...
EgyptSearch Forums Post New Topic  New Poll  Post A Reply
my profile | directory login | register | search | faq | forum home

  next oldest topic   next newest topic
» EgyptSearch Forums » Egyptology » Ancient Egyptian mummy genomes (Page 1)

 - UBBFriend: Email this page to someone!   This topic comprises 13 pages: 1  2  3  4  ...  11  12  13   
Author Topic: Ancient Egyptian mummy genomes
capra
Member
Member # 22737

Member Rated:
5
Icon 1 posted      Profile for capra     Send New Private Message       Edit/Delete Post   Reply With Quote 
Paper is out

https://www.nature.com/articles/ncomms15694

Only 3 samples with nuclear DNA data though. 2 Y hg J, 1 Y hg E1b1b1a1b2-V22.

The non-blurry mitochondrial DNA image clearly says M1, not M5. OK, that makes way more sense.

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

[excerpt methods and other sections, see link}

Verena J. Schuenemann1, 2 n1, Alexander Peltzer3, 4 n1, Beatrix Welte1, W. Paul van Pelt5, Martyna Molak6, Chuan-Chao Wang ORCID: orcid.org/0000-0001-9628-03074, Anja Furtwängler1, Christian Urban1, Ella Reiter1, Kay Nieselt ORCID: orcid.org/0000-0002-1283-70653, Barbara Teßmann7, Michael Francken1, Katerina Harvati1, 2, 8, Wolfgang Haak4, 9, Stephan Schiffels ORCID: orcid.org/0000-0002-1017-91504[…] & Johannes Krause1, 2, 4- Show fewer authors
Nature Communications 8, Article number: 15694 [2017}
doi:10.1038/ncomms15694


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


Introduction
Egypt provides a privileged setting for the study of population genetics as a result of its long and involved population history. Owing to its rich natural resources and strategic location on the crossroads of continents, the country had intense, historically documented interactions with important cultural areas in Africa, Asia and Europe ranging from international trade to foreign invasion and rule. Especially from the first millennium BCE onwards, Egypt saw a growing number of foreigners living and working within its borders and was subjected to an almost continuous sequence of foreign domination by Libyans, Assyrians, Kushites, Persians, Greeks, Romans, Arabs, Turks and Brits. The movement of people, goods and ideas throughout Egypt’s long history has given rise to an intricate cultural and genetic exchange and entanglement, involving themes that resonate strongly with contemporary discourse on integration and globalization1.

Until now the study of Egypt’s population history has been largely based on literary and archaeological sources and inferences drawn from genetic diversity in present-day Egyptians. Both approaches have made crucial contributions to the debate but are not without limitations. On the one hand, the interpretation of literary and archaeological sources is often complicated by selective representation and preservation and the fact that markers of foreign identity, such as, for example, Greek or Latin names and ethnics, quickly became ‘status symbols’ and were adopted by natives and foreigners alike2,3,4. On the other hand, results obtained by modern genetic studies are based on extrapolations from their modern data sets and make critical assumptions on population structure and time5. The analysis of ancient DNA provides a crucial piece in the puzzle of Egypt’s population history and can serve as an important corrective or supplement to inferences drawn from literary, archaeological and modern DNA data.

Despite their potential to address research questions relating to population migrations, genetic studies of ancient Egyptian mummies and skeletal material remain rare, although research on Egyptian mummies helped to pioneer the field of ancient DNA research with the first reported retrieval of ancient human DNA6. Since then progress has been challenged by issues surrounding the authentication of the retrieved DNA and potential contaminations inherent to the direct PCR method7. Furthermore, the potential DNA preservation in Egyptian mummies was met with general scepticism: The hot Egyptian climate, the high humidity levels in many tombs and some of the chemicals used in mummification techniques, in particular sodium carbonate, all contribute to DNA degradation and are thought to render the long-term survival of DNA in Egyptian mummies improbable8. Experimental DNA decay rates in papyri have also been used to question the validity and general reliability of reported ancient Egyptian DNA results9. The recent genetic analysis of King Tutankhamun’s family10 is one of the latest controversial studies that gave rise to this extensive scholarly debate11. New data obtained with high-throughput sequencing methods have the potential to overcome the methodological and contamination issues surrounding the PCR method and could help settle the debate surrounding ancient Egyptian DNA preservation8. However, the first high-throughput sequences obtained from ancient Egyptian mummies12 were not supported by rigorous authenticity and contamination tests.

Here, we provide the first reliable data set obtained from ancient Egyptians using high-throughput DNA sequencing methods and assessing the authenticity of the retrieved ancient DNA via characteristic nucleotide misincorporation patterns13,14 and statistical contamination tests15 to ensure the ancient origin of our obtained data.

By directly studying ancient DNA from ancient Egyptians, we can test previous hypotheses drawn from analysing modern Egyptian DNA, such as recent admixture from populations with sub-Saharan16 and non-African ancestries17, attributed to trans-Saharan slave trade and the Islamic expansion, respectively. On a more local scale, we aim to study changes and continuities in the genetic makeup of the ancient inhabitants of the Abusir el-Meleq community [Fig. 1}, since all sampled remains derive from this community in Middle Egypt and have been radiocarbon dated to the late New Kingdom to the Roman Period [cal. 1388BCE–426CE, Supplementary Data 1}. In particular, we seek to determine if the inhabitants of this settlement were affected at the genetic level by foreign conquest and domination, especially during the Ptolemaic [332–30BCE} and Roman [30BCE–395CE} Periods.


 -


Results
Samples and anthropological analysis

All 166 samples from 151 mummified individuals [for details of the 90 individuals included in the later analysis, see Supplementary Data 1} used in this study were taken from two anthropological collections at the University of Tübingen and the Felix von Luschan Skull Collection, which is now kept at the Museum of Prehistory of the Staatliche Museen zu Berlin, Stiftung preußischer Kulturbesitz [individuals: S3533, S3536, S3544, S3552, S3578, S3610}. According to the radiocarbon dates [Supplementary Data 1, see also ref. 18}, the samples can be grouped into three time periods: Pre-Ptolemaic [New Kingdom, Third Intermediate Period and Late Period}, Ptolemaic and Roman Period. During their conservation in the Tübingen and Berlin collections the remains underwent different treatments: some were preserved in their original mummified state, while others were macerated for anthropological analysis or due to conservation problems19.

In most cases, non-macerated mummy heads still have much of their soft tissue preserved. Some of the remains [individuals analysed in our study: 1543, 1547, 1565, 1577, 1611} have traces of gold leaf near the mouth and the cheekbone, which is characteristic for mummies from the Ptolemaic Period onwards20. In most cases the brain was removed and the excerebration route was highly likely transnasal, resulting in visible defects on the cribriform plate [for the individuals analysed in our study, see Supplementary Data 1}. In summary, the excellent bone preservation and the more or less good soft tissue preservation made a wide-ranging analysis possible19.

Recently, various studies were conducted on these remains, including a study on ancient Egyptian embalming resins, two ancient DNA studies and an anthropological examination of the macerated crania12,18,19,21. While the possibilities of a demographic reconstruction based on anthropological finds are naturally limited—due to incompleteness of the assemblage, the following anthropological observations were made on the assemblage: For a first assessment, computer tomographic scans of 30 mummies with soft tissue preservation were produced to describe sex [Supplementary Data 1}, age at death [Supplementary Data 1} and the macroscopic health status; the six macerated mummies were examined directly. It is notable that most of the individuals are early and late adults, and that subadult individuals are underrepresented [Supplementary Data 1}. It is possible that the sample’s demographic profile is the result of different burial treatments for adults and subadults, but it seems more likely that it is due to collection bias, with collectors favouring intact adult skulls. Almost all of the teeth show significant dentine exposure up to a total loss of the crown. This abrasion pattern is likely due to the food and food preparation itself, in particular for a cereal-rich diet containing a high proportion of coarse sandy particles. These particles act to abrade the dental tissues, allowing bacteria to penetrate the interior of the teeth. As a result, carious lesions or periapical processes appear in the analysed individuals [Supplementary Data 1}19.

For the DNA analysis we sampled different tissues [bone, soft tissue, tooth}, macerated and non-macerated, to test for human DNA preservation.

Processing and sequencing of the samples

We extracted DNA from 151 mummified human remains and prepared double-stranded Illumina libraries with dual barcodes22,23. Then we used DNA capture techniques for human mitochondrial DNA24 and for 1.24 million genomic single nucleotide polymorphisms [SNPs}25 in combination with Illumina sequencing, through which we successfully obtained complete human mitochondrial genomes from 90 samples and genome-wide SNP data from three male individuals passing quality control.

Comparison of the DNA preservation in different tissues

We tested different tissues for DNA preservation and applied strict criteria for authenticity on the retrieved mitochondrial and nuclear DNA to establish authentic ancient Egyptian DNA. First, DNA extracts from several tissues [that is, bone, teeth, soft tissue and macerated teeth} from 151 individuals were screened for the presence of human mitochondrial DNA [mtDNA} resulting in a total of 2,157 to 982,165 quality filtered mitochondrial reads per sample, and 11- to 4,236-fold coverage. To estimate, identify and filter out potential contamination we applied the program schmutzi15 with strict criteria for contamination and kept only samples with less than 3% contamination for further analysis. For a comparison of different source material [soft tissue, bone and teeth} ten individuals [Supplementary Table 1} were sampled multiple times. Yields of preserved DNA were comparable in bone and teeth but up to ten times lower in soft tissues [Fig. 2a, Supplementary Table 1}. Nucleotide misincorporation patterns characteristic for damaged ancient human DNA allowed us to assess the authenticity of the retrieved DNA13,14. The observed DNA damage patterns differed for the source materials with on average 19% damage in soft tissues and around 10% damage in bone tissue and teeth [Fig. 2b,c, Supplementary Table 1}. Importantly, mtDNA haplotypes were identical for all samples from the same individuals. Our results thus suggest that DNA damage in Egyptian mummies correlates with tissue type. The protection of bone and teeth by the surrounding soft tissue or the embalmment of soft tissue may have contributed to the observed differences.

Generation of nuclear data

In order to analyse the nuclear DNA we selected 40 samples with high mtDNA coverage and low mtDNA contamination. Using in solution enrichment for 1.2 million genome-wide SNPs26, we obtained between 3,632 and 508,360 target SNPs per sample [Supplementary Data 2}. Overall, the nuclear DNA showed poor preservation compared to the mtDNA as depicted by a high mitochondrial/nuclear DNA ratio of on average around 18,000. In many samples, nuclear DNA damage was relatively low, indicating modern contamination. We sequenced two libraries per sample: one untreated library to assess DNA damage, and one library treated with enzymatic damage repair27, which was used for downstream analysis. We applied strict criteria for further analysis: we considered only male samples with at least 8% average cytosine deamination rates at the ends of the reads from the untreated library, and with at least 150 SNPs on the X chromosome covered at least twice, in order to estimate contamination levels reliably. Three out of 40 samples fulfilling these criteria had acceptable nuclear contamination rates: Two samples from the Pre-Ptolemaic Periods [New Kingdom to Late Period} had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs. As shown below, to rule out any impact of potential contamination on our results, we analysed the three samples separately or replicated results using only the least contaminated sample.

Analysis of mitochondrial genomes

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


 -
a} Mitochondrial DNA haplogroup frequencies of three ancient and two modern-day populations, [b} Principal Component Analysis based on haplogroup frequencies: [sub-Saharan Africa [green}, North Africa [light green}, Near East [orange}, Europe [yellow}, ancient [blue}, [c} MDS of HVR-I sequence data: colour scheme as above; note that ancient groups were pooled, [d} Skygrid plot depicting effective population size estimates over the last 5,000 years in Egypt. Vertical bars indicate the ages of the analysed 90 mitochondrial genomes [three samples with genome-wide data highlighted in red}. Note that the values on y axis are given in female effective population size times generation time and were rescaled by 1:14.5 for the estimation of the studied population size [assuming 29-year generation time and equal male and female effective population sizes} [images by Kerttu Majander}.


Population size estimation using BEAST

The finding of a continuous population through time allowed us to estimate the effective population size [Ne} from directly radiocarbon-dated mitochondrial genomes using BEAST32. Our results show similar values of effective population size in the different ancient time periods with an average value of between ca. 48,000 and 310,000 [average 95% CI} inhabitants in the region and period under investigation [Fig. 3d, Supplementary Fig. 2, Supplementary Table 4}. This is important as it is the first time that such estimates can be contrasted with reported historic Egyptian census numbers from the neighbouring Fayum in the early Ptolemaic Period, which had a reported total population size of 85,000–95,000 inhabitants33.

Population genetic analysis of nuclear DNA

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


 -
a} Principal Component Analysis-based genome-wide SNP data of three ancient Egyptians, 2,367 modern individuals and 294 previously published ancient genomes, [b} subset of the full ADMIXTURE analysis [Supplementary Fig. 4}.


 -
[a} Outgroup f3-statistics measuring shared drift of the three ancient Egyptian samples and other modern and ancient populations, [b} The data shown in a, compared with the same estimates for modern Egyptians, ordered by shared drift with modern Egyptians, [c} Admixture f3-statistics, testing whether modern Egyptians are mixed from ancient Egyptians and some other source. The most negative Z-scores indicate the most likely source populations.

Estimating phenotypes

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

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

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

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

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

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

However, our results revise previous scepticism towards the DNA preservation in ancient Egyptian mummies due to climate conditions or mummification procedures8. The methodology presented here opens up promising avenues for future genetic research and can greatly contribute towards a more accurate and refined understanding of Egypt’s population history.

[ 04. June 2017, 11:09 PM: Message edited by: BlessedbyHorus ]

Posts: 660 | From: Canada | Registered: Mar 2017  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
Here we go!!! Enjoy the ride. I will start off reading the peer reviewed section. Interesting that the YDNA J is in Africa BEFORE the the Levant. Haber et al
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007  |  IP: Logged | Report this post to a Moderator
Askia_The_Great
Administrator
Member # 22000

Member Rated:
5
Icon 1 posted      Profile for Askia_The_Great     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by capra:
Paper is out

https://www.nature.com/articles/ncomms15694

Only 3 samples with nuclear DNA data though. 2 Y hg J, 1 Y hg E1b1b.

The non-blurry mitochondrial DNA image clearly says M1, not M5. OK, that makes way more sense.

Good read. At the end they say they don't rule out earlier SSA admixture. But I'm gonna read again to get my complete opinion.
Posts: 1891 | From: NY | Registered: Sep 2014  |  IP: Logged | Report this post to a Moderator
Ish Geber
Member
Member # 18264

Member Rated:
4
Icon 1 posted      Profile for Ish Geber     Send New Private Message       Edit/Delete Post   Reply With Quote 
Capra ,

Thanks for posting.

For the members. Let's stay objective and critical.

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | Report this post to a Moderator
Swenet
Member
Member # 17303

Member Rated:
4
Icon 1 posted      Profile for Swenet     Send New Private Message       Edit/Delete Post   Reply With Quote 
Thanks for the update  -
Posts: 8785 | From: Discovery Channel's Mythbusters | Registered: Dec 2009  |  IP: Logged | Report this post to a Moderator
capra
Member
Member # 22737

Member Rated:
5
Icon 1 posted      Profile for capra     Send New Private Message       Edit/Delete Post   Reply With Quote 
Estimated 6-15% African ancestry in the ancient samples, while modern Egyptians have 14-21%. And yes they used everyone's favourite True Negros the Yoruba for the sole SSA reference. [Big Grin]

3 samples with nuclear DNA are:

J2134 776-569 BC, mt hg J1d, Y hg J
J2911 769-560 BC, mt hg M1a1, Y hg J
J2888 97-2 BC, mt hg U6a2, Y hg E1b1b1a1b2-V22

So yes can be all Libyans, Hyksos, or Assyrians if that floats your boat. [Razz]

J2911 had the best coverage and least contamination. He had 2/2 + calls for derived rs1426654 in SLC24A5 and 0/7 + calls for derived s16891982 in SLC45A2. J2888 had 1 + call for rs1426654. So probably medium skin colour (sample is tiny and no data for other variants) - like modern Upper Egyptians maybe? Also brown eyes and lactose intolerant.

Posts: 660 | From: Canada | Registered: Mar 2017  |  IP: Logged | Report this post to a Moderator
zarahan aka Enrique Cardova
Member
Member # 15718

Icon 1 posted      Profile for zarahan aka Enrique Cardova     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Ish Gebor:
Capra ,

Thanks for posting.

For the members. Let's stay objective and critical.

Naturally distant West African Yoruba are the designated "sub-Saharan"
comparison group. Of interest would be the breakdown of their
ancient samples- dating and locations- they all seem rather recent-
quote:
"According to the radiocarbon
dates (Supplementary Data 1, see also ref. 18), the
samples can be grouped into three time periods: Pre-Ptolemaic
(New Kingdom, Third Intermediate Period and Late Period),
Ptolemaic and Roman Period."


The ancient data sample is also drawn from the north- Lower Egypt- where there
has long been more outside admixture. Hard to read more on tiny
phone screen but will check out later in more detail.

Posts: 5905 | From: The Hammer | Registered: Aug 2008  |  IP: Logged | Report this post to a Moderator
beyoku
Member
Member # 14524

Member Rated:
4
Icon 1 posted      Profile for beyoku     Send New Private Message       Edit/Delete Post   Reply With Quote 
This study is ****.

I retract all good I had to say about the authors and how "Smart" they were not to use Yoruba as the lone African SSA reference.

Posts: 2463 | From: New Jersey USA | Registered: Dec 2007  |  IP: Logged | Report this post to a Moderator
capra
Member
Member # 22737

Member Rated:
5
Icon 1 posted      Profile for capra     Send New Private Message       Edit/Delete Post   Reply With Quote 
Sample data is all in supplementary table 1. There are 3-4 samples from the New Kingdom but mtDNA only.

Probably Dinka or something would be a better reference. Genomes are now publicly available so we will probably see some amateur analysis in the near future. There is a lot to look at that wasn't in this paper.

Posts: 660 | From: Canada | Registered: Mar 2017  |  IP: Logged | Report this post to a Moderator
Concerned member of public
Banned
Member # 22355

Rate Member
Icon 10 posted      Profile for Concerned member of public   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
Game over Afrocentrists.

"Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details)."

- derived SLC24A5 in ancient Egyptians just like the ancient Sidonian samples. Like I always said, ancient Egyptians were light to medium brown in skin pigmentation, not dark brown ('black').

Posts: 949 | From: England | Registered: Oct 2015  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
I haven’t read the paper as yet but I speculated they would use a distant “SSA” like MButi but they used another distant SSA like YRI. They would not or could not possible use closer SSA, why, it will screw with their hypothesis. Understand the games. Of course M1 is African and found in SSA West and East and North of the Sahara.

Regardless 15% YRI is high!!


quote:
Originally posted by zarahan- aka Enrique Cardova:
quote:
Originally posted by Ish Gebor:
Capra ,

Thanks for posting.

For the members. Let's stay objective and critical.

Naturally distant West African Yoruba are the designated "sub-Saharan"
comparison group. Of interest would be the breakdown of their
ancient samples- dating and locations- they all seem rather recent-
quote:
"According to the radiocarbon
dates (Supplementary Data 1, see also ref. 18), the
samples can be grouped into three time periods: Pre-Ptolemaic
(New Kingdom, Third Intermediate Period and Late Period),
Ptolemaic and Roman Period."


The ancient data sample is also drawn from the north- Lower Egypt- where there
has long been more outside admixture. Hard to read more on tiny
phone screen but will check out later in more detail.


Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007  |  IP: Logged | Report this post to a Moderator
zarahan aka Enrique Cardova
Member
Member # 15718

Icon 1 posted      Profile for zarahan aka Enrique Cardova     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Cass/:
Game over Afrocentrists.

"Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details)."

- derived SLC24A5 in ancient Egyptians just like the ancient Sidonian samples. Like I always said, ancient Egyptians were light to medium brown in skin pigmentation, not dark brown ('black').

Get lost you moronic idiot. The samples are Late Period and they
are drawn from the north, an area always known to have more foreign admixture.
The only thing "over" is the feces dripping over your head.
Now run along back to your BNP "rally"..

Posts: 5905 | From: The Hammer | Registered: Aug 2008  |  IP: Logged | Report this post to a Moderator
Elmaestro
Moderator
Member # 22566

Member Rated:
5
Icon 1 posted      Profile for Elmaestro     Send New Private Message       Edit/Delete Post   Reply With Quote 
Uh oh..... Uh oh! Lmaoooooo I'm not saying NOTHING but some philosophies are in danger!!! I'm about to drop some HEAT in a few days too. Beyoku, Tukuler, you know where to find me. I'm off this for now.

PS Zaharan LET CASS ROCK, he's fucking himself up. Look at what I've been saying for the past 3-4 months.

Posts: 1781 | From: New York | Registered: Jul 2016  |  IP: Logged | Report this post to a Moderator
zarahan aka Enrique Cardova
Member
Member # 15718

Icon 1 posted      Profile for zarahan aka Enrique Cardova     Send New Private Message       Edit/Delete Post   Reply With Quote 
LOL.. true dat.. They admit limitations of study- quote:

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."

Posts: 5905 | From: The Hammer | Registered: Aug 2008  |  IP: Logged | Report this post to a Moderator
BrandonP
Member
Member # 3735

Icon 1 posted      Profile for BrandonP   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by beyoku:
This study is ****.

I retract all good I had to say about the authors and how "Smart" they were not to use Yoruba as the lone African SSA reference.

They do have a couple of Northeast African populations (Somalis and Ethiopian Jews) in the PCA, though you're right about the admixture graphs. Speaking of which, I perceive a special similarity in ancestry proportions to the three sampled Egyptian genomes and the Levantine Bronze Age (even more so than the Natufians or Neolithic). Which convinces me personally that there's a notable Bronze Age Levantine ancestry in this sample.

 -

Posts: 7069 | From: Fallbrook, CA | Registered: Mar 2004  |  IP: Logged | Report this post to a Moderator
Punos_Rey
Administrator
Member # 21929

Member Rated:
5
Icon 1 posted      Profile for Punos_Rey   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Cass/:
Game over Afrocentrists.

"Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details)."

- derived SLC24A5 in ancient Egyptians just like the ancient Sidonian samples. Like I always said, ancient Egyptians were light to medium brown in skin pigmentation, not dark brown ('black').

 -

[Roll Eyes] I love how Nazis think they have really one upped people. Type 4 skin in Northern Egyptian samples isn't a suprise at all. Still not Southern or Northern European, and several African populations south of the Sahara are also type 4. These people wouldn't have been any lighter than many of the Khoisan. [Roll Eyes]

 -

So going from a roughly San-like pigment to darker as you go further south(with admixture also skewing the phenotypical appearances), guess it'd be most accurate to say the Aegyptians were "mostly brown and black with a skinny desiccated look". [Razz]

Posts: 574 | From: Guinee | Registered: Jul 2014  |  IP: Logged | Report this post to a Moderator
Elmaestro
Moderator
Member # 22566

Member Rated:
5
Icon 1 posted      Profile for Elmaestro     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Punos_Rey:
quote:
Originally posted by Cass/:
Game over Afrocentrists.

"Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details)."

- derived SLC24A5 in ancient Egyptians just like the ancient Sidonian samples. Like I always said, ancient Egyptians were light to medium brown in skin pigmentation, not dark brown ('black').

 -

[Roll Eyes] I love how Nazis think they have really one upped people. Type 4 skin in Northern Egyptian samples isn't a suprise at all. Still not Southern or Northern European, and several African populations south of the Sahara are also type 4. These people wouldn't have been any lighter than many of the Khoisan. [Roll Eyes]

 -

So going from a roughly San-like pigment to darker as you go further south(with admixture also skewing the phenotypical appearances), guess it'd be most accurate to say the Aegyptians were "mostly brown and black with a skinny desiccated look". [Razz]

Dude, pay attention.

...cass is merely gum on the bottom of ones shoe at this point. Don't follow him off the rails

Posts: 1781 | From: New York | Registered: Jul 2016  |  IP: Logged | Report this post to a Moderator
Elijah The Tishbite
Member
Member # 10328

Rate Member
Icon 1 posted      Profile for Elijah The Tishbite     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
. 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.
A of that talk about Afro-loons is negated. Of course they used Yoruba when they admit themselves the SSA ancestry is from Nubia quite possibly and not a West African source.

The 3rd Intermediate Period already had an influx of foreign migration,, so the results are NOT surprising given the location and the time period.

Posts: 2595 | From: Vicksburg | Registered: Feb 2006  |  IP: Logged | Report this post to a Moderator
Concerned member of public
Banned
Member # 22355

Rate Member
Icon 10 posted      Profile for Concerned member of public   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
...cass is merely gum on the bottom of ones shoe at this point.
And yet, I made a prediction and was proven correct. I posted 2 months ago that ancient Egyptians would be carrying 1 of either derived SLC24A5 or SLC45A2. Afro-loons in that old thread said "no". [Roll Eyes] lol. Suddenly now they accept it, but down-play it as "recent foreign admixture".
Posts: 949 | From: England | Registered: Oct 2015  |  IP: Logged | Report this post to a Moderator
Elmaestro
Moderator
Member # 22566

Member Rated:
5
Icon 1 posted      Profile for Elmaestro     Send New Private Message       Edit/Delete Post   Reply With Quote 
Idiot, I made the same prediction. But why would I make such a prediction cass???
In fact I hope these mummies are FIXED for slc24a5 like their mtDNA suggest they'll be. Like Stuttgart, like the ancient Greeks will be, like non Ethiopian Jews are, like the Sudanese Copts are, like EEF are. Just understand that you cannot be simultaneously indigenous and foreign. But I've been sitting alone ahead of the game for months now.


So now, like you were saying these abusir samples show continuity right? Was it to the Copts, you said?

Posts: 1781 | From: New York | Registered: Jul 2016  |  IP: Logged | Report this post to a Moderator
BrandonP
Member
Member # 3735

Icon 1 posted      Profile for BrandonP   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
Also, I see an increase in Iranian ancestry in both modern Egyptians and other Middle Easterners compared to the ancient samples.

--------------------
Brought to you by Brandon S. Pilcher

My art thread on ES

And my books thread

Posts: 7069 | From: Fallbrook, CA | Registered: Mar 2004  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
Lol!! I couldn’t have said it better my-self.
Quote
“Just understand that you cannot be simultaneously indigenous and foreign.”. That goes to some of the brothas also.

Mind if I used that in the future? Plagiarism?

Also predict that Holocene North Africans(Mechta/Caspians) may carry derived forms of SLC45A2 and SLC24A5 but double alleles like most Europeans.

quote:
Originally posted by Elmaestro:
Idiot, I made the same prediction. But why would I make such a prediction cass???
In fact I hope these mummies are FIXED for slc24a5 like their mtDNA suggest they'll be. Like Stuttgart, like the ancient Greeks will be, like non Ethiopian Jews are, like the Sudanese Copts are, like EEF are. Just understand that you cannot be simultaneously indigenous and foreign. But I've been sitting alone ahead of the game for months now.


So now, like you were saying these abusir samples show continuity right? Was it to the Copts, you said?


Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007  |  IP: Logged | Report this post to a Moderator
beyoku
Member
Member # 14524

Member Rated:
4
Icon 1 posted      Profile for beyoku     Send New Private Message       Edit/Delete Post   Reply With Quote 
Notice they left Horners off that Admixture K Chart. Sneaky fvckers. LOL
Posts: 2463 | From: New Jersey USA | Registered: Dec 2007  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
Quote from Reviewers



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.

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.. It should be explained
why the previous work was not mentioned.


Lines 55-57: “However, methodological problems and contamination obstacles… hampered direct
investigations…”. What exactly were these problems and obstacles??

How many of them have an “identity” (e.g. name inscription)? (see
also comment 4).

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.”

--------------------
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  |  IP: Logged | Report this post to a Moderator
BrandonP
Member
Member # 3735

Icon 1 posted      Profile for BrandonP   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
EDIT: NM, I saw the peer review files.
Posts: 7069 | From: Fallbrook, CA | Registered: Mar 2004  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
Quote from Reviewers

--
Saharan admixture in more recent times” was shown in 2012 using genomewide
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.

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).

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.”

--

--------------------
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  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
Quote from Reviewers 3

--
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
--

--------------------
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  |  IP: Logged | Report this post to a Moderator
Concerned member of public
Banned
Member # 22355

Rate Member
Icon 1 posted      Profile for Concerned member of public   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Elmaestro:
Idiot, I made the same prediction. But why would I make such a prediction cass???
In fact I hope these mummies are FIXED for slc24a5 like their mtDNA suggest they'll be. Like Stuttgart, like the ancient Greeks will be, like non Ethiopian Jews are, like the Sudanese Copts are, like EEF are. Just understand that you cannot be simultaneously indigenous and foreign. But I've been sitting alone ahead of the game for months now.


So now, like you were saying these abusir samples show continuity right? Was it to the Copts, you said?

No Copts appear in the modern samples, but genome bloggers will run their own analyses soon though, probably including a Copt sample. People can already see the very close Coptic genetic ties to these Egyptian samples; some comments already made on this at Formbiodiversity.

Anyway, those Afrocentrists arguing the near-eastern ancestry is recent (late dynastic or Arab), are wrong-

quote:
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 ago. 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 deportation.
- Schuenemann et al. 2017
Posts: 949 | From: England | Registered: Oct 2015  |  IP: Logged | Report this post to a Moderator
Elmaestro
Moderator
Member # 22566

Member Rated:
5
Icon 1 posted      Profile for Elmaestro     Send New Private Message       Edit/Delete Post   Reply With Quote 
I .....don't have to wait for the bloggers
Posts: 1781 | From: New York | Registered: Jul 2016  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
We are back to Cape Verde!!!!! I am telling you guys deep analysis is require dof Cape Verdeans.
--

For those of you not getting what the reviewers are getting at.

Key points. Apparently MtDNA was found in other ancient Egyptians as much as 30%. I need to run that down. The current data is NOT consistent with that. Also they use only 3 YDNA to extrapolate , the reviewer is stating that would amount ot close to 7,000,000!!!! subsaharan slaves which is impossible. So the extrapolation is faulty.
SLC24A5 derived is at high frequency in Cape Verde and these people are very dark so the author cannot assume that these AEians were light brown. Furthermore there may be at least 20genes involved in pigmentation.

--------------------
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  |  IP: Logged | Report this post to a Moderator
Tukuler
multidisciplinary Black Scholar
Member # 19944

Icon 1 posted      Profile for Tukuler   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
PCA's leftmost AE circle
overlaps one Dinka
and touches another Dinka.

EDIT
those are neolithic Levant circles

Posts: 8179 | From: the Tekrur straddling Senegal & Mauritania | Registered: Dec 2011  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
To those who read the paper. Are they saying that only three(3) autosomal DNA was tested out of the 91 mummies. But the 91 linage was revealed but NOT the autosomal data of all 91???!!

Quote reviewer 4:
“This technique resulted in high-coverage mitochondrial genomes for 91 samples and an
additional set of autosomal SNPs for 3 of those samples.. “

--------------------
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  |  IP: Logged | Report this post to a Moderator
Concerned member of public
Banned
Member # 22355

Rate Member
Icon 1 posted      Profile for Concerned member of public   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
@ Xyyman

Derived SLC24A5 accounts for 25-38% of the skin colour variation between Sub-Saharan Africans and Europeans:

"Our results suggest that SLC24A5 explains between 25 and 38% of the European-African difference in skin melanin index."
- Lamason et al. 2005

Posts: 949 | From: England | Registered: Oct 2015  |  IP: Logged | Report this post to a Moderator
Tukuler
multidisciplinary Black Scholar
Member # 19944

Icon 1 posted      Profile for Tukuler   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
Aw, wha hoppen all that cock strutting
and superior objectivity and faith agenda.

The air is foul with the smell of counter to
geno-hamitic expectation butthurt hypocrisy.

 -

Posts: 8179 | From: the Tekrur straddling Senegal & Mauritania | Registered: Dec 2011  |  IP: Logged | Report this post to a Moderator
Forty2Tribes
Member
Member # 21799

Rate Member
Icon 1 posted      Profile for Forty2Tribes   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
I am days from being able to read it but the reference to SLC24A5 sounds like I'll be on some I told you sos. Yaruba as the true negro is funny too. By that standard I'm more Asian than these mummies.
Posts: 1254 | From: howdy | Registered: Mar 2014  |  IP: Logged | Report this post to a Moderator
xyyman
Member
Member # 13597

Rate Member
Icon 1 posted      Profile for xyyman   Author's Homepage         Edit/Delete Post   Reply With Quote 
reviewer 5"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.

According to the peer review response the author is arguing for E1b1b1 as non-African. GTFOH!

--------------------
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  |  IP: Logged | Report this post to a Moderator
Punos_Rey
Administrator
Member # 21929

Member Rated:
5
Icon 1 posted      Profile for Punos_Rey   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Tukuler:
Aw, wha hoppen all that cock strutting
and superior objectivity and faith agenda.

The air is foul with the smell of counter to
geno-hamitic expectation butthurt hypocrisy.

 -

Yeah as several of the guys lined up with their muskets ready for "afrocentrist"/black person target practice, I wasn't worried, and this is far from over.

 -

Posts: 574 | From: Guinee | Registered: Jul 2014  |  IP: Logged | Report this post to a Moderator
Swenet
Member
Member # 17303

Member Rated:
4
Icon 1 posted      Profile for Swenet     Send New Private Message       Edit/Delete Post   Reply With Quote 
 -

See Lurkers? Now how do people expect me to respond to the claim above that Dinka are close to the Abusir mummies and delusional chest thumping? What is stopping me from evoking words like cognitively challenged? Now, when I say that phrase it's going to be a problem again for using "insults". But what am I supposed to call that?

You just can't make this up.

Posts: 8785 | From: Discovery Channel's Mythbusters | Registered: Dec 2009  |  IP: Logged | Report this post to a Moderator
Ish Geber
Member
Member # 18264

Member Rated:
4
Icon 1 posted      Profile for Ish Geber     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by capra:
Estimated 6-15% African ancestry in the ancient samples, while modern Egyptians have 14-21%. And yes they used everyone's favourite True Negros the Yoruba for the sole SSA reference. [Big Grin]

3 samples with nuclear DNA are:

J2134 776-569 BC, mt hg J1d, Y hg J
J2911 769-560 BC, mt hg M1a1, Y hg J
J2888 97-2 BC, mt hg U6a2, Y hg E1b1b1a1b2-V22

So yes can be all Libyans, Hyksos, or Assyrians if that floats your boat. [Razz]

J2911 had the best coverage and least contamination. He had 2/2 + calls for derived rs1426654 in SLC24A5 and 0/7 + calls for derived s16891982 in SLC45A2. J2888 had 1 + call for rs1426654. So probably medium skin colour (sample is tiny and no data for other variants) - like modern Upper Egyptians maybe? Also brown eyes and lactose intolerant.

What is the obsession with the Yoruba? I don't understand, it's weird.

By the way, the dates above make sense.

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | Report this post to a Moderator
Elijah The Tishbite
Member
Member # 10328

Rate Member
Icon 1 posted      Profile for Elijah The Tishbite     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by beyoku:
Notice they left Horners off that Admixture K Chart. Sneaky fvckers. LOL

Do you know anything about Bahrriya Oasis?
Posts: 2595 | From: Vicksburg | Registered: Feb 2006  |  IP: Logged | Report this post to a Moderator
Mansamusa
Member
Member # 22474

Rate Member
Icon 1 posted      Profile for Mansamusa     Send New Private Message       Edit/Delete Post   Reply With Quote 
@ Swenet I just gobbled that up. lol.
Posts: 288 | From: Asia | Registered: Mar 2016  |  IP: Logged | Report this post to a Moderator
Concerned member of public
Banned
Member # 22355

Rate Member
Icon 14 posted      Profile for Concerned member of public   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
Another articl today (Nature News)
https://www.nature.com/news/mummy-dna-unravels-ancient-egyptians-ancestry-1.22069

Mummy DNA unravels ancient Egyptians’ ancestry


Genetic analysis reveals a close relationship with Middle Easterners, not central Africans.

The study, published on 30 May in Nature Communications1, includes data from 90 mummies buried between 1380 bc, during Egypt’s New Kingdom, and ad 425, in the Roman era. The findings show that the mummies’ closest kin were ancient farmers from a region that includes present-day Israel and Jordan. Modern Egyptians, by contrast, have inherited more of their DNA from central Africans.

Archaeological discoveries and historical documents suggest close ties between Egypt and the Middle East, but “it is very nice that this study has now provided empirical evidence for this at the genetic level”, says evolutionary anthropologist Omer Gokcumen of the State University of New York at Buffalo.

Both types of genomic material showed that ancient Egyptians shared little DNA with modern sub-Saharan Africans. Instead, their closest relatives were people living during the Neolithic and Bronze ages in an area known as the Levant. Strikingly, the mummies were more closely related to ancient Europeans and Anatolians than to modern Egyptians.

The researchers say that there was probably a pulse of sub-Saharan African DNA into Egypt roughly 700 years ago. The mixing of ancient Egyptians and Africans from further south means that modern Egyptians can trace 8% more of their ancestry to sub-Saharan Africans than can the mummies from Abusir el-Meleq.

The new data can’t explain why the ancient Egyptians were so tightly aligned with people from the Middle East. [Was it the result of migration, or were the Stone Age hunter-gatherers of northern Africa genetically similar to those of the Levant? It’s too early to tell, Krause says, but there’s a better chance now of getting answers. “This is the first glimpse of the genetic history of Egypt,” he says. “But it’s really just the start.”

Bold --- exactly. [Big Grin]

Posts: 949 | From: England | Registered: Oct 2015  |  IP: Logged | Report this post to a Moderator
Ish Geber
Member
Member # 18264

Member Rated:
4
Icon 1 posted      Profile for Ish Geber     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by zarahan- aka Enrique Cardova:
quote:
Originally posted by Ish Gebor:
Capra ,

Thanks for posting.

For the members. Let's stay objective and critical.

Naturally distant West African Yoruba are the designated "sub-Saharan"
comparison group. Of interest would be the breakdown of their
ancient samples- dating and locations- they all seem rather recent-
quote:
"According to the radiocarbon
dates (Supplementary Data 1, see also ref. 18), the
samples can be grouped into three time periods: Pre-Ptolemaic
(New Kingdom, Third Intermediate Period and Late Period),
Ptolemaic and Roman Period."


The ancient data sample is also drawn from the north- Lower Egypt- where there
has long been more outside admixture. Hard to read more on tiny
phone screen but will check out later in more detail.

Nice observation, …


quote:
Originally posted by .Charlie Bass.:
quote:
Originally posted by beyoku:
Notice they left Horners off that Admixture K Chart. Sneaky fvckers. LOL

Do you know anything about Bahrriya Oasis?
Repost:

Bahariyya E-V22 score = 21,95%

 -


Mixed Ethiopiansa E-V22 score = 25.00%

—Fulvio Cruciani (2007)


Fulani E-V22 score = 27.2%

E-V22 accounts for 27.2% and its highest frequency appears to be among Fulani, but it is also common in Nilo-Saharan speaking groups.

--Hisham Y. Hassan, Peter A. Underhill, Luca L. Cavalli-Sforza, and Muntaser E. Ibrahim

Y-Chromosome Variation Among Sudanese: Restricted Gene Flow, Concordance With Language, Geography, and History

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | Report this post to a Moderator
Mansamusa
Member
Member # 22474

Rate Member
Icon 1 posted      Profile for Mansamusa     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by xyyman:
We are back to Cape Verde!!!!! I am telling you guys deep analysis is require dof Cape Verdeans.
--

For those of you not getting what the reviewers are getting at.

Key points. Apparently MtDNA was found in other ancient Egyptians as much as 30%. I need to run that down. The current data is NOT consistent with that. Also they use only 3 YDNA to extrapolate , the reviewer is stating that would amount ot close to 7,000,000!!!! subsaharan slaves which is impossible. So the extrapolation is faulty.
SLC24A5 derived is at high frequency in Cape Verde and these people are very dark so the author cannot assume that these AEians were light brown. Furthermore there may be at least 20genes involved in pigmentation.

Not ancient DNA. Its DNA analysis of a modern Egyptian oases population.
Posts: 288 | From: Asia | Registered: Mar 2016  |  IP: Logged | Report this post to a Moderator
capra
Member
Member # 22737

Member Rated:
5
Icon 1 posted      Profile for capra     Send New Private Message       Edit/Delete Post   Reply With Quote 
ADMIXTURE graph will all samples (incl East Africans) is Supp Fig 4.
quote:
Originally posted by xyyman:
To those who read the paper. Are they saying that only three(3) autosomal DNA was tested out of the 91 mummies. But the 91 linage was revealed but NOT the autosomal data of all 91???!!

A cell typically contains hundreds of copies of the mitogenome, but it has only one nucleus. Hence it's generally much easier to recover mtDNA from ancient remains. These guys weren't buried in Siberia, don't expect too much.

Also I notice that all the samples were from a German museum collection - a large sample from one site over a considerable period of time. Explains why they chose this site. I'm guessing the Egyptian antiquities department isn't letting anyone get at their mummies.

Posts: 660 | From: Canada | Registered: Mar 2017  |  IP: Logged | Report this post to a Moderator
Ish Geber
Member
Member # 18264

Member Rated:
4
Icon 1 posted      Profile for Ish Geber     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Cass/:
Game over Afrocentrists.

"Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details)."

- derived SLC24A5 in ancient Egyptians just like the ancient Sidonian samples. Like I always said, ancient Egyptians were light to medium brown in skin pigmentation, not dark brown ('black').

How does this make a "game-over"? No-one claimed that ancient Egyptians were solely dark skinned.

It is all a bit more complicated.

quote:
The genotypic combination leading to a predicted phenotype of dark skin and non-brown eyes is unique and no longer present in contemporary European populations.


Figure 2 | Ancestral variants around the SLC45A2 (rs16891982, above) and SLC24A5 (rs1426654, below) pigmentation genes in the Mesolithic genome. The SNPs around the two diagnostic variants (red arrows) in these two genes were analysed. The resulting haplotype comprises neighbouring SNPs that are also absent in modern Europeans (CEU) (n5112) but present in Yorubans (YRI) (n5113). This pattern confirms that the La Bran ̃a 1 sample is older than the positive-selection event in these regions. Blue, ancestral; red, derived.


— Lalueza-Fox

quote:
Originally posted by Cass/:
quote:
...cass is merely gum on the bottom of ones shoe at this point.
And yet, I made a prediction and was proven correct. I posted 2 months ago that ancient Egyptians would be carrying 1 of either derived SLC24A5 or SLC45A2. Afro-loons in that old thread said "no". [Roll Eyes] lol. Suddenly now they accept it, but down-play it as "recent foreign admixture".
Remember this one?

quote:
Lalueza-Fox states: "However, the biggest surprise was to discover that this individual possessed African versions in the genes that determine the light pigmentation of the current Europeans, which indicates that he had dark skin, although we can not know the exact shade."
http://www.sciencedaily.com/releases/2014/01/140126134643.htm


And this one:

quote:
Frequencies display strong population differentiation, with the derived light skin pigmentation allele (A111T) fixed or nearly so in all European populations and the ancestral allele predominant in sub-Saharan Africa and East Asia (Lamason et al. 2005; Norton et al. 2007).

[...]

Phased haplotypes were retrieved from HapMap, Release 21. For phylogenetic analysis, graphs were drawn by the use of a simple nearest-neighbor approach and rooted by the use of ancestral alleles determined by comparison with other primate sequences.

[...]

"Of the remaining 10 common core haplotype groups, all ancestral at rs1426654, eight clearly have their origins in Africa (Figure 3B, Figure 4, and Table S4). Three early diverging haplotypes, C1, C2, and C4, are rare outside of Africa and clearly originated there."

--Victor A. Canfield et al.
Molecular Phylogeography of a Human Autosomal Skin Color Locus Under Natural Selection 2013


The above tells that this easily could have evolved within Africa, or at least nearby. Hence Bahariyya Egyptians.

Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | Report this post to a Moderator
Mansamusa
Member
Member # 22474

Rate Member
Icon 1 posted      Profile for Mansamusa     Send New Private Message       Edit/Delete Post   Reply With Quote 
We now have a saint in our midst--an anti-racist activist. lol
Posts: 288 | From: Asia | Registered: Mar 2016  |  IP: Logged | Report this post to a Moderator
Punos_Rey
Administrator
Member # 21929

Member Rated:
5
Icon 1 posted      Profile for Punos_Rey   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
Either Cass or Real Tawk (or both) under yet another pseudonym or one of their inbred kin.

--------------------
 -

Meet on the Level, act upon the Plumb, part on the Square.

Posts: 574 | From: Guinee | Registered: Jul 2014  |  IP: Logged | Report this post to a Moderator
BrandonP
Member
Member # 3735

Icon 1 posted      Profile for BrandonP   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Punos_Rey:
Either Cass or Real Tawk (or both) under yet another pseudonym or one of their inbred kin.

I believe it's Cass.
Posts: 7069 | From: Fallbrook, CA | Registered: Mar 2004  |  IP: Logged | Report this post to a Moderator
Mansamusa
Member
Member # 22474

Rate Member
Icon 1 posted      Profile for Mansamusa     Send New Private Message       Edit/Delete Post   Reply With Quote 
He got exposed; now he is trying to pull off a terrorist suicide attack by bringing the site down.
Posts: 288 | From: Asia | Registered: Mar 2016  |  IP: Logged | Report this post to a Moderator
  This topic comprises 13 pages: 1  2  3  4  ...  11  12  13   

Quick Reply
Message:

HTML is not enabled.
UBB Code™ is enabled.

Instant Graemlins
   


Post New Topic  New Poll  Post A Reply Close Topic   Feature Topic   Move Topic   Delete Topic next oldest topic   next newest topic
 - Printer-friendly view of this topic
Hop To:


Contact Us | EgyptSearch!

(c) 2015 EgyptSearch.com

Powered by UBB.classic™ 6.7.3