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Post by Noah on Dec 27, 2011 23:51:52 GMT -5
A recent genetics study by the commercial genetic testing company DNA Tribes analysed the DNA of an Ancient Egyptian pharaonic family from the Amarna site in Middle Egypt. Among the studied remains were those of the boy-king Tutankhamun, his young mother, and his relatives Amenhotep III and Yuya. The authors examined the autosomal STR profiles of the mummies based on 8 loci, and basically conclude that, of all the contemporary populations they studied -- including modern Egyptians -- all of the mummies by far shared greatest affinities with the Sub-Saharan samples (Southern African, African Great Lakes and Tropical West African). Admixture notwithstanding, Negroid peoples do not share any significant biological relations with modern Egyptians (who are the actual direct descendants of the Ancient Egyptians, as we'll see further below). That includes the neighboring Nilotes. Multiple studies have shown this, including the recent peer-reviewed Babiker et al. (2011), which analysed almost twice as many autosomal STRs as the DNA Tribes paper (15 vs. 8). This is an important specification because research has demonstrated that studies using only 10 autosomal loci have a huge statistical margin of error of over 30%. And that margin of error steadily decreases as one increases the number of markers analysed. "Thus the answer to the question “How often is a pair of individuals from one population genetically more dissimilar than two individuals chosen from two different populations?” depends on the number of polymorphisms used to define that dissimilarity and the populations being compared. The answer, can be read from Figure 2. Given 10 loci, three distinct populations, and the full spectrum of polymorphisms (Figure 2E), the answer is ≅ 0.3, or nearly one-third of the time. With 100 loci, the answer is ∼20% of the time and even using 1000 loci, ≅ 10%. However, if genetic similarity is measured over many thousands of loci, the answer becomes “never” when individuals are sampled from geographically separated populations."
www.genetics.org/content/176/1/351.full
This DNA Tribes paper uses even fewer loci than 10, so its margin of error is considerably higher than 30%. What good are genetic 'findings' that are around 40% likely to be wrong? Not especially useful let alone accurate. The comparatively weaker biological ties suggested in the DNA Tribes article between Horners & North Africans with the Amarna mummies relative to those posited between Negroid Africans with the Amarna mummies is another immediate red flag. Neither craniometric analyses nor dental studies nor cultural affinities nor historical data (including recorded self-perceptions) nor hair morphology nor linguistic research support such a privileged relationship. Quite the opposite. Except for obviously populations in North Africa & the Horn, the fact that kinky hair texture is the only hair form found in Africa also undermines a hypothesized Negroid origin for the Ancient Egyptians. As the anthropologist Jean Hiernaux has pointed out, " over most of the subcontinent, spiralled hair is the only category to be observed[...] the lowest frequencies of spiralled hair in sub-Saharan Africa have been observed in Ethiopia and Somalia, with a minimum in the Somali". Despite all of the above, the DNA Tribes paper would have us believe that modern Egyptians, North Africans in general & Horners are much less related to the Amarna Egyptian mummies than are Negroid Africans... almost as distantly related to the Amarna Egyptian mummies as are Northwest Europeans. In fact, in its Table 1 shown below, mummy KV55 (who is identified as "possibly Akhenaten or Smenkhkare") has a Match Likelihood Index/MLI score for Northwest Europe that is over twice that of its MLI for the Horn and North African samples and higher than all of the other circum-Meditternanean usual suspects' MLIs too (Levantine, Arabian, Aegean, Mesopotamian, etc.). But all of these MLI scores are likewise completely dwarfed by the Negroid populations' MLI scores. And not just with respect to mummy KV55, but vis-a-vis all of the mummies; especially Tutankhamun. So where did the Ancient Egyptians get their many Caucasoid affinities from, particularly their typical dark brown, cymotrichous (wavy) hair, if their nearest modern relatives are supposedly Negroid peoples? From spiralled-haired Nilotes? Not likely. Below are actual photos of two of the Amarna mummies, Yuya and Thuya, that the DNA Tribes data suggests share closer biological links with West/South/Southeast Africans than they do with even modern Egyptians. Yuya Thuya Bantu man... Yuya and Thuya relative? Egyptian man... not Yuya and Thuya relative? Somali man... not Yuya and Thuya relative? Besides Yuya and Thuya's very different facial structure and features, their hair is of the typical Ancient (and modern) Egyptian cymotrichous/wavy Caucasoid variety; the blonde appearance is due to the mummification process. The fact that the Meroites of Kush -- who shared morphological and cultural ties with the Ancient Egyptians to their north, and were actually considered on average to have had greater Sub-Saharan influences; see the Modern Nubians thread -- were found to be predominantly of Eurasian descent (~61%) also precludes Negroid origins for the related Egyptians. "The Hpal (np3,592) mitochondrial DNA marker is a selectively neutral mutation that is very common in sub-Saharan Africa and is almost absent in North African and European populations. It has been screened in a Meroitic sample from ancient Nubia through PCR amplification and posterior enzyme digestion, to evaluate the sub-Saharan genetic influences in this population. From 29 individuals analysed, only 15 yield positive amplifications, four of them (26.7%) displaying the sub-Saharan African marker. Hpa I (np3,592) marker is present in the sub-Saharan populations at a frequency of 68.7 on average. Thus, the frequency of genes from this area in the Merotic Nubian population can be estimated at around 39% (with a confidence interval from 22% to 55%). The frequency obtained fits in a south-north decreasing gradient of Hpa I (np3,592) along the African continent. Results suggest that morphological changes observed historically in the Nubian populations are more likely to be due to the existence of south-north gene flow through the Nile Valley than to in-situ evolution."
mathildasanthropologyblog.wordpress.com/2008/03/24/boring-dna-evidence-from-ancient-nubians/
From what I've been able to gather on the company, DNA Tribes' SNP work is generally considered reliable. Its autosomal STR tests (i.e. this study's methodology), however, are another matter entirely. Folks have been complaining about their inaccuracies for years. Some examples: --"The autosomal STR test from DNA Tribes is rather unreliable/inconsistent. The SNP test may not pinpoint to populations with 100% accuracy, but will rarely give results so wildly inaccurate as the DNA Tribes STR test."
--"Yeah, it is very unreliable, although my native population result was quite reliable, though global numbers were senseless. I noticed this question only because I saw earlier some small, but anyway interesting Asian admix values among Portugueses."
--"Although I am contrasted fully of Iberian Background, the analysis of DNA tribes show me that I'm overwhelming Chinese- Aboriginal Australian !!!! no European matches! They even tried to justify themselves with a possible "drift through Northern-Africa". Pleaseeeeeeeeee.... Not serious and a huge nonsense waste of money. of course, I don't recommend it at all"
So far, about three studies on the DNA profile of the Ancient Egyptians have been released. Two of them are questionable: the Swiss company iGENEA's claim that King Tut belongs to the common Western European paternal haplogroup R1b1a2, and of course this latest DNA Tribes misadventure. The third analysis of Ancient Egyptian DNA was recently conducted in Egypt by a team of researchers, including Professor Moamena Kamel of the Cairo University Medical School. Its results are legit & logical; they were aired in the PBS documentary Secrets of the Pharaohs. The scientists found that " the DNA confirmed a close relationship between the modern Egyptians living in the Nile Valley and the ancient workers who had been buried there." According to Professor Kamel, (transcripted from the video): "People who are living here, they are the same as the people who had been living 6000 years ago... And now the moderns are the descendants of these Ancient Egyptians." Since most modern Egyptians are the lineal descendants of the ancient Egyptians and are, per Kamel et al., also essentially still "the same" as the Ancient Egyptians (i.e. there's population continuity), the autosomal affinities of the modern Egyptians are a good indication of the biological makeup of their ancestors. On this point, various studies, including genome-wide analyses, have consistently shown modern Egyptians in general as being overwhelmingly of West Eurasian descent. That includes Upper Egyptians according to Omran et al. (2009): "Multi-dimensional scaling (MDS) based on pair-wise FST genetic distances of Upper Egyptian and other diverse global populations. OCE, Oceanian; ME, Middle Eastern; NAF, North African; EAS, East Asian; SSA, sub-Saharan African; UEGY, Upper Egyptian; SAS, South Asian; EUR, European. The figure shows that Oceania and American populations are very distant from Upper Egyptians (marked by a grey triangle) and other populations. The Upper Egyptian population is closer to the Middle Eastern, North African, South Asian and European populations than others." So the most that can be argued from this DNA Tribes study is that the Amarna royal dynasty may have largely, but not necessarily exclusively, been of non-Egyptian, West/South/Southeast African origin. In other words, they may have been among the group of foreigners that interrupted Ancient Egyptian rule at various periods throughout history, such as the Nubians, Persians, Greeks and Assyrians. As it turns out, a putative non-Egyptian origin for the Amarna pharaonic family is the only claim that the DNA Tribes authors make. They do not use their results on this group of royals to infer anything about the genetic makeup of the general Ancient Egyptian population. This is a sensible move on DNA Tribes' part since ruling classes, particularly in Africa, are often not of the same ancestral background as the commonfolk. However, as we already saw, even this somewhat conservative scenario is unlikely given the following: - Contra recommendations, the DNA Tribes study utilized a very small number of markers in reaching its conclusions. This results in a very large statistical margin of error/likelihood of being wrong; in this case, on the order of almost 40%.
- Just about all lines of evidence consistently affirm much closer ties between modern Egyptian, North & Horn African (i.e. Hamitic) populations with the Ancient Egyptians than between the Ancient Egyptians and Negroid peoples. That includes very obvious phenotypic factors such as hair form and general physical appearance.
- DNA Tribes' autosomal STR analyses have long had a reputation of unreliability and erratic matches.
- The related peoples of ancient Meroe were shown to be predominantly of Eurasian descent, and they are traditionally viewed as having been more Sub-Saharan admixed than were the Ancient Egyptians.
- A large-scale study on Ancient Egyptian DNA has already demonstrated that modern Egyptians are both direct descendants of and essentially the same people as the Ancient Egyptians.
- Those same modern Egyptians also have little biological ties with Negroid peoples.
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Post by Noah on Jan 6, 2012 22:10:37 GMT -5
There have been some new developments in the odd Amarna mummy saga. The DNA Tribes paper culled its raw data from an earlier Discovery Channel-financed, Egyptian-led study from 2010 by Albert Zink et al. that was published in the Journal of the American Medical Association (JAMA). It was this JAMA study's researchers that actually extracted the DNA from the mummies. The DNA Tribes authors just analysed the raw data, which had been made publicly available for independent analysis: Plugging the indicated STR values in the table above into one of the various free online population affiliation calculators (such as PopAffiliator), one consistently gets a Sub-Saharan affiliation for all of the Amarna mummies. This is in agreement with DNA Tribes' own analysis of the raw data. On its face, these results indeed suggest Sub-Saharan affinities for the Amarna royal family. However, the various lines of evidence discussed in the OP that preclude a Sub-Saharan biological origin for the Ancient Egyptians beg the question: Just how accurate is the JAMA raw data to begin with?The answer to that query is that it is apparently not very reliable at all. As it turns out, many geneticists have already expressed serious doubts about the validity of Zink et al.'s reported findings. These scientists have concluded that the likelihood of the indicated STR values actually being accurate is very low. This is due to a variety of reasons, chief among which is the difficulty of avoiding contaminating the mummy tissue with modern DNA (probably the single biggest obstacle to ancient DNA extraction). In plain language, this simply means that the DNA attributed by Zink et al. to the Amarna royals may actually be the DNA of people that physically handled/touched the mummies over the centuries and whose own DNA was then mistakenly analysed in lieu of the mummies' DNA. That's potentially a lot of people too. This scenario is highly likely given the lack of precautions that were apparently taken to prevent any such possible contamination. It is also especially likely given the fact that the reported Sub-Saharan affinities of the raw data are completely at odds with the already affirmed affinities shared between a general sample of Ancient Egyptian workers and modern Egyptians (see the Cairo University Medical School quote and link in the OP). By their own admission, the JAMA team didn't even get the same results each time. The following article published in Egyptological magazine's December 7, 2011 edition sums up the situation well: AWT Conference 2011 Review: Curse of the Pharaoh’s DNA (Jo Marchant)
Review by Kate Phizackerley.
Published on Egyptological, Magazine Reviews, 7th December 2011 (Edition 3).
Introduction
Many people were looking forward to hearing Jo Marchant speak about the DNA tests undertaken by Drs Zink, Pusch et al, and she didn’t disappoint. She was an outstanding speaker. She opened her talk by describing DNA itself, a topic which need not be repeated in this review, but which was useful for those in the audience who do not have a scientific background.
Marchant noted that the first study of ancient mummy DNA was conducted by Svante Pääbo in the 1980s whilst he was studying for his PhD at the University of Uppsala in Sweden, but is now himself sceptical of his results. The study of ancient DNA remains a subject of academic debate, with some experts believing that it is not possible to reliably sequence ancient DNA. Marchant was at pains to highlight that there are two camps, with a stark division between those who work on ancient DNA, especially human DNA, and those who believe it is not technically possible to produce valid results, with some labs refusing to take commissions. Throughout her lecture, Marchant presented the viewpoint from both sides of the debate, but her own position seemed to be that of a sceptic. The lecture needs to be considered in that context: an ancient DNA adherent might well have been more positive about some of the findings.
DNA from Egyptian Mummies
Contamination is a problem with studying DNA, which is why labs are such sterile environments and why controls should be run to eliminate the technicians’ DNA. Marchant described an early attempt to analyse the DNA of a woolly mammoth. It was later discovered that the published sequence was the project leader’s own DNA. Marchant explained how a process called Polymerase Chain Reaction (PCR)works by amplifying a small amount of DNA typically extracted from ancient, degraded samples in order to improve the size of the sample available for testing, and suggested (without discussing the evidence) that PCR is particularly susceptible to contamination from ancient DNA.
She explained why DNA from Egyptian mummies is particularly controversial. Mummies have been subjected to quite violent chemical processes during mummification, which are not entirely understood. (This was covered more extensively by Stephen Buckley in an earlier lecture.) They are then stored in fiercely hot, sometimes also rather damp, tombs and may have been disturbed and handled both in antiquity and by modern archaeologists. All of these conditions are bad for the preservation of DNA and Marchant said that computer studies have shown that DNA in Egyptian mummies can be preserved for no more than 500 years. “Preserved” in this case means that DNA strands are still long enough for analysis by the PCR method – over time the long strands of DNA break down into shorter and shorter pieces, eventually becoming too small for the minimum length for PCR analysis. (See conclusions at the end of the article for my views on this.) Scientists like Albert Zink and Helen Donoghue disagree and are still publishing papers . Marchant says that those scientists believe, instead, that mummification acts to preserve DNA.
Analysing the DNA of 18th Dynasty Royal Mummies
As most readers will know, the DNA of Tutankhamun and that of a dozen or so contemporary royal mummies was analysed and the results published in The Journal of the American Medical Association (JAMA) during 2010. The project was funded by the Discovery Channel for a series of TV documentaries and Marchant observed that some commentators are concerned that commercial considerations may have increased the pressure on the team to report newsworthy findings. The analysis was undertaken in Egypt by Egyptians, with Albert Zink and Carsten Pusch acting as consultants. The approach adopted was DNA fingerprinting – known as micro-satellite analysis / short tandem repeats (STR). For instance one of the loci examined is termed locus D13S317. A locus is the location in a DNA sequence of a specific gene. The same sequence of DNA can repeat at this location a variable number of times, from 7 repeats in some people up to 16 repeats for some others. DNA, and therefore the number of repeats, is inherited which is why it can be used to assess parentage given analysis of a sufficient number of loci. The team published the “most likely” family tree based on their reported findings and this is consistent with previous blood type analysis.
The study was criticised by a number of experts, and a subsequent JAMA edition carried a number of highly critical letters from other geneticists. Marchant listed the following key criticisms:
* It is hard to avoid contamination when taking samples from the long bones of a mummy * The study didn’t check the DNA of those involved in the sampling and analysis, so it is possible that their DNA could be eliminated * Nuclear DNA was tested but most teams working on ancient DNA believe that mitochondrial DNA is more reliable * DNA finger printing is rarely used for ancient DNA studies * PCR can create “stutter bands” (errors) through mis-amplification of DNA
Marchant reports that Zink has stated that the tests did not get the same results each time they were run and the results reported in the JAMA paper are those the team adjudged “most likely” based on “majority rule”.
On the positive side, the team didn’t find a Y-chromosome for any of the female mummies [author’s note: assuming that KV55 is male of course, and not all researchers yet are convinced of this]. This is encouraging as many of the team members were male so the results have not been contaminated by their Y-chromosome results. Marchant also reported that the team were expecting to publish mitochondrial DNA results during 2011 and that Zink believes the royal mummies are a special case, with DNA preserved by the exceptional standard of mummification the elite enjoyed.
Interestingly, Zink told Marchant that he does not believe that KV35YL can be Nefertiti but he is starting to suspect that KV21B could be – although he reports needing more results before this could be published.
Next Generation DNA Tests
The next generation of DNA tests have the potential to be successful with strands as short as 30 base pairs (c.f. 100 with PCR) so Marchant hopes that these tests might in time be used.
CT Scans and Tutankhamun’s Bones
Marchant concluded her talk by looking at Tutankhamun’s bones. His bones are broken in many places so it is hard to distinguish between pre-mortem breaks, damage during mummification and subsequent breaks. His sternum is missing and several ribs are broken.
Conclusion and Author’s Remarks
This is a subject of deep interest to me, so I wish to follow the review above with a personal assessment. There is no doubt that Marchant was one of the most skilled presenters and her ability to make technical matters accessible to a lay audience was very much appreciated by many. Her talk was widely applauded by attendees in conversations over coffee afterwards, and deservedly so because it was very, very good.
Reviewer’s Commentary
At the same time, I was rather disappointed for some of the same reasons for which I am unhappy with the original JAMA paper. While Marchant explained DNA and DNA testing with consummate skill, she made no attempt to explain the maths, or the various mathematical models she relied upon. For instance, she cited a computer study that showed that ancient DNA isn’t preserved beyond 100 years but didn’t state the source, the assumptions or even the results other than the headline. Similarly, while I agree with her dislike of Zink’s use of “majority rules” to present uncertain PCR results, I disagree with her conclusion that this is a major issue. Techniques like Bayesian inference can wrest results from uncertain data. What is clear, and Marchant herself made the point, is that it is important that Zink and colleagues publish the raw data so that independent analysis of the results can be undertaken.
For those reasons, I think Marchant leans overly to a sceptical position. There is indeed a great deal to criticise in the methodology and publication of the DNA study, and I have been quite vocal in my own criticisms on my News from the Valley of the Kings blog, including DNA Shows that KV55 Mummy Probably not Akhenaten (News from the Valley of the Kings, Phizackerley, 2010). My personal view is that the team did successfully sequence DNA from Tutankhamun and the other royal mummies but that the level of confidence in the results was badly reported: some of the results may not be as certain as the paper indicates and any partial results omitted from the paper might still be valuable if published and submitted to more detailed mathematical assessment.
In short, Marchant’s excellent talk was presented from the standpoint of a geneticist but overlooked that mathematics is an equally important discipline in interpreting ancient DNA results. It would be wrong to be overly critical of Marchant on this point. Within the context of a lecture to an enthusiast rather than academic audience, there was little scope to cover the mathematics in detail but I would have preferred that she had at least identified the areas in which the mathematics in the published paper could have been more thorough.
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Post by egypt1101 on Jan 10, 2012 13:00:28 GMT -5
I contacted DNATribes and this is the response they gave. It appears they did not want to admit the study was flawed (out of bias) or that they used so few loci to determine origins: Thank you for your interest in the recent Digest article. The 8 STR loci tested do not allow a fine level admixture analysis to identify percentages of ancestry from world regions or continents. However, in this case available results indicate the Amarna mummies have inherited several alleles that are most frequent in African populations, which suggests some African ancestry (not necessarily excluding other ancestral components) for these ancient individuals. Best regards, Lucas Martin DNA Tribes AND:Thank you for following up regarding your the recent Digest issue. The presence of some African specific alleles among the Amarna mummies does not necessarily exclude that ancient Egyptian populations were descended from multiple ancestral components (possibly including regional contacts related to modern populations of Egypt). These preliminary results only suggest that based on the 8 STR markers tested for the Amarna mummies, one of these ancestral components might have been indigenous to Africa. Best regards, Lucas Martin DNA Tribes And I contacted Mike at GenDNA. Here is what he had to say: The testing of only 8 Y-DNA markers would only give you a bare minimum amount of information about the ancestral origin of the direct paternal line. It may not even be enough to definitively place the paternal line in a specific major haplogroup. And, as far as being used for matching with others and finding genealogical connections, 8 markers is inadequate and although a minimum of 25 markers can be used, 37 markers or more are really needed to find meaningful matches. I would recommend the 37-marker test at [...]. So the testing of 8 loci is, as we already know, is extremely unreliable - inadequate - for placement of ancestry. One would expect a different outcome if more markers would have been tested. In fact, I would expect the finding to be more aligned with DNATribes previous article: dnatribes.com/dnatribes-digest-2009-02-28.pdfThe suggestion from DNATribes is unreliable. It goes against everything we know based on the genetic, linguistic, anthropologic and historical information that has been obtained for this NE African population. (note red emphasis mine)
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Post by Noah on Jan 10, 2012 21:02:50 GMT -5
Great initiative! The DNA Tribes representative appears to indicate all he really can given the unusual circumstances: a) The Amarna mummies probably also had non-African components.
b) We can't be confident about the relative percentages of each ancestral component since the 8 loci aren't enough to allow such a detailed resolution.
So it seems likes it's the sub-optimal number of markers and the JAMA raw data itself that are the problem. In their global genetic analysis based on Euclidean distance, the DNA Tribes researchers actually group their North African and Horn samples under the "Near Eastern" branch of their "Caucasian (West Eurasian)" genetic cluster. They group their other African samples separately under "Sub-Saharan African". The researchers attribute the overall clustering pattern to genetic contact/gene flow and to the degree of relative isolation from other regions. The dendrogram above of course pertains to modern populations. As such, it doesn't necessarily tell us much about the ancient Egyptians unless population continuity has been established, either with modern Egyptians or with other contemporary populations. Given the aforementioned Cairo University Medical School study explicitly asserting that its ancient Egyptian samples (pyramid builders, not royals) were genetically quite similar to its modern Egyptian ones, that genetic continuity between ancient and modern Egyptians has more or less already been established. So to find out what exactly those biological affinities were, we need look no further than the clustering pattern of the ancient Egyptians' direct descendants, the modern Egyptians. Loring Brace, among others, already suggested this population continuity a few years back. It didn't seem plausible that the Amarna mummies should cluster with West/South/Southeast Africans before even modern Egyptians. For one thing, if we assume that this royal family was of Egyptian origin (which is likely), then its members would've likely possessed certain phenotypic characteristics peculiar to both ancient and modern Egyptians that Sub-Saharan peoples in the main do not possess. Unique traits such as low bone mineral density. Afrocentrists would probably counter that the Ancient Egyptians had "tropical limb ratios" like Sub-Saharan Africans, so they must've had a "tropical African origin". But this is an exceedingly weak argument since: - Tropical limb proportions are not exclusive to Sub-Saharan Africans and never have been.
"The elongation of the distal segments of the limbs is also clearly related to the dissipation of metabolically generated heat. Since heat stress and latitude are clearly related, one would expect to find a correlation between the two sets of traits that are associated with adaptation to survival in areas of great ambient temperature-namely skin color and limb proportions. This is clearly the case in such areas as equatorial Africa, the tropical portions of South Asia, and northern Australia, although there is little covariation with other sets of inherited traits. In this regard, it is interesting to note that the limb proportions of the Predynastic Naqada people in Upper Egypt are reported to be “super-negroid,” meaning that the distal segments are elongated in the fashion of tropical Africans (Robins and Shute, 1986). It would be just as accurate to call them “super-Veddoid or “super-Carpentarian” since skin color intensification and distal limb elongation is apparent wherever people have been long-term residents of the tropics. The term “super-tropical” would be better since it implies the results of selection associated with a given latitude rather than the more “racially loaded” term “negroid.”"
wysinger.homestead.com/brace.pdf
- Neighboring peoples in South America from related ethnic groups were found to have evolved markedly different limb proportions due to one group having adapted to a higher, colder elevation than the others from lower, more tropical elevations.
"Living human populations from high altitudes in the Andes exhibit relatively short limbs compared with neighboring groups from lower elevations as adaptations to cold climates characteristic of high-altitude environments."
onlinelibrary.wiley.com/doi/10.1002/ajpa.20137/abstract
- Until quite recently, most Europeans -- who ultimately expanded into Europe from the Near East, not directly from tropical Africa -- had tropical limb ratios.
"Upper Palaeolithic humans not only were taller and had more robust bones in comparison with the Linear Band Pottery Culture Neolithic people; they also had longer limbs, a shorter trunk and, similar to modern African people, very long forearms and crural segments. The low brachial index* is a very recently acquired characteristic of White Europeans."
hormones.gr/preview.php?c_id=127
- Even African Americans do not consistently show the tropical limb ratios of their West African ancestors. While some are still tropically adapted, many others actually have a cold-adapted body plan as a consequence of both admixture with cold-adapted peoples (modern Europeans and Native Americans) and localized adaptation. And this change in their limb ratios at the population level did not take place over thousands of years, but instead over just a few hundred years of living in North America.
"The argument from morphology depends on the presupposition that body proportions are to a large degree genetically controlled. The fact that contemporary African Americans do not have tropical limb proportions but have in a few hundred years changed to more European body proportions (through adaptation to new climate plus intermixture with Europeans and First Nations Peoples) puts this claim into perspective (Pat Shipman, adjunct professor of biological anthropology, Pennsylvania State University, personal communication, 14 May 2004)."
books.google.ca/books?id=n7-BHoeyStgC&pg=PA350#v=onepage&q&f=false
It's now up to Zahi Hawass et al. to roll up their sleeves and conduct a proper genetic study on the Ancient Egyptians. This time hopefully they'll try and set up safeguards against modern DNA contamination. I'd also like to see them if possible focus more on the predynastic Egyptians, like the Naqada folks.
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Post by egypt1101 on Jan 10, 2012 23:01:41 GMT -5
Indeed. The whole study appears flawed from the start. As you previously quoted "the tests did not get the same results each time they were run and the results reported in the JAMA paper are those the team adjudged “most likely” based on “majority rule”If the data cannot be replicated, then it has no validity whatsoever and is therefore rendered worthless. There are actually more markers observed from a casual viewing of the documentary as seen on Discovery Channel: dsc.discovery.com/videos/king-tut-unwrapped-king-tuts-paternal-line.htmlThis equates to Tutankhamun belonging to R1b1a2 The JAMA report confirms/mentions 2 of the 16 DYS values as seen in the video above which would further confirm the screen shots were actual data and not concocted out of air as Afrocentrics claim. Also, regarding the "tropical limb length" issue, Zakrzewski's study was based on several Egyptian populations, the only population that was noted as having "tropical limb lengths" was the population at Gebelein, which was a Middle Kingdom Nubian settlement. “Stature and the pattern of body proportions were investigated in a series of six time-successive Egyptian populations in order to investigate the biological effects on human growth of the development and intensification of agriculture, and the formation of state-level social organization. Univariate analyses of variance were performed to assess differences between the sexes and among various time periods. Significant differences were found both in stature and in raw long bone length measurements between the early semipastoral population and the later intensive agricultural population. The size differences were greater in males than in females. This disparity is suggested to be due to greater male response to poor nutrition in the earlier populations, and with the increasing development of social hierarchy, males were being provisioned preferentially over females. Little change in body shape was found through time, suggesting that all body segments were varying in size in response to environmental and social conditions. The change found in body plan is suggested to be the result of the later groups having a more tropical (Nilotic) form than the preceding populations.” (“Variation In Ancient Egyptian Stature And Body Proportions” Sonia Zakrzewski 2003) The ancient Egyptians have been described as having a “Negroid” body plan (Robins, 1983). Variations in the proximal to distal segments of each limb were therefore examined. Of the ratios considered, only maximum humerus length to maximum ulna length (XLH/XLU) showed statistically significant change through time. This change was a relative decrease in the length of the humerus as compared with the ulna, suggesting the development of an increasingly African body plan with time. This may also be the result of Nubian mercenaries being included in the sample from Gebelein…The earliest evidence of Nubians living in Egypt comes during the OK. Throughout the MK, the pharaonic frontier lay on the Second Cataract (in present-day Sudan); during this period, movements northwards from Nubia are especially likely. Together with the known presence of Nubian mercenaries in Gebelein (Fischer, 1961), the MK sample may represent a Nubian rather than Egyptian population… (“Variation In Ancient Egyptian Stature And Body Proportions” Sonia Zakrzewski 2003) Robins, who Zakrzewski cites is refuting Robins negroid claim. However, Robins, who coined the so-called "super Negroid"term stated: “This does not mean that the ancient Egyptians were negroes; indeed, in their art they clearly distinguished between their own facial features and skin colour and those of people from further south.” Kemp affirms that the MK population at Gebelein was indeed Nubians: “…a group of Nubian bowmen were settled upstream from Thebes, in the vicinity of Gebelein, where a number of them were buried. Our only means of identification are small gravestones, the idiosyncratic hieroglyphs of which point to a date in the first Intermediate period. They identify themselves as Nubians by sometimes using…”Nehesy”. They are shown with bushy hair, darker skin colour, and a distinctive sash which hangs down the front of their kilts. They carry bows and arrows and sometimes attended by dogs. As riverine Nubians their cultural background is well known from excavations in Nubia itself and is quite distinctive. So far few traces of it have been found much to the north of Elephantine.” (“Ancient Egypt: Anatomy Of A Civilization” 2006 Barry Kemp) Goyon and Cardin also confirm the population consisted of Nubians: “The results for the MK are of particular interest, despite the small skeletal sample size studied from this period. This sample exhibited the greatest cranial sexual dimorphism. This may be a reflection of the unusual composition of the sample, deriving as it does from Gebelein. Evidence from stelae suggests that from the First Intermediate Period onwards, Gebelein had a colony of Nubian mercenaries, e.g. Stela Turin 1290. Six stelae from Gebelein indicate that these Nubians lived with and were buried near the Egyptian community that they served, and that they were buried in an Egyptian manner, whilst still being depicted as Nubian…The skeletal variation seen may therefore be the result of Nubian mercenaries marrying into Egyptian families and being buried within Egyptian (rather than Nubian) contexts, and thus that the MK sample studied comprises of a mixed Egyptian and Nubian population.” (“Proceedings Of The Ninth International Congress Of Egyptologists, Volume 2” 2007; Goyon, Cardin) So those "super Negroids" are mixed (their term), being roughly half Caucasoid. The nature of the body plan was also investigated by comparing the intermembral, brachial, and crural indices for these samples with values obtained from the literature. No significant differences were found in either index through time for either sex. The raw values in Table 6 suggest that Egyptians had the super-negroid body plan described by Robins (1983)…The sample studied originates from Gebelein in Upper Egypt. Interestingly, the only other sample deriving from Gebelein, an EPD sample, was found to be significantly biologically distant to the MK sample. This result suggests that there is no simple biological population continuity at Gebelein. Stele indicate that Nubian mercenaries lived, married, died, and were buried at this site over the MK period (Fischer, 1961). Previous research has suggested that this sample may include some of these Nubians… (“Variation In Ancient Egyptian Stature And Body Proportions” Sonia Zakrzewski 2003) Now anyone who studies ancient Egyptians will be familiar with "Ginger" an EPD Egyptian. Ginger is stated as being a "European type" (Egyptologist Najovits; 2003) and was discovered near Gebelein. This would explain why Ginger is "significantly biologically distant to the MK sample" for which there is "no simple biological population continuity at Gebelein". Nubians only arrived in Egypt during the OK as indicated by the study. This completely excludes Nubians as founders of the Egyptian populace - likewise excluding them from any type of contribution to the rise of the Egyptian state. Most notably is what Zakrzewski states below regarding tibia length in relation to the femur: "Of the Egyptian samples, only the Badarian and Early Dynastic period populations have shorter tibiae than predicted from femoral length." (“Variation In Ancient Egyptian Stature And Body Proportions” Sonia Zakrzewski 2003) The Afrocentrics gloss over this fact. Noteworthy are other studies which conclude: “cold-adapted” populations are known to have both relatively wide bodies and relatively short tibiae (Holliday, 1997, 1999; Ruff et al., 2005) Zakrzewski mentions the size of Egyptian mastoids: "The size of the mastoids was considered, but all Egyptian cranial material studied has relatively inflated mastoids as compared to other populations." (Zakrzewski; 2003) "Characters of Negroid skull: Small mastoid processes. medstudynotes.pgpreparation.in/2008/01/identification-of-race-from-skull.htmlEgyptians did not represent themselves as "tropical people" - nor did they depict themselves with "tropical" type hair - as one would expect coming from or having origins from a tropical environment. They refused to depict themselves in the same fashion as they did their neighbors to the south.
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Post by Noah on Jan 11, 2012 19:55:19 GMT -5
The Ancient Egyptians indeed rather tellingly contrasted the physical features of the Nilotes to their south from their own appearance. As discussed in the Modern Nubians thread, there's actually a stela featuring an inscription where Thutmose I boasts about how he defeated "the kinky-haired" (a byword here for "Negro" and the Noba in particular). On the other hand, the Ancient Egyptians depicted the peoples of the Land of Punt (which was probably further to their south and east) in a very similar fashion as themselves. They were also careful to differentiate the Puntites from Negroid peoples: "when Puntites and Africans are depicted on one and the same monument, care is taken to bring out the physical differences between them".
books.google.com/books?id=Z6nRkXHCoE4C&pg=PA58&lpg=PA58&dq=The+general+appearance+of+Puntites+in+the+temple+of+Hatshepsut&source=bl&ots=d4wEkM7sw4&sig=6_q8AqvCYZtheSagsLIwatTJhA8&hl=en&ei=ooivStSUB4fZlAey0LHQBg&sa=X&oi=book_result&ct=result&redir_esc=y#v=onepage&q=The%20general%20appearance%20of%20Puntites%20in%20the%20temple%20of%20Hatshepsut&f=false
What's especially bizarre is that there are Afrocentrists who now claim that non-kinky hair texture is indigenous to tropical Africa. This is despite the fact that not one study suggests this and that such hair texture is completely foreign to their own (typically West African) ancestors. Indeed, in every single African population where there's a notable incidence of such hair form, there's also an appreciable level of Eurasian ancestry since that's of course where that hair texture comes from in the first place. North Africans, Horners, the Tuareg, the Sahrawi -- you name it. That's why Jean Hiernaux, whom I quote in the OP, at one point describes kinky hair as "typically African". The Ancient Egyptians probably did have tropical limb proportions. But this in no way rules out West Eurasian affinities for them since West Asia already hosted tropically adapted peoples starting at least 100,000 years before present. The Skhul-Qafzeh skeletons of ancient Israel had a tropical body plan, and they were most certainly not Negroid. So did the proto-Caucasoid Cro-Magnons of Europe, who were the siblings of the Iberomaurusians of North Africa. Recall that Europeans only very recently developed cold-adapted limb proportions, and their ancestors ultimately expanded into Europe from the Near East. What does this tell us? It tells us that there were non-Negroid Near Easterners who were tropically adapted, just like the Ancient Egyptians. The fact that many African Americans are today cold-adapted tells us the opposite: that there are Negroid peoples who are cold-adapted, and they partially got that way through morphological adaptation over a very short period of time. Despite this, Afrocentrists argue that the tropical limb proportions of the Ancient Egyptians means that they were black, "Elongated Africans". According to them, this makes modern Egyptians and most North Africans biracial; a mixture of Elongated African and intrusive West Eurasian genes. What's most amusing and ironic about this theory is that the very man who created the "Elongated African" concept, Jean Hiernaux, explicitly and repeatedly states in his book The People of Africa that North Africans in general, including ancient and modern Egyptians, are basically Mediterranean peoples. "In this book the emphasis is on sub-Saharan Africa, the specifically African anthropological area. Because North Africa and Egypt belong much more to the Mediterranean and the area of Western Asia than to Africa in that which concerns physical anthropology, these regions will be touched on only briefly." Hiernaux also indicates that the Sahel is a region of admixture, but that certain Sahelian groups, like many Tuareg tribes, are still essentially Caucasoid. Based on multiple biological factors, he likewise describes many Afro-Asiatic-speaking populations in the Horn as essentially Caucasoid, albeit also possessing appreciable admixture. For example, he writes: "As repeatedly stressed here, reliance on a single indicator of an exotic genetic influence can be misleading. We are on much firmer ground in the case of populations which exhibit values near to the 'Arab' end of the scale for a number of independent traits: the probability that factors other than genetic admixture might generate such systematic affinities with Arabs is very low. Such is clearly the case for the populations of central Ethiopia[...]
The larger sample of northern Somali belonging to various groups, the best represented being the Warsingili, are much shorter (169 cm) and have a relatively narrower face and nose; apparently they are strongly Arabicized." Like the above, most of Hiernaux's work is actually quite logical and well-conceived. It's just been taken out-of-context and/or heavily distorted by Afrocentrists writing in secondary sources. Hiernaux was a colleague of Carleton Coon's, and they often referenced each other's work. Here's what Coon concluded on the overall body proportions of the Horners he examined, including the distal segments of the limbs (forearms and lower legs): "The hands and feet of all but the palpably negroid are small and extremely narrow, the lower legs and wrists usually spindly and ill-muscled. This attenuation of the distal segments of the limbs reaches its maximum among the Somalis[...] The bodily build of the African Hamites is typically Mediterranean in the ratio of arms, legs, and trunk, but the special attenuation of the extremities among the Somalis is a strong local feature, which finds its closest parallels outside the white racial group, in southern India and in Australia." This Mediterranean affinity in overall body proportions was further confirmed by the morphological study Billy et al. (1988), which analysed many of the very same samples that Hiernaux used in his earlier work: About the R1b affair, I'm not certain that King Tut belongs to the clade. Not necessarily because it's R1b per se, but because of how the STR values were actually obtained i.e. apparently through video screenshot glimpses of random figures. As such, we can't really be sure that that STR profile does, in fact, belong to him. I'm still open to the idea that it might, though. As we'll see later on in the month (once I hopefully finish up some new research that I'm working on), such a paternal ancestry is not completely ruled out; it's just less likely than the typical Egyptian/Hamitic E1b1b. I also think overemphasizing the possibility that Tut may carry other Y DNA haplogroups could perhaps be interpreted as a tacit admission that haplogroup E isn't of Hamitic origin... though the bulk of the evidence -- increasing by the month -- indicates that it is. So that's another thing we should be aware of.
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Post by Noah on Jan 11, 2012 20:12:35 GMT -5
We may have actually understated the sheer scale of the controversy surrounding the validity of the JAMA study's raw data. Nature magazine ran an interesting piece on the Amarna mummy debate in its April 2011 issue. Various researchers were quoted in it as taking exception to the inadequate "genetic fingerprinting" methodology used, to the point where the field is now described as "fractured". Thankfully, there are indications that next-generation sequencing techniques are already here. Researchers are about to use them on ancient Egyptian and other hoary remains, so this surreal episode should be sorted out soon enough. Ancient DNA: Curse of the Pharaoh's DNA
Some researchers claim to have analysed DNA from Egyptian mummies. Others say that's impossible. Could new sequencing methods bridge the divide?
Jo Marchant
Cameras roll as ancient-DNA experts Carsten Pusch and Albert Zink scrutinize a row of coloured peaks on their computer screen. There is a dramatic pause. "My god!" whispers Pusch, the words muffled by his surgical mask. Then the two hug and shake hands, accompanied by the laughter and applause of their Egyptian colleagues. They have every right to be pleased with themselves. After months of painstaking work, they have finally completed their analysis of 3,300-year-old DNA from the mummy of King Tutankhamun.
Featured in the Discovery Channel documentary King Tut Unwrapped last year and published in the Journal of the American Medical Association (JAMA)1, their analysis — of Tutankhamun and ten of his relatives — was the latest in a string of studies reporting the analysis of DNA from ancient Egyptian mummies. Apparently revealing the mummies' family relationships as well as their afflictions, such as tuberculosis and malaria, the work seems to be providing unprecedented insight into the lives and health of ancient Egyptians and is ushering in a new era of 'molecular Egyptology'. Except that half of the researchers in the field challenge every word of it.
Enter the world of ancient Egyptian DNA and you are asked to choose between two alternate realities: one in which DNA analysis is routine, and the other in which it is impossible. "The ancient-DNA field is split absolutely in half," says Tom Gilbert, who heads two research groups at the Center for GeoGenetics in Copenhagen, one of the world's foremost ancient-DNA labs.
Unable to resolve their differences, the two sides publish in different journals, attend different conferences and refer to each other as 'believers' and 'sceptics' — when, that is, they're not simply ignoring each other. The Tutankhamun study reignited long-standing tensions between the two camps, with sceptics claiming that in this study, as in most others, the results can be explained by contamination. Next-generation sequencing techniques, however, may soon be able to resolve the split once and for all by making it easier to sequence ancient, degraded DNA. But for now, Zink says, "It's like a religious thing. If our papers are reviewed by one of the other groups, you get revisions like 'I don't believe it's possible'. It's hard to argue with that."
Rise and fall
The disagreement stems from the dawn of ancient-DNA research. In the 1980s, a young PhD student called Svante Pääbo worked behind his supervisor's back at the University of Uppsala in Sweden to claim he had done what no one else had thought was possible: clone nuclear DNA from a 2,400-year-old Egyptian mummy2. Soon researchers realized that they could use a new technique called polymerase chain reaction (PCR) to amplify tiny amounts of DNA from ancient samples. There was a burst of excitement as DNA was reported from a range of ancient sources, including insects preserved in amber and even an 80 million-year-old dinosaur3.
Then came the fall. It turned out that PCR, susceptible to contamination at the best of times, is particularly risky when working with tiny amounts of old, broken-up DNA. Just a trace of modern DNA — say from an archaeologist who had handled a sample — could scupper a result. The 'dinosaur' DNA belonged to a modern human, as did Pääbo's pioneering clone. Once researchers began to adopt rigorous precautions4, including replicating results in independent labs, attempts to retrieve DNA from Egyptian mummies met with little success5.
That's no surprise, say sceptics. DNA breaks up over time, at a rate that increases with temperature. After thousands of years in Egypt's hot climate, they say, mummies are extremely unlikely to contain DNA fragments large enough to be amplified by PCR. "Preservation in most Egyptian mummies is clearly bad," says Pääbo, now at the Max Planck Institute for Evolutionary Anthroplogy in Leipzig and a leader in the field. Ancient-DNA researcher Franco Rollo of the University of Camerino in Italy went so far as to test how long mummy DNA might survive. He checked a series of papyrus fragments of various ages, preserved in the similar conditions to the mummies. He estimated that DNA fragments large enough to be identified by PCR — around 90 base pairs long — would have vanished after only around 600 years6.
Yet all the while, rival researchers have published a steady stream of papers on DNA extracted from Egyptian mummies up to 5,000 years old. Zink and his colleagues have tested hundreds of mummies, and claim to have detected DNA from a range of bacteria, including Mycobacterium tuberculosis, Corynebacterium diphtheriae and Escherichia coli, as well as the parasites responsible for malaria and leishmaniasis.
In a high-profile study last year, a team led by microbiologist Helen Donoghue at University College London reported finding DNA from M. tuberculosis in Dr Granville's mummy7 — named after physician Augustus Granville, the first person to autopsy a mummy, in 1825.
In the case of tuberculosis (TB) at least, Donoghue vehemently disagrees with the idea that DNA can't survive in Egyptian mummies. Mycobacteria such as M. tuberculosis have cell walls that are rich in lipids, which degrade slowly and protect the DNA, she argues. Donoghue claims that in many cases she has confirmed the presence of the bacterium by detecting these lipids directly. She says the extreme anti-contamination measures demanded by the big ancient-DNA labs are not as vital for ancient microbial DNA as they are for human DNA. After all, she says, modern diagnostic labs routinely detect TB using PCR — which suggests that the test is not as susceptible to contamination as the sceptics fear. In Donoghue's view, "some of the precautions they talk about are totally over the top compared to every diagnostic lab in the country".
The sceptics are unmoved. Without highly stringent controls in place, it's impossible to show that any microbial sequences are from ancient DNA and not from related modern microbes, says Gilbert. "How do you know you've got TB and not some other bacterium with a similar DNA sequence?" He and other critics believe that this entire body of research is based on wishful thinking.
The two groups have now grown tired of arguing. "It's largely dealt with by ignoring each other," says Ian Barnes, a molecular palaeontologist at Royal Holloway, University of London, who works on DNA from ancient animals, including mammoths. "There's enough dead stuff around, you're not obliged to get into anyone else's area."
A royal argument
After the JAMA study on Tutankhamun and his family, however, the arguments resumed in force. Studies of human DNA from Egyptian mummies are the most controversial of all. One reason is the high profile of the claims. Another is that contamination from modern human DNA is excruciatingly difficult to detect, because its genetic make-up is almost identical to that of a human mummy's. On top of that, restricted access to samples makes it hard to check any claims in an independent lab. After more than a century in which valuable artefacts flooded out of the country to museums and private collections all over the world, the Egyptian authorities imposed a ban on removing archaeological samples from Egypt. Most non-Egyptian researchers wanting to study mummies are limited to museum exhibits elsewhere.
The Tutankhamun project was carried out by an Egyptian team recruited by archaeologist Zahi Hawass, Egypt's top official in charge of antiquities. It was the first ancient-DNA study on royal mummies, and the country lacked the necessary expertise. So Hawass asked Zink, a prominent researcher at the EURAC Institute for Mummies and the Iceman in Bolzano, Italy, and Pusch, of the University of Tübingen, Germany, to act as consultants. The pair designed and oversaw the study, including the building of two dedicated labs in Cairo. The labs were partly paid for by the Discovery Channel, which filmed the project.
The researchers deny that the television involvement put them under excessive pressure to produce dramatic results. But working for the cameras did make a challenging project even tougher, says Pusch. "Each time they came in to film, we had to close the lab for a week to clean." Eventually the TV crew was banished and the lab scenes reconstructed.
In the end, the project seemed to be a wild success, and its findings drew wide press attention. The researchers claimed to have detected DNA from the malaria parasite Plasmodium falciparum in several of the mummies, including Tutankhamun, suggesting that the infection had contributed to their deaths. They also said they had retrieved fragments of human DNA from every mummy tested and used the data to construct a five-generation family tree, from Tutankhamun's great-grandparents to the two tiny bodies found in his tomb, identified as his stillborn children.
The whole episode has only raised eyebrows in the other half of the community. "I'm very sceptical," says Eske Willerslev, director of Copenhagen's Center for GeoGenetics, who co-authored a letter to JAMA disputing the results8. His major concern, shared by others, was the method of DNA analysis used. Rather than extracting and sequencing DNA, the team used a technique called genetic fingerprinting, which involves measuring the size of the DNA products that have been amplified by PCR. It is rarely used in ancient-DNA studies, say critics, because without sequence data it is especially difficult to rule out contamination. And on a well-handled mummy such as Tutankhamun, say sceptics, contamination could be rife.
Bones of contention
The Tutankhamun team carried out many controls, including replication of the tests by different teams in the two labs and comparing the mummy DNA fingerprints with those of the research team to cross-check for contamination. Zink and Pusch add that the samples were taken from within the mummies' bones where, they say, contaminating DNA should not have reached.
Zink and Pusch think that the mummification process protected the DNA from degrading in the hot tomb by removing water, which is required for the main mechanism of DNA decay, called depurination. Egyptian embalmers dried bodies with natron, a naturally occurring mixture of salts, immediately after death. "The Egyptians really knew how to preserve a body," says Zink. "They got rid of the water very fast." Tutankhamun was also smothered with embalming and anointing materials, thought to contain ingredients such as bitumen, plant oils and beeswax, and Pusch believes it gave the DNA additional protection from the damaging effects of water. Hawass was not directly involved in the DNA research, but he stands by the team's conclusions, saying that the DNA in Egyptian mummies seems to be well preserved.
"There are a number of things right about the paper," says David Lambert, an ancient-DNA researcher and evolutionary biologist at Griffith University in Nathan, Queensland. Lambert points out that the Tutankhamun team was not able to amplify Y-chromosome markers from the female mummies, which argues against contamination from modern archaeologists, who are generally male. In unpublished work, he says he has amplified DNA from mummified ibises, a sacred bird in ancient Egypt. "We're confident that traditional PCR methods work with some of the material that we've got," he says.
Sceptics, however, doubt that there was sufficient DNA left in Tutankhamun for the result to be real. They say that a mummified body would soon soak up any moisture available in the atmosphere, especially into its porous bones. When British archaeologist Howard Carter first opened Tutankhamun's coffins in 1925, he reported that they had been damaged by humidity. But it is difficult for anyone else to replicate the DNA work without permission to access the samples.
The Tutankhamun study has left the field more divided than ever, with clear frustration on both sides. "I don't understand people's harshness," Pusch says. "This is pioneering work." He and Zink say that they are sequencing DNA from the mitochondria and Y chromosomes of the mummies, and plan to publish these results this year.
But now, after years of conflict, strides in sequencing technology are changing the game. The newest techniques can read much shorter fragments — easily down to the 30 base pairs that might be found in a 2,000-year-old Egyptian mummy. "That pushes the [DNA] survival time a long way back," says Gilbert. "Things that we wrote off in the past, we can now get genomes on." And, crucially, the speed of the techniques makes it much easier to sequence a sample multiple times and to rule out contamination by checking for patterns of damage characteristic of ancient DNA.
Last year, these techniques enabled Willerslev, Gilbert and their colleagues to publish the full genome sequence of a palaeo-Eskimo from Greenland that is some 4,000 years old9. Within weeks, teams led by Pääbo published the genome of a 38,000-year-old Neanderthal10 and a previously unknown hominin from southern Siberia11. Meanwhile Zink's team is on the brink of publishing the genome of Ötzi the Iceman.
All these specimens were preserved in the cold — but Willerslev is already using next-generation techniques to extract DNA from various South American mummies, some of which have been preserved in warmer conditions. "Some are definitely working," he says. But, he adds, he is finding tremendous variability in whether samples yield DNA — a possible reason why Egyptian mummies have yielded such conflicting results. With the cost of sequencing falling sharply, researchers are lining up to try the techniques on Egyptian mummies.
Zink and Pusch are now negotiating the complex political path towards using next-generation techniques on Tutankhamun and his kin. "We would love to do this," says Zink. "It would absolutely make sense. The problem is to do it in Egypt." With no samples allowed out of the country, they would have to take the sequencing machines to Cairo, an expensive proposition. And there is concern, says Zink, that such work might yield politically sensitive information about the genetic origin of the pharaohs, and whether any of their descendants are alive today. "This goes right to their history."
Still, Zink is optimistic that next-generation sequencing will help to bring the fractured field back together. "I think it is really time to bring together the different sides and stop arguing about each other's work," he says. "With next-generation sequencing, people can't just say 'I don't like it'. People have to discuss the work based on the data themselves." Willerslev agrees, offering a rare olive branch. "I think we will find that the believers have been too uncritical," he says. "But the sceptics have probably been too conservative."
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Post by egypt1101 on Jan 6, 2013 22:32:50 GMT -5
I've been re-analyzing the JAMA paper as well as DNATribes. Could it be possible JAMA is correct but DNATribes wrong? In the JAMA paper, there are only two published values: DYS393=13 Y-GATA-H4=11 When plugged into WAHP we get an outcome of R1b 88%. This would agree with the Discovery Channel documentary and what genetic forums on the interent relay. As far as DNATribes, they seem to zone in on only two of 8 alleles: D18S51=19 and D21S11=34 and ignore the other six. They further state that these alleles: "today are more frequent in populations of Africa than in other parts of the world."This leads me to conclude that it wasn't so in the past. Further, with a little investigative research, I have found that the D21S11=34 allele can be found across ALL populations and the highest frequency is represented in the Asian Balinese population. D18S51=19 is found in the Asian Balti group, and is just as high in the Xhosa (African) group, both at 13.8%. It's found in 1.1% of Egyptians and 3.6% of both Berbers and European Americans. alfred.med.yale.eduSo DNATribes appears to be misleading in this aspect, neither alleles are African specific, much less "black" specific.
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Post by Noah on Jan 7, 2013 10:07:57 GMT -5
I haven't yet had the opportunity to re-examine the Amarna values. However, I do think you may be onto something because many of the autosomal markers in Zink's more recent Ramesses III paper show non-Sub-Saharan affinities. They are quite bizarre overall, actually.
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Post by Noah on Jan 8, 2013 17:28:00 GMT -5
I took the initiative and ran Tutankhamun's microsatellite marker values in the table above through the Earth Human Short Tandem Repeat Allele Frequencies Database (EHSTRAFD)'s Allele Frequency Global Tracking (AFGT) module. Like Ramesses III's results, Tut's alleles showed a highest incidence amongst modern South Asian communities. There were also some secondary links with Sub-Saharan African, Amerindian, East Asian and Eastern European groups. TUTANKHAMUN (KV62)Locus: D13S317*Allele: 10 (1st parent) 1. Yupik - South-Western Alaska, United States (42.5%) 2. Madia-Gond - Maharashtra, India (28%) 3. Inupiat - Northern Alaska, United States (26.61%) 4. Athabaskan - Alaska, United States (22.77%) 5. Ximeng - Inner Mongolia (20.5%) Population affinity: Inuit, South Asian, MongolianAllele: 12 (2nd parent) 1. Guinean - Guinea-Bissau (48%) 2. Arab - Zriba, Tunisia (47.8%) 3. Afro-Caribbean - United Kingdom (45.5%) 4. African American - Jamaica (45.49%) 5. Berber - Ghardaia, Algeria (44.3%) Population affinity: West African, Northwest AfricanLocus: D7S820Allele: 10 (1st parent) 1. Hutu - Nyarurema, Rwanda (44%) 2. Tutsi - Central Rwanda (43.103%) 3. Arab - Zriba, Tunisia (42.2%) 4. Argentine - Salta, Argentina (41.7%) 5. Mozambican - Maputo, Mozambique (39.1%) Population affinity: Sub-Saharan African, Northwest African, AmerindianAllele: 15 (2nd parent) 1. Buddhist - Ladakh, India (2.8%) 2. Katkari - Maharashtra, India (1.6%) 3. Berber - Southern Morocco (1%) 4. Northern Arab - Dubai Emirate (0.5%) 5. Chinese - Eastern China (0.5%) Population affinity: Indian, Berber, ChineseLocus: D2S1338Allele: 16 (1st parent) 1. Old Believers - North-Eastern Poland (8.8%) 2. Old Believers - North-Eastern Poland (8.8%) 3. Albanian - Kosovo (8.1%) 4. Tutsi - Central Rwanda (8.065%) 5. Saudi Arabian - Dubai Emirate (8%) Population affinity: Eastern European, Tutsi, Gulf ArabAllele: 26 (2nd parent) 1. Lithuanian - North-Eastern Poland (3.6%) 2. Japanese - Japan (3.3%) 3. Caucasian - United States (3%) 4. Romanian - Bucharest, Romania (2.9%) 5. Romanian - Bucharest, Romania (2.9%) Population affinity: Eastern European, JapaneseLocus: D21S11*Allele: 29 (1st parent) 1. Argon - Ladakh, India (34.8%) 2. Arab - Zriba, Tunisia (33.3%) 3. Chinese - Macau, China (32.8%) 4. Egyptian - Cairo, Egypt (32.5%) 5. Albanian - Kosovo (31.6%) Population affinity: Indian, North African, Chinese, AlbanianAllele: 34 (2nd parent) 1. Colombian - Boyaca, Colombia (4.5%) 2. Satnami - Chhattisgarh, India (2.6%) 3. Brazilian - Pernambuco, Brazil (2.4%) 4. Angolan - Cabinda, Angola (2.27%) 5. Khatri - Uttar Pradesh, India (2.2%) Population affinity: Amerindian, Sub-Saharan African, South AsianLocus: D16S539Allele: 8 (1st parent) 1. Jat - Uttar Pradesh, India (12.8%) 2. Tibetan - Gannan, China (12.2%) 3. Tamil - Tamil Nadu, India (12.08%) 4. Madia-Gond - Maharashtra, India (12%) 5. Katkari - Maharashtra, India (10.8%) Population affinity: Indian, ChineseAllele: 13 (2nd parent) 1. Bosnian - Bosnia and Herzegovina (24.4%) 2. Native American - Michigan, United States (24.14%) 3. Kurmi - Uttar Pradesh, India (23.5%) 4. Colombian - Bogota, Colombia (22.28%) 5. Caucasian - Transylvania, Romania (21.9%) Population affinity: Eastern European, Amerindian, South AsianLocus: D18S51Allele: 19 (1st parent) 1. Botswananian - Botswana (17.3%) 2. Baiti - Ladakh, India (13.8%) 3. Arab - Zriba, Tunisia (12.8%) 4. Fang - Bioko, Equatorial Guinea (12.75%) 5. Angolan - Cabinda, Angola (12.73%) Population affinity: Sub-Saharan African, Indian, Northwest AfricanAllele: 19 (2nd parent) 1. Botswananian - Botswana (17.3%) 2. Baiti - Ladakh, India (13.8%) 3. Arab - Zriba, Tunisia (12.8%) 4. Fang - Bioko, Equatorial Guinea (12.75%) 5. Angolan - Cabinda, Angola (12.73%) Population affinity: Sub-Saharan African, Indian, Northwest AfricanLocus: CSF1POAllele: 6 (1st parent) 1. Katkari - Maharashtra (4.9%) 2. Black - Cape Town, South Africa (1.5%) 3. Mara - Mizoram, India (1.1%) 4. Asian-derived Brazilian - Sao Paulo, Brazil (0.9%) 5. White - Cape Town, South Africa (7.6%) Population affinity: South Asian, Sub-Saharan African (Khoisan?), Amerindian*Allele: 12 (2nd parent) 1. Lai - Mizoram, India (59.8%) 2. Han - Henan, China (58.9%) 3. Mahadeo-Koli - Maharashtra, India (55.7%) 4. Salishan - United States (50%) 5. Saskatchewan - United States (49.37%) Population affinity: South Asian, Chinese, AmerindianLocus: FGAAllele: 23 (1st parent) 1. Han - Henan, China (26.6%) 2. Han - South-Eastern, China (26.2%) 3. South Korean - South Korea (25.4%) 4. Chaoshan - Chaoshan, China (24.3%) 5. Han - Shaanxi, China (24.14%) Population affinity: East AsianAllele: 23 (2nd parent) 1. Han - Henan, China (26.6%) 2. Han - South-Eastern, China (26.2%) 3. South Korean - South Korea (25.4%) 4. Chaoshan - Chaoshan, China (24.3%) 5. Han - Shaanxi, China (24.14%) Population affinity: East Asian*asterisk=alleles whose top 100 AFGT matches are exclusively Eurasian
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Post by egypt1101 on Jan 8, 2013 21:35:49 GMT -5
Great observation, Noah! That is also a very nice utility which is proven to be very useful!
These markers in total seem to hold more weight with Caucasoid and Mongoloid types than with Sub Saharans. We know that there were no American Indians in ancient Egypt and we can also conclude, based on genetic studies, that there were no Bantuids in Egypt either. The mere fact that these markers are also found in Caucasoids, dispels the DNATribes myth. Frequencies does not always equal origins.
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Post by Noah on Jan 9, 2013 20:05:11 GMT -5
Great observation, Noah! That is also a very nice utility which is proven to be very useful! These markers in total seem to hold more weight with Caucasoid and Mongoloid types than with Sub Saharans. We know that there were no American Indians in ancient Egypt and we can also conclude, based on genetic studies, that there were no Bantuids in Egypt either. The mere fact that these markers are also found in Caucasoids, dispels the DNATribes myth. Frequencies does not always equal origins. What's nice about the AFGT module is that you can actually see what the top 100 population matches are in the database for each allele. There's no guessing involved as to how a Match Likelihood Index or other similarity metric may have come about since we can actually see the constituent parts. Also notice how in the DNA Tribes table in the opening thread post, no Indian or Amerindian populations appear to have been included for comparison against the Amarna microsatellite values. Perhaps this is why Sub-Saharan Africans occupied the top three MLI spots? Had the researchers included Indian samples in their analysis, South Asia probably would have topped the table. But what do we make of the continued lack of close matches between the Amarna mummies' microsatellite profiles and those of modern Egyptians and Horners in the AFGT module (where they are again both included as reference populations)? Why do Tunisians from time to time appear as top matches on certain alleles on certain loci, while Egyptians and Horners do not? I think this may come down to the provenance and movements of the original haplogroup E1b1a carriers, a clade which today has slightly higher frequencies in Northwest Africa than in the Northeast. Perhaps they were originally of Libyan or Western Hamitic stock?
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Post by egypt1101 on Jan 14, 2013 15:50:12 GMT -5
What's nice about the AFGT module is that you can actually see what the top 100 population matches are in the database for each allele. There's no guessing involved as to how a Match Likelihood Index or other similarity metric may have come about since we can actually see the constituent parts. Also notice how in the DNA Tribes table in the opening thread post, no Indian or Amerindian populations appear to have been included for comparison against the Amarna microsatellite values. Perhaps this is why Sub-Saharan Africans occupied the top three MLI spots? Had the researchers included Indian samples in their analysis, South Asia probably would have topped the table.But what do we make of the continued lack of close matches between the Amarna mummies' microsatellite profiles and those of modern Egyptians and Horners in the AFGT module (where they are again both included as reference populations)? Why do Tunisians from time to time appear as top matches on certain alleles on certain loci, while Egyptians and Horners do not? I think this may come down to the provenance and movements of the original haplogroup E1b1a carriers, a clade which today has slightly higher frequencies in Northwest Africa than in the Northeast. Perhaps they were originally of Libyan or Western Hamitic stock? DNATribes lacks a lot to be desired and they give no information on how they arrived at their MLI scores. Their article is NOT peer-reviewed and does NOT agree with the vast amount of peer-reviewed studies on the subject. I was reviewing the JAMA paper and the only two haplotype values they publish are stated in the following sentence: "Markers DYS393 and Y-GATA-H4 showed identical allele constellations (repeat motif located in the microsatellite allele reiterated 13 and 11 times, respectively)" If we plug DYS393=13 and Y-GATA-H4=11 into WAHP, it gives a score of 88% R1b. This would be in agreement with and validate the Discovery Channel documentary results.
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Post by Noah on Jan 14, 2013 22:12:36 GMT -5
DNATribes lacks a lot to be desired and they give no information on how they arrived at their MLI scores. Their article is NOT peer-reviewed and does NOT agree with the vast amount of peer-reviewed studies on the subject. I was reviewing the JAMA paper and the only two haplotype values they publish are stated in the following sentence: "Markers DYS393 and Y-GATA-H4 showed identical allele constellations (repeat motif located in the microsatellite allele reiterated 13 and 11 times, respectively)" If we plug DYS393=13 and Y-GATA-H4=11 into WAHP, it gives a score of 88% R1b. This would be in agreement with and validate the Discovery Channel documentary results. We can't really make any definite predictions as to what paternal haplogroup Tutankhamun may have belonged to based on those two allele values. This is because the Jama researchers indicate that they actually tested fourteen other Y-DNA STRs, or sixteen markers in total: DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, DYS448. Experimentation with plugging in different values on Whit Athey's Haplogroup Predictor (WHAP) shows that so much as one change can often produce a drastic difference in the predicted haplogroup. This unfortunately means that we can only wait until the remaining fourteen other STR values are released to the public or leaked before making a prediction on Tut's paternal lineage.
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Post by Noah on Jan 14, 2013 22:13:26 GMT -5
According to DNA Tribes, after Tutankhamun, Thuya is the Amarna royal with the next highest Match Likelihood Index/MLI scores relative to the Southern African, African Great Lakes and Tropical West African Sub-Saharan regions. To see if this is perhaps another error (likely caused at least in part by an omission of South Asian and Amerindian reference populations), I ran Thuya's microsatellite marker values in the table above through EHSTRAFD's AFGT module. Like both Ramesses III's and Tut's results, Thuya's alleles showed a highest occurence amongst modern South Asian communities. There were also some secondary links with Sub-Saharan African, Amerindian, East Asian and Eastern European groups. If this is how the Ancient Egyptian royals with allegedly the most Sub-Saharan affinities are panning out, one can only imagine what the situation is with, say, Yuya, who DNA Tribes scored as having a much lower MLI vis-a-vis the Sub-Saharan reference populations. THUYA (KV46)Locus: D13S317*Allele: 9 (1st parent) 1. Huastecos Amerindian - San Luis Potosi, Mexico (37.64%) 2. Native American - Northern Ontario, Canada (36.4%) 3. Huasteco Amerindian - Huasteca, Mexico (36.4%) 4. Otomi Amerindian (Hna-hnu) - Tenango de Doria & San Bartolo Tutotepec, Mexico (35.5%) 5. Hna-hnu Amerindian - Hidalgo, Mexico (34.94%) Population affinity: AmerindianAllele: 12 (2nd parent) 1. Guinean - Guinea-Bissau (48%) 2. Arab - Zriba, Tunisia (47.8%) 3. Afro-Caribbean - United Kingdom (45.5%) 4. African American - Jamaica (45.49%) 5. Berber - Ghardaia, Algeria (44.3%) Population affinity: West African, Northwest AfricanLocus: D7S820Allele: 10 (1st parent) 1. Hutu - Nyarurema, Rwanda (44%) 2. Tutsi - Central Rwanda (43.103%) 3. Arab - Zriba, Tunisia (42.2%) 4. Argentine - Salta, Argentina (41.7%) 5. Mozambican - Maputo, Mozambique (39.1%) Population affinity: Sub-Saharan African, Northwest African, AmerindianAllele: 13 (2nd parent) 1. Baiti - Ladakh, India (14.7%) 2. Thakur - Uttar Pradesh, India (12.9%) 3. Honduras - Honduras (8.49%) 4. Berber - Ghardaia, Algeria (8%) 5. Han - South-Eastern China (7.1%) Population affinity: Indian, Amerindian, Berber, ChineseLocus: D2S1338Allele: 19 (1st parent) 1. Huasteco Amerindian - Huasteca, Mexico (39.2%) 2. Otomi Amerindian (Hna-hnu) - Tenango de Doria & San Bartolo Tutotepec (29%) 3. Mestizo - Valley of Mexico, Mexico (26.9%) 4. Malay - Malaysia (24.3%%) 5. Thai - Thailand (24.2%) Population affinity: Amerindian, Southeast AsianAllele: 26 (2nd parent) 1. Lithuanian - North-Eastern Poland (3.6%) 2. Japanese - Japan (3.3%) 3. Caucasian - United States (3%) 4. Romanian - Bucharest, Romania (2.9%) 5. Romanian - Bucharest, Romania (2.9%) Population affinity: Eastern European, JapaneseLocus: D21S11Allele: 26 (1st parent) 1. Thakur - Uttar Pradesh, India (4.7%) 2. Katkari - Maharashtra, India (2.9%) 3. Byelorussian - North-Eastern Poland (2.4%) 4. Arab - Zriba, Tunisia (2.2%) 5. Old Believers - North-Eastern Poland (31.6%) Population affinity: Indian, Eastern European, TunisianAllele: 35 (2nd parent) 1. Guinean - Guinea-Bissau (6.5%) 2. African American - Florida, United States (4.79%) 3. Thakur - Uttar Pradesh, India (4.7%) 4. Gabonese - Gabon (4.2%) 5. African American - Jamaica (4.12%) Population affinity: West African, IndianLocus: D16S539Allele: 11 (1st parent) 1. Inupiat - Northern Alaska, United States (61.47%) 2. Arab - Zriba, Tunisia (45.5%) 3. Madia-Gond - Maharashtra, India (44%) 4. Yemenit - Dubai Emirate, United Arab Emirates (41.1%) 5. Yadav - Bihar, India (39.5%) Population affinity: Inuit, Tunisian, Indian, YemeniAllele: 13 (2nd parent) 1. Bosnian - Bosnia and Herzegovina (24.4%) 2. Native American - Michigan, United States (24.14%) 3. Kurmi - Uttar Pradesh, India (23.5%) 4. Colombian - Bogota, Colombia (22.28%) 5. Caucasian - Transylvania, Romania (21.9%) Population affinity: Eastern European, Amerindian, South AsianLocus: D18S51**Allele: 8 (1st parent) 1. Katkari - Maharashtra, India (2.8%) 2. Pawara - Maharashtra, India (0.9%) 3. South Korean - South Korea (0.2%) 4. Caucasian - Transylvania, Romania (0.2%) 5. South Korean - South Korea (0.2%) Population affinity: Indian, Korean, CaucasianAllele: 19 (2nd parent) 1. Botswananian - Botswana (17.3%) 2. Baiti - Ladakh, India (13.8%) 3. Arab - Zriba, Tunisia (12.8%) 4. Fang - Bioko, Equatorial Guinea (12.75%) 5. Angolan - Cabinda, Angola (12.73%) Population affinity: Sub-Saharan African, Indian, Northwest AfricanLocus: CSF1POAllele: 7 (1st parent) 1. Guinean - Guinea-Bissau (11%) 2. Angolan - Cabinda, Angola (8.18%) 3. African American - Alabama, United States (8.06%) 4. Hutu - Nyarurema, Rwanda (8%) 5. Afro-Caribbean - United Kingdom (7.6%) Population affinity: Sub-Saharan African*Allele: 12 (2nd parent) 1. Lai - Mizoram, India (59.8%) 2. Han - Henan, China (58.9%) 3. Mahadeo-Koli - Maharashtra, India (55.7%) 4. Salishan - United States (50%) 5. Saskatchewan - United States (49.37%) Population affinity: South Asian, Chinese, AmerindianLocus: FGAAllele: 24 (1st parent) 1. Baiti - Ladakh, India (29.3%) 2. Pawara - Maharashtra, India (27.6%) 3. Bamileke - Cameroon (25%) 4. Tamil - Southern India (25%) 5. Ximeng - Inner Mongolia, China (24.9%) Population affinity: Indian, West African, ChineseAllele: 26 (2nd parent) 1. Mestizo - Guatemala (14.5%) 2. Otomi Amerindian (Hna-hnu) - Tenango de Doria & San Bartolo Tutotepec, Mexico (14%) 3. Hna-hnu Amerindian - Hidalgo, Mexico (13.86%) 4. Argentine - Salta, Argentina (12.5%) 5. Argentine - Neuquen, Argentina (12.16%) Population affinity: Amerindian*asterisk=alleles whose top 100 AFGT matches are exclusively Eurasian**double asterisk=rare allele
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