Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
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
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PEER REVIEW FILE (easier to read at link above)
Reviewers' comments: Reviewer #1 (Remarks to the Author): This is an interesting paper that presents important insights into the genetic history of the ancient Egyptian population. To my knowledge, this work represents the first detailed population genetic study on ancient Egyptian mummified material, by the reconstruction of 91 mitochondrial genomes and three genome-wide datasets. It has to be acknowledged that the authors applied strict quality controls and thereby managed to unequivocally proof the authenticity of their findings. Based on this data, the long-lasting and often dogmatic discussion on whether ancient DNA could survive in ancient Egyptian mummies can be finally put to rest. Both, the molecular approach and the data analysis was very well done and the results provide new and important insights into the continuity of the population of the ancient Egyptian site and the shared ancestry of the ancient Egyptians with Near Easterners. The work represents an important contribution to the study of ancient human history in Egypt. Nevertheless, the work could be further improved by providing more details on the investigated mummies and a more detailed analysis of a possible foreign influence at the site. It would be interesting to understand if the methodological approach could allow to identify single individuals that have a different origin, such as Ptolemaic or Roman, and what it would tell us about burial practice and mummification techniques. In the following, I have listed some specific comments: 1.I would have liked to see some comments on the debate about DNA preservation in ancient Egypt and in particular the mentioning of some previous work. I think it would strengthen the impact of this paper, if the authors would underline the importance of their findings with regard to the general skeptics on the presence of ancient DNA in hot and arid climates. 2.I am particularly surprised that the authors have not cited the previous work on the material that derives from the same collection. As far as I understand, Khairat et al. (J. Appl. Genet., 2013) and Lalremruata et al. (Plos One, 2013), also used samples from the mummy collection at the University of Tuebingen. As the authors of this work have used some radiocarbon dates from Lalremruata et al. (see Suppl.), I assume that the samples were taken from the same collection. It should be explained why the previous work was not mentioned. 3.Lines 55-57: “However, methodological problems and contamination obstacles… hampered direct investigations…”. What exactly were these problems and obstacles?? I assume that a major part of the problem was the disbelief of many scholars that ancient DNA could survive in Egyptian mummies due to the hot climate. What were the other reasons? Why has it become possible now? (see also comment 1) 4.Lines 66-72. Evidence for foreign influence: Is this true for the studied samples? What do we know about the mummies regarding names, burial practice, coffin styles, etc.? This is an interesting point! Why didn’t the authors use their data to proof or disproof this assumption? The authors should mention whether they tried to see any foreign influence and how could this have influence their analysis! 5.Lines 75-77. “In particular, the site holds much promise for studying changes in its population structure from the late Dynastic Period to the present day.” Why is this the case? Is it due to the better DNA preservation in the later mummies?? Please explain! 6.Line 78. 151 mummified remains: It would have been interesting to learn more about these mummies. Is there any information on the age and sex of the mummies? How were they mummified? How is the state of preservation? How many of them have an “identity” (e.g. name inscription)? (see also comment 4). 7.Line 92. Yields of preserved DNA: What’s about the preservation of non-human DNA? Did the authors have a look into the metagenomics data? It is surprising to see that the authors, who published a series of articles on ancient pathogen DNA, didn’t check for the presence of diseases such as TB, malaria or toxoplasmosis, which were all reported in previous studies. Please comment. 8.Lines 98-99. DNA damage in mummies: Is this true for all mummies or just Egyptian mummies? Is this influenced by the mummification process? Could it be different in natural mummies? 9.Lines 137-140. “The affinity to the Middle East finds further support by the Y-chromosome haplogroups…” This is true, but the two haplogroups are believed to have different origins (J Western Asia, E1b1b1 North Africa). Moreover, both individuals with haplogroup J are from the pre-ptolemaic period and the individual with haplogroup E from the Ptolemaic period. Does this tell us something about their origin or any differences? The authors should comment on this. 10.Line 144. “The finding of a continuous population…” Is it really a continuous population, or are the foreign influences in the Ptolemaic-Roman period probably too little to be accounted?? Would it be possible at all to trace down foreigners with this approach?? Please comment! 11.Conclusions. What are the particular challenges of working with ancient Egyptian mummies? (see comment 3.). It seems that there was some work published on ancient pathogen DNA in Egypt, but very little on human DNA. What is the reason? Was it mainly a methodological problem, such as the non-availability of high-throughput sequencing and enrichment or are there particular issues with contamination or inhibition? I think it could be interesting for the reader to understand the potential and obstacles of working with Egyptian mummies. 12.Conclusions. The authors should discuss the possible influence and presence of foreigners at the archaeological site Abusir el-Meleq and how their approach could be used to detect it. Although there appears to be a continuity in the overall population, there could be maybe some single individuals that originate from the Ptolemaic or Roman population. Would it be possible to identify those people and could this help to understand the use of certain mummification practices? 13.Conclusions. I agree that in other sites, especially in the south of Egypt, there could be a much higher influence of Sub-Saharan populations. It is well known that there were close trading connections to Nubia and other Sub-Saharan areas during the Middle and New Kingdom. What does this mean for the interpretation of your findings? Reviewer #2 (Remarks to the Author): This paper is written like similarly structured ancient DNA papers, with a focus on the production of the dataset, a set of standard analyses performed for small sample sizes and extrapolation to prehistorical conclusions. The problem with this approach is that for the majority of studies, prior genetic analysis (and archaeological etc) has already been performed. The ancient DNA papers largely ignore the other fields and are written ‘hypothesis-free.’ Their scientific value becomes limited as each new paper attempts to devise and answer hypotheses that are often longstanding, involving significant repetition. This paper should and could be re-written to answer a question. It would start with a review of prior historical and genetic work performed on Egyptian populations, narrow down to 1-2 specific hypotheses (Can we confirm that slave trade into Egpyt and Near East occurring in the past XX centuries changed the genetic composition of Egyptians represented by urban cohorts in Cairo?) Is this a paper about success in sequencing ancient Egyptians or about resolving the population history of Egyptians given new mtDNA data? Unfortunately, the authors appear to have ignored several earlier papers on Egyptians (see below for 3 examples, there may be others). Their primary result, stated in the abstract as “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” was shown in 2012 using genome- wide SNP array data from Egyptians (Henn et al., PLoS Genetics: Table 1). That is, the sub-Saharan African ancestry is of recent origin in Egyptians dating to AD 1250 (~24 generations ago). Indeed those authors argued that the source of this sub-Saharan ancestry is more likely to be Nilotic than West African as modeled in the current analyses. This is especially problematic as it is the only result reported in the Abstract itself. And again in the conclusion: "By comparing ancient with modern Egyptians, we remarkably found an influx of additional Sub-Saharan African ancestry after the Roman Period, which is visible at both mitochondrial and autosomal level.” This result is not remarkable, it is what is expected given prior published analyses. For example, Kujanova et al. (2009) analysis of mtDNA and Y-chromosomal data from an Egyptian oasis isolate from middle Egypt is not cited. They found that sub-Saharan mtDNA L-lineages constituted 30% of their dataset, indicating a strong sub-Saharan component on the maternal side, which was largely absent on the Y (6% M2-derived lineages). Kujanova et al. also argued for a recent migration event to account for the L lineages: “The absence of any signs of local accumulation of diversity in the L haplotypes in el-Hayez seems to favor the idea of these lineages being recent introductions into the Egyptian Western Desert.” And in Pagani et al. (2015, AJHG) show that "the average proportion of non-African ancestry in the Egyptians to be 80% and dated the midpoint of the admixture event by using ALDER to around 750 years ago (Table S2), consistent with the Islamic expansion and dates reported previously.” In contrasting this paper with another similar high-profile journal paper, Pagani et al. (2015) AJHG, I do not find the results in this manuscript to be major scientific contribution and would be more appropriate for a specialized journal. Section beginning line 144: The authors report apparent congruity between their population sizes estimates and those from the Fayum in the Ptoleimac Period with a 95% credible interval range between 50,000 - 280,000. 1) This is the Ne estimated from mtDNA. In order to compare with the true Ne it need to be scaled 4-fold. 2) The Y-axis scale on Figure 3D does not match the results reported in the text. Indeed the Ne appears to be between 1-2 million durin the Ptolemaic period (black line). 3) Assuming even that the numbers in the text are correct, (115,000 50th estimate) the scaling for females vs. female+male as reported in the historical record would indicate a large divergence between the genetic and historical estimates. 4) No prior on the mutation rate, which will strong influence Ne, is given in the supplement. This is the appropriate place to integrate assumption of g (generation time) Line 197: Lazaridis et al. (2014) contained 18 Egyptian sample of uncertain provenance (Cairo-urban area). Other autosomal SNP array datasets at least including many more individuals are not used here. Contrasting 3 individuals to 18 contemporary ones in order to indicate extrapolate evidence for a pattern that" 6 and 7 million Sub-Saharan slaves to Northern Africa over a span of some 1250 years” seems a strong extrapolation on its own. As the authors admit. Line 180: "This individual had a derived allele at the SLC24A5 locus, which encodes for light skin pigmentation…” SLC24A5 is among at least 20 skin pigmentation genes known to contribute to melanin variability in contemporary human populations. It alone does not ‘encode’ for light skin pigmentation. Indeed, many individuals in Cape Verde, Africa carry this allele (which does lighten pigmentation, accounting for 7% of the variance in pigmentation) but their overall phenotype would be still be twice as dark as an average European (Beleza et al. 2013, PLoS Genetics). Note 8: Test of Population Continuity: the analysis here was not described. Other than collapsing mtDNA lineages into haplogroup frequencies to compare ancient and contemporary groups, there is no description of what the actual test was. Even if the method was described in Brandt et al. (2013) [not even in the main text, only in their supplement], the authors should lay out the assumptions, parameter choices and models invoked in using this method. Why for example, is TPC preferable over Approximate Bayesian Computation models typically used to test the relative liklihood of two different population demographies (in this case continuity w/ minimal drift vs. migration). Reviewer #3 (Remarks to the Author): In this very well written, concise yet informative manuscript, Verena Schuenemann and colleagues report genetic data obtained from ancient Egyptian mummies. Because DNA is not very well preserved in mummies, the authors used capture techniques to enrich their libraries for specific human target regions. This technique resulted in high-coverage mitochondrial genomes for 91 samples and an additional set of autosomal SNPs for 3 of those samples. When comparing to modern data, the authors find convincing evidence of an influx of Sub-Saharen alleles in more recent times. To obtain these results, the authors used by now well established analysis techniques, which were applied carefully to the degree I can judge. The analyses does appear sound and I do not have any concern that the observed genetic differences between ancient and modern Egyptians is real. I’m less confident that this result is surprising given the archaeological and historical knowledge of the region. I’m not a specialist of that history, but I would have enjoyed reading this paper much more if the introduction and discussion / conclusion would relate this finding better with the existing literature on the Egyptian history. Just stating that “Egypt provides a privileged setting for studying population history” fails a bit short of discussing open questions the study of Egyptian mummies might help to settle. Indeed, the way the paper is pitched know the real emphasis is just put on the fact that DNA could be obtained from mummies. Another aspect that I feel is missing is a brief discussion on how the bias from only studying individuals that were mummified (as compared to random individuals from the ancient Egypt) might have let to the lack of a Sub-Saharan component in the ancient individuals. I just found one type: L123: three (instead of tree) REVIEWERS' COMMENTS: Reviewer #1 (Remarks to the Author): The authors have taken into consideration all my comments and the revised manuscript has improved significantly. However, I do not fully agree with the response to my first query and the way the introduction was modified accordingly (lines 84-105). Although it is true that most of the previous work was done in the "PCR era of ancient DNA", it does not necessarily mean that the previous findings were mainly the result of modern contamination. In particular, as most of the criticism was based on a general assumption that DNA may not survive in hot and dry climates. In this work, the authors have successfully demonstrated otherwise and they should therefore come to the conclusion that the general doubts on preservation of ancient DNA in Egyptian mummies (e.g. citations 8,9) were premature. It is true and highly appreciated that the authors performed the first in-depth ancient DNA analysis using high-throughput sequencing methods, so there is no need to generally doubt previous work that was done on Egyptian mummies. I would once more recommend that the authors present the previous work in a more balanced way, mentioning the issues with the PCR based approach, but also acknowledge that DNA seems to survive in ancient Egyptian mummies despite previous skepticism. If the authors are willing to address this issue, I would be happy to accept the manuscript for publication. Reviewer #3 (Remarks to the Author): This is now the second time I review this manuscript and I'm pleased to see that the manuscript has greatly improved from its initial version. In particular, the presented research is now appropriately embedded in the general historical context of the region and the authors now mention the specific questions or hypothesis they test more explicitly. I also remain happy with the analyses presented. It is indeed questionable how accurate ancient admixture rates can be learned from either a single locus (mtDNA) or just three samples in a case in which admixture is so recent that ancestry blocks are necessarily large and the variation in admixture rates between individuals expected to be very high. However, the authors are aware and transparent about these shortcomings in their data. Yet, as a result, the presented results do still not go much beyond confirming some previously noted findings and the real contribution of the work seems to be the success in obtaining reliable genetic data from Egyptian mummies. The importance of that finding to the relevant community is something I can not judge. I just stumbled across one typo: on L164: repetition of “still”. "Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods" by Verena J. Schuenemann and colleagues Response to reviewer comments: Please find below a point by point response to the comments made by each of the three reviewers. Their individual comments are in black, the matching response in blue. Reviewer #1: Q1. I would have liked to see some comments on the debate about DNA preservation in ancient Egypt and in particular the mentioning of some previous work. I think it would strengthen the impact of this paper, if the authors would underline the importance of their findings with regard to the general skeptics on the presence of ancient DNA in hot and arid climates. Answer: We have substantially rewritten the introduction (lines: 84-105) to address results (or lack thereof) from previous studies and questions about the feasibility to retrieve ancient human DNA from samples from hot and arid climates. Q2. I am particularly surprised that the authors have not cited the previous work on the material that derives from the same collection. As far as I understand, Khairat et al. (J. Appl. Genet., 2013) and Lalremruata et al. (Plos One, 2013), also used samples from the mummy collection at the University of Tuebingen. As the authors of this work have used some radiocarbon dates from Lalremruata et al. (see Suppl.), I assume that the samples were taken from the same collection. It should be explained why the previous work was not mentioned. Answer: It is correct that we used 5 radiocarbon dates reported in Lalremruate et al. 2013 and generated 85 new ones. The study Khairat et al. 2013 is now cited in our revised introduction: lines 103-105. All studies on the Tuebingen mummy collection (Lalremruate et al. 2013, Khairat et al. 2013, Nicholson et al. 2011 and Welte 2016) are now cited in our revised sample description: lines 173-175. Q3. Lines 55-57: “However, methodological problems and contamination obstacles... hampered direct investigations...”. What exactly were these problems and obstacles?? I assume that a major part of the problem was the disbelief of many scholars that ancient DNA could survive in 1 Egyptian mummies due to the hot climate. What were the other reasons? Why has it become possible now? (see also comment 1) Answer: This is not a matter of beliefs, but based on the fact that many/most of the early studies did not withstand the scrutiny of ancient DNA authentication criteria. These are particularly important when reporting results from challenging climates (see e.g. Bollongino et al. 2008, Comptes Rendus Palevol 7(2):91-98). Many of the studies of Egyptian remains were conducted in the classical ‘PCR era of ancient DNA’, a technique which favors intact DNA molecules and is thus prone to modern human DNA contamination. It furthermore does not allow to study DNA damage patterns, that were found to be among the most reliable criteria for ancient DNA authenticity (Stoneking & Krause 2011). It is well known that the length of ancient DNA molecules is around 50bp and the overall amount of DNA damage roughly correlates with (thermal) age (Matthew Collins, Susanna Sawyer etc…), which makes STR profiling (up to 350 bp!) rather difficult. NGS techniques have the advantage to utilise the large number of independent DNA fragments (usually not accessible to PCR) in order to study contamination. Further, many previous studies have used muscle tissue, which we clearly show to be the least promising/appropriate material when studying ancient DNA. We expanded our discussion on preservation conditions and previous work in the introduction (lines: 84-105), however much of this debate can be found in Lorenzen et al. 2010 and was not repeated here. Q4. Lines 66-72. Evidence for foreign influence: Is this true for the studied samples? What do we know about the mummies regarding names, burial practice, coffin styles, etc.? This is an interesting point! Why didn’t the authors use their data to proof or disproof this assumption? The authors should mention whether they tried to see any foreign influence and how could this have influence their analysis! Answer: We have extensively rewritten the introduction and sample information to include all available contextual information on the individuals under study (lines: 111-137, 162-172). Unfortunately, this information is scarce and not sufficient to formulate strong hypotheses that could be tested in a formal manner. This issue is now detailed in our discussion: lines 361- 371. We do, however, fully address the reliability of our sample as being representative of the community at the time (see discussion: lines: 371-385). 2 Q5. Lines 75-77. “In particular, the site holds much promise for studying changes in its population structure from the late Dynastic Period to the present day.” Why is this the case? Is it due to the better DNA preservation in the later mummies?? Please explain! Answer: Unfortunately, mummies from the Old till early New Kingdom are not present at the site or and not included in our data set, which focusses on the three consecutive periods. The site is mainly occupied during the Late Period till Roman times according to written sources, and thus would allow the study of an extended temporal transect. We furthermore find in more than 50% of all remains authentic ancient DNA preserved, suggesting this to be an ideal site for further studies. We removed the sentence and included a more intensive introduction and discussion of the site, see Q1 and Q4. Q6. Line 78. 151 mummified remains: It would have been interesting to learn more about these mummies. Is there any information on the age and sex of the mummies? How were they mummified? How is the state of preservation? How many of them have an “identity” (e.g. name inscription)? (see also comment 4). Answer: As mentioned in response to Q4, the individual information is scarce. We have included all available information and anthropological data (see lines: 176-192) in the revised manuscript and supplementary information now. Q7. Line 92. Yields of preserved DNA: What’s about the preservation of non-human DNA? Did the authors have a look into the metagenomics data? It is surprising to see that the authors, who published a series of articles on ancient pathogen DNA, didn’t check for the presence of diseases such as TB, malaria or toxoplasmosis, which were all reported in previous studies. Please comment. Answer: We used our latest metagenomic pipeline (Herbig et al. 2016 biorxiv) in order to find evidence for authentic ancient pathogens, we however failed to find any clear signal for the pathogens reported in previous studies. More analyses on teeth and individuals with clear pathological lesions might be more promising for future research on ancient pathogens from Egyptian mummies. 3 Q8. Lines 98-99. DNA damage in mummies: Is this true for all mummies or just Egyptian mummies? Is this influenced by the mummification process? Could it be different in natural mummies? Answer: To our knowledge, there is no comprehensive and comparative survey on mummies from a global variety published to date. For natural mummies, such as for example from Peru (dry mummies) or the Tyrolean iceman (ice mummy), there seems to be no general pattern observable other than those from high altitudes, i.e. ‘perma-frost-conditions, show higher yields of authentic DNA and reduced damage patterns (e.g. Iceman, Saqqaq). To our knowledge, no systematic tests have yet been done on mummies, as for example for bones and eggshells in Allentoft et al (2012). There have been attempts to simulate DNA decay by burying material and investigating after several years how much DNA damage was introduced, these results were however inconclusive. Q9. Lines 137-140. “The affinity to the Middle East finds further support by the Y- chromosome haplogroups...” This is true, but the two haplogroups are believed to have different origins (J Western Asia, E1b1b1 North Africa). Moreover, both individuals with haplogroup J are from the pre-ptolemaic period and the individual with haplogroup E from the Ptolemaic period. Does this tell us something about their origin or any differences? The authors should comment on this. Answer: (to be included in the manuscript and referenced here) We agree with the reviewer that Y chromosomal haplogroup J is suggested to have arisen in the ancient Near East. However, the current distribution of E1b1b1 in North Africa could also be caused by the back migration from the Near East to Africa that have already been proposed by several authors (Hammer et al. Genetics 1997, 145:787–805; Hammer et al. Mol Biol Evol 1998, 15:427–441; Hammer MF, et al. Mol Biol Evol 2001, 18:1189–1203). The high frequencies of haplogroup R1-M173 in Cameroon also supported the back migration from Eurasia to Africa in Cruciani et al. Am J Hum Genet 2002, 70:1197–1214. Since it’s still unclear whether E1b1b evolved in Northeast Africa or the Near East, we do not attempt to interpret the presence of the two haplogroups as evidence for distinct population affinities for our three Mummy samples and we removed that argument from our study. 4 Q10. Line 144. “The finding of a continuous population...” Is it really a continuous population, or are the foreign influences in the Ptolemaic-Roman period probably too little to be accounted?? Would it be possible at all to trace down foreigners with this approach?? Please comment! Answer: The method used for the population continuity test relies on a set of priors such as generation time and total population size in the respective area. We evaluated a set of different population sizes as priors in our analysis as well as different generation times to test whether these substantially change our initial analysis. They did not change our initial finding of genetic continuity, which is why we believe that our results hold even for a larger number of parameters that could be applied here. The test of population continuity is not capable/designed to detect outliers. In general, the level of genetic resolution (mostly mitogenomes) does not allow us to identify ‘foreigners’, mostly due to the lack of comparable population data. However, we would be able to spot outliers (i.e. potential foreigners) from our nuclear DNA data via PCA and/or Admixture. The data from our three successfully genotyped samples do suggest that they belonged to the same population. Q11. Conclusions. What are the particular challenges of working with ancient Egyptian mummies? (see comment 3.). It seems that there was some work published on ancient pathogen DNA in Egypt, but very little on human DNA. What is the reason? Was it mainly a methodological problem, such as the non-availability of high-throughput sequencing and enrichment or are there particular issues with contamination or inhibition? I think it could be interesting for the reader to understand the potential and obstacles of working with Egyptian mummies. Answer: Please see answers to Q3 and Q8, and our revised introduction. Q12. Conclusions. The authors should discuss the possible influence and presence of foreigners at the archaeological site Abusir el-Meleq and how their approach could be used to detect it. Although there appears to be a continuity in the overall population, there could be maybe some single individuals that originate from the Ptolemaic or Roman population. Would it be possible to identify those people and could this help to understand the use of certain mummification practices? Answer: We have substantially extended the introduction (lines 111-137) and discussion (lines 361-385, 420-432) to address to point. The data from our three successfully genotyped samples do not 5 suggest a foreign origin, so can be considered representing the local community profile. The contextual evidence does not allow a detailed examination of variations in mummification practices. Q13. Conclusions. I agree that in other sites, especially in the south of Egypt, there could be a much higher influence of Sub-Saharan populations. It is well known that there were close trading connections to Nubia and other Sub-Saharan areas during the Middle and New Kingdom. What does this mean for the interpretation of your findings? Answer: We have addressed this point in our revised discussion (see lines 395-405). As an alternative explanation this would only mean that modern-day Egyptians might resemble more closely ancient Egyptians from the south. However, in the absence of data from southern sites, this also remains speculative. Reviewer #2: Q1: This paper is written like similarly structured ancient DNA papers, with a focus on the production of the dataset, a set of standard analyses performed for small sample sizes and extrapolation to prehistorical conclusions. The problem with this approach is that for the majority of studies, prior genetic analysis (and archaeological etc) has already been performed. The ancient DNA papers largely ignore the other fields and are written ‘hypothesis-free.’ Their scientific value becomes limited as each new paper attempts to devise and answer hypotheses that are often longstanding, involving significant repetition. This paper should and could be re- written to answer a question. It would start with a review of prior historical and genetic work performed on Egyptian populations, narrow down to 1-2 specific hypotheses (Can we confirm that slave trade into Egpyt and Near East occurring in the past XX centuries changed the genetic composition of Egyptians represented by urban cohorts in Cairo?) Is this a paper about success in sequencing ancient Egyptians or about resolving the population history of Egyptians given new mtDNA data? Answer: As in our previous version, we had clearly framed the aims of our study: i) a proof of concept that Modern Sequencing technology produces data of previously problematic samples, ii) to evaluate the degree of continuity between the ancient and modern Egyptian population, [and iii)...]. As such, the article is not hypothesis-free. Neither are we ignorant of other fields. In 6 particular, in the revised manuscript we have extensively included information from historical and archaeological sources (see Introduction and Discussion). Q2: Unfortunately, the authors appear to have ignored several earlier papers on Egyptians (see below for 3 examples, there may be others). Their primary result, stated in the abstract as “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” was shown in 2012 using genome-wide SNP array data from Egyptians (Henn et al., PLoS Genetics: Table 1). That is, the sub-Saharan African ancestry is of recent origin in Egyptians dating to AD 1250 (~24 generations ago). Indeed those authors argued that the source of this sub-Saharan ancestry is more likely to be Nilotic than West African as modeled in the current analyses. This is especially problematic as it is the only result reported in the Abstract itself. And again in the conclusion: "By comparing ancient with modern Egyptians, we remarkably found an influx of additional Sub-Saharan African ancestry after the Roman Period, which is visible at both mitochondrial and autosomal level.” This result is not remarkable, it is what is expected given prior published analyses. Answer: We acknowledge the oversight not having mentioned the 2012 study by Henn and colleagues, which is now included in our revised manuscript. We confirm their conclusions based on our modern Egyptian data, in particular do we confirm a time estimate for pulse-like admixture from Sub-Sahara Africa 700 years ago. However, the LD-based method used in Henn et al. 2012 (and confirmed by us) cannot distinguish between a pulse-like admixture and continuous migration. Using the direct observation from 2,000 year old Egyptians, which we estimate to have had 8% African ancestry, we get a more complete picture of the time course of African migration into the region than what can be extrapolated from modern data alone. Q3: For example, Kujanova et al. (2009) analysis of mtDNA and Y-chromosomal data from an Egyptian oasis isolate from middle Egypt is not cited. They found that sub-Saharan mtDNA L- lineages constituted 30% of their dataset, indicating a strong sub-Saharan component on the maternal side, which was largely absent on the Y (6% M2-derived lineages). Kujanova et al. also argued for a recent migration event to account for the L lineages: “The absence of any signs of local accumulation of diversity in the L haplotypes in el-Hayez seems to favor the idea of these lineages being recent introductions into the Egyptian Western Desert.” Answer: We thank reviewer 2 for pointing out this dataset, which we’ve now included in the analysis and interpretation of our revised manuscript. We merged the dataset with the previously used 7 one by Pagani et al. (2015, AJHG). Nevertheless, the resulting statistics did only show effects at the 3rd decimal point and hence did not alter or affect our interpretation. We see this as further evidence that the origin of the dataset does not alter the statistics and the available datasets cover modern Egyptian diversity quite well. Q4: And in Pagani et al. (2015, AJHG) show that "the average proportion of non-African ancestry in the Egyptians to be 80% and dated the midpoint of the admixture event by using ALDER to around 750 years ago (Table S2), consistent with the Islamic expansion and dates reported previously.” Answer: Our results are consistent with a model of ancient Egypt being predominantly of near Eastern ancestry, with about 10% African ancestry, which increased up to about 18% in modern times. As we now clearly state, this is qualitatively in line with the Henn et al. study from 2012. On the level of a mixture proportion of 80% non-African ancestry, we agree with Pagani et al., but we clearly show that 2,000 years ago, Egypt was more Near-Eastern, not less, as proposed by the model in Pagani et al. with non-African ancestry appearing more recently. We discuss this in the Discussion section (see line 406 to 419). Q5: Section beginning line 144: The authors report apparent congruity between their population sizes estimates and those from the Fayum in the Ptoleimac Period with a 95% credible interval range between 50,000 - 280,000. 1) This is the Ne estimated from mtDNA. In order to compare with the true Ne it need to be scaled 4-fold. 2) The Y-axis scale on Figure 3D does not match the results reported in the text. Indeed the Ne appears to be between 1-2 million durin the Ptolemaic period (black line). 3) Assuming even that the numbers in the text are correct, (115,000 50th estimate) the scaling for females vs. female+male as reported in the historical record would indicate a large divergence between the genetic and historical estimates. 4) No prior on the mutation rate, which will strong influence Ne, is given in the supplement. This is the appropriate place to integrate assumption of g (generation time). Answer: The apparent discordance between Figure 3D and the numbers given in the text stems from the fact that the figure shows unscaled results of the SkyGrid inference (given in the female effective population size times the generation time; Ne x T). To estimate the approximate effective population size for the studied population, which could be compared with the population size from the historical records, we scaled the estimated values by dividing them by generation time (we assumed 25 years) and doubled them to account for the whole (male and 8 female) population (assuming equal male to female Ne ratio). We agree that this rescaling was not described explicitly enough, which might have made the results unclear. We modified the figure caption (figures 3d, S2) as well as the relevant methods’ section so that the rescaling is more clearly described. Regarding the mutation rate prior, we used an uninformative CTMC prior and thus all the temporal information in the inference (which drives estimation of mutation rate and the codependent parameters) came solely from ages of the samples. We modified the text accordingly to make this more clear. Q6: Line 197: Lazaridis et al. (2014) contained 18 Egyptian sample of uncertain provenance (Cairo-urban area). Other autosomal SNP array datasets at least including many more individuals are not used here. Contrasting 3 individuals to 18 contemporary ones in order to indicate extrapolate evidence for a pattern that" 6 and 7 million Sub-Saharan slaves to Northern Africa over a span of some 1250 years” seems a strong extrapolation on its own. As the authors admit. Answer: We cannot easily include SNP data sets that were generated on a different platform than the Affymetrix Human Origins array. But given the fact that we almost exactly confirm results from Henn et al. who used a different data set, we are confident that as far as our modern Egyptian data is concerned, we have a good representation. As far as ancient Egypt is concerned, we indeed have only three samples from a specific region, but we acknowledge the limits of our conclusions clearly in the Discussion. We also highlight that we do incorporate 100 modern Egyptian Mitogenomes from Pagani et al. and exactly confirm their report of 80% non-African ancestry at the mitochondrial level, again suggesting that our modern Egyptian sample is broadly representative at the level of the analysis performed here. Q7: Line 180: "This individual had a derived allele at the SLC24A5 locus, which encodes for light skin pigmentation...” SLC24A5 is among at least 20 skin pigmentation genes known to contribute to melanin variability in contemporary human populations. It alone does not ‘encode’ for light skin pigmentation. Indeed, many individuals in Cape Verde, Africa carry this allele (which does lighten pigmentation, accounting for 7% of the variance in pigmentation) but their overall phenotype would be still be twice as dark as an average European (Beleza et al. 2013, PLoS Genetics). Answer: 9 We changed the sentence (lines: 346-348) to “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 Anatolia (40), consistent with the ancestral affinity shown above” Q8: Note 8: Test of Population Continuity: the analysis here was not described. Other than collapsing mtDNA lineages into haplogroup frequencies to compare ancient and contemporary groups, there is no description of what the actual test was. Even if the method was described in Brandt et al. (2013) [not even in the main text, only in their supplement], the authors should lay out the assumptions, parameter choices and models invoked in using this method. Why for example, is TPC preferable over Approximate Bayesian Computation models typically used to test the relative liklihood of two different population demographies (in this case continuity w/ minimal drift vs. migration). Answer: We have extended the description of our analysis both in the methods part of the manuscript and our supplementary information for clarification and to explain our main findings. Our intention to use the TPC as applied in Brandt et al. 2013 was to evaluate with a simple method whether we can assume genetic continuity (null hypothesis) between our ancient groups and modern-day populations. We agree that complex ABC models would have been the ideal choice to explore alternative scenarios that could explain discontinuity under varying parameters (drift, migration, time, etc.), but were not deemed necessary given that we can more reliably estimate the origin and timing of admixture with nuclear data. Reviewer #3: Q1: I’m less confident that this result is surprising given the archaeological and historical knowledge of the region. I’m not a specialist of that history, but I would have enjoyed reading this paper much more if the introduction and discussion / conclusion would relate this finding better with the existing literature on the Egyptian history. Just stating that “Egypt provides a privileged setting for studying population history” fails a bit short of discussing open questions the study of Egyptian mummies might help to settle. Indeed, the way the paper is pitched know the real emphasis is just put on the fact that DNA could be obtained from mummies. Answer: We have substantially rewritten the introduction, sample collection and discussion to include more background information on Egypt’s history (lines: 57-69), the archaeological site (lines: 111-137, 361-385) and the sample collection (lines: 149-192) in particular. 10 Another aspect that I feel is missing is a brief discussion on how the bias from only studying individuals that were mummified (as compared to random individuals from the ancient Egypt) might have let to the lack of a Sub-Saharan component in the ancient individuals. Answer: We agree that taphonomic and collection bias could indeed be a factor influencing the interpretation of our results. Please see our revised discussion for reasons why we think that our sample is largely representative of the local community at the time (lines: 372-385). Of note, mummification was already quite common from the late Period on and we thus expect mainly middle class individuals at this site. I just found one type: L123: three (instead of tree) Answer: Thanks, we have fixed it.
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posted
Same samples used. mummy collection at the University of Tuebingen
Lalremruate et al. 2013
Molecular Identification of Falciparum Malaria and Human Tuberculosis Co-Infections in Mummies from the Fayum Depression (Lower Egypt)
At a time after 1800 BC, due to unexpected increase in flow discharge, the level of the lake raised considerably (ca 18 to 20 masl) and most of the areas occupied by the Middle Kingdom installations were drawn [16], [20]. The dam was breached and the Fayum depression became once more uninhabitable. The lake still stood at around the same level or even higher when Herodotus saw it in the mid-5th century BC and apparently remained that way until early Ptolemaic times [16], [22].
The second large scale reclamation of the Fayum started under the Ptolemies [Ptolemy I Soter (310- 282 BC) and Ptolemy II Philadelphos (282-246 BC)] [22]. It probably took as long as 30 years to lower the level of the lake to two meters below sea level reaching the same level it had during the Old Kingdom.
The Lahun embankment (a five kilometers embankment from the northern side of the Lahun Gap at al-Lahun) constructed under the Ptolemies was used to divert the annual influx of Nile water. Lake Quarun, therefore, dropped to 5 meters below the sea level and the newly exposed land was colonized by Macedonian soldiers [16], [22]. The campaign of land reclamation appears to have started in the eastern area of the Fayum, in the meris of Herakleides, then continued in the southern area, corresponding to the meris of Polemon and, lastly, into the western area in the meris of Themistos [22].
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More about Abusir-el-Meleq and the Heka Khasut(Hyksos/Aamu) burials analyzed in this study:
The first Predynastic graves were discovered at Abusir el-Meleq by Otto Rubensohn in his 1902–4 expedition, which also revealed priests’ graves of the Late period and scattered burials from the 18th Dynasty. Under the auspices of the German Orient- Gesellschaft, Georg Möller excavated the Predynastic cemetery in 1905–6, also exposing several burials of the Hyksos period (15th–16th Dynasties). From Encyclopedia of the Archaeology of Ancient Egypt
Thus far genotyped native Ancient Egyptians mummies like Ramses III, Amenhotep III, King Tut all have revealed affiliations with modern SS Africans. For example, Ramses III was determined to be E1b1a by the British Medical Journal study(BMJ).
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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.
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quote:Q4. Lines 66-72. Evidence for foreign influence: Is this true for the studied samples? What do we know about the mummies regarding names, burial practice, coffin styles, etc.? This is an interesting point! Why didn’t the authors use their data to proof or disproof this assumption? The authors should mention whether they tried to see any foreign influence and how could this have influence their analysis!
Answer:
We have extensively rewritten the introduction and sample information to include all available contextual information on the individuals under study (lines: 111-137, 162-172). Unfortunately, this information is scarce and not sufficient to formulate strong hypotheses that could be tested in a formal manner.This issue is now detailed in our discussion: lines 361- 371. We do, however, fully address the reliability of our sample as being representative of the community at the time (see discussion: lines: 371-385).
So the information on these mummies is scares and not sufficient to formulate strong hypotheses that could be tested in a formal manner.
quote:Q5. Lines 75-77. “In particular, the site holds much promise for studying changes in its population structure from the late Dynastic Period to the present day.” Why is this the case? Is it due to the better DNA preservation in the later mummies?? Please explain!
Answer:
Unfortunately, mummies from the Old till early New Kingdom are not present at the site or and not included in our data set, which focusses on the three consecutive periods. The site is mainly occupied during the Late Period till Roman times according to written sources, and thus would allow the study of an extended temporal transect.
We furthermore find in more than 50% of all remains authentic ancient DNA preserved, suggesting this to be an ideal site for further studies.
We removed the sentence and included a more intensive introduction and discussion of the site, see Q1 and Q4.
How is it possible for them to make a claim that these mummies represent all of Egyptian history, while here they clearly state that the site represents mainly occupation during the Late Period till Roman times according to written sources. And at the same time they write "Unfortunately, mummies from the Old till early New Kingdom are not present at the site or and not included in our data set, which focusses on the three consecutive periods."
Perhaps it's me, but that's just weird.
quote:Q6. Line 78. 151 mummified remains: It would have been interesting to learn more about these mummies. Is there any information on the age and sex of the mummies? How were they mummified? How is the state of preservation? How many of them have an “identity” (e.g. name inscription)? (see also comment 4).
Answer:
As mentioned in response to Q4, the individual information is scarce. We have included all available information and anthropological data (see lines: 176-192) in the revised manuscript and supplementary information now.
Again, the individual information is scarce? In other words, they don't know who they've tested.
quote: Q9. Lines 137-140. “The affinity to the Middle East finds further support by the Y- chromosome haplogroups...” This is true, but the two haplogroups are believed to have different origins (J Western Asia, E1b1b1 North Africa). Moreover, both individuals with haplogroup J are from the pre-ptolemaic period and the individual with haplogroup E from the Ptolemaic period. Does this tell us something about their origin or any differences? The authors should comment on this.
Answer: (to be included in the manuscript and referenced here)
We agree with the reviewer that Y chromosomal haplogroup J is suggested to have arisen in the ancient Near East. However, the current distribution of E1b1b1 in North Africa could also be caused by the back migration from the Near East to Africa that have already been proposed by several authors (Hammer et al. Genetics 1997, 145:787–805; Hammer et al. Mol Biol Evol 1998, 15:427–441; Hammer MF, et al. Mol Biol Evol 2001, 18:1189–1203). The high frequencies of haplogroup R1-M173 in Cameroon also supported the back migration from Eurasia to Africa in Cruciani et al. Am J Hum Genet 2002, 70:1197–1214. Since it’s still unclear whether E1b1b evolved in Northeast Africa or the Near East, we do not attempt to interpret the presence of the two haplogroups as evidence for distinct population affinities for our three Mummy samples and we removed that argument from our study.
Then this rediclious 1997, 1998, 2001 Hammer citation. Yet, Hammer in his later work, if I am not mistaken stated that it has an East African origin, but many authors have confirmed the East African origin as well. And I am not even going to touch R1-M173 (2002), since Cruciani et al is assigning a totally different story in his revised phylogenetic tree (2012). It's clear these authors are biased.
Since they have the gusto to claim that it’s still unclear whether E1b1b evolved in Northeast Africa or the Near East, and thus did not attempt to interpret the presence of the two haplogroups as evidence for distinct population affinities for our three Mummy samples and they removed that argument from their study.
However, there was deliberately no mentioning that the Masalit and Fur populations carry the nucleotide.
They also mentioned E-V22, but due to their biases didn't expect this to have presence in the Sahara-Sahel region going back thousands of years prior to the rise of ancient Egypt. The irony is that it is found in regions, which historical data accounts for as the proto-civilization for ancient Egypt.
They are contradicting their own claims here. And the paper clearly lacked detailed specifics, however this didn't stop them to make outrageous claims.
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quote: Q10. Line 144. “The finding of a continuous population...” Is it really a continuous population, or are the foreign influences in the Ptolemaic-Roman period probably too little to be accounted?? Would it be possible at all to trace down foreigners with this approach?? Please comment!
Answer:
The method used for the population continuity test relies on a set of priors such as generation time and total population size in the respective area. We evaluated a set of different population sizes as priors in our analysis as well as different generation times to test whether these substantially change our initial analysis. They did not change our initial finding of genetic continuity, which is why we believe that our results hold even for a larger number of parameters that could be applied here.
The test of population continuity is not capable/designed to detect outliers. In general, the level of genetic resolution (mostly mitogenomes) does not allow us to identify ‘foreigners’, mostly due to the lack of comparable population data. However, we would be able to spot outliers (i.e. potential foreigners) from our nuclear DNA data via PCA and/or Admixture. The data from our three successfully genotyped samples do suggest that they belonged to the same population.
So, what was the proximate population size? Why don't they elaborate on this, why does this remain unanswered? And what was the given method?
It's especially odd, since they themselves stated that it was a site, which represented mainly occupation during the Late Period till Roman times according to written sources.
quote:Q12. Conclusions. The authors should discuss the possible influence and presence of foreigners at the archaeological site Abusir el-Meleq and how their approach could be used to detect it. Although there appears to be a continuity in the overall population, there could be maybe some single individuals that originate from the Ptolemaic or Roman population. Would it be possible to identify those people and could this help to understand the use of certain mummification practices?
Answer:
We have substantially extended the introduction (lines 111-137) and discussion (lines 361-385, 420-432) to address to point. The data from our three successfully genotyped samples do not suggest a foreign origin, so can be considered representing the local community profile. The contextual evidence does not allow a detailed examination of variations in mummification practices.
This is somewhat what confusing. They are local community and not foreign. But they can't determine whether E1b1b1 was local to the community? But they do consider Hg J and R to be foreign? Okay.
quote: Q13. Conclusions. I agree that in other sites, especially in the south of Egypt, there could be a much higher influence of Sub-Saharan populations. It is well known that there were close trading connections to Nubia and other Sub-Saharan areas during the Middle and New Kingdom. What does this mean for the interpretation of your findings?
Answer:
We have addressed this point in our revised discussion (see lines 395-405). As an alternative explanation this would only mean that modern-day Egyptians might resemble more closely ancient Egyptians from the south. However, in the absence of data from southern sites, this also remains speculative.
So, let me get this straight. The archeological and anthropological data on these mummies, including the site thus lacks evidence, which they formulate as "scares".
However the sites occupation is only dated to Late Period till Roman times according to written sources, while other sites at south are thousands of years older. And anthropological data shows that these early Neolithic inhabitants from the South represent those modern ethnicities from the South. So how can it be that these authors have doubt, without "their substantial evidence"?
Repeat:
Unfortunately, mummies from the Old till early New Kingdom are not present at the site or and not included in our data set, which focusses on the three consecutive periods.
From my understanding the older remains are found in the Deep South, starting at Central Sudan, which show a clear link to the rise of ancient Egypt. Older mummies are found in upper Egypt, thousands of years prior to the given Abusir settlement.
Again, I sense prejudice.
quote: The cemetery called HK43, belonging to the non-elite (or workers) segment of the predynastic population, is located on the southern side of the site beside the Wadi Khamsini. Work here in 1996 when a land reclamation scheme threatened its preservation and excavations continued until 2004, resulting in the discovery of a minimum of 452 graves holding over 500 individuals of Naqada IIB-IIC date (roughly 3650-3500BC).
quote:”As a result of their facial prognathism, the Badarian sample has been described as forming a morphological cluster with Nubian, Tigrean, and other southern (or "Negroid") groups (Morant, 1935, 1937; Mukherjee et al., 1955; Nutter, 1958, Strouhal, 1971; Angel, 1972; Keita, 1990). Cranial nonmetric trait studies have found this group to be similar to other Egyptians, including much later material (Berry and Berry, 1967, 1972), but also to be significantly different from LPD material (Berry et al., 1967). Similarly, the study of dental nonmetric traits has suggested that the Badarian population is at the centroid of Egyptian dental samples (Irish, 2006), thereby suggesting similarity and hence continuity across Egyptian time periods. From the central location of the Badarian samples in Figure 2, the current study finds the Badarian to be relatively morphologically close to the centroid of all the Egyptian samples. The Badarian have been shown to exhibit greatest morphological similarity with the temporally successive EPD (Table 5). Finally, the biological distinctiveness of the Badarian from other Egyptian samples has also been demonstrated (Tables 6 and 7).
These results suggest that the EDyn do form a distinct morphological pattern. Their overlap with other Egyptian samples (in PC space, Fig. 2) suggests that although their morphology is distinctive, the pattern does overlap with the other time periods. These results therefore do not support the Petrie concept of a Dynastic race" (Petrie, 1939; Derry, 1956). Instead, the results suggest that the Egyptian state was not the product of mass movement of populations into the Egyptian Nile region, but rather that it was the result of primarily indigenous development combined with prolonged small-scale migration, potentially from trade, military, or other contacts.
This evidence suggests that the process of state formation itself may have been mainly an indigenous process, but that it may have occurred in association with in-migration to the Abydos region of the Nile Valley. This potential in-migration may have occurred particularly during the EDyn and OK. A possible explanation is that the Egyptian state formed through increasing control of trade and raw materials, or due to military actions, potentially associated with the use of the Nile Valley as a corridor for prolonged small scale movements through the desert environment."
--Sonia R. Zakrzewski. (2007).
Population Continuity or Population Change: Formation of the Ancient Egyptian State. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 132:501-509)
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quote: Q2: Unfortunately, the authors appear to have ignored several earlier papers on Egyptians (see below for 3 examples, there may be others). Their primary result, stated in the abstract as “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” was shown in 2012 using genome-wide SNP array data from Egyptians (Henn et al., PLoS Genetics: Table 1). That is, the sub-Saharan African ancestry is of recent origin in Egyptians dating to AD 1250 (~24 generations ago). Indeed those authors argued that the source of this sub-Saharan ancestry is more likely to be Nilotic than West African as modeled in the current analyses. This is especially problematic as it is the only result reported in the Abstract itself. And again in the conclusion: "By comparing ancient with modern Egyptians, we remarkably found an influx of additional Sub-Saharan African ancestry after the Roman Period, which is visible at both mitochondrial and autosomal level.” This result is not remarkable, it is what is expected given prior published analyses.
Answer:
We acknowledge the oversight not having mentioned the 2012 study by Henn and colleagues, which is now included in our revised manuscript. We confirm their conclusions based on our modern Egyptian data, in particular do we confirm a time estimate for pulse-like admixture from Sub-Sahara Africa 700 years ago. However, the LD-based method used in Henn et al. 2012 (and confirmed by us) cannot distinguish between a pulse-like admixture and continuous migration. Using the direct observation from 2,000 year old Egyptians, which we estimate to have had 8% African ancestry, we get a more complete picture of the time course of African migration into the region than what can be extrapolated from modern data alone.
The part that is missing from Brenna Henn in their citation is:however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood.
Ironically this is the population component, relavant to the rise of ancient Egypt. So why not include these pastoral groups into the paper?
quote: ”Many of the sites reveal evidence of important interactions between Nilotic and Saharan groups during the formative phases of the Egyptian Predynastic Period (e.g. Wadi el-Hôl, Rayayna, Nuq’ Menih, Kurkur Oasis). Other sites preserve important information regarding the use of the desert routes during the Protodynastic and Pharaonic Periods,particularly during periods of political and military turmoil in the Nile Valley (e.g. Gebel Tjauti, Wadi el-Hôl)."
quote:There is now a sufficient body of evidence from modern studies of skeletal remains to indicate that the ancient Egyptians, especially southern Egyptians, exhibited physical characteristics that are within the range of variation for ancient and modern indigenous peoples of the Sahara and tropical Africa.
In general, the inhabitants of Upper Egypt and Nubia had the greatest biological affinity to people of the Sahara and more southerly areas
[...]
Any interpretation of the biological affinities of the ancient Egyptians must be placed in the context of hypothesis informed by the archaeological, linguistic, geographic or other data.
In this context the physical anthropological evidence indicates that the early Nile Valley populations can be identified as part of an African lineage, but exhibiting local variation.
This variation represents the short and long term effects of evolutionary forces, such as gene flow, genetic drift, and natural selection influenced by culture and geography”
--Kathryn A. Bard (STEPHEN E. THOMPSON Egyptians, physical anthropology of Physical anthropology) (1999, 2005, 2015)
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Q5: Section beginning line 144: The authors report apparent congruity between their population sizes estimates and those from the Fayum in the Ptoleimac Period with a 95% credible interval range between 50,000 - 280,000. 1) This is the Ne estimated from mtDNA. In order to compare with the true Ne it need to be scaled 4-fold. 2) The Y-axis scale on Figure 3D does not match the results reported in the text. Indeed the Ne appears to be between 1-2 million durin the Ptolemaic period (black line). 3) Assuming even that the numbers in the text are correct, (115,000 50th estimate) the scaling for females vs. female+male as reported in the historical record would indicate a large divergence between the genetic and historical estimates. 4) No prior on the mutation rate, which will strong influence Ne, is given in the supplement. This is the appropriate place to integrate assumption of g (generation time).
Answer:
The apparent discordance between Figure 3D and the numbers given in the text stems from the fact that the figure shows unscaled results of the SkyGrid inference (given in the female effective population size times the generation time; Ne x T). To estimate the approximate effective population size for the studied population, which could be compared with the population size from the historical records, we scaled the estimated values by dividing them by generation time (we assumed 25 years) and doubled them to account for the whole (male and female) population (assuming equal male to female Ne ratio). We agree that this rescaling was not described explicitly enough, which might have made the results unclear. We modified the figure caption (figures 3d, S2) as well as the relevant methods’ section so that the rescaling is more clearly described.
Regarding the mutation rate prior, we used an uninformative CTMC prior and thus all the temporal information in the inference (which drives estimation of mutation rate and the codependent parameters) came solely from ages of the samples. We modified the text accordingly to make this more clear.
What is this population size from the historical records, they have compared? What is the source they used?
quote:
Q6: Line 197: Lazaridis et al. (2014) contained 18 Egyptian sample of uncertain provenance (Cairo-urban area). Other autosomal SNP array datasets at least including many more individuals are not used here. Contrasting 3 individuals to 18 contemporary ones in order to indicate extrapolate evidence for a pattern that" 6 and 7 million Sub-Saharan slaves to Northern Africa over a span of some 1250 years” seems a strong extrapolation on its own. As the authors admit.
Answer:
We cannot easily include SNP data sets that were generated on a different platform than the Affymetrix Human Origins array. But given the fact that we almost exactly confirm results from Henn et al. who used a different data set, we are confident that as far as our modern Egyptian data is concerned, we have a good representation. As far as ancient Egypt is concerned, we indeed have only three samples from a specific region, but we acknowledge the limits of our conclusions clearly in the Discussion. We also highlight that we do incorporate 100 modern Egyptian Mitogenomes from Pagani et al. and exactly confirm their report of 80% non-African ancestry at the mitochondrial level, again suggesting that our modern Egyptian sample is broadly representative at the level of the analysis performed here.
How do they know there was sub Saharan slaves, when it is recorded that the Islamic expansion took place. And it's a given that the Hajj is one the pillars in Islamic traditions. Historical accounts show that African Muslims have been vey dedicated. Why was this never taken into consideration, instead of the "centuries-old" armchair-theorized slave trade.
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quote: Q7: Line 180: "This individual had a derived allele at the SLC24A5 locus, which encodes for light skin pigmentation...” SLC24A5 is among at least 20 skin pigmentation genes known to contribute to melanin variability in contemporary human populations. It alone does not ‘encode’ for light skin pigmentation. Indeed, many individuals in Cape Verde, Africa carry this allele (which does lighten pigmentation, accounting for 7% of the variance in pigmentation) but their overall phenotype would be still be twice as dark as an average European (Beleza et al. 2013, PLoS Genetics).
Answer:
We changed the sentence (lines: 346-348) to “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 Anatolia (40), consistent with the ancestral affinity shown above”
The authors clearly ignore the question and African populations all together as such, including those from the Sahara-Sahel region and up North. They go directly to Neolithic Anatolia. And how does this fit their local, non-foreign model?
Are Neolithic Anatolians tropical adapted in body portions and limb ratio?
quote:
Q8: Note 8: Test of Population Continuity: the analysis here was not described. Other than collapsing mtDNA lineages into haplogroup frequencies to compare ancient and contemporary groups, there is no description of what the actual test was. Even if the method was described in Brandt et al. (2013) [not even in the main text, only in their supplement], the authors should lay out the assumptions, parameter choices and models invoked in using this method. Why for example, is TPC preferable over Approximate Bayesian Computation models typically used to test the relative liklihood of two different population demographies (in this case continuity w/ minimal drift vs. migration).
Answer:
We have extended the description of our analysis both in the methods part of the manuscript and our supplementary information for clarification and to explain our main findings. Our intention to use the TPC as applied in Brandt et al. 2013 was to evaluate with a simple method whether we can assume genetic continuity (null hypothesis) between our ancient groups and modern-day populations. We agree that complex ABC models would have been the ideal choice to explore alternative scenarios that could explain discontinuity under varying parameters (drift, migration, time, etc.), but were not deemed necessary given that we can more reliably estimate the origin and timing of admixture with nuclear data.
This again contradicts previous claims, which seems to have a consistent pattern.
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quote:Originally posted by Andromeda2025: Same samples used. mummy collection at the University of Tuebingen
Lalremruate et al. 2013
Molecular Identification of Falciparum Malaria and Human Tuberculosis Co-Infections in Mummies from the Fayum Depression (Lower Egypt)
At a time after 1800 BC, due to unexpected increase in flow discharge, the level of the lake raised considerably (ca 18 to 20 masl) and most of the areas occupied by the Middle Kingdom installations were drawn [16], [20]. The dam was breached and the Fayum depression became once more uninhabitable. The lake still stood at around the same level or even higher when Herodotus saw it in the mid-5th century BC and apparently remained that way until early Ptolemaic times [16], [22].
The second large scale reclamation of the Fayum started under the Ptolemies [Ptolemy I Soter (310- 282 BC) and Ptolemy II Philadelphos (282-246 BC)] [22]. It probably took as long as 30 years to lower the level of the lake to two meters below sea level reaching the same level it had during the Old Kingdom.
The Lahun embankment (a five kilometers embankment from the northern side of the Lahun Gap at al-Lahun) constructed under the Ptolemies was used to divert the annual influx of Nile water. Lake Quarun, therefore, dropped to 5 meters below the sea level and the newly exposed land was colonized by Macedonian soldiers [16], [22]. The campaign of land reclamation appears to have started in the eastern area of the Fayum, in the meris of Herakleides, then continued in the southern area, corresponding to the meris of Polemon and, lastly, into the western area in the meris of Themistos [22].
Thanks, nice post.
"To substantiate those speculations, molecular analyses were carried out on sixteen mummified heads recovered from the necropolis of Abusir el Meleq (Fayum) dating from the 3rd Intermediate Period (1064- 656 BC) to the Roman Period (30 BC- 300 AD)."
At least we now know that it's a Fayum settlement. This opens the gate, to understanding these mummies better.
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quote:Originally posted by Amun-Ra The Ultimate: More about Abusir-el-Meleq and the Heka Khasut(Hyksos/Aamu) burials analyzed in this study:
The first Predynastic graves were discovered at Abusir el-Meleq by Otto Rubensohn in his 1902–4 expedition, which also revealed priests’ graves of the Late period and scattered burials from the 18th Dynasty. Under the auspices of the German Orient- Gesellschaft, Georg Möller excavated the Predynastic cemetery in 1905–6, also exposing several burials of the Hyksos period (15th–16th Dynasties). From Encyclopedia of the Archaeology of Ancient Egypt
Thus far genotyped native Ancient Egyptians mummies like Ramses III, Amenhotep III, King Tut all have revealed affiliations with modern SS Africans. For example, Ramses III was determined to be E1b1a by the British Medical Journal study(BMJ).
More nice info on the settlement.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by Amun-Ra The Ultimate: Citation from the study:
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.
Never knew the Canaan were the Hyksos.
"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 Levant".
quote: “While commonly believed to represent Greek settlers in Egypt, the Faiyum portraits instead reflect the complex synthesis of the predominant Egyptian culture and that of the elite Greek minority in the city. According to Walker, the early Ptolemaic Greek colonists married local women and adopted Egyptian religious beliefs, and by Roman times, their descendants were viewed as Egyptians by the Roman rulers, despite their own self-perception of being Greek. The dental morphology of the Roman-period Faiyum mummies was also compared with that of earlier The dental morphology of the Roman-period Faiyum mummies was also compared with that of earlier Egyptian populations, and was found to be "much more closely akin" to that of ancient Egyptians than to Greeks or other European populations. “
--Irish JD (2006).
"Who were the ancient Egyptians? Dental affinities among Neolithic through postdynastic peoples.". Am J Phys Anthropol 129
quote: "Still, it appears that the process of state formation involved a large indigenous component. Outside influence and admixture with extraregional groups primarily occurred in Lower Egypt—perhaps during the later dynastic, but especially in Ptolmaic and Roman times (also Irish, 2006). No large-scale population replacement in the form of a foreign dynastic ‘race’ (Petrie, 1939) was indicated. Our results are generally consistent with those of Zakrzewski (2007). Using craniometric data in predynastic and early dynastic Egyptian samples, she also concluded that state formation was largely an indigenous process with some migration into the region evident. The sources of such migrants have not been identified; inclusion of additional regional and extraregional skeletal samples from various periods would be required for this purpose."
--Schillaci MA, Irish JD, Wood CC. 2009
Further analysis of the population history of ancient Egyptians.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by Ish Gebor: Reviewer #1:
quote: Q10. Line 144. “The finding of a continuous population...” Is it really a continuous population, or are the foreign influences in the Ptolemaic-Roman period probably too little to be accounted?? Would it be possible at all to trace down foreigners with this approach?? Please comment!
Answer:
The method used for the population continuity test relies on a set of priors such as generation time and total population size in the respective area. We evaluated a set of different population sizes as priors in our analysis as well as different generation times to test whether these substantially change our initial analysis. They did not change our initial finding of genetic continuity, which is why we believe that our results hold even for a larger number of parameters that could be applied here.
The test of population continuity is not capable/designed to detect outliers. In general, the level of genetic resolution (mostly mitogenomes) does not allow us to identify ‘foreigners’, mostly due to the lack of comparable population data. However, we would be able to spot outliers (i.e. potential foreigners) from our nuclear DNA data via PCA and/or Admixture. The data from our three successfully genotyped samples do suggest that they belonged to the same population.
So, what was the proximate population size? Why don't they elaborate on this, why does this remain unanswered? And what was the given method?
It's especially odd, since they themselves stated that it was a site, which represented mainly occupation during the Late Period till Roman times according to written sources.
quote:Q12. Conclusions. The authors should discuss the possible influence and presence of foreigners at the archaeological site Abusir el-Meleq and how their approach could be used to detect it. Although there appears to be a continuity in the overall population, there could be maybe some single individuals that originate from the Ptolemaic or Roman population. Would it be possible to identify those people and could this help to understand the use of certain mummification practices?
Answer:
We have substantially extended the introduction (lines 111-137) and discussion (lines 361-385, 420-432) to address to point. The data from our three successfully genotyped samples do not suggest a foreign origin, so can be considered representing the local community profile. The contextual evidence does not allow a detailed examination of variations in mummification practices.
This is somewhat what confusing. They are local community and not foreign. But they can't determine whether E1b1b1 was local to the community? But they do consider Hg J and R to be foreign? Okay.
quote: Q13. Conclusions. I agree that in other sites, especially in the south of Egypt, there could be a much higher influence of Sub-Saharan populations. It is well known that there were close trading connections to Nubia and other Sub-Saharan areas during the Middle and New Kingdom. What does this mean for the interpretation of your findings?
Answer:
We have addressed this point in our revised discussion (see lines 395-405). As an alternative explanation this would only mean that modern-day Egyptians might resemble more closely ancient Egyptians from the south. However, in the absence of data from southern sites, this also remains speculative.
So, let me get this straight. The archeological and anthropological data on these mummies, including the site thus lacks evidence, which they formulate as "scares".
However the sites occupation is only dated to Late Period till Roman times according to written sources, while other sites at south are thousands of years older. And anthropological data shows that these early Neolithic inhabitants from the South represent those modern ethnicities from the South. So how can it be that these authors have doubt, without "their substantial evidence"?
Repeat:
Unfortunately, mummies from the Old till early New Kingdom are not present at the site or and not included in our data set, which focusses on the three consecutive periods.
From my understanding the older remains are found in the Deep South, starting at Central Sudan, which show a clear link to the rise of ancient Egypt. Older mummies are found in upper Egypt, thousands of years prior to the given Abusir settlement.
Again, I sense prejudice.
quote: The cemetery called HK43, belonging to the non-elite (or workers) segment of the predynastic population, is located on the southern side of the site beside the Wadi Khamsini. Work here in 1996 when a land reclamation scheme threatened its preservation and excavations continued until 2004, resulting in the discovery of a minimum of 452 graves holding over 500 individuals of Naqada IIB-IIC date (roughly 3650-3500BC).
quote:”As a result of their facial prognathism, the Badarian sample has been described as forming a morphological cluster with Nubian, Tigrean, and other southern (or "Negroid") groups (Morant, 1935, 1937; Mukherjee et al., 1955; Nutter, 1958, Strouhal, 1971; Angel, 1972; Keita, 1990). Cranial nonmetric trait studies have found this group to be similar to other Egyptians, including much later material (Berry and Berry, 1967, 1972), but also to be significantly different from LPD material (Berry et al., 1967). Similarly, the study of dental nonmetric traits has suggested that the Badarian population is at the centroid of Egyptian dental samples (Irish, 2006), thereby suggesting similarity and hence continuity across Egyptian time periods. From the central location of the Badarian samples in Figure 2, the current study finds the Badarian to be relatively morphologically close to the centroid of all the Egyptian samples. The Badarian have been shown to exhibit greatest morphological similarity with the temporally successive EPD (Table 5). Finally, the biological distinctiveness of the Badarian from other Egyptian samples has also been demonstrated (Tables 6 and 7).
These results suggest that the EDyn do form a distinct morphological pattern. Their overlap with other Egyptian samples (in PC space, Fig. 2) suggests that although their morphology is distinctive, the pattern does overlap with the other time periods. These results therefore do not support the Petrie concept of a Dynastic race" (Petrie, 1939; Derry, 1956). Instead, the results suggest that the Egyptian state was not the product of mass movement of populations into the Egyptian Nile region, but rather that it was the result of primarily indigenous development combined with prolonged small-scale migration, potentially from trade, military, or other contacts.
This evidence suggests that the process of state formation itself may have been mainly an indigenous process, but that it may have occurred in association with in-migration to the Abydos region of the Nile Valley. This potential in-migration may have occurred particularly during the EDyn and OK. A possible explanation is that the Egyptian state formed through increasing control of trade and raw materials, or due to military actions, potentially associated with the use of the Nile Valley as a corridor for prolonged small scale movements through the desert environment."
--Sonia R. Zakrzewski. (2007).
Population Continuity or Population Change: Formation of the Ancient Egyptian State. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 132:501-509)
I believe according to the Malaria study of the Fayum depression, the area has been de- populated on several occasions do to the fluctuations of the Nile. Thus making population continuity highly variable over millennia.
Posts: 165 | From: Miami Beach, Florida | Registered: Jun 2017
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quote:Originally posted by Andromeda2025: I believe according to the Malaria study of the Fayum depression, the area has been de- populated on several occasions do to the fluctuations of the Nile. Thus making population continuity highly variable over millennia.
That comes off as logical.
I have posted this source a few times already, but now it starts to make sense.
quote: The ancient settlement of Abusir el-Malek sat on a small rise in the fertile floodplain between the Faiyum and the Nile. By 1500 B.C., it was a prosperous settlement with many temples and a vast burial ground and buildings stretching across a large area.
Excavations in the early twentieth century revealed burials centered on a cult honoring Osiris, the Egyptian god of the afterlife. The earliest evidence of occupation at the site dates from around 3000 B.C., with the majority of burials beginning 1,500 years later. The cemetery continued to be used for centuries, with the earlier shaft tombs being filled with later burials from the Greek, Roman, and Islamic periods. Thousands of individuals were buried at the site over hundreds of years of use.
quote:Originally posted by Amun-Ra The Ultimate: More about Abusir-el-Meleq and the Heka Khasut(Hyksos/Aamu) burials analyzed in this study:
The first Predynastic graves were discovered at Abusir el-Meleq by Otto Rubensohn in his 1902–4 expedition, which also revealed priests’ graves of the Late period and scattered burials from the 18th Dynasty. Under the auspices of the German Orient- Gesellschaft, Georg Möller excavated the Predynastic cemetery in 1905–6, also exposing several burials of the Hyksos period (15th–16th Dynasties). From Encyclopedia of the Archaeology of Ancient Egypt
Thus far genotyped native Ancient Egyptians mummies like Ramses III, Amenhotep III, King Tut all have revealed affiliations with modern SS Africans. For example, Ramses III was determined to be E1b1a by the British Medical Journal study(BMJ).
Saying they found hyksos period mummies doesn't mean the mummies they found were hyksos. Do you have any other citations that would suggest the presence of hyksos burials?
Posts: 2508 | From: . | Registered: Nov 2011
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quote:Originally posted by Amun-Ra The Ultimate: More about Abusir-el-Meleq and the Heka Khasut(Hyksos/Aamu) burials analyzed in this study:
The first Predynastic graves were discovered at Abusir el-Meleq by Otto Rubensohn in his 1902–4 expedition, which also revealed priests’ graves of the Late period and scattered burials from the 18th Dynasty. Under the auspices of the German Orient- Gesellschaft, Georg Möller excavated the Predynastic cemetery in 1905–6, also exposing several burials of the Hyksos period (15th–16th Dynasties). From Encyclopedia of the Archaeology of Ancient Egypt
Thus far genotyped native Ancient Egyptians mummies like Ramses III, Amenhotep III, King Tut all have revealed affiliations with modern SS Africans. For example, Ramses III was determined to be E1b1a by the British Medical Journal study(BMJ).
Saying they found hyksos period mummies doesn't mean the mummies they found were hyksos. Do you have any other citations that would suggest the presence of hyksos burials?
The mummies at earliest estimate 1338 BC but most are not as old Of the three mummies with nuclear genome data the oldest is 769 BC
The Hyksos were expelled in 1550 BC
That means these mummies aren't Hyksos
Asiatics migrated into Northern Egypt en mass in the 12th Dynasty -> 1800 bc and established settlements in the North - particularly in the Delta and were militarily and politically dominant until the 18th Dynasty. The Hyksos were neutralized, *militarily* by southern warrior kings... but I very much doubt that Asiatic demographic infiltration, invasion, migration and settlement was ever resolved by the southern kings.
I don't think that the various Canaanite populations were ever expelled from Northern Egypt... they just became Egyptianized; the Hyksos were already in the process of adopting features of Egyptian culture, and were probably encouraged to complete the adoption of culture and identity.
I maintain that the Abusir mummies are not representative.
Posts: 1568 | From: Pluto | Registered: Sep 2008
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I maintain that the Abusir mummies are not representative.
What if an mtdna analysis on the Amarna had similar maternal DNA?
Then I would accept the results. Late period samples at a time of foreign domination do not sway me. I need early dynastic samples - particularly from the south.
Posts: 1568 | From: Pluto | Registered: Sep 2008
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posted
Nah lioness is catching me off guard, she/he/them iirc has posted the most evidence or arguments (probably tied with Ish) for these mummies being representatives of not "native" burials, why ask that question about the mtdna profiles? With all you've contributed do you believe that the Armana culture would be just as Asian?
Posts: 1781 | From: New York | Registered: Jul 2016
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quote:Originally posted by Amun-Ra The Ultimate: More about Abusir-el-Meleq and the Heka Khasut(Hyksos/Aamu) burials analyzed in this study:
The first Predynastic graves were discovered at Abusir el-Meleq by Otto Rubensohn in his 1902–4 expedition, which also revealed priests’ graves of the Late period and scattered burials from the 18th Dynasty. Under the auspices of the German Orient- Gesellschaft, Georg Möller excavated the Predynastic cemetery in 1905–6, also exposing several burials of the Hyksos period (15th–16th Dynasties). From Encyclopedia of the Archaeology of Ancient Egypt
Thus far genotyped native Ancient Egyptians mummies like Ramses III, Amenhotep III, King Tut all have revealed affiliations with modern SS Africans. For example, Ramses III was determined to be E1b1a by the British Medical Journal study(BMJ).
Saying they found hyksos period mummies doesn't mean the mummies they found were hyksos. Do you have any other citations that would suggest the presence of hyksos burials?
I maintain that the Abusir mummies are not representative.
What if an mtdna analysis on the Amarna had similar maternal DNA?
Do you expect the Armanas to carry T, J, X, W and R?
I bet, you will get no answer on this.
quote:Originally posted by Elmaestro: Nah lioness is catching me off guard, she/he/them iirc has posted the most evidence or arguments (probably tied with Ish) for these mummies being representatives of not "native" burials, why ask that question about the mtdna profiles? With all you've contributed do you believe that the Armana culture would be just as Asian?
Perhaps it skipped me, but what has the lioness posted on Abusir that made you convinced?
In terms of amount of posts there is no one other than the lioness with a ridiculous amount of Posts: 31625 since Registered: Jan 2010.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Genetic kinship analyses revealed identical haplotypes in both mummies (table 1⇓); using the Whit Athey’s haplogroup predictor, we determined the Y chromosomal haplogroup E1b1a. The testing of polymorphic autosomal microsatellite loci provided similar results in at least one allele of each marker (table 2⇓). Although the mummy of Ramesses III’s wife Tiy was not available for testing, the identical Y chromosomal DNA and autosomal half allele sharing of the two male mummies strongly suggest a father-son relationship.
--Zahi Hawass, Somaia Ismai et al.
Revisiting the harem conspiracy and death of Ramesses III: anthropological, forensic, radiological,and genetic study
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:1) So all these single SNPs have been found individually in these 91 mummies?
2) Why are most of the SNPs so low in frequency?
3) What is known about any of these remains, other than what is being shown?
4) Basically they claim that L* SNPs were never in northeast (Egypt) Africa, which is laughable at best.
How do you know the SNP is so low in frequency? I don't know how to read these charts... Another question, reading the text it has at the bottom, is it saying that only 2 of these mummies tested positive for relatively lighter skin?
Posts: 2508 | From: . | Registered: Nov 2011
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quote:Originally posted by Oshun: How do you know the SNP is so low in frequency? I don't know how to read these charts...
He made that up
quote:Originally posted by Oshun: Another question, reading the text it has at the bottom, is it saying that only 2 of these mummies tested positive for relatively lighter skin?
No, of the 3 mummies tested for nuclear genome data they found two of them carrying these genes. They didn't test the other mummies for that No
Posts: 42920 | From: , | Registered: Jan 2010
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quote:Originally posted by Oshun: How do you know the SNP is so low in frequency? I don't know how to read these charts...
He made that up
quote:Originally posted by Oshun: Another question, reading the text it has at the bottom, is it saying that only 2 of these mummies tested positive for relatively lighter skin?
No, of the 3 mummies tested for nuclear genome data they found two of them carrying these genes. They didn't test the other mummies for that No
It was not made up, it shows in the data. Remember your aren't that great at math.
But instead of being so concerned with this, how come the "remaining mummies" only show single SNP's and no remaining ancestral DNA? I have prossed this question to you a few times already, but for some reason you keep running away from this. Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by the lioness,: The mummies at earliest estimate 1338 BC but most are not as old Of the three mummies with nuclear genome data the oldest is 769 BC
**The Hyksos were expelled in 1550 BC**
That means these mummies aren't Hyksos burials
As Swenet has pointed out, both archaeological and skeletal evidence show significant demographic change to Lower Egypt from the end of the Middle Kingdom through the New Kingdom period. When historical sources say the Egyptians expelled the Hyksos, they usually specify the Hyksos elite or ruling families. This does not mean all Hyksos or even Asiatic peoples in the Delta were expelled. And this does not exclude the possibility that these Hyskos (elite or not) or other Asiatics could have intermarried and mixed with the indigenes especially since it is known that the Hyksos did adopt Egyptian culture and for the most part assimilate.
Again, I'm not saying the Abusir mummies tested were necessarily Hyksos or even of Hyksos ancestry per say but what makes you so confident that they are pristine' Egyptians with no foreign admixture??
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posted
^ In addition to that, I know Toby Wilkinson in his Rise and Fall of Ancient Egypt mentioned substantial Libyan immigration into Lower Egypt during the Third Intermediate Period. Assuming these Libyans were the lighter-skinned type from the northern Libyan coast, maybe they could be another source of foreign admixture?
quote:Originally posted by Tyrannohotep: ^ In addition to that, I know Toby Wilkinson in his Rise and Fall of Ancient Egypt mentioned substantial Libyan immigration into Lower Egypt during the Third Intermediate Period. Assuming these Libyans were the lighter-skinned type from the northern Libyan coast, maybe they could be another source of foreign admixture?
what would the genetic difference be?
Posts: 42920 | From: , | Registered: Jan 2010
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posted
^ Why don't you tell us, since you seem to have a thing for all things 'Berber' and Maghrebi. Meanwhile you haven't explained the genetic difference between the Egyptians and say the neolithic Anatolians whom the authors say share a common ancestry.
Posts: 26239 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
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
_________________________
PEER REVIEW FILE (easier to read at link above)
Reviewers' comments: Reviewer #1 (Remarks to the Author): This is an interesting paper that presents important insights into the genetic history of the ancient Egyptian population. To my knowledge, this work represents the first detailed population genetic study on ancient Egyptian mummified material, by the reconstruction of 91 mitochondrial genomes and three genome-wide datasets. It has to be acknowledged that the authors applied strict quality controls and thereby managed to unequivocally proof the authenticity of their findings. Based on this data, the long-lasting and often dogmatic discussion on whether ancient DNA could survive in ancient Egyptian mummies can be finally put to rest. Both, the molecular approach and the data analysis was very well done and the results provide new and important insights into the continuity of the population of the ancient Egyptian site and the shared ancestry of the ancient Egyptians with Near Easterners. The work represents an important contribution to the study of ancient human history in Egypt. Nevertheless, the work could be further improved by providing more details on the investigated mummies and a more detailed analysis of a possible foreign influence at the site. It would be interesting to understand if the methodological approach could allow to identify single individuals that have a different origin, such as Ptolemaic or Roman, and what it would tell us about burial practice and mummification techniques. In the following, I have listed some specific comments: 1.I would have liked to see some comments on the debate about DNA preservation in ancient Egypt and in particular the mentioning of some previous work. I think it would strengthen the impact of this paper, if the authors would underline the importance of their findings with regard to the general skeptics on the presence of ancient DNA in hot and arid climates. 2.I am particularly surprised that the authors have not cited the previous work on the material that derives from the same collection. As far as I understand, Khairat et al. (J. Appl. Genet., 2013) and Lalremruata et al. (Plos One, 2013), also used samples from the mummy collection at the University of Tuebingen. As the authors of this work have used some radiocarbon dates from Lalremruata et al. (see Suppl.), I assume that the samples were taken from the same collection. It should be explained why the previous work was not mentioned. 3.Lines 55-57: “However, methodological problems and contamination obstacles… hampered direct investigations…”. What exactly were these problems and obstacles?? I assume that a major part of the problem was the disbelief of many scholars that ancient DNA could survive in Egyptian mummies due to the hot climate. What were the other reasons? Why has it become possible now? (see also comment 1) 4.Lines 66-72. Evidence for foreign influence: Is this true for the studied samples? What do we know about the mummies regarding names, burial practice, coffin styles, etc.? This is an interesting point! Why didn’t the authors use their data to proof or disproof this assumption? The authors should mention whether they tried to see any foreign influence and how could this have influence their analysis! 5.Lines 75-77. “In particular, the site holds much promise for studying changes in its population structure from the late Dynastic Period to the present day.” Why is this the case? Is it due to the better DNA preservation in the later mummies?? Please explain! 6.Line 78. 151 mummified remains: It would have been interesting to learn more about these mummies. Is there any information on the age and sex of the mummies? How were they mummified? How is the state of preservation? How many of them have an “identity” (e.g. name inscription)? (see also comment 4). 7.Line 92. Yields of preserved DNA: What’s about the preservation of non-human DNA? Did the authors have a look into the metagenomics data? It is surprising to see that the authors, who published a series of articles on ancient pathogen DNA, didn’t check for the presence of diseases such as TB, malaria or toxoplasmosis, which were all reported in previous studies. Please comment. 8.Lines 98-99. DNA damage in mummies: Is this true for all mummies or just Egyptian mummies? Is this influenced by the mummification process? Could it be different in natural mummies? 9.Lines 137-140. “The affinity to the Middle East finds further support by the Y-chromosome haplogroups…” This is true, but the two haplogroups are believed to have different origins (J Western Asia, E1b1b1 North Africa). Moreover, both individuals with haplogroup J are from the pre-ptolemaic period and the individual with haplogroup E from the Ptolemaic period. Does this tell us something about their origin or any differences? The authors should comment on this. 10.Line 144. “The finding of a continuous population…” Is it really a continuous population, or are the foreign influences in the Ptolemaic-Roman period probably too little to be accounted?? Would it be possible at all to trace down foreigners with this approach?? Please comment! 11.Conclusions. What are the particular challenges of working with ancient Egyptian mummies? (see comment 3.). It seems that there was some work published on ancient pathogen DNA in Egypt, but very little on human DNA. What is the reason? Was it mainly a methodological problem, such as the non-availability of high-throughput sequencing and enrichment or are there particular issues with contamination or inhibition? I think it could be interesting for the reader to understand the potential and obstacles of working with Egyptian mummies. 12.Conclusions. The authors should discuss the possible influence and presence of foreigners at the archaeological site Abusir el-Meleq and how their approach could be used to detect it. Although there appears to be a continuity in the overall population, there could be maybe some single individuals that originate from the Ptolemaic or Roman population. Would it be possible to identify those people and could this help to understand the use of certain mummification practices? 13.Conclusions. I agree that in other sites, especially in the south of Egypt, there could be a much higher influence of Sub-Saharan populations. It is well known that there were close trading connections to Nubia and other Sub-Saharan areas during the Middle and New Kingdom. What does this mean for the interpretation of your findings? Reviewer #2 (Remarks to the Author): This paper is written like similarly structured ancient DNA papers, with a focus on the production of the dataset, a set of standard analyses performed for small sample sizes and extrapolation to prehistorical conclusions. The problem with this approach is that for the majority of studies, prior genetic analysis (and archaeological etc) has already been performed. The ancient DNA papers largely ignore the other fields and are written ‘hypothesis-free.’ Their scientific value becomes limited as each new paper attempts to devise and answer hypotheses that are often longstanding, involving significant repetition. This paper should and could be re-written to answer a question. It would start with a review of prior historical and genetic work performed on Egyptian populations, narrow down to 1-2 specific hypotheses (Can we confirm that slave trade into Egpyt and Near East occurring in the past XX centuries changed the genetic composition of Egyptians represented by urban cohorts in Cairo?) Is this a paper about success in sequencing ancient Egyptians or about resolving the population history of Egyptians given new mtDNA data? Unfortunately, the authors appear to have ignored several earlier papers on Egyptians (see below for 3 examples, there may be others). Their primary result, stated in the abstract as “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” was shown in 2012 using genome- wide SNP array data from Egyptians (Henn et al., PLoS Genetics: Table 1). That is, the sub-Saharan African ancestry is of recent origin in Egyptians dating to AD 1250 (~24 generations ago). Indeed those authors argued that the source of this sub-Saharan ancestry is more likely to be Nilotic than West African as modeled in the current analyses. This is especially problematic as it is the only result reported in the Abstract itself. And again in the conclusion: "By comparing ancient with modern Egyptians, we remarkably found an influx of additional Sub-Saharan African ancestry after the Roman Period, which is visible at both mitochondrial and autosomal level.” This result is not remarkable, it is what is expected given prior published analyses. For example, Kujanova et al. (2009) analysis of mtDNA and Y-chromosomal data from an Egyptian oasis isolate from middle Egypt is not cited. They found that sub-Saharan mtDNA L-lineages constituted 30% of their dataset, indicating a strong sub-Saharan component on the maternal side, which was largely absent on the Y (6% M2-derived lineages). Kujanova et al. also argued for a recent migration event to account for the L lineages: “The absence of any signs of local accumulation of diversity in the L haplotypes in el-Hayez seems to favor the idea of these lineages being recent introductions into the Egyptian Western Desert.” And in Pagani et al. (2015, AJHG) show that "the average proportion of non-African ancestry in the Egyptians to be 80% and dated the midpoint of the admixture event by using ALDER to around 750 years ago (Table S2), consistent with the Islamic expansion and dates reported previously.” In contrasting this paper with another similar high-profile journal paper, Pagani et al. (2015) AJHG, I do not find the results in this manuscript to be major scientific contribution and would be more appropriate for a specialized journal. Section beginning line 144: The authors report apparent congruity between their population sizes estimates and those from the Fayum in the Ptoleimac Period with a 95% credible interval range between 50,000 - 280,000. 1) This is the Ne estimated from mtDNA. In order to compare with the true Ne it need to be scaled 4-fold. 2) The Y-axis scale on Figure 3D does not match the results reported in the text. Indeed the Ne appears to be between 1-2 million durin the Ptolemaic period (black line). 3) Assuming even that the numbers in the text are correct, (115,000 50th estimate) the scaling for females vs. female+male as reported in the historical record would indicate a large divergence between the genetic and historical estimates. 4) No prior on the mutation rate, which will strong influence Ne, is given in the supplement. This is the appropriate place to integrate assumption of g (generation time) Line 197: Lazaridis et al. (2014) contained 18 Egyptian sample of uncertain provenance (Cairo-urban area). Other autosomal SNP array datasets at least including many more individuals are not used here. Contrasting 3 individuals to 18 contemporary ones in order to indicate extrapolate evidence for a pattern that" 6 and 7 million Sub-Saharan slaves to Northern Africa over a span of some 1250 years” seems a strong extrapolation on its own. As the authors admit. Line 180: "This individual had a derived allele at the SLC24A5 locus, which encodes for light skin pigmentation…” SLC24A5 is among at least 20 skin pigmentation genes known to contribute to melanin variability in contemporary human populations. It alone does not ‘encode’ for light skin pigmentation. Indeed, many individuals in Cape Verde, Africa carry this allele (which does lighten pigmentation, accounting for 7% of the variance in pigmentation) but their overall phenotype would be still be twice as dark as an average European (Beleza et al. 2013, PLoS Genetics). Note 8: Test of Population Continuity: the analysis here was not described. Other than collapsing mtDNA lineages into haplogroup frequencies to compare ancient and contemporary groups, there is no description of what the actual test was. Even if the method was described in Brandt et al. (2013) [not even in the main text, only in their supplement], the authors should lay out the assumptions, parameter choices and models invoked in using this method. Why for example, is TPC preferable over Approximate Bayesian Computation models typically used to test the relative liklihood of two different population demographies (in this case continuity w/ minimal drift vs. migration). Reviewer #3 (Remarks to the Author): In this very well written, concise yet informative manuscript, Verena Schuenemann and colleagues report genetic data obtained from ancient Egyptian mummies. Because DNA is not very well preserved in mummies, the authors used capture techniques to enrich their libraries for specific human target regions. This technique resulted in high-coverage mitochondrial genomes for 91 samples and an additional set of autosomal SNPs for 3 of those samples. When comparing to modern data, the authors find convincing evidence of an influx of Sub-Saharen alleles in more recent times. To obtain these results, the authors used by now well established analysis techniques, which were applied carefully to the degree I can judge. The analyses does appear sound and I do not have any concern that the observed genetic differences between ancient and modern Egyptians is real. I’m less confident that this result is surprising given the archaeological and historical knowledge of the region. I’m not a specialist of that history, but I would have enjoyed reading this paper much more if the introduction and discussion / conclusion would relate this finding better with the existing literature on the Egyptian history. Just stating that “Egypt provides a privileged setting for studying population history” fails a bit short of discussing open questions the study of Egyptian mummies might help to settle. Indeed, the way the paper is pitched know the real emphasis is just put on the fact that DNA could be obtained from mummies. Another aspect that I feel is missing is a brief discussion on how the bias from only studying individuals that were mummified (as compared to random individuals from the ancient Egypt) might have let to the lack of a Sub-Saharan component in the ancient individuals. I just found one type: L123: three (instead of tree) REVIEWERS' COMMENTS: Reviewer #1 (Remarks to the Author): The authors have taken into consideration all my comments and the revised manuscript has improved significantly. However, I do not fully agree with the response to my first query and the way the introduction was modified accordingly (lines 84-105). Although it is true that most of the previous work was done in the "PCR era of ancient DNA", it does not necessarily mean that the previous findings were mainly the result of modern contamination. In particular, as most of the criticism was based on a general assumption that DNA may not survive in hot and dry climates. In this work, the authors have successfully demonstrated otherwise and they should therefore come to the conclusion that the general doubts on preservation of ancient DNA in Egyptian mummies (e.g. citations 8,9) were premature. It is true and highly appreciated that the authors performed the first in-depth ancient DNA analysis using high-throughput sequencing methods, so there is no need to generally doubt previous work that was done on Egyptian mummies. I would once more recommend that the authors present the previous work in a more balanced way, mentioning the issues with the PCR based approach, but also acknowledge that DNA seems to survive in ancient Egyptian mummies despite previous skepticism. If the authors are willing to address this issue, I would be happy to accept the manuscript for publication. Reviewer #3 (Remarks to the Author): This is now the second time I review this manuscript and I'm pleased to see that the manuscript has greatly improved from its initial version. In particular, the presented research is now appropriately embedded in the general historical context of the region and the authors now mention the specific questions or hypothesis they test more explicitly. I also remain happy with the analyses presented. It is indeed questionable how accurate ancient admixture rates can be learned from either a single locus (mtDNA) or just three samples in a case in which admixture is so recent that ancestry blocks are necessarily large and the variation in admixture rates between individuals expected to be very high. However, the authors are aware and transparent about these shortcomings in their data. Yet, as a result, the presented results do still not go much beyond confirming some previously noted findings and the real contribution of the work seems to be the success in obtaining reliable genetic data from Egyptian mummies. The importance of that finding to the relevant community is something I can not judge. I just stumbled across one typo: on L164: repetition of “still”. "Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods" by Verena J. Schuenemann and colleagues Response to reviewer comments: Please find below a point by point response to the comments made by each of the three reviewers. Their individual comments are in black, the matching response in blue. Reviewer #1: Q1. I would have liked to see some comments on the debate about DNA preservation in ancient Egypt and in particular the mentioning of some previous work. I think it would strengthen the impact of this paper, if the authors would underline the importance of their findings with regard to the general skeptics on the presence of ancient DNA in hot and arid climates. Answer: We have substantially rewritten the introduction (lines: 84-105) to address results (or lack thereof) from previous studies and questions about the feasibility to retrieve ancient human DNA from samples from hot and arid climates. Q2. I am particularly surprised that the authors have not cited the previous work on the material that derives from the same collection. As far as I understand, Khairat et al. (J. Appl. Genet., 2013) and Lalremruata et al. (Plos One, 2013), also used samples from the mummy collection at the University of Tuebingen. As the authors of this work have used some radiocarbon dates from Lalremruata et al. (see Suppl.), I assume that the samples were taken from the same collection. It should be explained why the previous work was not mentioned. Answer: It is correct that we used 5 radiocarbon dates reported in Lalremruate et al. 2013 and generated 85 new ones. The study Khairat et al. 2013 is now cited in our revised introduction: lines 103-105. All studies on the Tuebingen mummy collection (Lalremruate et al. 2013, Khairat et al. 2013, Nicholson et al. 2011 and Welte 2016) are now cited in our revised sample description: lines 173-175. Q3. Lines 55-57: “However, methodological problems and contamination obstacles... hampered direct investigations...”. What exactly were these problems and obstacles?? I assume that a major part of the problem was the disbelief of many scholars that ancient DNA could survive in 1 Egyptian mummies due to the hot climate. What were the other reasons? Why has it become possible now? (see also comment 1) Answer: This is not a matter of beliefs, but based on the fact that many/most of the early studies did not withstand the scrutiny of ancient DNA authentication criteria. These are particularly important when reporting results from challenging climates (see e.g. Bollongino et al. 2008, Comptes Rendus Palevol 7(2):91-98). Many of the studies of Egyptian remains were conducted in the classical ‘PCR era of ancient DNA’, a technique which favors intact DNA molecules and is thus prone to modern human DNA contamination. It furthermore does not allow to study DNA damage patterns, that were found to be among the most reliable criteria for ancient DNA authenticity (Stoneking & Krause 2011). It is well known that the length of ancient DNA molecules is around 50bp and the overall amount of DNA damage roughly correlates with (thermal) age (Matthew Collins, Susanna Sawyer etc…), which makes STR profiling (up to 350 bp!) rather difficult. NGS techniques have the advantage to utilise the large number of independent DNA fragments (usually not accessible to PCR) in order to study contamination. Further, many previous studies have used muscle tissue, which we clearly show to be the least promising/appropriate material when studying ancient DNA. We expanded our discussion on preservation conditions and previous work in the introduction (lines: 84-105), however much of this debate can be found in Lorenzen et al. 2010 and was not repeated here. Q4. Lines 66-72. Evidence for foreign influence: Is this true for the studied samples? What do we know about the mummies regarding names, burial practice, coffin styles, etc.? This is an interesting point! Why didn’t the authors use their data to proof or disproof this assumption? The authors should mention whether they tried to see any foreign influence and how could this have influence their analysis! Answer: We have extensively rewritten the introduction and sample information to include all available contextual information on the individuals under study (lines: 111-137, 162-172). Unfortunately, this information is scarce and not sufficient to formulate strong hypotheses that could be tested in a formal manner. This issue is now detailed in our discussion: lines 361- 371. We do, however, fully address the reliability of our sample as being representative of the community at the time (see discussion: lines: 371-385). 2 Q5. Lines 75-77. “In particular, the site holds much promise for studying changes in its population structure from the late Dynastic Period to the present day.” Why is this the case? Is it due to the better DNA preservation in the later mummies?? Please explain! Answer: Unfortunately, mummies from the Old till early New Kingdom are not present at the site or and not included in our data set, which focusses on the three consecutive periods. The site is mainly occupied during the Late Period till Roman times according to written sources, and thus would allow the study of an extended temporal transect. We furthermore find in more than 50% of all remains authentic ancient DNA preserved, suggesting this to be an ideal site for further studies. We removed the sentence and included a more intensive introduction and discussion of the site, see Q1 and Q4. Q6. Line 78. 151 mummified remains: It would have been interesting to learn more about these mummies. Is there any information on the age and sex of the mummies? How were they mummified? How is the state of preservation? How many of them have an “identity” (e.g. name inscription)? (see also comment 4). Answer: As mentioned in response to Q4, the individual information is scarce. We have included all available information and anthropological data (see lines: 176-192) in the revised manuscript and supplementary information now. Q7. Line 92. Yields of preserved DNA: What’s about the preservation of non-human DNA? Did the authors have a look into the metagenomics data? It is surprising to see that the authors, who published a series of articles on ancient pathogen DNA, didn’t check for the presence of diseases such as TB, malaria or toxoplasmosis, which were all reported in previous studies. Please comment. Answer: We used our latest metagenomic pipeline (Herbig et al. 2016 biorxiv) in order to find evidence for authentic ancient pathogens, we however failed to find any clear signal for the pathogens reported in previous studies. More analyses on teeth and individuals with clear pathological lesions might be more promising for future research on ancient pathogens from Egyptian mummies. 3 Q8. Lines 98-99. DNA damage in mummies: Is this true for all mummies or just Egyptian mummies? Is this influenced by the mummification process? Could it be different in natural mummies? Answer: To our knowledge, there is no comprehensive and comparative survey on mummies from a global variety published to date. For natural mummies, such as for example from Peru (dry mummies) or the Tyrolean iceman (ice mummy), there seems to be no general pattern observable other than those from high altitudes, i.e. ‘perma-frost-conditions, show higher yields of authentic DNA and reduced damage patterns (e.g. Iceman, Saqqaq). To our knowledge, no systematic tests have yet been done on mummies, as for example for bones and eggshells in Allentoft et al (2012). There have been attempts to simulate DNA decay by burying material and investigating after several years how much DNA damage was introduced, these results were however inconclusive. Q9. Lines 137-140. “The affinity to the Middle East finds further support by the Y- chromosome haplogroups...” This is true, but the two haplogroups are believed to have different origins (J Western Asia, E1b1b1 North Africa). Moreover, both individuals with haplogroup J are from the pre-ptolemaic period and the individual with haplogroup E from the Ptolemaic period. Does this tell us something about their origin or any differences? The authors should comment on this. Answer: (to be included in the manuscript and referenced here) We agree with the reviewer that Y chromosomal haplogroup J is suggested to have arisen in the ancient Near East. However, the current distribution of E1b1b1 in North Africa could also be caused by the back migration from the Near East to Africa that have already been proposed by several authors (Hammer et al. Genetics 1997, 145:787–805; Hammer et al. Mol Biol Evol 1998, 15:427–441; Hammer MF, et al. Mol Biol Evol 2001, 18:1189–1203). The high frequencies of haplogroup R1-M173 in Cameroon also supported the back migration from Eurasia to Africa in Cruciani et al. Am J Hum Genet 2002, 70:1197–1214. Since it’s still unclear whether E1b1b evolved in Northeast Africa or the Near East, we do not attempt to interpret the presence of the two haplogroups as evidence for distinct population affinities for our three Mummy samples and we removed that argument from our study. 4 Q10. Line 144. “The finding of a continuous population...” Is it really a continuous population, or are the foreign influences in the Ptolemaic-Roman period probably too little to be accounted?? Would it be possible at all to trace down foreigners with this approach?? Please comment! Answer: The method used for the population continuity test relies on a set of priors such as generation time and total population size in the respective area. We evaluated a set of different population sizes as priors in our analysis as well as different generation times to test whether these substantially change our initial analysis. They did not change our initial finding of genetic continuity, which is why we believe that our results hold even for a larger number of parameters that could be applied here. The test of population continuity is not capable/designed to detect outliers. In general, the level of genetic resolution (mostly mitogenomes) does not allow us to identify ‘foreigners’, mostly due to the lack of comparable population data. However, we would be able to spot outliers (i.e. potential foreigners) from our nuclear DNA data via PCA and/or Admixture. The data from our three successfully genotyped samples do suggest that they belonged to the same population. Q11. Conclusions. What are the particular challenges of working with ancient Egyptian mummies? (see comment 3.). It seems that there was some work published on ancient pathogen DNA in Egypt, but very little on human DNA. What is the reason? Was it mainly a methodological problem, such as the non-availability of high-throughput sequencing and enrichment or are there particular issues with contamination or inhibition? I think it could be interesting for the reader to understand the potential and obstacles of working with Egyptian mummies. Answer: Please see answers to Q3 and Q8, and our revised introduction. Q12. Conclusions. The authors should discuss the possible influence and presence of foreigners at the archaeological site Abusir el-Meleq and how their approach could be used to detect it. Although there appears to be a continuity in the overall population, there could be maybe some single individuals that originate from the Ptolemaic or Roman population. Would it be possible to identify those people and could this help to understand the use of certain mummification practices? Answer: We have substantially extended the introduction (lines 111-137) and discussion (lines 361-385, 420-432) to address to point. The data from our three successfully genotyped samples do not 5 suggest a foreign origin, so can be considered representing the local community profile. The contextual evidence does not allow a detailed examination of variations in mummification practices. Q13. Conclusions. I agree that in other sites, especially in the south of Egypt, there could be a much higher influence of Sub-Saharan populations. It is well known that there were close trading connections to Nubia and other Sub-Saharan areas during the Middle and New Kingdom. What does this mean for the interpretation of your findings? Answer: We have addressed this point in our revised discussion (see lines 395-405). As an alternative explanation this would only mean that modern-day Egyptians might resemble more closely ancient Egyptians from the south. However, in the absence of data from southern sites, this also remains speculative. Reviewer #2: Q1: This paper is written like similarly structured ancient DNA papers, with a focus on the production of the dataset, a set of standard analyses performed for small sample sizes and extrapolation to prehistorical conclusions. The problem with this approach is that for the majority of studies, prior genetic analysis (and archaeological etc) has already been performed. The ancient DNA papers largely ignore the other fields and are written ‘hypothesis-free.’ Their scientific value becomes limited as each new paper attempts to devise and answer hypotheses that are often longstanding, involving significant repetition. This paper should and could be re- written to answer a question. It would start with a review of prior historical and genetic work performed on Egyptian populations, narrow down to 1-2 specific hypotheses (Can we confirm that slave trade into Egpyt and Near East occurring in the past XX centuries changed the genetic composition of Egyptians represented by urban cohorts in Cairo?) Is this a paper about success in sequencing ancient Egyptians or about resolving the population history of Egyptians given new mtDNA data? Answer: As in our previous version, we had clearly framed the aims of our study: i) a proof of concept that Modern Sequencing technology produces data of previously problematic samples, ii) to evaluate the degree of continuity between the ancient and modern Egyptian population, [and iii)...]. As such, the article is not hypothesis-free. Neither are we ignorant of other fields. In 6 particular, in the revised manuscript we have extensively included information from historical and archaeological sources (see Introduction and Discussion). Q2: Unfortunately, the authors appear to have ignored several earlier papers on Egyptians (see below for 3 examples, there may be others). Their primary result, stated in the abstract as “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” was shown in 2012 using genome-wide SNP array data from Egyptians (Henn et al., PLoS Genetics: Table 1). That is, the sub-Saharan African ancestry is of recent origin in Egyptians dating to AD 1250 (~24 generations ago). Indeed those authors argued that the source of this sub-Saharan ancestry is more likely to be Nilotic than West African as modeled in the current analyses. This is especially problematic as it is the only result reported in the Abstract itself. And again in the conclusion: "By comparing ancient with modern Egyptians, we remarkably found an influx of additional Sub-Saharan African ancestry after the Roman Period, which is visible at both mitochondrial and autosomal level.” This result is not remarkable, it is what is expected given prior published analyses. Answer: We acknowledge the oversight not having mentioned the 2012 study by Henn and colleagues, which is now included in our revised manuscript. We confirm their conclusions based on our modern Egyptian data, in particular do we confirm a time estimate for pulse-like admixture from Sub-Sahara Africa 700 years ago. However, the LD-based method used in Henn et al. 2012 (and confirmed by us) cannot distinguish between a pulse-like admixture and continuous migration. Using the direct observation from 2,000 year old Egyptians, which we estimate to have had 8% African ancestry, we get a more complete picture of the time course of African migration into the region than what can be extrapolated from modern data alone. Q3: For example, Kujanova et al. (2009) analysis of mtDNA and Y-chromosomal data from an Egyptian oasis isolate from middle Egypt is not cited. They found that sub-Saharan mtDNA L- lineages constituted 30% of their dataset, indicating a strong sub-Saharan component on the maternal side, which was largely absent on the Y (6% M2-derived lineages). Kujanova et al. also argued for a recent migration event to account for the L lineages: “The absence of any signs of local accumulation of diversity in the L haplotypes in el-Hayez seems to favor the idea of these lineages being recent introductions into the Egyptian Western Desert.” Answer: We thank reviewer 2 for pointing out this dataset, which we’ve now included in the analysis and interpretation of our revised manuscript. We merged the dataset with the previously used 7 one by Pagani et al. (2015, AJHG). Nevertheless, the resulting statistics did only show effects at the 3rd decimal point and hence did not alter or affect our interpretation. We see this as further evidence that the origin of the dataset does not alter the statistics and the available datasets cover modern Egyptian diversity quite well. Q4: And in Pagani et al. (2015, AJHG) show that "the average proportion of non-African ancestry in the Egyptians to be 80% and dated the midpoint of the admixture event by using ALDER to around 750 years ago (Table S2), consistent with the Islamic expansion and dates reported previously.” Answer: Our results are consistent with a model of ancient Egypt being predominantly of near Eastern ancestry, with about 10% African ancestry, which increased up to about 18% in modern times. As we now clearly state, this is qualitatively in line with the Henn et al. study from 2012. On the level of a mixture proportion of 80% non-African ancestry, we agree with Pagani et al., but we clearly show that 2,000 years ago, Egypt was more Near-Eastern, not less, as proposed by the model in Pagani et al. with non-African ancestry appearing more recently. We discuss this in the Discussion section (see line 406 to 419). Q5: Section beginning line 144: The authors report apparent congruity between their population sizes estimates and those from the Fayum in the Ptoleimac Period with a 95% credible interval range between 50,000 - 280,000. 1) This is the Ne estimated from mtDNA. In order to compare with the true Ne it need to be scaled 4-fold. 2) The Y-axis scale on Figure 3D does not match the results reported in the text. Indeed the Ne appears to be between 1-2 million durin the Ptolemaic period (black line). 3) Assuming even that the numbers in the text are correct, (115,000 50th estimate) the scaling for females vs. female+male as reported in the historical record would indicate a large divergence between the genetic and historical estimates. 4) No prior on the mutation rate, which will strong influence Ne, is given in the supplement. This is the appropriate place to integrate assumption of g (generation time). Answer: The apparent discordance between Figure 3D and the numbers given in the text stems from the fact that the figure shows unscaled results of the SkyGrid inference (given in the female effective population size times the generation time; Ne x T). To estimate the approximate effective population size for the studied population, which could be compared with the population size from the historical records, we scaled the estimated values by dividing them by generation time (we assumed 25 years) and doubled them to account for the whole (male and 8 female) population (assuming equal male to female Ne ratio). We agree that this rescaling was not described explicitly enough, which might have made the results unclear. We modified the figure caption (figures 3d, S2) as well as the relevant methods’ section so that the rescaling is more clearly described. Regarding the mutation rate prior, we used an uninformative CTMC prior and thus all the temporal information in the inference (which drives estimation of mutation rate and the codependent parameters) came solely from ages of the samples. We modified the text accordingly to make this more clear. Q6: Line 197: Lazaridis et al. (2014) contained 18 Egyptian sample of uncertain provenance (Cairo-urban area). Other autosomal SNP array datasets at least including many more individuals are not used here. Contrasting 3 individuals to 18 contemporary ones in order to indicate extrapolate evidence for a pattern that" 6 and 7 million Sub-Saharan slaves to Northern Africa over a span of some 1250 years” seems a strong extrapolation on its own. As the authors admit. Answer: We cannot easily include SNP data sets that were generated on a different platform than the Affymetrix Human Origins array. But given the fact that we almost exactly confirm results from Henn et al. who used a different data set, we are confident that as far as our modern Egyptian data is concerned, we have a good representation. As far as ancient Egypt is concerned, we indeed have only three samples from a specific region, but we acknowledge the limits of our conclusions clearly in the Discussion. We also highlight that we do incorporate 100 modern Egyptian Mitogenomes from Pagani et al. and exactly confirm their report of 80% non-African ancestry at the mitochondrial level, again suggesting that our modern Egyptian sample is broadly representative at the level of the analysis performed here. Q7: Line 180: "This individual had a derived allele at the SLC24A5 locus, which encodes for light skin pigmentation...” SLC24A5 is among at least 20 skin pigmentation genes known to contribute to melanin variability in contemporary human populations. It alone does not ‘encode’ for light skin pigmentation. Indeed, many individuals in Cape Verde, Africa carry this allele (which does lighten pigmentation, accounting for 7% of the variance in pigmentation) but their overall phenotype would be still be twice as dark as an average European (Beleza et al. 2013, PLoS Genetics). Answer: 9 We changed the sentence (lines: 346-348) to “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 Anatolia (40), consistent with the ancestral affinity shown above” Q8: Note 8: Test of Population Continuity: the analysis here was not described. Other than collapsing mtDNA lineages into haplogroup frequencies to compare ancient and contemporary groups, there is no description of what the actual test was. Even if the method was described in Brandt et al. (2013) [not even in the main text, only in their supplement], the authors should lay out the assumptions, parameter choices and models invoked in using this method. Why for example, is TPC preferable over Approximate Bayesian Computation models typically used to test the relative liklihood of two different population demographies (in this case continuity w/ minimal drift vs. migration). Answer: We have extended the description of our analysis both in the methods part of the manuscript and our supplementary information for clarification and to explain our main findings. Our intention to use the TPC as applied in Brandt et al. 2013 was to evaluate with a simple method whether we can assume genetic continuity (null hypothesis) between our ancient groups and modern-day populations. We agree that complex ABC models would have been the ideal choice to explore alternative scenarios that could explain discontinuity under varying parameters (drift, migration, time, etc.), but were not deemed necessary given that we can more reliably estimate the origin and timing of admixture with nuclear data. Reviewer #3: Q1: I’m less confident that this result is surprising given the archaeological and historical knowledge of the region. I’m not a specialist of that history, but I would have enjoyed reading this paper much more if the introduction and discussion / conclusion would relate this finding better with the existing literature on the Egyptian history. Just stating that “Egypt provides a privileged setting for studying population history” fails a bit short of discussing open questions the study of Egyptian mummies might help to settle. Indeed, the way the paper is pitched know the real emphasis is just put on the fact that DNA could be obtained from mummies. Answer: We have substantially rewritten the introduction, sample collection and discussion to include more background information on Egypt’s history (lines: 57-69), the archaeological site (lines: 111-137, 361-385) and the sample collection (lines: 149-192) in particular. 10 Another aspect that I feel is missing is a brief discussion on how the bias from only studying individuals that were mummified (as compared to random individuals from the ancient Egypt) might have let to the lack of a Sub-Saharan component in the ancient individuals. Answer: We agree that taphonomic and collection bias could indeed be a factor influencing the interpretation of our results. Please see our revised discussion for reasons why we think that our sample is largely representative of the local community at the time (lines: 372-385). Of note, mummification was already quite common from the late Period on and we thus expect mainly middle class individuals at this site. I just found one type: L123: three (instead of tree) Answer: Thanks, we have fixed it.
quote: Q5. Lines 75-77. “In particular, the site holds much promise for studying changes in its population structure from the late Dynastic Period to the present day.” Why is this the case? Is it due to the better DNA preservation in the later mummies?? Please explain! Answer: Unfortunately, mummies from the Old till early New Kingdom are not present at the site or and not included in our data set, which focusses on the three consecutive periods. The site is mainly occupied during the Late Period till Roman times according to written sources, and thus would allow the study of an extended temporal transect. We furthermore find in more than 50% of all remains authentic ancient DNA preserved, suggesting this to be an ideal site for further studies.
quote:Q10. Line 144. “The finding of a continuous population...” Is it really a continuous population, or are the foreign influences in the Ptolemaic-Roman period probably too little to be accounted?? Would it be possible at all to trace down foreigners with this approach?? Please comment! Answer: The method used for the population continuity test relies on a set of priors such as generation time and total population size in the respective area. We evaluated a set of different population sizes as priors in our analysis as well as different generation times to test whether these substantially change our initial analysis. They did not change our initial finding of genetic continuity, which is why we believe that our results hold even for a larger number of parameters that could be applied here.
Questioning the continuity was on the right track to a potentially insightful investigation. However, if there were any problems in population continuity, it'd be between the Old Kingdom and New Kingdom, not between the Late period to the Ptolomaic. The Second intermediate period was a period where this land was ruled by foreigners and much of it's population didn't come on to the scene until the Late Period. We don't know where the Egyptians who migrated into the area during the Late period came from. They admit they have no way of testing for that. Who were the small band of villagers before people arrived in the late period? The original predynastic villagers of Abusir el-Meleq seemed to be a mix of Upper and Lower Egyptians.
quote:Q13. Conclusions. I agree that in other sites, especially in the south of Egypt, there could be a much higher influence of Sub-Saharan populations. It is well known that there were close trading connections to Nubia and other Sub-Saharan areas during the Middle and New Kingdom. What does this mean for the interpretation of your findings? Answer: We have addressed this point in our revised discussion (see lines 395-405). As an alternative explanation this would only mean that modern-day Egyptians might resemble more closely ancient Egyptians from the south. However, in the absence of data from southern sites, this also remains speculative.
I'm with Keita on this one. I guess Ramses and the Amarna results are....speculative? But it's not being speculative to take these mummies to be "authentic" Egyptians with no foreign mixture despite foreign names in the tombs because...they tested the three consecutive time periods that all date after mass migration into the country? Understand that it'd make sense for the mummies to seem as one population because any additional mixture into Lower Egypt would've most likely happened many many centuries prior. Though again I personally think a lot of first peoples to come back to Lower Egypt as the Sahara dried were people with notable NE ancestry (and yes, I include Abusir el Meleq as Lower Egypt, because the Egyptians did). Abusir el Meleq seems to have in the predynastic been a combination of Lower and Upper Egypt. But if this site wasn't really populated until the Late period (and was considered Lower Egyptian by the Egyptians) the added shock of a more mixed north could explain these findings as well. I think Upper and Lower Egypt shared common ancestors, but also had ancestry that made them distinct.
quote:Originally posted by Tyrannohotep: ^ In addition to that, I know Toby Wilkinson in his Rise and Fall of Ancient Egypt mentioned substantial Libyan immigration into Lower Egypt during the Third Intermediate Period. Assuming these Libyans were the lighter-skinned type from the northern Libyan coast, maybe they could be another source of foreign admixture?
Interesting observation. Most of these mummies date during or after a time in Egypt where Libyans were had been stationed in the nome of Abusir el Meleq belonged to. Some Libyans assimilated to religious practices that could've had them buried here. It's probably unlikely, should any Libyans have been in the tombs, that they were a direct transplant. Because of lack of Libyan names noted in Abusir el-Meleq, I'd take that to mean that if there were any Libyans they probably (much like Asiatic foreigners), assimilated into Egypt, or were the assimilated offspring of Libyans and Egyptians.
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