Where are the Ancient Egyptians From? Old Kingdom DNA Ancestry - Archaeological Science Ep 18

Back in February, I did an episode on the DNA of an ancient Egyptian who lived during the Old Kingdom, also known as the Age of the Pyramids. This genome was presented in a recent doctoral thesis, and in that thesis, it was found that the Old Kingdom Egyptian derived most of his ancestry from that seen in the Natufians, an epipaleolithic West Asian population indigenous to the Levant and associated with the first agricultural practices there. Now, this ancient Egyptian man's nucleogenome has been re-sequenced to higher coverage, and the findings were recently published in the journal Nature. This is the highest quality ancient Egyptian genome published to date, and the results have revealed exciting, and perhaps unexpected, new affinities between this Old Kingdom Egyptian and nearby ancient populations. I'm Madam Archaeologist, your go-to informant on everything archaeology, and in this episode, I'll go over the updated ancestry of the Old Kingdom Egyptian, reveal the exciting new genetic connection with the nearby population, and consider how his DNA relates to later ancient Egyptians and the Egyptians today. Let's start off with a question. Who was the ancient Egyptian man whose nucleogenome was sequenced? We don't know his name, but we can learn a few things about him from his burial and the scientific analysis of his bones. He lived between 44 to 64 years of age, probably closer to 60, and was interred inside a ceramic pot placed within a rock-cut tomb at Numirat in Upper Egypt. His teeth were radiocarbon dated to between 2855 and 2570 BC, coinciding with the early dynastic period and Old Kingdom in ancient Egyptian chronology, with archaeological evidence favoring an Old Kingdom date. This tells us that he lived shortly after the unification of Upper and Lower Egypt around 3100 BC. His manner of burial suggests that he would have enjoyed a higher social status in Old Kingdom Egyptian society, but an analysis of his skeleton pointed towards a life of physical labor, the patterns of which suggest that he might have had a career as a potter. The analysis of isotopic signatures in his teeth further suggests that he was a local Egyptian. If you'd like to learn more about stable isotope analysis, I discussed this in my episode What Can We Learn About a Person From Their Bones? Here, the isotope signatures in the Numirat individual's teeth were consistent with a childhood spent in the Nile Valley, and throughout his life, he had no idea that, more than 4500 years later, he would be famous for becoming the first Old Kingdom Egyptian to have his nuclear genome published. Let's dive into his DNA. Here are two PCA plots. PCA stands for Principal Component Analysis and allows us to visually compare individuals within and between populations. The left PCA plot shows the position of the Numirat individual, represented by the red circle, in comparison to global populations, while the one on the right takes a closer look by just comparing ancient and modern populations from North Africa and West Asia. In the left image, we can see that he clusters with present-day West Asians, represented here in blue, and then on the right, we see that he falls near the intersection of what we call two clines. A cline is a gradient of genetic variation. It represents a gradual change in allele frequencies across a geographical area. One here is called the Levant Iran Paleolithic cline, and the other is called the Morocco Paleolithic West Asia cline. In terms of relationships to ancient individuals, he plots close to two ancient Egyptians from a later period in Egypt's dynastic history, represented by these purple diamonds, and Neolithic individuals from the Levant, represented by orange squares on one side, and Middle Neolithic samples from Morocco on the other. This analysis suggests that the Numirat individual had closer genetic affinities to West Asians and North Africans, but we need to use other tools to dig deeper. Archaeogeneticists commonly employ a statistical tool called QPATOM to model the ancestry of ancient individuals, or even whole populations, and estimate ancestry proportions. A model is just a combination of possible ancestral sources. Models that give us a p-value of at least 0.05 are considered statistically significant, or a good fit with the data, while models yielding p-values under 0.05 can be rejected. In other words, QPATOM tests whether an individual or population can be modeled as a mixture of different source populations and estimates the percentages. The best working model here saw that about 77.6 plus or minus 3.8 percent of the ancestry of the Numirat individual was most similar to that seen in the Middle Neolithic population from a site in Morocco called Skirat Razi, while the rest of his ancestry, or 22.4 plus or minus 3.8 percent, was related to Neolithic Mesopotamians from about 9 to 8,000 BC. Let's unpack this. First of all, what was the ancestry of the Middle Neolithic Moroccans? The Middle Neolithic Skirat Razi population was represented by three genomes and published in this paper, Northwest African Neolithic Initiated by Migrants from Iberia and the Levant. They could be modeled as deriving 76.4 plus or minus 4 percent of their ancestry from sources related to the Neolithic Levant, and 23.6 plus or minus 4 percent related to the local North African Iberomorosians. The Iberomorosians themselves were admixed between ancient Levantines and ancient North Africans. If you'd like to learn more about them, I have dedicated an entire episode to their DNA. But to give you some context for this video, in a recent study, the Iberomorosians from Grotte de Pigeon near Tafralt in Eastern Morocco, who lived roughly 14 to 15,000 years ago, were modeled as deriving roughly 60.8 percent of their DNA from an Atufian-like source, so ancient Levantine, and about 39.2 percent of their DNA from an ancestral North African lineage. This ancestral North African lineage is very ancient and diverged from Sub-Saharan African lineages around the same time that the lineage leading to non-Africans did, that is tens of thousands of years ago. It is distinct from all Sub-Saharan African and non-African populations, and so it represents a truly ancient indigenous North African lineage. So overall, the Middle Neolithic Skira-Tirazi population had strong genetic ties to the Levant, coming from more recently arrived individuals harboring Levantine ancestry alongside much more ancient Levantine hunter-gatherers who had contributed their DNA to the Iberomorosian gene pool, and they harbored ancient North African ancestry as well. This ancient Levantine genetic connection is unfortunately barely discussed in the Old Kingdom paper's main text. We find some discussion in the supplementary information document, where you can see that QP Adam modeling, using even more ancient or distal sources, found that a three-way model comprising 67.3 plus or minus 3.7 percent Neolithic Levantine, 18.4 plus or minus 3.1 percent Epipaleolithic Morocco, and 14.3 plus or minus 4.6 percent Neolithic Zagros, that is farmers from Iran, was also a good fit for modeling the New Era individual's ancestry. Two of these sources, the Epipaleolithic Moroccans and the Neolithic Levantines, as we already know, can also be used to successfully model the ancestry of the Middle Neolithic population of Skira-Tirazi, telling us that the Middle Neolithic Moroccans and ancient Egyptians derive their ancestries from very similar sources. But, as we can see, New Era differs from these ancient Moroccans in deriving some ancestry from the Eastern Fertile Crescent as well. There's also a small paragraph in the supplementary information that mentions that the ancestral composition of Neolithic North Africans is comprised of more ancient sources, including Levantines, but it would have been nice to include this in the main text because it ties with the archaeological evidence for the spread of farming into Egypt, which I'll discuss in a second. Now, this affinity to Middle Neolithic populations from Morocco doesn't make the ancient Egyptians Moroccan. It is more like the ancient Egyptians and ancient Moroccans shared a significant genetic heritage. As populations from the Levant moved out of West Asia and into North Africa, Egypt would have been their first stop, and it is highly likely that at least one of the groups that settled in Egypt were Levantine farmers, because not only do we find this ancient Levantine connection in the DNA, but when we look at the archaeological record, domesticated crops show up in Egypt from the late 6th and 5th millennia BC onwards, and these crops are Near Eastern in origin, suggesting that farmers from the Levant migrated directly into Egypt and settled there, bringing agriculture with them. That said, how many waves of migration out of the Levant into North Africa took place during Neolithic cannot be deduced from our current data. What we can say is that the Middle Neolithic population of Skira Razi best represents most of the ancestry seen in the individual. This doesn't mean that they are the direct ancestors of the Old Kingdom Egyptians. Rather, both the ancient Egyptians and ancient Moroccans derived part of their ancestries from the same or genetically very similar ancestral groups. While migration from Morocco to Egypt sometime after the start of the Neolithic could have taken place, the genetic and archaeological data together point towards a broader genetic heritage shared by populations across North Africa. The authors of the study themselves suggest the possibility of shared ancestry across the region at that time and that the local Neolithic populations of Egypt gave rise to the dynastic Egyptians. One thing that stands out to me in the Neorite individual's updated ancestry estimate was the Epipaleolithic Moroccan. This is very interesting because it's the first time an indigenous North African component is being detected in an ancient Egyptian. I wonder if when the Neolithic farmers from the Levant came into the region, they mixed with some of these North Africans in Egypt, or if this component was introduced by later admixture with other North African groups. This can be clarified by getting DNA out of Neolithic samples from Egypt, which will prove difficult, but I am optimistic that if any DNA remains in them at all, archaeogeneticists will be able to piece enough of their genomes together for population level studies in the future. That roughly 22% ancestry related to so-called Neolithic Mesopotamians is also very interesting, and according to the Old Kingdom paper's supplementary information, the Neolithic Mesopotamians they used derived their ancestry from sources related to Caucasus hunter-gatherers, or Neolithic Iranians, who are closely related, and the rest mainly from Levantines. Chalcolithic Iranians derived their ancestry from similar sources to Neolithic Mesopotamians and lived closer in time to the Neorite individual, but when tested in a two-way model with Middle Neolithic Morocco, the model was rejected, yielding a p-value of 0.01, while Neolithic Mesopotamia was not rejected, yielding a p-value of 0.12, and this model is, in fact, the best-fitting model here. Together, these suggest that the Iranian Neolithic-related component seen in the Neorite individual's three-way distal model was most likely derived from Neolithic Mesopotamians, or a closely related source who harbored Iranian Neolithic-related ancestry. This is a fascinating finding because Mesopotamia and Egypt witnessed the emergence of the two first Bronze Age civilizations, and this new DNA evidence suggests that people from these two regions weren't just sharing ideas, they were actually exchanging genes. It would be interesting to find out when and how this so-called Mesopotamian component was introduced to Egypt. Was it during or around the Bronze Age, or was it earlier, during the Neolithic? This ancestral component is hard to trace with just one Old Kingdom genome because it is best represented by a source dated to about 9-8000 BC, that's thousands of years before the Neorite individual lived. When farming first emerged, the first farmers in the three main regions, the Levant, Anatolia, and Iran, emerged largely from their respective regions' local hunter-gatherers, who were all genetically distinct, with the side note that Iranians were genetically close to Caucasus hunter-gatherers. As time went on, throughout the Neolithic, Chalcolithic, and Bronze Age, these groups admixed with each other, reducing genetic differentiation between West Asian populations. Such gene flow could have extended into Egypt as well. But if this ancestry came later in this timeline, then the movement of people from the region of Mesopotamia could have been the means by which new ideas, like the potter's reel and writing, spread to Egypt, because these emerged in Mesopotamia before they are found in Egypt. These are all just hypotheses right now, the timing of this admixture, and how many migrations took place needs testing with further samples. How this ancestry got to Egypt also needs figuring out. For example, if it came via intermediaries harbouring a large component of Neolithic Mesopotamian ancestry, then which populations were these? We'll only be able to gain a clearer picture once Neolithic genomes from Egypt and many other early dynastic and old kingdom samples have been sequenced. Getting more Neolithic to Bronze Age samples from the Near East would also help to refine our picture and find possible intermediaries. The more ancient populations tested, the better. Now, when we compare these results to the doctoral thesis, it's not that the doctoral thesis was wrong when it said that the New Era individual had predominantly Natufian or Levantine-derived ancestry. It's just that since the researchers were able to get better coverage of his nuclear genome, they gained greater insights into his genetic ancestry. New affinities with groups were revealed because 1. the resequenced data captured more SNPs than the original attempt, and 2. genetic research on ancient North Africa has advanced quite a bit in the last couple of years. Also, that Levantine connection discussed in the thesis is still there, as we've seen, it just unfortunately wasn't elaborated on more in the new paper, at least not to the same extent as in the thesis. Perhaps because by the time of the emergence of the state, the Levantines that had settled in Egypt and other parts of North Africa had already been in the region for a long time, and so the dynastic Egyptians emerged to a great extent from local populations, but with the caveat that these populations derived their genetic ancestries from more ancient populations, a large portion of which were Levantine in origin. The paper also published a facial reconstruction of the New Era individual. This was based mainly on his skull, and if you notice, the reconstruction has been done in black and white because, unfortunately, phenotypic predictions based on his DNA were not very sound. Information on some genes were missing, for example, the New Era individual carried derived alleles at RS1426654 on gene SLC24A5, which is the strongest gene associated with lightening of skin pigmentation in western Eurasians today, but he was missing information on the second most important gene, SLC45A2, and many other genes that affect phenotypic traits, and so any predictions are inconclusive. The researchers didn't see his genotype as giving us evidence of what his skin and hair color most likely were, and so because of this, they decided to do the reconstruction in black and white and without head or facial hair. I really appreciate them having made note of this because in the past, a lot of guesswork has gone into these reconstructions, but then the reconstruction is treated as if it's fact. For example, with Cheddar Man, the researchers didn't get a complete profile for genes related to skin color. They were missing some genes entirely, and for some, they only got information on one of the copies, note that you have two copies of each gene, and so the researchers guessed which alleles Cheddar Man would have carried for some genes and went with his phenotypic predictions based on that. His eyes also had a chance of being green instead of blue, and yet they went with blue, but most people don't know this. You have to go to the paper's supplementary materials to find this out. Maybe their guess was correct, but that's what the reconstruction is based on, I guess. That the researchers here admitted they don't have enough evidence to give us a reconstruction of the Old Kingdom Egyptian with skin and hair color was a really honest approach to their work, and I really appreciate that they didn't make any guesses and then have their facial reconstruction presented in the press as if it's fact. More reconstructions need to be approached like this. But of course, if someone's profile is complete, we have all the alleles and predictions come back that this person has an extremely high chance of having had a specific eye, skin, or hair color, then by all means, go ahead and make the facial reconstruction based What about the Egyptians who lived after the Old Kingdom? Are they related to the Old Kingdom Egyptians? In 2017, nuclear data from three mummies excavated at the site of Abusir el-Melek were published. Two of these were dated to the Third Intermediate to Late Period and one to Greco-Roman times. The original study found close connections between these individuals and Near Easterners, particularly Neolithic and Bronze Age Levantines. Now, the Third Intermediate Period individuals were remodeled in light of the newly generated Old Kingdom data. Two two-way models yielded significant p-values. In one model, they derived 44.5 plus or minus 5.7 percent of their ancestry from that seen in the New Eirat individual and 55.5 plus or minus 5.7 percent from Bronze Age Levantine groups, while in the other, one source was 35.5 plus or minus 5.6 percent Middle Neolithic Morocco, represented again by Skirat Rwazi, and the other 64.5 plus or minus 5.6 percent Bronze Age Levantine. Given that the ancestry seen in the Middle Neolithic population of Skirat Rwazi represents much of the ancestry seen in the Old Kingdom Egyptian, this suggests that this ancestry was more widespread in Egypt and that the Third Intermediate Period Egyptians thus derived a good portion of their ancestry from earlier Egyptians. These new models don't change the overall conclusion of the 2017 study, that these Later Ancient Egyptians were genetically close to Neolithic and Bronze Age Levantines, because as we've seen, the Middle Neolithic Moroccans carried a significant Neolithic Levantine-related genetic component, and the Third Intermediate Period individuals also carried an ancestral component best represented by Bronze Age Levantines. So, the Levantine connection still stands strong. However, this remodeling does help to expand our picture because it tells us that these Later Egyptians were, at least in part, descended from earlier Egyptians and tells us that there was both continuity and change in Ancient Egypt's gene pool over time. It's also worth noting that in the thesis, admixture analysis suggested that around 90% of the New Erat individuals' ancestry was Natufian-like and 10% Ancient Ethiopian-like. But then when tested statistically, Ethiopian ancestry was rejected. The thesis concluded that background noise was the most plausible reason for this Ethiopian component showing up in admixture. The new study proves this inference right, as the higher quality genome did not show ancestry from Sub-Saharan African populations in either admixture analysis or cupiadum, even from nearby East Africa. This paper then also supports the suggestion, based on previous DNA studies and both modern and ancient Egyptians, that Sub-Saharan ancestry increased or arrived in Egypt more recently. The new paper analyzed the genomes of present-day Egyptians too and found both substantial heterogeneity in the modern Egyptian population and also significant links with their land's ancient past. They found most Egyptians today derive about 32.1 to 74.7% of their ancestry from sources related to the Old Kingdom New Erat individual. The paper states, I quote, If tracing the ancestry of many present-day Egyptians in our study to the Bronze Age, much of it would be found in groups related to New Erat or alternatively to sources best represented by Middle Neolithic Morocco, from which approximately 80% of New Erat's ancestry derives. The second most common ancestry component is related to the Bronze Age Levant, consistent This suggests that modern Egyptians have strong ties to the ancient Egyptians, being their descendants, but that they have also received additional admixture in post-dynastic periods, which is expected given Egypt's rich history and position as a crossroads. Notably, modern Egyptians have acquired a substantial amount of Sub-Saharan African ancestry. The new paper dates the influx of this Sub-Saharan ancestry to about 27 generations ago, or roughly the 13th-14th century AD. This is in line with estimates given in a paper on modern Egyptians, which gave a date of roughly 25 generations ago, and the 2017 paper, which gave an estimate of 24 generations ago. Together, these suggest that the Sub-Saharan African DNA seen in modern-day Egyptians came largely from admixture that took place during the Middle Ages. Egypt has been a really hard region to sample for ancient One, heat acts as a catalyst for DNA degradation, and two, many individuals have been mummified, the materials of which used in the process can be harmful to DNA. But with advancements in the field of archaeogenetics, we are finally starting to fill in this large gap in our genetic history of the world. Getting a high-quality genome from an Old Kingdom Egyptian is one of the biggest archaeogenetic accomplishments of the decade. This Old Kingdom individual derived his ancestry from sources best represented by the Middle Neolithic Moroccans and Neolithic Mesopotamians. These sources, in turn, derived their ancestry from more ancient groups, originating largely in the Levant, but also in other parts of West Asia and also North Africa. The study overall suggests that the ancient Egyptians shared a significant genetic heritage with other ancient North Africans, and that they also had genetic connections to West Asians. While we only have one published genome from the Old Kingdom, I want to stress that one genome isn't just one genome, because that person got his DNA from his parents, who got their DNA from their parents, and so on. And so one genome, unless it's from an immigrant, can give us interesting insights into a population's genetic history. The fact that the later Third Intermediate Period Egyptians derived a good portion of their DNA from that seen in the Nuerat individual also suggests that this Old Kingdom Egyptian's DNA was more widespread in Egypt. And so even though we need more genomes to gain a more complete picture of the DNA of the ancient Egyptians, at least a part of the ancient Egyptian population can be represented by this ancestry. This year has seen a few really great papers published on the DNA of ancient North Africans, and I'm looking forward to what's coming next. As usual, if you have any thoughts, feel free to drop a comment and subscribe for more cool content where it goes from informants on everything archaeology to Madame Archaeologist.