posted
ElMaestro was correct - The Abusir data is manipulated
During my "ban" here on ES I was able to hone in my skills and confirm that the Abusir dataset was manipulated and the CODIS STR was removed.......deliberately
I can confirm that CODIS STR which shows geographic affinity like with the King Tuts Amarnas was REMOVED!!! From the Abusir..at least for JK2888 @ THO1 Chromosome 11 and TPOX @ Chromosome 2.
I can now map out the entire genome of many samples and confirm whether the author is ling or not and expose some of the tricks they are too.
I am not sure how ElMaestro knew it was removed unless he did the analysis like I just did but he was correct. (He is not sharing info?) They are not there. I haven't pulled up all the CODIS STR's but from what I pulled out so far...the CODIS STR is NOT there in the Abusir unlike the Amarna's. To those who want to do a deep dive. Here is some help at ESR but in Summary
Anyways. A major break through!!!!!!
I have it...sort of. Well it looks like the CODIS STRs were indeed "removed' from the Abusir before they were made "freely" available on-line. I have NOT completed the entire dataset but the fact is some if not all the CODIS STR is not there. I did not need LobSTR software. The BAmAnalysis kit cited above did the trick. Anyone can do it. This is how
Here is the process:
1. Run the BAMAnaylsis Software as described above(Windows based). And obtain the VCF files for the Abusirs. 2. Use MS Excel to open the VCF files. You can open one Chromosome VCF file at a time. In this example I used Chr 2 3. The region of interest and CODIS repeats can be obtained manually or visually see table below. Eg TPOX CODIS lies in region 1493425 - 1493456 on Chromosome 2. 4. As you can see that region is NOT there....In other words it was either "removed' deliberately or not recoverable via aDNA degradation. 5. If we do this analysis for ALL CODIS STR and they are not present for ALL Abusir then we can safely assume it was removed for nefarious reasons. 6. Some of the Abusir aDNA was removed or deleted. My guess it is the "African" portion
So what ElMaestro hinted at was correct. The CODIS STR DNA material was removed. Yes, they learnt from their mistake with the Amarnas.
It took me almost 2 months working on this.
Sage I know you are meticulous and patient and this is what is needed.
But we have to find another way.. I am thinking TreeMix or some other software. TreeMix should be able to identify the "parental" population between the Abusir and Africans.
I will do a couple more Abusirs to confirm the CODIS data was removed deliberately If it was removed we can assume the result...they skewed the results by removing the CODIS STR data. Anyways I am a little embarrassed. I had the answer in front of me a few weeks ago and missed it. Here is the result...
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posted
To those who can follow. The CODIS STRs are located at specific positions on the human genome eg THO1 is on Chromosome #11 between positions 2192318-2192345. See the highlighted sections(red) in that spreadsheets. Those locations are ....gone! ...gone!...gone!!!. SMH, typical shyster Europeans! Crooked to the core!! Now why would they remove the CODIS STRs before making the genome available to the public? Tic! Toc!
What did I tell you all. It is impossible for the Amarnas to be sub-saharan Africans and the Abusir living 50miles away not be SSA also!
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Without promising. You gimme CODIS STRs w/t values. I'll try comparing against frequency data. I can only be that much of a colleague.
Everybody knows how far crabs in a basket get. Yet everybody still clawing individually or pulling others down. Even though they know a chain of crabs could ramp them all out the basket.
posted
Not sure "I" follow you or "you" follow me.
There is no CODIS STR for the ABusir #Jk2888. They were removed. Therefore there are "no repeats" detected therefore "no frequency". If the CODIS STR was available then we can manually count the repeats and punch it into the popaffl link. It is that simple. The repeats(n) are in the 2nd table above.
BAManalysis Kit can spit out the genome/SNP positions for any data file eg Abusir. Beauty?s ...it is Windows based. I could have solved this 2 weeks ago but because I hit a road block with the Computer I was using I decided to retrace my steps with Windows and Bam Analysis kit. STRait Razor aleardy told me that the CODIS STRS were removed. Now BamAnlaysis kit running on Excel also confirmed it. I assume STRScan and HIPSTR will give same result. These are up and running on my Ubuntu system .
quote:Originally posted by Tukuler: Without promising. You gimme CODIS STRs w/t values. I'll try comparing against frequency data. I can only be that much of a colleague.
Everybody knows how far crabs in a basket get. Yet everybody still clawing individually or pulling others down. Even though they know a chain of crabs could ramp them all out the basket.
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The process: 1. download the Bam files for the Abusir. 2. Using appropriate Software in Windows or Ubuntu(preferred) index the file. Samtools, BamAnaylsis Kit, Picaud Tools etc to get the *.VCF file 3. Pull up the VCF file in Excel and go to the Chromosome of interest and location. The locations for the CODIS STR can be found on-line and is in that 2nd Table. 4. The CODIS STR are NOT there! It was deleted by the researchers.
We now need to run ADMIXTURE to our repertoire and TreeMix. Just started getting my head around TreeMIx. Why TreeMix and other tools? "DIRECTION" of migration can be determined through these applications!!!
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posted
@ Sage and others. Here is another interesting breakthrough. Now we can pull Skoglund Ancient African dataset and play with it. Frequency of STRs??!!! We should be able to tell Which African population Luxmanda , Malawi_Hora8100BP or even Taforalt is closest to.
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posted
OP, is it your argument that the Abusir el-Meleq mummies would appear more sub-Saharan if the CODIS STRs were included? Do you think STRs have more say on biological affinity than the other genetic data they used?
posted
@ Sage. Let me explain. I now have the process(outlined above)tools to pull CODIS STR data from BAM files whether it is Abusir or any other genome.
In processing the ABusir JK2888 it was observe that the CODIS STRS are NOT there. They are gone ...they were never uploaded within the BAM files. ELMaestro susggested that when I first clued in on how these STRs can be extracted. He told me "go for it". When I did ....see above and on ESR..... JK2888 definitely do NOT have COODiS STR unlike the Amarnas.
Of course the follow-up question is
1. Was it deliberately removed before uploading. 2. Or for this mummy, JK2888, the sample was too degraded. But why at ALL the STR sites there is degradation and/or missing data?. This leads me to believing it was deliberately removed.
Dont' take my word for it...do the analysis yourself. It is outlined above and on ESR.
Now we have the process we can do this for all 93 Abusir mummies. So again the follow-up would be ...Are ALL the CODIS STRs removed from ALL the Abusir mummies? You or Anyone can run a few and give us the results. Now...If ALL CODIS STRs are NOT present on ALL Abusir...what does that imply?
Keeping in mind it looks like BAM(autosomal) files are available for the 93 mummies but only 3 were deeply analyzed. Go on-line you will see it.
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posted
No insult intended young man but because you ask that question tells me you don't fully understand how this thing works.
Yes, CODIS STR is still used by Police Agencies around the world. Not Autosomal SNPs ie affinity through frequency. Why? Linkage disequilibrium (LD)! STR not SNP will assign population affinity.
That is why the STR was removed from the Abusir. We seem to forget some modern Europeans are 80% African based upon UNSUPERVISED SNP analysis. 80%!!!! In other words if the computers are NOT tricked into removing African DNA Europeans are 80% African. One of the few methods to "separate" Africans from Europeans is through CODIS STRs . That is why the Amarna came back African and not European. If SNPS are used then there is TreeMix or some sort of "filtering" software to determine ancestral population. I have no doubt if SNPs were used instead of CODIS STRs the Amarnas will also come out as "Eurasian" just as the Abusir.
anyone can do it..
quote:Originally posted by Tyrannohotep: OP, is it your argument that the Abusir el-Meleq mummies would appear more sub-Saharan if the CODIS STRs were included? Do you think STRs have more say on biological affinity than the other genetic data they used?
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posted
I have no doubt if SNPs were used instead of CODIS STRs the Amarnas will also come out as "Eurasian" just as the Abusir.
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posted
To those who can follow this stuff. My 2 months of exile was worth it. Aside from the fact there is numerous software out there for John Public to perform his own analysis I found out that there will be an "African" reference genome coming out soon. That will be a game changer.
Reference-GRCh38 is European based and as Daniel Shriner pointed out the "reference" used can have a dramatic impact on your results as he showed with the Natfuians having at least 29% African ancestry when initial reports said zero SSA ancestry.
My guess is when the African reference genome is used via independent analysis...game over ....with all the lies Reich, Paabo and the crew keeping spewing.
GRCh38 is the Genome Reference Consortium Human genome build 38. As of May 7, 2014 it is the standard reference assembly sequence used by NCBI. Unlike other sequences, GRCh38 is not from one individual's genome sequence, but is built from reference sequences of different individuals.Aug 14, 2014
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posted
This is result from one Abusir using another software. Notice, yes, there is Sub-Saharan African ancestry
And here is another
And another
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posted
If you all haven't connected the dots as yet. ...I will oblige.
Don't be caught up between Mediterranean and Europeans , Paleo African, Neo African and North West African etc. That is part of the label game. As I said on the entire human genome(UNSUPERVISED), Europeans and Africans share >80% of their DNA. So what they are labeling "European" may be "African". Understand the game. Genes mimic geography - Sforza et al - and always had. That said. Where are the differences between European and African? IBD blocks or CODIS STR. That is why STR are so important in criminal(FBI) work. SNP cannot be used. STR tells the "race" per the FBI not the SNP. Keep in mind Luxmanda was 60% European(Sardinian) using SNP but she will be 100% sub-Saharan when her CODIS STR are analyzed. Just as some of the hunter gatherers of Africa. The Hadza are 30% Europeans but 100% sub-saharan African via CODIS STR.
Confusing? Again. LD, Linkage disequilibrium
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On one hand, it could be they're Africans and that discrepancies between the two are a byproduct of supervised data. However if we were to be more conservative and look over that, this information would still be very strange. An Egyptian mummy with more European ancestry than the Near East? And not just by a slight margin-- 80 percent European? Western Europe harbors more of a percentage of the mummy ancestry than all of Asia? Maybe they're African, maybe this research downplays too much their admission of finding foreign names (including some from Europe) in the tombs.
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quote:Originally posted by Tyrannohotep: OP, is it your argument that the Abusir el-Meleq mummies would appear more sub-Saharan if the CODIS STRs were included? Do you think STRs have more say on biological affinity than the other genetic data they used?
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posted
Just finished Abusir JK2134. And yes, CODIS STR @ TPOX is gone! Gone! Gone! lol!
Crooked Europeans!
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Three samples were selected for down-stream analysis: JK2134, JK2888 and JK2911.
Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details). For further genes such as SLC45A2, LCT and EDAR we were unable to find derived alleles for both JK2888 and JK2911. For JK2134, there was no sufficient coverage after quality filtering at all the specific sites, which is why the analysis revealed no further clues.
Finally, we analysed several functionally relevant SNPs in sample JK2911, which had low contamination and relatively high coverage. This individual had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia41, consistent with the ancestral affinity shown above. Other relevant SNPs carry the ancestral allele, including HERC2 and LCT, which suggest dark-coloured eyes and lactose intolerance.
Three samples were selected for down-stream analysis: JK2134, JK2888 and JK2911.
Our analysis fur
quote:Originally posted by beyoku: ^ Why did you post this when we are talking about STRs?
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posted
I assume he, Lioness , is making the reader aware of the mummies.
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posted
The discussion is already about the mummies. We know about the mummies...we are talking about missing STR data and have seen that SNP data posted before.
@XYYMAN - Still think these folks would not be sitting on mummies and not publishing data? What would you do if you got the raw data PRIOR to the STR scrub?
Posts: 2463 | From: New Jersey USA | Registered: Dec 2007
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Genes (Basel). 2018 Mar; 9(3): 135. Published online 2018 Mar 1. doi: [10.3390/genes9030135] PMCID: PMC5867856 PMID: 29494531
Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens
Odile Loreille,1,* Shashikala Ratnayake,2 Adam L. Bazinet,2 Timothy B. Stockwell,2 Daniel D. Sommer,2 Nadin Rohland,3 Swapan Mallick,3 Philip L.F. Johnson,4 Pontus Skoglund,5 Anthony J. Onorato,1 Nicholas H. Bergman,2 David Reich,3,6 and Jodi A. Irwin1
Nuclear DNA testing in forensics is currently based on autosomal short tandem repeat (STR) loci, and, thus, STRs would be the logical target marker for individual identification purposes. Unfortunately, due to their relatively large size, successful targeted amplification of STRs is rare with highly degraded samples. In addition, STRs are difficult to recover from shotgun data in these types of specimens. Not only is the full length of the repeat region rarely intact, but small recovered fragments of repetitive sequence are also unlikely to include enough genome-specific flanking regions to allow for proper mapping. Single nucleotide polymorphisms (SNPs), however, can be used for individual identification [97,98,99], and these could be typed using hybridization capture and HTS. SNPs are already being targeted by the ancient DNA community to determine Y haplogroups [74,88,100], assess kinship [89], and test models of human population history and evolution [41,61,62,64,65,66,100,101,102]. For these types of questions, thousands of nuclear SNPs are often targeted, and low coverage of even a subset is generally sufficient to answer the question at hand.
The haplotype (deposited in GenBank under accession number MG736653) belongs to mitochondrial DNA lineage U5b2b5, but the specific sequence has not been previously reported in the 35,942 mtGenomes stored in the NCBI GenBank database (as of October 2017).
When only the mtDNA sequences recovered from ancient Egyptian human remains are considered, the Djehutynakht sequence most closely resembles a U5a lineage from sample JK2903, a 2000-year-old skeleton from Abusir el-Meleq
Of the three mummies, a couple that xyyman mentioned individually, that were anaylzed for Y-DNA one individual, one third were African, North African
Posts: 42930 | From: , | Registered: Jan 2010
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posted
So let me see if I have this right... STRs would be better to use than SNPs to determine population affinity but since they are claiming they cannot recover the STRs they are using SNP? Not sure I'm understanding.
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quote:Originally posted by Oshun: So let me see if I have this right... STRs would be better to use than SNPs to determine population affinity but since they are claiming they cannot recover the STRs they are using SNP? Not sure I'm understanding.
that used to be true but methods have improved
" For these types of questions, thousands of nuclear SNPs are often targeted, and low coverage of even a subset is generally sufficient to answer the question at hand."
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quote:Originally posted by Oshun: So let me see if I have this right... STRs would be better to use than SNPs to determine population affinity but since they are claiming they cannot recover the STRs they are using SNP? Not sure I'm understanding.
We won't know until more people check more mummies. I'm hella busy. I might try one.
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Why cry over spilt milk (the Abusir CODIS STRs which don't exist)? Why not examine Abusir SNPs relevant to geographic origin?
quote:Originally posted by xyyman: What did I tell you all. It is impossible for the Amarnas to be sub-saharan Africans and the Abusir living 50miles away not be SSA also!
First of all, the Abusir mummies sampled come from the late periods of Egyptian history with heavy foreign influence while the Amarna royal family is an indigenous family from Upper Egypt.
Second, you again fall for the Eurocentric trap of a monolithic 'Sub-Saharan' category. Yet the same autosomal data shows that Sub-Saharans are diverse. So how can Africans be divided into solely into Sub-Saharan and North African?
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posted
Good point. So we need to move on to Geneteic software that can determine "direction" of migration. Like TreemiX. Even software that determine "age" of genetic material ie ALDER? Compare age of SNPs in the NEar East vs Africa...keeping mind Africa and the Levant "share" SNPs.
But you missing the point. Why would ALL the STRs be removed???!!! Why? Not 1 or 2 or 3. But ALL!!!!! Gone! Gone! Gone!
Anyways..
I am looking into ALDER now..
ALDER: Admixture-induced Linkage Disequilibrium for Evolutionary Relationships
Current release: ALDER v1.03 (March 5, 2013) The ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture described in:
Loh P-R, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, and Berger B. Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium. Genetics, 2013
quote:Originally posted by Tukuler: Why cry over spilt milk (the Abusir CODIS STRs which don't exist)? Why not examine Abusir SNPs relevant to geographic origin?
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posted
You do realize EM speaks from both sides of his mouth. I went back to some of his post and it hit me that he does a lot of double talk.
And don't speak for him. Let him speak for himself. Keep in mind he is a "showman".
quote:Originally posted by Fourty2Tribes: No response from ElMaestro. Maybe this isn't how he thought it was manipulated.
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posted
Again you are distracted, you don't get it ....there is no(2.21%) Near East DNA in the Abusir.....depending on the software used. 3000bc, African extended to the Near EAst. And they know that. That is why ONLY the Bedoiuns are closest to the Abusir ...
quote:Originally posted by : the Abusir mummies sampled come from the late periods of Egyptian history with heavy foreign influence
Second, you again fall for the Eurocentric trap of a monolithic 'Sub-Saharan' category. Yet the same autosomal data shows that Sub-Saharans are diverse. So how can Africans be divided into solely into Sub-Saharan and North African?
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What did I tell you all. It is impossible for the Amarnas to be sub-saharan Africans and the Abusir living 50miles away not be SSA also!
First of all, the Abusir mummies sampled come from the late periods of Egyptian history with heavy foreign influence while the Amarna royal family is an indigenous family from Upper Egypt.
Second, you again fall for the Eurocentric trap of a monolithic 'Sub-Saharan' category. Yet the same autosomal data shows that Sub-Saharans are diverse. So how can Africans be divided into solely into Sub-Saharan and North African?
.
.
above, earliest oldest mummy samples Abusir El-Meleq Keep in mind it's mtDNA groups .
.
Three samples were selected for down-stream analysis: JK2134, JK2888 and JK2911. None were earliest mummies
African YDNA 36) JK2888 date BC 97-2 YDNA E1b1b1a1a2 mtDNA U6a2 _____________________
Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens
When only the mtDNA sequences recovered from ancient Egyptian human remains are considered, the Djehutynakht sequence most closely resembles a U5a lineage from sample JK2903, a 2000-year-old skeleton from Abusir el-Meleq
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quote:Originally posted by xyyman: Good point. So we need to move on to Geneteic software that can determine "direction" of migration. Like TreemiX.
Not possible an Treemix doesn't do that
quote:Originally posted by xyyman: Even software that determine "age" of genetic material ie ALDER? Compare age of SNPs in the NEar East vs Africa...keeping mind Africa and the Levant "share" SNPs.
But you missing the point. Why would ALL the STRs be removed???!!! Why? Not 1 or 2 or 3. But ALL!!!!! Gone! Gone! Gone!
Nuclear DNA testing in forensics is currently based on autosomal short tandem repeat (STR) loci, and, thus, STRs would be the logical target marker for individual identification purposes. Unfortunately, due to their relatively large size, successful targeted amplification of STRs is rare with highly degraded samples. In addition, STRs are difficult to recover from shotgun data in these types of specimens. Not only is the full length of the repeat region rarely intact, but small recovered fragments of repetitive sequence are also unlikely to include enough genome-specific flanking regions to allow for proper mapping. Single nucleotide polymorphisms (SNPs), however, can be used for individual identification [97,98,99], and these could be typed using hybridization capture and HTS. SNPs are already being targeted by the ancient DNA community to determine Y haplogroups [74,88,100], assess kinship [89], and test models of human population history and evolution [41,61,62,64,65,66,100,101,102]. For these types of questions, thousands of nuclear SNPs are often targeted, and low coverage of even a subset is generally sufficient to answer the question at hand. __________________________________
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Anyways..... Quote: "Inclusion of the 1000 Genomes Project, NorthAfrican and Khoe-San (Khoisan) populations in principal component analysis (Extended Data Figs 3–5, and Supplementary Figs 1 and 2) suggested possible HG ancestry among southern Niger-Congo groups—highlighted by clustering towards the Khoe-San, in addition to confirming a cline towards Eurasian populations. **‘Unsupervised’** (that is, without including known information on individual ancestry) ADMIXTURE9 (https://www.genetics.ucla.edu/software/admixture/) analysis including the 1000 Genomes Project and Human Origins data sets (Fig. 1), also supported evidence for substantial Eurasian and HG ancestry in SSA (Fig. 1 and Extended Data Fig. 6)."
quote: "An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations (Supplementary Note 5). Given limited archaeological and linguistic evidence for the presence of Khoe-San populations in West Africa, this extant HG admixture might represent ancient populations, consistent with the presence of mass HG graves from the early Holocene period comprising skeletons with distinct morphological features15, and with evidence of HG rock art dating to this period in the western Sahara16,17. In East Africa, our analyses suggested that Mbuti rainforest HG populations most closely represented ancient HG mixing populations (Supplementary Note 5), with admixture dating to,3,000 years ago, suggesting that HG ancestry here is likely to be older than previously reported18. T"
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posted
All I really have to say is that I did not assume or make any public accusation about why the codis Regions were absent in the abusir three. All I reported was that they weren’t there. Other than that Xyyman did a fine job I didn’t think he’d be capable or have the drive to see it through..
We still have no proof anything was removed “deliberately”. Do if that’s what folks chose to beleive don’t quote me as saying so.
@xyyman Also objectivity isn’t double talking... it’s called suppressing ones biases for credibility. When you learn more about genetics and run shit on your own you will see more clearly. Everything won’t go the way you want it to.
Posts: 1781 | From: New York | Registered: Jul 2016
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quote:Originally posted by Elmaestro: All I really have to say is that I did not assume or make any public accusation about why the codis Regions were absent in the abusir three. All I reported was that they weren’t there. Other than that Xyyman did a fine job I didn’t think he’d be capable or have the drive to see it through..
We still have no proof anything was removed “deliberately”. Do if that’s what folks chose to beleive don’t quote me as saying so.
@xyyman Also objectivity isn’t double talking... it’s called suppressing ones biases for credibility. When you learn more about genetics and run shit on your own you will see more clearly. Everything won’t go the way you want it to.
why not just email Wolfgang Haak, Stephan Schiffels or Johannes Krause?
the contact addresses are right on the article
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posted
Because the process of getting the aDNA from these samples required gathering very short reads amplifying them and mapping them to a Href. Aligning a relatively low amount of super short base pair sequences to STR regions is ridiculous. I already know this.
It makes no sense for me to pursue this further given the fact that I’m also aware that they targeted HOIII regions for sequencing.
The best answer I would get is “we left out codis regions because the reads were terribly unreliable” the most likely answer is “we were not able to receive data from these regions due to limitations of our method and the conditions of our samples” .
So even if they did purposefully omit data it’ll take me nowhere. Xyyman on the other hand is pretty good at presenting information. So I guess the more he or someone like him learns and posts the more people will understand what I’m trying to say. And in that case you should ask him to email themPosts: 1781 | From: New York | Registered: Jul 2016
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posted
ALDER looking promising to determine if SNPs/Gene blocks are older in Africa vs the Levant.
Trying to run it now. Remember LD is important due to recombination. Apparently on some Chr LD is much higher.
Anyways when installing and running ALDER the libraries MUST be installed.
''Summary of what you are going to install:
BLAS Lapack Lapacke FFTW, and OpenMP ''
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Want ancient forensic STRs? Gotta use the tools designed for the job. Hulk strength or Ant-man finesse? Whole genome mining or 13 CODIS STR pinpointing? What kit was born to run with degraded ancient STR DNA?
Why did Keita and them use popaffiliator. Any penny ante amateur can do that. No. They should a done better. They should a wrote for a grant and used The AmpFLSTR MiniFiler PCR Amplification Kit by Thermo Fisher Scientific
The MiniFiler kit is the world's first commercially available reagent kit for generating genetic profiles from aged, compromised, or damaged DNA samples.
The Identifiler kit and the AmpFℓSTR Minifiler kit (Applied Biosystems) were used for amplification of 8 polymorphic microsatellites of the nuclear genome (D13S317, D7S820, D2S1338, D21S11, D16S539, D18S51, CSF1PO, FGA).
Image for example only. Not actual Hawass (2010) data.
AmpFℓSTR® MiniFiler™ PCR Amplification Kit Put to the Ultimate Test with Ancient Egyptian Mummy Identification Project (PDF) Applied Biosystems Technology and Scientific Experts Help Egypt's Supreme Council of Antiquities Initiate Groundbreaking Forensic Work, Forensic News, (October 2007)
Success Story: Genotyping of degraded and ancient DNA samples using AmpFℓSTR® MiniFiler™ PCR Amplification Kit (PDF) RNDr.Daniel Vanek, Ph.D., Director, Forensic DNA Service, Prague, Czech Republic
But by all means write Krause and Keita too. Write anybody with the money, tools, human resources, and access to the mummies.
quote:Originally posted by Elmaestro: Because the process of getting the aDNA from these samples required gathering very short reads amplifying them and mapping them to a Href. Aligning a relatively low amount of super short base pair sequences to STR regions is ridiculous. I already know this.
It makes no sense for me to pursue this further given the fact that I’m also aware that they targeted HOIII regions for sequencing.
So even if they did purposefully omit data it’ll take me nowhere. Xyyman on the other hand is pretty good at presenting information. So I guess the more he or someone like him learns and posts the more people will understand what I’m trying to say. And in that case you should ask him to email them
"To track down the suspect, investigators had created a fake profile on GEDmatch and uploaded DNA from a 1980 crime scene, where it matched a distant relative of the man eventually arrested."
John Law circumvented formal request for data. He just became an uploader via illegal identity theft.
posted
Great Job Xyyman . You have provided more evidence of how Geneticist are using population genetics to promote white supremacy while attempting to erase us from history. It is sad that Black geneticist refuse to tell the truth about our history--and instead promote the status quo
-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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posted
1. yes we have no other choice but to mine STRs from whole genome s or use some other tool. I believe Keita did the same as all of us novices which is used popaffli . I am alarmed a respected person of his caliber did not do a deep dive instead just a superficial critique of Abusir paper. Makes me second guess his motive.
2. " that Black geneticist" ? They all work through the Reich Lab or Max Planck! As is said on ESR. Lazaridis and David Reich are playing "good Cop bad Cop". Lazarade is the good cop. He throws us a bone ever so often. Eg "North African was the ancestral population to Natufians and the North Africans has a deeper connection to Europeans than the Levant(Dzudzuana population) "
Quote: "Whole genome mining or 13 CODIS STR pinpointing? What kit was born to run with degraded ancient STR DNA?
They should a done better.(Keita)
The AmpFLSTR MiniFiler PCR Amplification Kit"
Quote: "It is sad that Black geneticist refuse to tell the truth about our history--and instead promote the status quo."
-------------------- 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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My Advice to those who are computer literate or adept is load up(download) these publicly available files. Learn to use the software tools and freely available data files that are on-line. I placed several links on ESR while I was exiled from on ES..
I have some of these tools up and running.
Here is what works - ALDER, TreeMix, Bam Analysis Kit, GTK Kit, GlacTool, STRScan, HipSTR, STRait Razor, SAMTools etc SAMTools is critical!!! Or Picaud.
I am still struggling with LobSTR version 4.06. LobSTR ver 3.0.0 is embedded in the BAMAnalysis kit along with BEDtools. See ESR on how to retrieve the *.VCF files on the ancient DNA. Still struggling also with BEDTools and BEDops ..stand alone.
Also there are online applications(some you need to pay a small fee) that will process your data aDNA for you.
I have to thank one poster on ESR who hit me up with some valuable links which helped me overcome some road-Blocks. I believe he/she wants to remain anonymous
1. They obtain the data from the lab equipment 2. Using freely available software 3. Interpret the results 4. Spin their interpretation. 5. YOU CAN DO THE SAME!!!!!...if you get your hands on the dataset...some are free.
-------------------- 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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-------------------- 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
This is interesting. Unsupervised analysis shows SUBSTANTIAL "Eurasian" ancestry in Sub-Saharan Africa. This "Eurasian" ancestry goes from West TO East then South. The ancient African ancestry ie Ghost population is related to Khoi-San who seem to have been much further North. So many studies have confirmed substantial Eurasian ancestry in sub-saharan Africa but they play games that the Abusirs have no sub-saharan DNA.
Quote: "We used principal component analysis to explore relationships among AGVP populations (Extended Data Figs 2–5, Supplementary Figs 1 and 2). PC1 appeared to represent a cline extending **from West** and East African populations towards Ethiopian populations, possibly suggesting **Eurasian gene flow,** while PC2 separated West African and South/East African populations (Extended Data Fig. 2). Inclusion of the 1000 Genomes Project, North African and Khoe-San (Khoisan) populations in principal component analysis (Extended Data Figs 3–5, and Supplementary Figs 1 and 2) suggested possible HG ancestry among southern Niger-Congo groups—highlighted by clustering towards the Khoe-San, in addition to confirming a cline towards Eurasian populations. ****‘Unsupervised’**** (that is, without including known information on individual ancestry) ADMIXTURE9 (https://www.genetics.ucla.edu/software/admixture/) analysis including the 1000 Genomes Project and Human Origins data sets (Fig. 1), also supported evidence for substantial Eurasian and HG ancestry in SSA (Fig. 1 and Extended Data Fig. 6)."
-------------------- 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
Dr Winters may find this interesting. Is the Lakeside burials in the Western Sahara related to Khoi_San people and NOT other West African types?
Ref #15 15. Sereno, P. C. et al. Lakeside cemeteries in the Sahara: 5000 years of holocene population and environmental change. PLoS ONE 3, e2995 (2008).
----------------- Quote: "An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations (Supplementary Note 5). Given limited archaeological and linguistic evidence for the presence Of Khoe-San populations in West Africa, this extant HG admixture might represent ancient populations, consistent with the presence of mass HG graves from the early Holocene period comprising skeletons with distinct morphological features***15***, and with evidence of HG rock art dating to this period in the western Sahara16,17. In East Africa, our analyses suggested that Mbuti rainforest tHG populations most closely represented ancient HG mixing populations (Supplementary Note 5), with admixture dating to,3,000 years ago, suggesting that HG ancestry here is likely to be older than previously reported18. The primary source of HG admixture in Zulu and Sotho populations was from Khoe-San populations (Fig. 2 and Supplementary Note 5), consistent with linguistic assimilation of click consonants among these populations."
--------------------- If I am reading this correctly are they stating that
1. Ancient Africa, primarily SSA, were sub-divided into diverse Hunter Gatherer camps 2. East Africans are more related to MButi HG while West Africans are NOT related to Mbuti ...or Biaka but Kho-San HG 3. The Holocene Skeletal material of West Africa are morphologically related to Khoi-San and not modern day Igbo-YRI type. 5. This observation is made AFTER "Eurasian" ancestry is masked or removed from Sub-Saharan Africans. 6. This substantial "Eurasian" ancestry is what differentiates Most Sub-Saharan African when we used "Unspuervised" ie not manipulated DNA Testing. Holy Shyte! Lol!
-------------------- 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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