 was rejected. In the case all permutations were rejected, the model with the best P-value is represented. Being that KDR001 formed a decent fit with two sources of ancestry, I aimed to get the other populations a 2-way model. Single donor populations were periodically added to the models with rejected sources. For simplicity only 4 candidate populations were selected as donors. The best fitting Near Eastern ancestor, A north African ancestor, the best fitting East African Forager ancestor and a Nilotic Ancestor.
Similar to the PCA, We can see KDR001 shows a similar genetic make up with Pastoral-Neolithic East Africans and is differentiated by the presence of Nilotic ancestry represented by the Dinka. The most similar compositions were held by late Rift Valley Pastoral populations, at Hyrax hill and Molo caves as well as the first ancient East African pastoralist with published genomes, Tanzania’s Luxmanda.15 (A three way model for KDR001 involving early Neolithic Moroccans from site Ifri n Amer Moussa is respectable though yields a slightly lower P-value)
What can we quickly takeaway
Much cannot be said outside of what the “leaked” abstract above can confirm. I say so due to the extremely poor (though available) coverage of the specimen. At first glance it might not come as a surprise that the genetic profile of East African Pastoralists could be found so far north. It is seldom accepted that the origin of Cushitic people who share a similar Autosomal make up had their origin in the upper Nile valley. However the idea that this genetic make-up is associated with Cushitic speakers had been purported in aDNA studies of Ancient east Africa and modern Southern Africa.16–18 Though the Autosomal make up of the populations are similar there are key differences between Pastoral-Neolithic (PN) populations of East Africa and Contemporary Cushitic, Horn (and Ancient Sudanese) populations that I will reveal in a future post. One tidbit, is the propensity of PN populations to trend towards East African foragers. How this relates to Kadruka is noticeable when one scans the PCA chart. There is a likelihood that Neolithic Sudanese populations could reveal North East African substructure poorly encapsulated in available populations. But what can be said now, is that Kadruka does have a great association with Pastoral neolithic populations though not particularly indistinguishable.
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