New DNA Evidence for the Ancient Egyptians - Archaeological Science Ep 7

I have a breakthrough to share on the DNA of the ancient Egyptians. Back in December, I did an episode on this topic focusing on this paper published in 2017, which linked mummies from the site of Abu Sir el-Malek to the Near East, particularly to an area called the Levant. This is a very important DNA study because it was the first, and at the time that I released the episode only, paper that published data on the nuclear genomes of ancient Egyptians. Nuclear means considering all of someone's DNA, and not just markers that tell us about direct maternal or paternal lines. It was also revolutionary in that it showed us that we can get nuclear DNA from mummies. In that sense, it was a big stepping stone in the study of ancient Egyptian population history. Most ancient DNA studies just focus on haplogroups, which only tell us about someone's ancient direct maternal or paternal lines. And those may tell us something, but they don't give us a full picture of someone's genetic ancestry. Meanwhile, the nuclear genome does. My video received mixed reactions, but alas, we can't argue with DNA. However, it does require a great deal of interpretation, which archaeogeneticists are specialized in. And as we collect more and more ancient DNA samples, our interpretations will become more refined. Now, we have the nuclear genome of an Egyptian from the Old Kingdom, the time of the pyramid builders, published in a doctoral thesis that was made available online on the 1st of February 2025. Combining this genome with the 2017 study, we are gaining interesting insights into who the ancient Egyptians were at the genetic level. I'm Madam Archaeologist, your go-to informant on everything archaeology, and in this episode, I'll revisit the DNA of the ancient Egyptians in light of new genetic data. I'll also discuss archaeological evidence for migrations and combine this with the ancient DNA studies to give a well-rounded emerging picture of who the ancient Egyptians were, and hopefully finally settle the debate on their origins. Buckle up, folks. So, who were the ancient Egyptians, and where did they come from? This doctoral thesis, just released online, included the first sequenced data on a human genome dated to the Old Kingdom. The sample comes from a male who was buried inside a pot placed within a rock-cut tomb at the Cemetery of Numerat, located in the 16th Nome of Upper Egypt. The ancient Egyptians had divided their land into 42 Nomes, or Sepat, which refer to provinces, out of which 20 were in Lower Egypt and 22 were in Upper Egypt. The sample is referred to in the to not have been attacked by grave robbers. The rock-cut tomb suggests that he was of a higher social status, but his grave wasn't as rich, suggesting that he wasn't part of the highest ranking members of society. Radiocarbon dating placed his remains between 2868 and 2492 BC, which coincides with Dynasties 3 and 4, as suggested by his burial. Ancient Egyptian history is divided into a series of Dynasties, which are then grouped into larger periods depending on political stability. Dynasties 3 and 4 are part of the Old Kingdom. This was an exciting time because it was the age of the pyramid builders. This new genomic data ties, once again, the ancient Egyptians to the Levant. Comparing the Numerat man's nuclear DNA to the DNA of other ancient populations as well as modern ones, it was found that at least 90% of his DNA was derived from Natufians, an epipaleolithic population who lived in the Levant and are associated with early cereal cultivation. In one test called Admixture Analysis, NUE001 was found to share the same ancestry as populations currently living in the Arabian Peninsula as well as a group called Bedouin where ancestry is ultimately derived from the Levantine epipaleolithic Natufians. While roughly 10% of NUE001's DNA was similar to the DNA of a 4,500-year-old Ethiopian, another test called Outgroup-F3 confirmed the affinity between NUE001 and the Natufians, but another test rejected any genetic ancestry coming from East Africa, suggesting that that 10% on the initial Admixture test was just background noise. In genetic sequencing, background noise refers to mistakes in sequences. These are more common in genetic studies than you might think. A bit of background noise is actually present in all DNA sequences, and so long as your sequence is generally high quality, it's not a big deal. Programs are usually able to work around it. Here are the results as presented in the thesis. I quote, QPADM ancestry modeling confirmed that NUE001 could not be modeled as a mixture of Levant Natufian and East Africa Late Stone Age ancestries. Same for the two 3rd Intermediate Period Egyptians. The low ancestry component estimate with Admixture could result from background noise, making it unlikely that NUE001 carried East African-related ancestry." Those two 3rd Intermediate Period Egyptians mentioned there were from the 2017 Abusir el-Malek study. Also, a simple definition of QPADM is that it is a statistical tool that helps archaeogeneticists study Admixture between populations in ancient samples. The thesis later concluded, I quote, that NUE001 derived the majority of his ancestry from ancestry present in the Natufians from the end quote. This not only tells us about this old kingdom Egyptians' genetic ancestry, it also suggests that there was a strong genetic connection between Egyptians at the time of the pyramid builders and populations from the Near East. And I wouldn't be surprised if ancient genomes from the bulk of Egypt came back as Natufian as well, because of the fact that archaeologists have found animals and crops domesticated initially in the Near East at early agricultural settlements up and down the Nile, meaning Near Eastern farmers likely settled in both Lower and Upper Egypt. We have these findings presented at a symposium on biomolecular archaeology held in Toulouse back in 2021. It was a follow-up to the 2017 study on mummies from Abusir el-Malek, which I will get to shortly. Although this research only focused on mitochondrial DNA, which traces direct maternal ancestry, it included a wider ranging sample. Mummies and skeletons from six sites up and down the Nile spanning approximately 4,000 years of ancient Egyptian history were sampled. Their mitochondrial haplogroups matched those estimated for the Abusir el-Malek individuals, adding support to the hypothesis that Near Eastern populations had settled along the Nile. At the moment, we just have this summary from the conference, but I hope the findings get published soon because I want to know which specific sites these individuals came from and which specific haplogroups were estimated. Regardless, the findings add support to the hypothesis based on the finding of Near Eastern crops in Egypt that Near Easterners had settled both in the Delta and along the Nile Valley before the rise of the ancient Egyptian state. Exactly when these Near Eastern populations, who were very likely farmers carrying Natufian-derived ancestry based on the Old Kingdom genome, settled in Egypt needs to be confirmed with even older genomes. Based on current archaeological evidence, people first started practicing agriculture in the Near East in an area we call the Fertile Crescent around 11 to 12,000 years ago. Likewise, many domesticated animals we rely on today were first domesticated in the Near East. If you'd like to learn more about the domestication process, check out my episode, The Reality of Domestication. Now, the finding of Near Eastern crops in the earliest agricultural settlements in Egypt suggests that Near Eastern farmers likely migrated into Egypt before the rise of the Egyptian state. Some scholars even suspect a possible Levantine origin for the Baderian culture, that is the earliest prehistoric culture in Upper Egypt to be associated with agriculture. However, this connection is often neglected in archaeological discussions of the neolithicization of Egypt. That Near Eastern domesticates spread to Egypt is a known fact, but the how is only sometimes touched on. This is in sharp contrast to neolithic Europe, where for the longest time the introduction of Near Eastern crops and animals into Europe was attributed to the migration of Near Eastern farmers and then this was confirmed with ancient DNA. The Old Kingdom genome prompts us to rethink the origins of farming in Egypt. Let's take a quick look at what we know about the spread of Near Eastern plants and animals into Egypt. The oldest domesticates that have been identified archaeologically in Egypt are animals, specifically cattle and goats. These date uncontroversially the earliest to the late 7th millennium BC and mainly to the 6th millennium. Their bones appear at archaeological sites in Egypt's western and eastern deserts. There's some debate over whether the earliest domesticated cattle in Egypt were brought from the Near East or whether these animals were domesticated independently in Egypt, but the goat's wild counterpart, the wild bazaar, is only indigenous to the Caucasus and Zagros mountains and archaeological evidence suggests that goats were introduced to North Africa from the Near East. During the 5th millennium BC, the number of sites with domesticated animals of Near Eastern origin multiplies in the western desert and domesticated animals appear in the Nile Valley as well. At this time, the pig, another species whose domestication began in the Near East, can be added to the animal bone assemblages. It is also from the late 6th and 5th millennium BC onwards that we finally begin seeing evidence for domesticated crops in the Egyptian archaeological record, such as emmerwheat, which was one of the first cereals in the world to be domesticated. Emmerwheat's wild progenitor only grows naturally in Israel, Jordan, southwestern Syria, Lebanon, southeastern Turkey, northern Iraq, and western Iran. Some other Near Eastern crops found at early agricultural settlements in Egypt include barley, lentils, and flax, and have been recorded at sites in the delta and in the Nile Valley. Evidence for Near Eastern crops have been found, for example, at Sais, Marim de Beni Salama, El Omari, in the Fayum region, and in the El Badari region, where they were associated with Badarian sites. This evidence suggests indirectly that there was migration from the Near East into Egypt during the Holocene and before the rise of the unified Egyptian state around 3000 BC, and the strong Natufian component in the Old Kingdom genome supports this, as do the mitochondrial haplogroups from the unpublished study. It's possible that there were smaller-scale migrations first that brought goats and possibly cattle to the western and eastern deserts, while more impactful waves likely took place in the 6th and 5th millennia BC, when farmers brought agriculture with them and set up the first agriculture-based settlements in Egypt. There could have been an even older migration, since DNA from 15,000-year-old skeletons found in Morocco showed that they derived around two-thirds of their ancestry from the Natufians. The timing of the migrations into Egypt can hopefully be clarified with future DNA studies. Another interesting and important question we need to ask is, how do the Abusir el-Malek mummies from the 2017 paper relate to the Old Kingdom Egyptian? This was explored in the doctoral thesis as well. Abusir el-Malek is located in the 20th nomen of Upper Egypt. In the 2017 paper, the Abusir el-Malek individuals who had their nuclear genome analyzed, clustered very closely with both ancient and modern Levantine populations on this PCA plot. PCA stands for Principal Component Analysis, and it's a very useful tool in population studies. There are too many technical details to go over, but essentially, different populations are plotted on the graph, and then you can see where your sample fits. If it clusters with a group, then it suggests close genetic relatedness between your sample and the population it clusters with. Two of the ancient Egyptian individuals used in this study dated to between the 3rd Intermediate Period and Late Period, although for the sake of simplicity, I'll refer to these simply as mummies from the 3rd Intermediate Period, while one individual was dated to Graeco-Roman times. According to the thesis, the 3rd Intermediate Period mummies derived about 80 to 90 some percent of their ancestry from that seen in the Old Kingdom skeleton, aka Natufian derived ancestry, and the rest from two other populations from the Bronze Age near east. The thesis states, I quote, We found evidence that the 3rd Intermediate Period Egyptians are consistent with being admixed between two West Asian populations dated to the Early Bronze Age and the Old Kingdom Egyptian represented by NUE001. Using QPADM, we could estimate the 3rd Intermediate Period Egyptians to be admixed with 16.3 ± 9.4% and 83.7 ± 9.4% ancestry from Early Bronze Age individuals from the Levant and NUE001, or 6.1 ± 15.7% and 83.7 ± 15.7% ancestry from Early Bronze Age individuals from Turkey and NUE001. End quote. The Abusir Elmelek mummies also had some Caucasus hunter-gatherer derived ancestry. This small Bronze Age West Asian component could have come from the Hyksos mixing with Egyptians. The Hyksos were a group of Levantines who settled in Egypt starting probably from the 12th Dynasty onwards and managed to rule over Lower Egypt during the 2nd Intermediate Period. Their rule is referred to by Egyptologists as Dynasty 15. At the time of the Epipaleolithic and into the Neolithic, when West Asians shifted towards living in sedentary settlements and farming, four genetic populations existed in the Near East, these are Levant Natufians, Anatolia Epipaleolithic, Iran Mesolithic, and Caucasus hunter-gatherers. DNA studies show that each of these populations were each genetically differentiated, with the exception of Iranian Mesolithic and Caucasus hunter-gatherers being closely related. Genetic studies also show us that the first farmers in the Levant, Anatolia, and Iran each emerged from the local hunter-gatherer population in their respective area. As time went on, there was greater mobility within the region, so that during the Chalcolithic Period and Bronze Age, Near Eastern populations were not as genetically differentiated anymore. In other words, all these populations were mixing with one another, acquiring each other's genes. The Hyksos moved into Egypt probably from the end of Egypt's 12th Dynasty onwards, so from the early 2nd millennium BC, that's after this mixing started taking place. Therefore, they likely brought DNA from West Asian populations other than Natufian with them. This is just one hypothesis, although it fits nicely with the historical record. The comparison between the Old Kingdom genome and the genomes of the Abusir el-Melek mummies is very interesting because it shows a great degree of continuity, genetically, between Egyptians of the Old Kingdom and Egyptians living during the Third Intermediate Period. And that's why even though we only have one genome from the Old Kingdom, I believe that that genome represents the indigenous Ancient Egyptian population, because that Natufian DNA remained strong 2,000 years later. Now, some of you may still be thinking that the Nuerat individual could have been an immigrant. Well, that's extremely unlikely and I'll tell you why. Remember the first farmers in the Levant, Iran, and Anatolia emerged from the respective local hunter-gatherer populations in each area who were all genetically differentiated. Then the genomes of Near Easterners from the Chalcolithic and Bronze Age Period showed mixing between these groups. So if the Nuerat individual was an immigrant, his DNA should have come back as a mixture of different Near Eastern populations. That he came back just about purely Natufian suggests that he's descended from a group or groups of people who moved out of the Levant before that genetic mixing took place in the Near East. So who were the Ancient Egyptians? By the time the Egyptian civilization had emerged and the Egyptians were writing texts, they saw themselves as their own population from a land they likely named based on the Nile Valley's fertile soil, that is the silt that's deposited along the Nile River after its inundation. But genetically, they were descended from Near Eastern populations, specifically the Natufians from the Levant. Over time, they acquired some DNA from other Near Eastern groups. Whether there was any Sub-Saharan input in ancient times needs to be tested with more genomes. When we compare the Old Kingdom genome to the Abu Sir al-Malek mummies, there was no increase in Sub-Saharan African DNA at all. This also adds some support to the title of the 2017 study, that an increase in Sub-Saharan African DNA took place much later in Egypt's history. However, we know that Nubians and Ancient Egyptians interacted, so some Egyptians may have acquired a bit of Nubian DNA over time, but we have yet to see that in the ancient DNA evidence. Nevertheless, what we might call the Indigenous Ancient Egyptians, the ones who witnessed the rise of the Egyptian civilization, were very likely the descendants of settlers carrying Natufian ancestry. Whether those settlers mixed with populations that had existed in the Egyptian deserts or not, and where exactly those desert populations originated from, need more study. It's possible that West Asian groups had settled in Egypt before the settlers who brought agriculture, both based on the finding of domesticated West Asian animals in Egypt's desert regions, and the fact that DNA from 15,000-year-old Moroccan skeletons showed that they derived around two-thirds of their ancestry from the Natufians. The Moroccan study indicates that there were pre-Neolithic migrations from West Asia into North Africa. More ancient DNA studies will hopefully confirm the nature of migrations from West Asia into Egypt, and specifically how early the populations carrying Natufian ancestry first moved into the region. I'm very excited that this research on ancient DNA has come out, because we have such an amazing civilization, but so little is known about their origins genetically in comparison to places like Europe or the Near East. Lots of great genetic research has been done on those regions, so it's really exciting that we're finally getting information on the ancient Egyptians. Some questions still remain though. For example, we have yet to compare the DNA of the general population to the pharaohs. Don't forget to give this video a like and subscribe for more cool content by your go-to informant on everything archaeology, Madam Archaeologist.