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    Default Ancient Egyptian mummy genomes (Schuenemann et al. 2017)

    The paper is finally out:

    Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

    Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

    [...]

    On a more local scale, we aim to study changes and continuities in the genetic makeup of the ancient inhabitants of the Abusir el-Meleq community (Fig. 1), since all sampled remains derive from this community in Middle Egypt and have been radiocarbon dated to the late New Kingdom to the Roman Period (cal. 1388BCE–426CE, Supplementary Data 1). In particular, we seek to determine if the inhabitants of this settlement were affected at the genetic level by foreign conquest and domination, especially during the Ptolemaic (332–30BCE) and Roman (30BCE–395CE) Periods.



    [...]

    Analysis of mitochondrial genomes
    The 90 mitochondrial genomes fulfilling our criteria (>10-fold coverage and <3% contamination) were grouped into three temporal categories based on their radiocarbon dates (Supplementary Data 1), corresponding to Pre-Ptolemaic Periods (n=44), the Ptolemaic Period (n=27) and the Roman Period (n=19) (Supplementary Data 1). To test for genetic differentiation and homogeneity we compared haplogroup composition, calculated FST-statistics28 and applied a test for population continuity29 (Supplementary Table 2, Supplementary Data 3,4) on mitochondrial genome data from the three ancient and two modern-day populations from Egypt and Ethiopia, published by Pagani and colleagues17, including 100 modern Egyptian and 125 modern Ethiopian samples (Fig. 3a). We furthermore included data from the El-Hayez oasis published by Kujanová and colleagues30. We observe highly similar haplogroup profiles between the three ancient groups (Fig. 3a), supported by low FST values (<0.05) and P values >0.1 for the continuity test. Modern Egyptians share this profile but in addition show a marked increase of African mtDNA lineages L0–L4 up to 20% (consistent with nuclear estimates of 80% non-African ancestry reported in Pagani et al.17). Genetic continuity between ancient and modern Egyptians cannot be ruled out by our formal test despite this sub-Saharan African influx, while continuity with modern Ethiopians17, who carry >60% African L lineages, is not supported (Supplementary Data 5). To further test genetic affinities and shared ancestry with modern-day African and West Eurasian populations we performed a principal component analysis (PCA) based on haplogroup frequencies and Multidimensional Scaling of pairwise genetic distances. We find that all three ancient Egyptian groups cluster together (Fig. 3b), supporting genetic continuity across our 1,300-year transect. Both analyses reveal higher affinities with modern populations from the Near East and the Levant compared to modern Egyptians (Fig. 3b,c). The affinity to the Middle East finds further support by the Y-chromosome haplogroups of the three individuals for which genome-wide data was obtained, two of which could be assigned to the Middle-Eastern haplogroup J, and one to haplogroup E1b1b1 common in North Africa (Supplementary Table 3). However, comparative data from a contemporary population under Roman rule in Asia Minor, from the Roman city Ağlasun today in Turkey31, did not reveal a closer relationship to the ancient Egyptians from the Roman period (Fig. 3b,c).



    [...]

    Population genetic analysis of nuclear DNA
    On the nuclear level we merged the SNP data of our three ancient individuals with 2,367 modern individuals34,35 and 294 ancient genomes36 and performed PCA on the joined data set. We found the ancient Egyptian samples falling distinct from modern Egyptians, and closer towards Near Eastern and European samples (Fig. 4a, Supplementary Fig. 3, Supplementary Table 5). In contrast, modern Egyptians are shifted towards sub-Saharan African populations. Model-based clustering using ADMIXTURE37 (Fig. 4b, Supplementary Fig. 4) further supports these results and reveals that the three ancient Egyptians differ from modern Egyptians by a relatively larger Near Eastern genetic component, in particular a component found in Neolithic Levantine ancient individuals36 (Fig. 4b). In contrast, a substantially larger sub-Saharan African component, found primarily in West-African Yoruba, is seen in modern Egyptians compared to the ancient samples. In both PCA and ADMIXTURE analyses, we did not find significant differences between the three ancient samples, despite two of them having nuclear contamination estimates over 5%, which indicates no larger impact of modern DNA contamination. We used outgroup f3-statistics38 (Fig. 5a,b) for the ancient and modern Egyptians to measure shared genetic drift with other ancient and modern populations, using Mbuti as outgroup. We find that ancient Egyptians are most closely related to Neolithic and Bronze Age samples in the Levant, as well as to Neolithic Anatolian and European populations (Fig. 5a,b). When comparing this pattern with modern Egyptians, we find that the ancient Egyptians are more closely related to all modern and ancient European populations that we tested (Fig. 5b), likely due to the additional African component in the modern population observed above. By computing f3-statistics38, we determined whether modern Egyptians could be modelled as a mixture of ancient Egyptian and other populations. Our results point towards sub-Saharan African populations as the missing component (Fig. 5c), confirming the results of the ADMIXTURE analysis. We replicated the results based on f3-statistics using only the least contaminated sample (with <1% contamination estimate) and find very similar results (Supplementary Fig. 5), confirming that the moderate levels of modern DNA contamination in two of our samples did not affect our analyses. Finally, we used two methods to estimate the fractions of sub-Saharan African ancestry in ancient and modern Egyptians. Both qpAdm35 and the f4-ratio test39 reveal that modern Egyptians inherit 8% more ancestry from African ancestors than the three ancient Egyptians do, which is also consistent with the ADMIXTURE results discussed above. Absolute estimates of African ancestry using these two methods in the three ancient individuals range from 6 to 15%, and in the modern samples from 14 to 21% depending on method and choice of reference populations (see Supplementary Note 1, Supplementary Fig. 6, Supplementary Tables 5–8). We then used ALDER40 to estimate the time of a putative pulse-like admixture event, which was estimated to have occurred 24 generations ago (700 years ago), consistent with previous results from Henn and colleagues16. While this result by itself does not exclude the possibility of much older and continuous gene flow from African sources, the substantially lower African component in our ∼2,000-year-old ancient samples suggests that African gene flow in modern Egyptians occurred indeed predominantly within the last 2,000 years.





    Estimating phenotypes
    Finally, we analysed several functionally relevant SNPs in sample JK2911, which had low contamination and relatively high coverage. This individual had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia41, consistent with the ancestral affinity shown above. Other relevant SNPs carry the ancestral allele, including HERC2 and LCT, which suggest dark-coloured eyes and lactose intolerance (Supplementary Table 9).


    Discussion
    This study demonstrates that the challenges of ancient DNA work on Egyptian mummies can be overcome with enrichment strategies followed by high-throughput DNA sequencing. The use of ancient DNA can greatly contribute towards a more accurate and refined understanding of Egypt’s population history. More specifically, it can supplement and serve as a corrective to archaeological and literary data that are often unevenly distributed across time, space and important constituents of social difference (such as gender and class) as well as modern genetic data from contemporary populations that may not be fully representative of past populations.

    The archaeological site Abusir el-Meleq was inhabited from at least 3250BCE until about 700CE and was of great religious significance because of its active cult to Osiris, the god of the dead, which made it an attractive burial site for centuries2. Written sources indicate that by the third century BCE Abusir el-Meleq was at the centre of a wider region that comprised the northern part of the Herakleopolites province, and had close ties with the Fayum and the Memphite provinces, involving the transport of wheat, cattle-breeding, bee-keeping and quarrying42. In the early Roman Period, the site appears to have been the main centre in its own district42. Abusir el-Meleq’s proximity to, and close ties with, the Fayum are significant in the context of this study as the Fayum in particular saw a substantial growth in its population during the first hundred years of Ptolemaic rule, presumably as a result of Greek immigration33,43. Later, in the Roman Period, many veterans of the Roman army—who, initially at least, were not Egyptian but people from disparate cultural backgrounds—settled in the Fayum area after the completion of their service, and formed social relations and intermarried with local populations44. Importantly, there is evidence for foreign influence at Abusir el-Meleq. Individuals with Greek, Latin and Hebrew names are known to have lived at the site and several coffins found at the cemetery used Greek portrait image and adapted Greek statue types to suit ‘Egyptian’ burial practices2,45. The site’s first excavator, Otto Rubensohn, also found a Greek grave inscription in stone as well as a writing board inscribed in Greek46. Taken together with the multitude of Greek papyri that were written at the site, this evidence strongly suggests that at least some inhabitants of Abusir el-Meleq were literate in, and able to speak, Greek45. However, a general issue concerning the site is that several details of the context of the individuals analysed in this study were lost over time. All of the material was excavated by Rubensohn in the early twentieth century, whose main interest was to obtain literary papyri from cartonnage rather than to excavate human remains47. As is customary for the time, Rubensohn’s archaeological records are highly incomplete and many of the finds made by him were removed undocumented from their contexts. Furthermore, many of his excavation diaries and notes were destroyed during the Second World War19. This lack of context greatly diminishes the possibility of ‘thick description’ of the analysed individuals, at least in terms of their names, titles and materially expressed identity. However, the finds nevertheless hold much promise for a long-term study of population dynamics in ancient Egypt. Abusir el-Meleq is arguably one of the few sites in Egypt, for which such a vast number of individuals with such an extensive chronological spread are available for ancient DNA analysis. Although we only analysed mummified remains, there is little reason to believe that the burials Rubensohn excavated belonged exclusively to a group of prosperous inhabitants on the basis of the far published references to excavation diaries and Rubensohn’s preliminary reports that permit a basic reconstruction. Rather it seems arguable that the complete spectrum of society is represented, ranging from Late Period priests’ burials that stand out by virtue of their size and contents to simple inhumations that are buried with little to no grave goods2. The widespread mummification treatments in the Ptolemaic and Roman Periods in particular, leading to a decline in standards and costs48 and the generally modest appearance of many burials further supports this assessment.

    By comparing ancient individuals from Abusir el-Meleq with modern Egyptian reference populations, we found an influx of sub-Saharan African ancestry after the Roman Period, which corroborates the findings by Henn and colleagues16. Further investigation would be needed to link this influx to particular historic processes. Possible causal factors include increased mobility down the Nile and increased long-distance commerce between sub-Saharan Africa and Egypt49. Trans-Saharan slave trade may have been particularly important as it moved between 6 and 7 million sub-Saharan slaves to Northern Africa over a span of some 1,250 years, reaching its high point in the nineteenth century50. However, we note that all our genetic data were obtained from a single site in Middle Egypt and may not be representative for all of ancient Egypt. It is possible that populations in the south of Egypt were more closely related to those of Nubia and had a higher sub-Saharan genetic component, in which case the argument for an influx of sub-Saharan ancestries after the Roman Period might only be partially valid and have to be nuanced. Throughout Pharaonic history there was intense interaction between Egypt and Nubia, ranging from trade to conquest and colonialism, and there is compelling evidence for ethnic complexity within households with Egyptian men marrying Nubian women and vice versa51,52,53. Clearly, more genetic studies on ancient human remains from southern Egypt and Sudan are needed before apodictic statements can be made.

    The ancient DNA data revealed a high level of affinity between the ancient inhabitants of Abusir el-Meleq and modern populations from the Near East and the Levant. This finding is pertinent in the light of the hypotheses advanced by Pagani and colleagues, who estimated that the average proportion of non-African ancestry in Egyptians was 80% and dated the midpoint of this admixture event to around 750 years ago17. Our data seem to indicate close admixture and affinity at a much earlier date, which is unsurprising given the long and complex connections between Egypt and the Middle East. These connections date back to Prehistory and occurred at a variety of scales, including overland and maritime commerce, diplomacy, immigration, invasion and deportation54. Especially from the second millennium BCE onwards, there were intense, historically- and archaeologically documented contacts, including the large-scale immigration of Canaanite populations, known as the Hyksos, into Lower Egypt, whose origins lie in the Middle Bronze Age Levant54.

    Our genetic time transect suggests genetic continuity between the Pre-Ptolemaic, Ptolemaic and Roman populations of Abusir el-Meleq, indicating that foreign rule impacted the town’s population only to a very limited degree at the genetic level. It is possible that the genetic impact of Greek and Roman immigration was more pronounced in the north-western Delta and the Fayum, where most Greek and Roman settlement concentrated43,55, or among the higher classes of Egyptian society55. Under Ptolemaic and Roman rule, ethnic descent was crucial to belonging to an elite group and afforded a privileged position in society55. Especially in the Roman Period there may have been significant legal and social incentives to marry within one’s ethnic group, as individuals with Roman citizenship had to marry other Roman citizens to pass on their citizenship. Such policies are likely to have affected the intermarriage of Romans and non-Romans to a degree55. Additional genetic studies on ancient human remains from Egypt are needed with extensive geographical, social and chronological spread in order to expand our current picture in variety, accuracy and detail.

    However, our results revise previous scepticism towards the DNA preservation in ancient Egyptian mummies due to climate conditions or mummification procedures8. The methodology presented here opens up promising avenues for future genetic research and can greatly contribute towards a more accurate and refined understanding of Egypt’s population history.
    Last edited by Semitic Duwa; 2017-05-30 at 17:05.


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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    Do we know what the haplotypes are for the 2 J samples? Maybe one of them is related to me.. also very interesting.."We find that ancient Egyptians are most closely related to Neolithic and Bronze Age samples in the Levant, as well as to Neolithic Anatolian and European populations (Fig. 5a,b). " I believe this is equivalent to saying Copts closely cluster with neolithic and bronze age samples from levant..

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    Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times.
    Ło kurwa... [Holy fuck] he he he...

    Now we need a pre dynastic/ early Egypt please.
    and the IEEE Milestone for breaking the Enigma Code goes to... Polish Cipher Bureau 1932-39

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    Nothing surprising tbh

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    According to the supplement, JK2888 was E-V22. JK2134 and JK2911 are just J.

    These three samples basically seem to cluster in between Levant_Neolithic and Jordan_EBA:



    - - - Updated - - -

    Quote Originally Posted by SomaliSuldaan View Post
    Nothing surprising tbh
    The haplogroups do not surprise me either, though I'd take some of the stuff the authors say with a grain of salt.


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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    More from the supplement:

    Note 6: Y-chromosomal & phenotypic analysis
    Chuanchao Wang, Alexander Peltzer

    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 (77-79). The high frequencies of haplogroup R1-M173 in
    Cameroon also supported the back migration from Eurasia to Africa (80). Since
    it’s still unclear whether E1b1b evolved in Northeast Africa or the Near East, we
    were deciding against attempting to conclude whether the two haplogroups
    provide information about different paternal origin information in our three
    Mummy samples
    .

    For our phenotypic analysis, we investigated a set of SNPs thought to be affected
    by selection in our samples. Only high-quality (q > 30) bases were counted. We
    were able to find derived alleles for the genes SLC24A5 (rs1426654), which are
    known to be responsible for lighter skin pigmentation in JK2888 and JK2911.
    Our further tests whether the genes SLC45A2 (rs16891982), LCT (rs4988235),
    EDAR (rs3827760) and HERC2 (rs12913832) revealed no derived alleles for
    both JK2888 and JK2911. For JK2134, no sufficient coverage after quality
    filtering was given at the specific sites, which is why the analysis revealed no
    further clues (see Supplementary Table 6 for details). LCT is responsible for
    lactase persistence in Europe (81, 82). The SNPs at SLC24A5 and SLC45A2 are
    responsible for lighter skin pigmentation (83). The SNP at EDAR affects tooth
    morphology and hair thickness (84, 85).
    The SNP at HERC2 is the primary
    determinant of light eye colour in present-day Europeans (86, 87).


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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    Quote Originally Posted by Desertrose View Post
    Do we know what the haplotypes are for the 2 J samples?
    Not yet

    Maybe one of them is related to me..
    That's definitely a possibility. But we don't even know whether they're J1 or J2 yet. If they're J1, it's likely one of them is J1-ZS241, since the presence of J1-P58 alongside Iran_Chl-like ancestry is almost undoubtedly due to NW Semitic speakers such as the Hyksos (and J1-ZS241* has been found in Egypt).

    I believe this is equivalent to saying Copts closely cluster with neolithic and bronze age samples from levant..
    From the looks of it, the Copts will be near-identical to these AE samples.


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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    Finally, lol. I would love to see their autosomal DNA to compare them to today's populations.

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    Quote Originally Posted by Semitic Duwa View Post
    Not yet



    That's definitely a possibility. But we don't even know whether they're J1 or J2 yet. If they're J1, it's likely one of them is J1-ZS241, since the presence of J1-P58 alongside Iran_Chl-like ancestry is almost undoubtedly due to NW Semitic speakers such as the Hyksos (and J1-ZS241* has been found in Egypt).



    From the looks of it, the Copts will be near-identical to these AE samples.
    Is there a gedmatch calculator that measure iranian chalcolithic? Also, do we know if we will get gedmatch kit numbers for these ancient cuties?

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    JK2889, JK2925 and JK2984 carry mtDNA haplogroup U7, this also could've arrived with the Aamu/Asiatics.


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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