Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
[excerpt methods and other sections, see link}
Verena J. Schuenemann1, 2 n1, Alexander Peltzer3, 4 n1, Beatrix Welte1, W. Paul van Pelt5, Martyna Molak6, Chuan-Chao Wang ORCID: orcid.org/0000-0001-9628-03074, Anja Furtwängler1, Christian Urban1, Ella Reiter1, Kay Nieselt ORCID: orcid.org/0000-0002-1283-70653, Barbara Teßmann7, Michael Francken1, Katerina Harvati1, 2, 8, Wolfgang Haak4, 9, Stephan Schiffels ORCID: orcid.org/0000-0002-1017-91504[…] & Johannes Krause1, 2, 4- Show fewer authors Nature Communications 8, Article number: 15694 [2017} doi:10.1038/ncomms15694
Abstract Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.
Introduction Egypt provides a privileged setting for the study of population genetics as a result of its long and involved population history. Owing to its rich natural resources and strategic location on the crossroads of continents, the country had intense, historically documented interactions with important cultural areas in Africa, Asia and Europe ranging from international trade to foreign invasion and rule. Especially from the first millennium BCE onwards, Egypt saw a growing number of foreigners living and working within its borders and was subjected to an almost continuous sequence of foreign domination by Libyans, Assyrians, Kushites, Persians, Greeks, Romans, Arabs, Turks and Brits. The movement of people, goods and ideas throughout Egypt’s long history has given rise to an intricate cultural and genetic exchange and entanglement, involving themes that resonate strongly with contemporary discourse on integration and globalization1.
Until now the study of Egypt’s population history has been largely based on literary and archaeological sources and inferences drawn from genetic diversity in present-day Egyptians. Both approaches have made crucial contributions to the debate but are not without limitations. On the one hand, the interpretation of literary and archaeological sources is often complicated by selective representation and preservation and the fact that markers of foreign identity, such as, for example, Greek or Latin names and ethnics, quickly became ‘status symbols’ and were adopted by natives and foreigners alike2,3,4. On the other hand, results obtained by modern genetic studies are based on extrapolations from their modern data sets and make critical assumptions on population structure and time5. The analysis of ancient DNA provides a crucial piece in the puzzle of Egypt’s population history and can serve as an important corrective or supplement to inferences drawn from literary, archaeological and modern DNA data.
Despite their potential to address research questions relating to population migrations, genetic studies of ancient Egyptian mummies and skeletal material remain rare, although research on Egyptian mummies helped to pioneer the field of ancient DNA research with the first reported retrieval of ancient human DNA6. Since then progress has been challenged by issues surrounding the authentication of the retrieved DNA and potential contaminations inherent to the direct PCR method7. Furthermore, the potential DNA preservation in Egyptian mummies was met with general scepticism: The hot Egyptian climate, the high humidity levels in many tombs and some of the chemicals used in mummification techniques, in particular sodium carbonate, all contribute to DNA degradation and are thought to render the long-term survival of DNA in Egyptian mummies improbable8. Experimental DNA decay rates in papyri have also been used to question the validity and general reliability of reported ancient Egyptian DNA results9. The recent genetic analysis of King Tutankhamun’s family10 is one of the latest controversial studies that gave rise to this extensive scholarly debate11. New data obtained with high-throughput sequencing methods have the potential to overcome the methodological and contamination issues surrounding the PCR method and could help settle the debate surrounding ancient Egyptian DNA preservation8. However, the first high-throughput sequences obtained from ancient Egyptian mummies12 were not supported by rigorous authenticity and contamination tests.
Here, we provide the first reliable data set obtained from ancient Egyptians using high-throughput DNA sequencing methods and assessing the authenticity of the retrieved ancient DNA via characteristic nucleotide misincorporation patterns13,14 and statistical contamination tests15 to ensure the ancient origin of our obtained data.
By directly studying ancient DNA from ancient Egyptians, we can test previous hypotheses drawn from analysing modern Egyptian DNA, such as recent admixture from populations with sub-Saharan16 and non-African ancestries17, attributed to trans-Saharan slave trade and the Islamic expansion, respectively. On a more local scale, we aim to study changes and continuities in the genetic makeup of the ancient inhabitants of the Abusir el-Meleq community [Fig. 1}, since all sampled remains derive from this community in Middle Egypt and have been radiocarbon dated to the late New Kingdom to the Roman Period [cal. 1388BCE–426CE, Supplementary Data 1}. In particular, we seek to determine if the inhabitants of this settlement were affected at the genetic level by foreign conquest and domination, especially during the Ptolemaic [332–30BCE} and Roman [30BCE–395CE} Periods.
Results Samples and anthropological analysis
All 166 samples from 151 mummified individuals [for details of the 90 individuals included in the later analysis, see Supplementary Data 1} used in this study were taken from two anthropological collections at the University of Tübingen and the Felix von Luschan Skull Collection, which is now kept at the Museum of Prehistory of the Staatliche Museen zu Berlin, Stiftung preußischer Kulturbesitz [individuals: S3533, S3536, S3544, S3552, S3578, S3610}. According to the radiocarbon dates [Supplementary Data 1, see also ref. 18}, the samples can be grouped into three time periods: Pre-Ptolemaic [New Kingdom, Third Intermediate Period and Late Period}, Ptolemaic and Roman Period. During their conservation in the Tübingen and Berlin collections the remains underwent different treatments: some were preserved in their original mummified state, while others were macerated for anthropological analysis or due to conservation problems19.
In most cases, non-macerated mummy heads still have much of their soft tissue preserved. Some of the remains [individuals analysed in our study: 1543, 1547, 1565, 1577, 1611} have traces of gold leaf near the mouth and the cheekbone, which is characteristic for mummies from the Ptolemaic Period onwards20. In most cases the brain was removed and the excerebration route was highly likely transnasal, resulting in visible defects on the cribriform plate [for the individuals analysed in our study, see Supplementary Data 1}. In summary, the excellent bone preservation and the more or less good soft tissue preservation made a wide-ranging analysis possible19.
Recently, various studies were conducted on these remains, including a study on ancient Egyptian embalming resins, two ancient DNA studies and an anthropological examination of the macerated crania12,18,19,21. While the possibilities of a demographic reconstruction based on anthropological finds are naturally limited—due to incompleteness of the assemblage, the following anthropological observations were made on the assemblage: For a first assessment, computer tomographic scans of 30 mummies with soft tissue preservation were produced to describe sex [Supplementary Data 1}, age at death [Supplementary Data 1} and the macroscopic health status; the six macerated mummies were examined directly. It is notable that most of the individuals are early and late adults, and that subadult individuals are underrepresented [Supplementary Data 1}. It is possible that the sample’s demographic profile is the result of different burial treatments for adults and subadults, but it seems more likely that it is due to collection bias, with collectors favouring intact adult skulls. Almost all of the teeth show significant dentine exposure up to a total loss of the crown. This abrasion pattern is likely due to the food and food preparation itself, in particular for a cereal-rich diet containing a high proportion of coarse sandy particles. These particles act to abrade the dental tissues, allowing bacteria to penetrate the interior of the teeth. As a result, carious lesions or periapical processes appear in the analysed individuals [Supplementary Data 1}19.
For the DNA analysis we sampled different tissues [bone, soft tissue, tooth}, macerated and non-macerated, to test for human DNA preservation.
Processing and sequencing of the samples
We extracted DNA from 151 mummified human remains and prepared double-stranded Illumina libraries with dual barcodes22,23. Then we used DNA capture techniques for human mitochondrial DNA24 and for 1.24 million genomic single nucleotide polymorphisms [SNPs}25 in combination with Illumina sequencing, through which we successfully obtained complete human mitochondrial genomes from 90 samples and genome-wide SNP data from three male individuals passing quality control.
Comparison of the DNA preservation in different tissues
We tested different tissues for DNA preservation and applied strict criteria for authenticity on the retrieved mitochondrial and nuclear DNA to establish authentic ancient Egyptian DNA. First, DNA extracts from several tissues [that is, bone, teeth, soft tissue and macerated teeth} from 151 individuals were screened for the presence of human mitochondrial DNA [mtDNA} resulting in a total of 2,157 to 982,165 quality filtered mitochondrial reads per sample, and 11- to 4,236-fold coverage. To estimate, identify and filter out potential contamination we applied the program schmutzi15 with strict criteria for contamination and kept only samples with less than 3% contamination for further analysis. For a comparison of different source material [soft tissue, bone and teeth} ten individuals [Supplementary Table 1} were sampled multiple times. Yields of preserved DNA were comparable in bone and teeth but up to ten times lower in soft tissues [Fig. 2a, Supplementary Table 1}. Nucleotide misincorporation patterns characteristic for damaged ancient human DNA allowed us to assess the authenticity of the retrieved DNA13,14. The observed DNA damage patterns differed for the source materials with on average 19% damage in soft tissues and around 10% damage in bone tissue and teeth [Fig. 2b,c, Supplementary Table 1}. Importantly, mtDNA haplotypes were identical for all samples from the same individuals. Our results thus suggest that DNA damage in Egyptian mummies correlates with tissue type. The protection of bone and teeth by the surrounding soft tissue or the embalmment of soft tissue may have contributed to the observed differences.
Generation of nuclear data
In order to analyse the nuclear DNA we selected 40 samples with high mtDNA coverage and low mtDNA contamination. Using in solution enrichment for 1.2 million genome-wide SNPs26, we obtained between 3,632 and 508,360 target SNPs per sample [Supplementary Data 2}. Overall, the nuclear DNA showed poor preservation compared to the mtDNA as depicted by a high mitochondrial/nuclear DNA ratio of on average around 18,000. In many samples, nuclear DNA damage was relatively low, indicating modern contamination. We sequenced two libraries per sample: one untreated library to assess DNA damage, and one library treated with enzymatic damage repair27, which was used for downstream analysis. We applied strict criteria for further analysis: we considered only male samples with at least 8% average cytosine deamination rates at the ends of the reads from the untreated library, and with at least 150 SNPs on the X chromosome covered at least twice, in order to estimate contamination levels reliably. Three out of 40 samples fulfilling these criteria had acceptable nuclear contamination rates: Two samples from the Pre-Ptolemaic Periods [New Kingdom to Late Period} had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs. As shown below, to rule out any impact of potential contamination on our results, we analysed the three samples separately or replicated results using only the least contaminated sample.
Analysis of mitochondrial genomes
The 90 mitochondrial genomes fulfilling our criteria [>10-fold coverage and <3% contamination} were grouped into three temporal categories based on their radiocarbon dates [Supplementary Data 1}, corresponding to Pre-Ptolemaic Periods [n=44}, the Ptolemaic Period [n=27} and the Roman Period [n=19} [Supplementary Data 1}. To test for genetic differentiation and homogeneity we compared haplogroup composition, calculated FST-statistics28 and applied a test for population continuity29 [Supplementary Table 2, Supplementary Data 3,4} on mitochondrial genome data from the three ancient and two modern-day populations from Egypt and Ethiopia, published by Pagani and colleagues17, including 100 modern Egyptian and 125 modern Ethiopian samples [Fig. 3a}. We furthermore included data from the El-Hayez oasis published by Kujanová and colleagues30. We observe highly similar haplogroup profiles between the three ancient groups [Fig. 3a}, supported by low FST values [<0.05} and P values >0.1 for the continuity test. Modern Egyptians share this profile but in addition show a marked increase of African mtDNA lineages L0–L4 up to 20% [consistent with nuclear estimates of 80% non-African ancestry reported in Pagani et al.17}. Genetic continuity between ancient and modern Egyptians cannot be ruled out by our formal test despite this sub-Saharan African influx, while continuity with modern Ethiopians17, who carry >60% African L lineages, is not supported [Supplementary Data 5}. To further test genetic affinities and shared ancestry with modern-day African and West Eurasian populations we performed a principal component analysis [PCA} based on haplogroup frequencies and Multidimensional Scaling of pairwise genetic distances. We find that all three ancient Egyptian groups cluster together [Fig. 3b}, supporting genetic continuity across our 1,300-year transect. Both analyses reveal higher affinities with modern populations from the Near East and the Levant compared to modern Egyptians [Fig. 3b,c}. The affinity to the Middle East finds further support by the Y-chromosome haplogroups of the three individuals for which genome-wide data was obtained, two of which could be assigned to the Middle-Eastern haplogroup J, and one to haplogroup E1b1b1 common in North Africa [Supplementary Table 3}. However, comparative data from a contemporary population under Roman rule in Asia Minor, from the Roman city Ağlasun today in Turkey31, did not reveal a closer relationship to the ancient Egyptians from the Roman period [Fig. 3b,c}.
a} Mitochondrial DNA haplogroup frequencies of three ancient and two modern-day populations, [b} Principal Component Analysis based on haplogroup frequencies: [sub-Saharan Africa [green}, North Africa [light green}, Near East [orange}, Europe [yellow}, ancient [blue}, [c} MDS of HVR-I sequence data: colour scheme as above; note that ancient groups were pooled, [d} Skygrid plot depicting effective population size estimates over the last 5,000 years in Egypt. Vertical bars indicate the ages of the analysed 90 mitochondrial genomes [three samples with genome-wide data highlighted in red}. Note that the values on y axis are given in female effective population size times generation time and were rescaled by 1:14.5 for the estimation of the studied population size [assuming 29-year generation time and equal male and female effective population sizes} [images by Kerttu Majander}.
Population size estimation using BEAST
The finding of a continuous population through time allowed us to estimate the effective population size [Ne} from directly radiocarbon-dated mitochondrial genomes using BEAST32. Our results show similar values of effective population size in the different ancient time periods with an average value of between ca. 48,000 and 310,000 [average 95% CI} inhabitants in the region and period under investigation [Fig. 3d, Supplementary Fig. 2, Supplementary Table 4}. This is important as it is the first time that such estimates can be contrasted with reported historic Egyptian census numbers from the neighbouring Fayum in the early Ptolemaic Period, which had a reported total population size of 85,000–95,000 inhabitants33.
Population genetic analysis of nuclear DNA
On the nuclear level we merged the SNP data of our three ancient individuals with 2,367 modern individuals34,35 and 294 ancient genomes36 and performed PCA on the joined data set. We found the ancient Egyptian samples falling distinct from modern Egyptians, and closer towards Near Eastern and European samples [Fig. 4a, Supplementary Fig. 3, Supplementary Table 5}. In contrast, modern Egyptians are shifted towards sub-Saharan African populations. Model-based clustering using ADMIXTURE37 [Fig. 4b, Supplementary Fig. 4} further supports these results and reveals that the three ancient Egyptians differ from modern Egyptians by a relatively larger Near Eastern genetic component, in particular a component found in Neolithic Levantine ancient individuals36 [Fig. 4b}. In contrast, a substantially larger sub-Saharan African component, found primarily in West-African Yoruba, is seen in modern Egyptians compared to the ancient samples. In both PCA and ADMIXTURE analyses, we did not find significant differences between the three ancient samples, despite two of them having nuclear contamination estimates over 5%, which indicates no larger impact of modern DNA contamination. We used outgroup f3-statistics38 [Fig. 5a,b} for the ancient and modern Egyptians to measure shared genetic drift with other ancient and modern populations, using Mbuti as outgroup. We find that ancient Egyptians are most closely related to Neolithic and Bronze Age samples in the Levant, as well as to Neolithic Anatolian and European populations [Fig. 5a,b}. When comparing this pattern with modern Egyptians, we find that the ancient Egyptians are more closely related to all modern and ancient European populations that we tested [Fig. 5b}, likely due to the additional African component in the modern population observed above. By computing f3-statistics38, we determined whether modern Egyptians could be modelled as a mixture of ancient Egyptian and other populations. Our results point towards sub-Saharan African populations as the missing component [Fig. 5c}, confirming the results of the ADMIXTURE analysis. We replicated the results based on f3-statistics using only the least contaminated sample [with <1% contamination estimate} and find very similar results [Supplementary Fig. 5}, confirming that the moderate levels of modern DNA contamination in two of our samples did not affect our analyses. Finally, we used two methods to estimate the fractions of sub-Saharan African ancestry in ancient and modern Egyptians. Both qpAdm35 and the f4-ratio test39 reveal that modern Egyptians inherit 8% more ancestry from African ancestors than the three ancient Egyptians do, which is also consistent with the ADMIXTURE results discussed above. Absolute estimates of African ancestry using these two methods in the three ancient individuals range from 6 to 15%, and in the modern samples from 14 to 21% depending on method and choice of reference populations [see Supplementary Note 1, Supplementary Fig. 6, Supplementary Tables 5–8}. We then used ALDER40 to estimate the time of a putative pulse-like admixture event, which was estimated to have occurred 24 generations ago [700 years ago}, consistent with previous results from Henn and colleagues16. While this result by itself does not exclude the possibility of much older and continuous gene flow from African sources, the substantially lower African component in our ∼2,000-year-old ancient samples suggests that African gene flow in modern Egyptians occurred indeed predominantly within the last 2,000 years.
a} Principal Component Analysis-based genome-wide SNP data of three ancient Egyptians, 2,367 modern individuals and 294 previously published ancient genomes, [b} subset of the full ADMIXTURE analysis [Supplementary Fig. 4}.
[a} Outgroup f3-statistics measuring shared drift of the three ancient Egyptian samples and other modern and ancient populations, [b} The data shown in a, compared with the same estimates for modern Egyptians, ordered by shared drift with modern Egyptians, [c} Admixture f3-statistics, testing whether modern Egyptians are mixed from ancient Egyptians and some other source. The most negative Z-scores indicate the most likely source populations.
Estimating phenotypes
Finally, we analysed several functionally relevant SNPs in sample JK2911, which had low contamination and relatively high coverage. This individual had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia41, consistent with the ancestral affinity shown above. Other relevant SNPs carry the ancestral allele, including HERC2 and LCT, which suggest dark-coloured eyes and lactose intolerance [Supplementary Table 9}.
Discussion This study demonstrates that the challenges of ancient DNA work on Egyptian mummies can be overcome with enrichment strategies followed by high-throughput DNA sequencing. The use of ancient DNA can greatly contribute towards a more accurate and refined understanding of Egypt’s population history. More specifically, it can supplement and serve as a corrective to archaeological and literary data that are often unevenly distributed across time, space and important constituents of social difference [such as gender and class} as well as modern genetic data from contemporary populations that may not be fully representative of past populations.
The archaeological site Abusir el-Meleq was inhabited from at least 3250BCE until about 700CE and was of great religious significance because of its active cult to Osiris, the god of the dead, which made it an attractive burial site for centuries2. Written sources indicate that by the third century BCE Abusir el-Meleq was at the centre of a wider region that comprised the northern part of the Herakleopolites province, and had close ties with the Fayum and the Memphite provinces, involving the transport of wheat, cattle-breeding, bee-keeping and quarrying42. In the early Roman Period, the site appears to have been the main centre in its own district42. Abusir el-Meleq’s proximity to, and close ties with, the Fayum are significant in the context of this study as the Fayum in particular saw a substantial growth in its population during the first hundred years of Ptolemaic rule, presumably as a result of Greek immigration33,43. Later, in the Roman Period, many veterans of the Roman army—who, initially at least, were not Egyptian but people from disparate cultural backgrounds—settled in the Fayum area after the completion of their service, and formed social relations and intermarried with local populations44. Importantly, there is evidence for foreign influence at Abusir el-Meleq. Individuals with Greek, Latin and Hebrew names are known to have lived at the site and several coffins found at the cemetery used Greek portrait image and adapted Greek statue types to suit ‘Egyptian’ burial practices2,45. The site’s first excavator, Otto Rubensohn, also found a Greek grave inscription in stone as well as a writing board inscribed in Greek46. Taken together with the multitude of Greek papyri that were written at the site, this evidence strongly suggests that at least some inhabitants of Abusir el-Meleq were literate in, and able to speak, Greek45. However, a general issue concerning the site is that several details of the context of the individuals analysed in this study were lost over time. All of the material was excavated by Rubensohn in the early twentieth century, whose main interest was to obtain literary papyri from cartonnage rather than to excavate human remains47. As is customary for the time, Rubensohn’s archaeological records are highly incomplete and many of the finds made by him were removed undocumented from their contexts. Furthermore, many of his excavation diaries and notes were destroyed during the Second World War19. This lack of context greatly diminishes the possibility of ‘thick description’ of the analysed individuals, at least in terms of their names, titles and materially expressed identity. However, the finds nevertheless hold much promise for a long-term study of population dynamics in ancient Egypt. Abusir el-Meleq is arguably one of the few sites in Egypt, for which such a vast number of individuals with such an extensive chronological spread are available for ancient DNA analysis. Although we only analysed mummified remains, there is little reason to believe that the burials Rubensohn excavated belonged exclusively to a group of prosperous inhabitants on the basis of the far published references to excavation diaries and Rubensohn’s preliminary reports that permit a basic reconstruction. Rather it seems arguable that the complete spectrum of society is represented, ranging from Late Period priests’ burials that stand out by virtue of their size and contents to simple inhumations that are buried with little to no grave goods2. The widespread mummification treatments in the Ptolemaic and Roman Periods in particular, leading to a decline in standards and costs48 and the generally modest appearance of many burials further supports this assessment.
By comparing ancient individuals from Abusir el-Meleq with modern Egyptian reference populations, we found an influx of sub-Saharan African ancestry after the Roman Period, which corroborates the findings by Henn and colleagues16. Further investigation would be needed to link this influx to particular historic processes. Possible causal factors include increased mobility down the Nile and increased long-distance commerce between sub-Saharan Africa and Egypt49. Trans-Saharan slave trade may have been particularly important as it moved between 6 and 7 million sub-Saharan slaves to Northern Africa over a span of some 1,250 years, reaching its high point in the nineteenth century50. However, we note that all our genetic data were obtained from a single site in Middle Egypt and may not be representative for all of ancient Egypt. It is possible that populations in the south of Egypt were more closely related to those of Nubia and had a higher sub-Saharan genetic component, in which case the argument for an influx of sub-Saharan ancestries after the Roman Period might only be partially valid and have to be nuanced. Throughout Pharaonic history there was intense interaction between Egypt and Nubia, ranging from trade to conquest and colonialism, and there is compelling evidence for ethnic complexity within households with Egyptian men marrying Nubian women and vice versa51,52,53. Clearly, more genetic studies on ancient human remains from southern Egypt and Sudan are needed before apodictic statements can be made.
The ancient DNA data revealed a high level of affinity between the ancient inhabitants of Abusir el-Meleq and modern populations from the Near East and the Levant. This finding is pertinent in the light of the hypotheses advanced by Pagani and colleagues, who estimated that the average proportion of non-African ancestry in Egyptians was 80% and dated the midpoint of this admixture event to around 750 years ago17. Our data seem to indicate close admixture and affinity at a much earlier date, which is unsurprising given the long and complex connections between Egypt and the Middle East. These connections date back to Prehistory and occurred at a variety of scales, including overland and maritime commerce, diplomacy, immigration, invasion and deportation54. Especially from the second millennium BCE onwards, there were intense, historically- and archaeologically documented contacts, including the large-scale immigration of Canaanite populations, known as the Hyksos, into Lower Egypt, whose origins lie in the Middle Bronze Age Levant54.
Our genetic time transect suggests genetic continuity between the Pre-Ptolemaic, Ptolemaic and Roman populations of Abusir el-Meleq, indicating that foreign rule impacted the town’s population only to a very limited degree at the genetic level. It is possible that the genetic impact of Greek and Roman immigration was more pronounced in the north-western Delta and the Fayum, where most Greek and Roman settlement concentrated43,55, or among the higher classes of Egyptian society55. Under Ptolemaic and Roman rule, ethnic descent was crucial to belonging to an elite group and afforded a privileged position in society55. Especially in the Roman Period there may have been significant legal and social incentives to marry within one’s ethnic group, as individuals with Roman citizenship had to marry other Roman citizens to pass on their citizenship. Such policies are likely to have affected the intermarriage of Romans and non-Romans to a degree55. Additional genetic studies on ancient human remains from Egypt are needed with extensive geographical, social and chronological spread in order to expand our current picture in variety, accuracy and detail.
However, our results revise previous scepticism towards the DNA preservation in ancient Egyptian mummies due to climate conditions or mummification procedures8. The methodology presented here opens up promising avenues for future genetic research and can greatly contribute towards a more accurate and refined understanding of Egypt’s population history.
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Supplementary Data 3 Comparison of mitochondrial and nuclear Haplogroups. As the nuclear results do not have any specific enrichment applied for mitochondrial DNA retrieval, there are cases where the position was either not covered (yellow) or covered with less than 3 reads (red). Matching mutations were marked in green respectively between both captures. ____________________________
I had a glitch so the headings are messed up Maybe somebody else can post it
soma haplogroups listed:
J1d U6a2 M1a1
______________
also see
4. Supplementary Data 4 Results of the genetic distance computation with Arlequin between 56 populations from Europe, Africa, the middle East, Asia and the Ancient Egyptian metapopulation investigated in this study. 5. Supplementary Data 5 Results and details of a population continuity test between our investigated three ancient Egyptian populations and modern populations from Egypt and Ethiopia in the respective region.
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Because modern people care about the Afrocentrist question, the extent of Sub-Saharan African ancestry is highlighted in this paper. I do not think this is actually the most interesting aspect. But I’ll get to that. Since this post will be read by a fair number of people I’ll talk about the relationship of ancient and modern Egyptians to (Northern) Europeans and Sub-Saharan Africans.
The figure to the left is looking at 90 ancient Egyptian mitochondrial genomes (and some modern ones in the two rightmost columns). Since mtDNA is copious it was relatively easy to extract and analyze. Haplogroup L, the red to orange shades in the bar plots, are associated without dispute with Sub-Saharan Africa. Haplogroup U6, M1 and a few others may be “back to Africa” variants of different periods (they are generally found in Afro-Asiatic groups).
What you can see is that somewhat more than half of Ethiopia’s mtDNA lineages are L, in keeping with the whole genome estimate of Sub-Saharan African ancestry in most Cushitic populations. In Egypt there is a difference over time; haplogroup L goes from low frequencies to much higher frequencies in modern periods. The ~20% fraction in the modern samples is in line with the population wide admixture one sees in modern Egyptians of Sub-Saharan admixture.
I actually recomputed the haplogroups to a finer granularity from the supplements. A quick inspection of mtDNA haplogroup frequencies shows that ancient Egyptians are not typical of modern Europeans. Not that much H, and lots of T, J and K. What that does remind me of are Early European Farmers. These people, who brought agriculture to Europe from Anatolia contributed a large fraction of the ancestry of modern Southern Europeans, and a lesser component to Northern Europeans.
Butultimately what’s great about this paper is that they have ancient autosomal DNA. That is, genome-wide results.
They got three samples of reasonably high quality. More precisely: “Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs.”
You can see the three samples on this bar plot. What is interesting is that they’re all pretty similar.
What you can see here is that to a great extent ancient Egyptians were descended from a population closely related to Natufians, or Natufians themselves. This easily explains the mtDNA affinity to Neolithic farmers: Natufians and Anatolian Neolithic populations were sister populations. The f3 statistic which looks at shared drift shows an affinity of ancient Egyptians with ancient farmer populations with Near Eastern provenance, but also with modern Sardinians. This is a common pattern, as ancient groups do not have later migration waves, with the Sardinians the modern population closest to this.
You see in the bar plot that northern Levantine populations are placed between Anatolian Neolithics and Natufians, as one might expect based on their geographical position and gene flow between these two regions. Additionally, the cyan color is associated with eastern farmers from the Zagros. I’ve already talked about gene flow from this area to the Levant recently. If you compare the Bronze Age Sidon samples I think you’ll see broad affinities with these Late Period Egyptians.
The PCA gives us results consonant with the model-based clustering. If you plot the genetic variation of ancient Egyptians they’re closest to Neolithic eastern Mediterranean populations. No great surprise.
Not the modern Egyptians. Why? It’s pretty clearly because modern Egyptians are shifted toward Sub-Saharan Africans. But there is also another component: modern Egyptians have more of the cyan eastern farmer component. What could this be?
An immediate thought comes to mind. We focus a great deal on Sub-Saharan African slavery. One reason is that it is visible. Black Africans are physically distinct from most Middle Eastern populations. But Egypt was long the center of another slave trade: “white slaves” from the Caucasus. Circassians. For hundreds of years Mamluks were recruited from the Caucasus as military slaves. They eventually became the ruling class of Egypt, until their decimation in the 19th century under Muhammad Ali (who himself was an Albanian Ottoman who never learned to speak Arabic well).
As noted in the paper earlier work looking at patterns in ancestry tracts and LD decay had made it obvious that much of the admixture of Sub-Saharan ancestry in Egypt, as in much of the Middle East, is relatively recent. In particular, it dates to the Islamic period, when trade and conquest took on new dimensions in Africa and north into Central Asia. One way ethnic minorities like Assyrians and Lebanese Christians differ from their Muslim neighbors is that they have much lower fractions of Sub-Saharan African ancestry, and no East Asian component. The latter might surprise, but remember that Central Asian Turkic slaves have been prominent in Muslim armies since at least the 9th century.
But some of the Sub-Saharan ancestry in Egyptians is old. The ancient Egyptian samples have it. To have none of it would seem strange, considering the history of contact between Nubia and Egypt, dating back to the Old Kingdom. Second, there is evidence of low levels of Sub-Saharan African gene flow into Southern Europeans. How did that happen? The highest fractions are in Spain, and can there be attributed to the Moorish period. But that explanation does not hold in much of Italy, where there are a few percent of haplogroup L. This probably is due to south-to-north gene flow across the Mediterranean during the Classical period. Some of the peoples on the south shore of the Mediterranean almost certainly already had some Sub-Saharan African admixture.
Not getting into the details of it, there are ways to explicitly model gene flow into a target population from donors defined by a phylogeny. In this case the authors tested various models of gene flow from Sub-Saharan Africans and Eurasians (non-Africans) to generate allele frequency patterns we see in modern Egyptians and ancient Egyptians.
What they consistently found is that modern Egyptians are about twice as much Sub-Saharan African as ancient Egyptians. The proportions for modern Egyptians ranged from ~10 to ~20 percent Sub-Saharan African against a Eurasian background, with a bias toward the higher values (depending on which populations you put into the phylogeny for non-Africans), and ~0 to ~10 percent for the ancient Egyptians, again with a bias toward the higher values. The pattern is consistent in these tests.
An issue here is that we’re going off three samples. That being said, the authors observe that despite differences in contamination/quality and time period they’re very concordant with each other. If I had to bet I think Old Kingdom samples would have somewhat less Sub-Saharan and eastern farmer ancestry. But the basic pattern persisted down to the Roman period, and was only shifted by admixture due to slavery.
And not to belabor the point, but a paper from a few years ago which had some Copt samples looks familiar in its broad outlines. You see that the Copts have very little Sub-Saharan African ancestry, though it does seem to be evident (the marker set is in the hundreds of thousands of SNPs). Additionally, they are quite distinct from the Qatari Arab sample.
Unfortunately the data for this paper just published is not on the European Nucleotide Archive. I really want to dig a little deeper into it.
What are the takeaways here? Egypt has been the sink for a lot of migration and gene flow over the past several thousand years, and probably earlier. Not surprising considering that it was relatively wealthy in the aggregate. The Natufian population that the Late Period Egyptians resemble the most did not have Sub-Saharan African ancestry according to earlier research. These Late Period Egyptians do have some. This is reasonable in light of the long interaction with Nubia which is historically attested. Similarly, there was clearly gene flow from Southwest Asia. This is again historically attested, especially in the Nile Delta (though foreign garrisons of mercenaries are recorded in Upper Egypt as well).
The Roman period probably did introduce some gene flow from Southeast Europe and Southwest Asia. But these populations are not that distinct from Egyptians.
Similarly, the Islamic period also brought in different peoples from Arabia and the Caucasus. But the most salient dynamic during the Islamic period was a massive trans-Saharan slave trade (though the Caucasus impact may have been comparable, and I think these results support the proposition that it was).
It seems entirely likely that the Copts are descended from a mix of Roman era Egyptians. Not only do they resemble the people in the Fayum portraits, but the circumstantial genetic data is that they have fewer “exotic” components which increased in frequency during the Islamic era. This would be exactly parallel to ethno-religious minorities in the Levant and Iraq.
One curious element to me is the suggestion gene flow before ~5,000 BCE between Sub-Saharan Africa and the lower Nile valley was low. If it hadn’t been low, it seems unlikely that the fraction of Sub-Saharan ancestry (or shift in that direction in relation to other Eurasians) in Copts would be so small.
So what explains the lack of earlier gene flow? I think the answer is going to be the fact that the human demographic landscape is characterized by lots of local population extinctions. As ancient DNA sampling coverage gets better and better meta-population dynamics are coming into focus, and we see gene flow, and die offs, in several areas. It is fashionable to say that human population variation is characterized by clines. But much of this clinal aspect is an outcome of the period after massive admixture over the last ~10,000 years.
And yet it may not be that the period before the Holocene was not clinal. Rather, it may be that large depopulations of areas of human occupation fragmented clinal ranges, and resulted in new range expansions from “core” zones.
About ~8,000 years ago there was a major desertification period in the Sahara desert. Many trans-Saharan populations may have gone extinct during this time due to rapid climate change. Eventually repopulation may have occurred from outside of the Sahara, so that post-Natufian Levantines and Sub-Saharan Africans from what today call the Sahel pushed up and down the Nile drainage basic respectively, meeting in the zone of Nubia on the boundary of history and prehistory.
Unlike many other areas of the world we have a long attested record of Egyptian history. As we get more mummy samples it seems likely that we’re get a crisper, clearer, picture. And the time transects will not be narrative blind; we already know the general arc of Egyptian history. If, for example, we see a new ancestral component around ~1500 B.C., in Egypt it’s not mysterious what this might be: the Hyksos.
This is just the prologue to a fascinating book that will be written over the next decade.
Posts: 42919 | From: , | Registered: Jan 2010
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How come no one's interested in wondering what Egypt was like before 2k BC? The author specifically mentions that while there was always a component to the results we see in northern Egypt (at least), there had been a significant increase in these lineages within that part of Egypt (minimum) as it entered the New Kingdom period. It is for this reason he attributes the geneflow to historical periods of foreign contact and invasion. The coalesence date doesn't extend to predynastic/Early Dynastic period.
It's not that I'm saying it's impossible that Pre Dynastic and Early Dynastic Egyptians were exactly like the samples in this period, but if so why was the author so cautious about inferring that? Why would he focus on periods of foreign invasion instead of Levanite farmers of the predynastic based on the coalescence dates his team found? And if that data was masked out, what then would the it have shown? The author also say that before making a generalized statement we need to make sure the increased inflow they're deeming "SSA" wasn't just from local southern Egyptians and Nubians. Southern Egyptian and Sudanese data is needed for a complete picture. Especially data that is older.
Even some of the stuff before 2k BC may present a more homogenized picture that probably wasn't there at the start of state formation. At the start, northern and southern Egyptians carried morphological distinctions that so far, are being ascribed to different ecological niches. Although it could be that the surrounding peoples may have also played a role in this too.
Posts: 2508 | From: . | Registered: Nov 2011
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quote:Originally posted by Oshun: How come no one's interested in wondering what Egypt was like before 2k BC? The author specifically mentions that while there was always a component to the results we see in the New Kingdom period, it significantly increased at around this point in time. It is for this reason he attributes the geneflow to historical periods of foreign contact. It's not that I'm saying it's impossible that Pre Dynastic and Old Kingdom Egyptians were exactly like the samples in this period, but if so why was the author so cautious about this? Why would he focus on periods of foreign invasion based on the coalescence dates his team found? And if that data was masked out, what then would the data have shown? The author also say that before making a generalized statement we need to make sure the inflow they're deeming "SSA" wasn't just from local southern Egyptians and Nubians. Southern Egyptian and Sudanese data is needed for a complete picture. Especially data that is older. Even some of the stuff before 2k BC may present a more homogenized picture that probably wasn't there at the start of state formation. At the start, northern and southern Egyptians carried morphological distinctions that so far, are being ascribed to different ecological niches. Although it could be that the surrounding peoples may have also played a role in this too.
Who is "no one"? You mean the folks who wrote this paper?
This report is obviously cannon fodder for all the amateurs on forums to debate over until they get access to another round of DNA tests on AE mummies held by Egypt. The issue is whether the Egyptian government will grant permission to do another set of tests. Of course anyone with half a brain would see this report is useless in understanding Egypts overall DNA make up even during the period studied. Keep in mind that this era was when the Kushites conquered Egypt. So are we to believe those Kushites had the same DNA picture? Of course not. So the key is to see what happens with the Egyptian government and even Sudanese government. These samples were taken from mummies in museums outside of Egypt.
But regardless the fundamental issue is that the Haplogroups L0 - L4 are assigned as sub Saharan by these folks. I doubt these people will change that assignment even in the presence of Sudanese and Upper Egyptian DNA samples. Now unless there is a "surprise" discovery, most would expect those Sudanese samples to have more L DNA lineages. They have already assigned the label and reinforced the idea that North Africa was distinct from "sub Saharan" Africa in terms of DNA.
Posts: 8889 | Registered: May 2005
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Ok maybe not "no one" literally but very few people seem interested to place any focus on the coalescence dates the author states. Should just note that I'd since edited when I said Old Kingdom to Early Dynastic. Technically these lineages could've been starting to present themselves in greater quantity by the late Old Kingdom period. This makes some sort of response to Pagani's findings that Egyptian mixture changed 750 years ago. But Where did Pagani take his samples? Were these southern Egyptians or northern Egyptians?
Posts: 2508 | From: . | Registered: Nov 2011
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quote:Originally posted by Oshun: Ok maybe not "no one" literally but very few people seem interested to place any focus on the coalescence dates the author states. Should just note that I'd since edited when I said Old Kingdom to Early Dynastic. Technically these lineages could've been starting to present themselves in greater quantity by the late Old Kingdom period. This makes some sort of response to Pagani's findings that Egyptian mixture changed 750 years ago. But Where did Pagani take his samples? Were these southern Egyptians or northern Egyptians?
The point of the paper is that they are able to actually get better DNA samples from ancient mummies. That means the more mummies they can test the better. We can theorize until the cows come home. Once you actually get the data that will be the more definitive answer. And it is up to the Egyptian government to allow them to sample more "famous" mummies. Expect them to drag this out ad infinitum as they begin sampling more individual mummies of different eras and from different places.
To my mind, the question becomes whether Southern Egyptians and Sudanese carry L lineages or some kind of "other". My hunch is there will be more L lineages in those groups. Note it is odd but even with all this talk about Nubia there hasn't been much study of so-called Nubian DNA, modern or otherwise. You would think that would be better than postulating based on limited data sets.
Posts: 8889 | Registered: May 2005
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No offense Lioness but there is already like three threads on this...
Mod edit: + the lioness has added some of the original text from and images from the article that was finally published May 31 Now moved to the first page of the stickied earlier version of the thread of the same title Ancient Egyptian mummy genomes Pages http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=009694Posts: 1891 | From: NY | Registered: Sep 2014
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