Design From September 2007 to October 2009, royal mummies underwent detailed anthropological, radiological, and genetic studies as part of the King Tutankhamun Family Project. Mummies distinct from Tutankhamun's immediate lineage served as the genetic and morphological reference. To authenticate DNA results, analytical steps were repeated and independently replicated in a second ancient DNA laboratory staffed by a separate group of personnel. Eleven royal mummies dating from circa 1410-1324 BC and suspected of being kindred of Tutankhamun and 5 royal mummies dating to an earlier period, circa 1550-1479 BC, were examined.
These results were repeatedly obtained with DNA extracted from 2 to 4 different biopsies per mummy; moreover, they differed from the Y profiles of the male laboratory staff and were independently reproduced twice in a second laboratory physically isolated from the first, data-generating laboratory.
Pusch and Zink admit that their data, as to be expected for such difficult samples, was not always 100% clear. So they tested every microsatellite several times in samples from different locations on each mummy, and used a "majority rule" to decide on the result. "If we do the experiment 30 times on one mummy, we might get 18 the same," says Pusch. Then they used a computer programme to work out the most probable family tree for the resulting genotypes.
Zink says that he would be happy to discuss the results with other researchers but that he would be reluctant to share raw data, because the need to use the majority rule means "there could be a lot of arguing".
What about mtDNA? In fact, the researchers say that they have isolated mtDNA, but chose not to include it in the JAMA paper as they are still working on it. "We face problems getting clear results," says Zink. MtDNA sequences would give researchers their first insight into the genetic origins of the pharaohs - a potentially explosive issue - so "we want to be 100% sure", says Zink. He and Pusch are planning a paper on this, along with an analysis of the male mummies' Y chromosomes - later this year. The JAMA paper was "just the opening ceremony", says Pusch.
Overall, Pusch says he is disappointed by the criticism that the paper has received. "I don't understand people's harshness," he says. "These people have never worked on royal mummies. Give us a little bit more time, to show people that more is to come."
But Lorenzen is not swayed. "There has been so much coverage of this, but no mention of the criticisms," she says. "It is very frustrating."
So, is this one of the most exciting developments in Egyptology, and will 2011 bring our first insight into the genetic origins of the pharaohs? Or is this a case of researchers under huge pressure for results seeing what they want to see? Pusch and Zink seem to me to be talented and tenacious researchers working in very difficult circumstances. But they need to provide the methodological details and raw data that will convince other experts of the validity of their work.
--Jo Marchant , Jan 2011
______________________
Jo Marchant is an award-winning science journalist based in London. She has a PhD in genetics and medical microbiology from St Bartholomew's Hospital Medical College in London, and an MSc in Science Communication from Imperial College London. She has worked as an editor at New Scientist and at Nature and her articles have appeared in publications including The Guardian, Wired, and The Observer Review.
She’s the author of Decoding the Heavens, which was shortlisted for the 2009 Royal Society Prize for Science Books, and The Shadow King. Her latest book is Cure: A Journey Into the Science of Mind Over Body.
related Marchant article in science journal Nature, April 2011:
they tested every microsatellite several times in samples from different locations on each mummy, and used a "majority rule" to decide on the result. "If we do the experiment 30 times on one mummy, we might get 18 the same," says Pusch.
^^ I don't see another source for this alleged statement by Pusch other than Jo Marchant. He is one of the lead researchers on the Zink team.
Also this:
quote: 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”.
-- Egyptological, Magazine Reviews, 7th December 2011
I don't see other reference to the Zink team having used “most likely” and “majority rule” methodology.
Oshun is wondering if the Zink et al JAMA report says
quote: results were repeatedly obtained with DNA extracted from 2 to 4 different biopsies per mummy; moreover, they differed from the Y profiles of the male laboratory staff and were independently reproduced twice in a second laboratory physically isolated from the first, data-generating laboratory.
^^ It seems conclusive, the implication of clear results
But the other remarks, not in the journal article but supposedly made by it's authors don't seem conclusive " If we do the experiment 30 times on one mummy, we might get 18 the same"
So if you look at the separate source data sets and " results were repeatedly obtained" does this mean they got the same results each time?
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Bitch
This is not a complete posting of the study with hi-lites as I demanded but just another rehashing of Marchant and though Zink&Pusch are criticized where is Marchant critiqued?
Where is the source where Zink/Pusch themselves publish the words Marchant claims?
Marchant is a journalist Z&P are geneticists All that roorag Marchant bio is an appeal to authority fallacy.
She has the education but where are any studies Marchant (co)authored?
Where are scholarly peer reviewed rebuttals of Hawass (2010)? This Link &Pusch study has 218 citations by other scholarly peer reviewed studies and reports.
Quite simply, it is not questionable to other serious researchers in the field of genetics and bioanthropology else produce their published (not blogged) critiques.
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Precision from
Identifications of ancient Egyptian royal mummies from the 18th Dynasty reconsidered M.E. Habicht, A.S. Bouwman andF.J. Rühli* Version of Record online: 25 JAN 2016 DOI: 10.1002/ajpa.22909
Some of these mummies—some vitally important ancestors of the Thutmoside royal house ruling in the 18th Dynasty—have been recently investigated by means of molecular genetics (Hawass et al., 2010).
That investigation triggered many theories and a major controversy in the field of Egyptology
The aim of this study is to review all available evidence for the identification of some of the most famous ancient Egyptian royal mummies. This overview of all methods used may help to identify more conclusive evidence for identification.
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
More from the above source
Claims that it is not possible to extract authentic DNA from Egyptian mummies (Marota et al., 2002; Gilbert et al., 2005; Lorenzen and Willerslev, 2010) can be challenged by the fact that recent studies were able to identify ancient animal DNA in Egyptian crocodile and cat mummies (Hekkala et al., 2011; Kurushima et al., 2012; Marchant, 2014). New technology, such as Next Generation Sequencing will make it easier to identify contamination and separate it from authentic DNA. From all methods applied to identify royal mummies, molecular genetics are the most reliable together with accurate information from the historic inscriptions provided by archaeological research
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Molecular genetics
Woodward made the first attempt at genetic analyses of some of these mummies, but the results remained unpublished; however, some information was only shown in a documentary movie (Woodward et al., 2001; Habicht, 2014b, pp 52–53, 88; Marchant, 2014).
He discovered inbreeding at the beginning and at the end of the 18th Dynasty and proposed that the mummy CG 61074 really is Amenhotep III. After the millennium, molecular genetics opened a new door into the past, but the feasibility of acquiring authentic ancient DNA from Egyptian mummies is still debated. Another project to obtain genetic profile of the Pharaohs by Sakuji Yoshimura was turned down in 2000 (Marchant, 2014).
Zink and Nerlich postulated that DNA analysis was feasible based on the lower temperature in the tombs, the beneficial fact that mummies are dry and that natron increases the pH-value (Zink and Nerlich, 2003). The success rate of amplifying DNA by PCR from ancient samples is generally 50–60% (Zink et al., 2001).
Other studies, based on the decay rate of DNA in papyrus rejected the idea that authentic DNA from ancient Egypt could survive at all (Marota et al., 2002). Factors such as humidity, chemical agents, temperature, and modern contamination are a challenge for molecular genetic studies (Gilbert et al., 2005).
A study on the extent of modern contamination was presented by Malmström, investigating animal remains for human DNA: all 29 samples contained human DNA, but in 25 cases authentic animal DNA was found also (Malmström et al., 2005).
To eliminate contamination, procedures were developed to assure the collection of authentic ancient DNA (Yang and Watt, 2005; Bouwman et al., 2006; Anderung et al., 2008).
To ensure authentic and credible data they suggest:
Extraction of clean samples in new excavations, the traditional cleaning of bones must be avoided no washing, no chemicals, and separate storage from modern samples; and investigators should handle them only with gloves and wear forensic suits.
For old material, which is possibly contaminated, a decontamination strategy should be used first.
Search for criteria of authenticity (short DNA strands of less than 300 base pairs and authentic aDNA should contain modified bases).
UV irradiation and removal of the surface material, extraction from the bone cortex or dentine.
For the Tutankhamun Family project, such safety protocols were applied (Richards et al., 1995; Gad, 2010; Gabolde, 2013a). Several facts speak clearly in favor of authentic aDNA:
All female genetic profiles were negative for Y-Chromosome markers.
All male mummies showed homozygous (i.e., hemizygous) Y-chromosomal profiles.
The profiles and haplotypes of all mummies showed individual differences and therefore could not have originated from the same source of putative contaminant DNA.
The combination of nuclear data (Y- and autosomal chromosome–related markers) complemented each other.
Different biopsies and extractions on each mummy resulted in reproducible genotypes.
This is not a complete posting of the study with hi-lites as I demanded
You think I respond to your demands? You are a low class savage. I made this thread for Oshun and put it in ES forum so that Swenet or beyoku might comment
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quote:Originally posted by the lioness,: So if you look at the separate source data sets and " results were repeatedly obtained" does this mean they got the same results each time?
Both the news articles and the Hawass et al paper say that the results they ultimately settled on were replicated. Both statements acknowledge that they got DNA they could not reproduce. The results they couldn't reproduce were discarded.
No different from the results obtained by the following paper. They couldn't reproduce most of the results obtained by Adcock et al. When this happens you don't throw the baby out with the bathwater. You just hone in on the data that you can replicate (in this case, WLH4's mtDNA S2).
quote:PCR Amplification for Mitochondrial Sequences Using the Original Material Used by Adcock et al. (3). We present here results of research using the remaining original DNA extracts (WLH3 and KS8) from the work by Adcock et al. (3). We commenced by amplifying sections of the first and second hypervariable sections of the human mitochondrial control region by PCR in an attempt to replicate the original results. For WLH3, all 38 clones had transitions relative to the rCRS at nucleotide positions (nps) 16,224 and 16,311. Ten clones carried transitions at nps 146 and 200 (SI Appendix, Table S7). For KS8, all 23 clones had transitions relative to the rCRS at nps 16,223 and 16,278, 5 of these clones carried an additional transversion at np 16,259, and an additional 8 clones amplified carried transitions at nps 146 and 152. These results show the presence of a DNA template that is most likely of European origin (haplogroup K) and that matches the sequence from Gregory J. Adcock (Australian National University, Canberra, Australia) in the products amplified from WLH3 (SI Appendix, Table S7). The motifs T16224C and T16311C are diagnostic for haplogroup K (www.Phylotree.org; build 16). These results are not consistent with those returned by Adcock et al. (3) for WLH3 and KS8 from the same extracts. We deliberately chose to use different primers and PCR conditions that those used by Adcock et al. (3) to avoid the likelihood of PCR artifacts previously identified. Rather, they are clearly indicative of copurified contaminants. Because all PCR blanks did not show any amplified product and because the results were repeated in separate PCR assays, we suggest that the DNA was present in the original extracts.
posted
@ youngster. Did you read that paper? I believe it looks like they are saying Adcock "deliberately" falsify the results . It was more than a contamination issue .
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posted
Didn't read it yet, gramps. I only gave it a superficial glance, so far. Any specific excerpts that gave you that idea or was it an impression you got?
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. For WLH3, however, we found a total of five European mtDNA contaminants,” presumably” derived from peopling handling the remains.
. As a further control against contamination within the laboratory, it may also prove beneficial to “sequence the genomes of all of those who handled the remains”
In relation to the four landmark claims made by Adcock et al. (3), we were unable to verify that the original study recovered any authentic Aboriginal Australian mitochondrial sequences from the four Willandra Lakes samples that they studied (claim 1). The contamination observed for WLH3 and the absence of human DNA for KS8 suggest that the validity of the originally reported sequences should be reappraised in light of the technological advances available to this study.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
Reading the Adcock paper it looks like he was trying to lay claim that AMH did NOT originate from Africa. Now keep in mind this was written when aDNA was in it’s infancy. Back in 2001. NGS was not available then. PCR was the norm.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
Good observations. Some people were really pushing the "OOA doesn't explain things" narrative which is ascribed to Adcock by these authors. I'd have to re-read Adcock et al to see how much they were on that bandwagon, but I do remember the whole Lake Mungo's age controversy and rope tugging. It is kind of convenient that a team with those beliefs get the results they're expecting to the degree that they did and that others can't seem to replicate as you said with NGS. Although, if there was bias at play, it might not have been deliberate bias. Also, the bulk of Adcock's results might still be replicated in the future as the authors of this paper note.
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