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Post by djoser-xyyman on Mar 4, 2019 10:45:00 GMT -5
Finally. My trek is over for ADMIXTURE. So one Abusir jk2134 is non-African(possible contamination reading the preamble?) and the other two are pure Africans(red). More African than even Afro-barbados and Ethiopians. This is impossible. All 3 has to be African not just two!!! Creating the Admixture charts is outlined above(coding). It is simpler than I thought. 1. Download bam files of the Abusir 2. Index with samtools 3. Align to hg19(abusir) 4. Create your global compare datasets. Also align with hg19. 5. Merge Abusirs with the "YOUR" globals datasets. 6. Create your abusir-global dataset and create plink bed files 7. run the plink bed files through admixture 8. plot your admixture files with genesis or some such tool. This is my K2 I will clean up and plot K3-K10 with clean labels. Important point to note is using different source global datasets and overlapping SNPs give different results.
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Post by djoser-xyyman on Mar 4, 2019 10:51:20 GMT -5
Key scripts and code are as follows: gatk --java-options "-Xmx8G" HaplotypeCaller -R reference.fasta -I input.bam -O output.vcf gatk HaplotypeCaller -R hg19.fa -I JK2134.bam -O JK2134-bam.vcf samtools index ~/workingfolder/JK2888.bam samtools index ~/workingfolder/JK2911.bam gatk HaplotypeCaller -R hg19.fa -I JK2911.bam -O JK2911-bam.vcf gatk HaplotypeCaller -R hg19.fa -I JK2888.bam -O JK2888-bam.vcf bgzip JK2134-bam.vcf bgzip JK2888-bam.vcf bgzip JK2911-bam.vcf tabix -p vcf JK2911-bam.vcf.gz tabix -p vcf JK2134-bam.vcf.gz tabix -p vcf JK2888-bam.vcf.gz MERGING Abusir WITH my Dataset vcf-merge abusir-bam.vcf.gz main-sample-admixture-test-set.vcf.gz | bgzip -c > abusir-global.vcf.gz detected that all genotypes are missing for a SNP locus. Please apply quality-control filters to remove such loci. plink --bfile abusir-global --geno 0.999 --make-bed --out abusir-global-fix admixture abusir-global-fix.bed 2 plink --vcf abusir-global.vcf.gz --const-fid 0 --make-bed --out abusir-global CONVERT VCF to bed in PLINK jk2888-jk-2134-jk-2911-out.vcf plink --vcf jk2888-jk-2134-jk-2911-out.vcf --make-bed --out abusirpop Read more: egyptsearchreloaded.proboards.com/thread/2766/abusir-strs-finally-africans?page=10#ixzz5hDcs3cxD
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Post by djoser-xyyman on Mar 4, 2019 12:29:55 GMT -5
Apparently they had a contamination issue.... Quotes: Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
Verena J. SchuenemannGeneration of nuclear data quote: "In order to analyse the nuclear DNA we selected 40 samples with high mtDNA coverage and low mtDNA contamination. Using in solution enrichment for 1.2 million genome-wide SNPs26, we obtained between 3,632 and 508,360 target SNPs per sample Overall, the nuclear DNA showed poor preservation compared to the mtDNA as depicted by a high mitochondrial/nuclear DNA ratio of on average around 18,000. In many samples, nuclear DNA damage was relatively low, indicating modern contamination. Three out of 40 samples fulfilling these criteria had acceptable nuclear contamination rates Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs. As shown below, to rule out any impact of potential contamination on our results, we analysed the three samples separately or **replicated results using only the least contaminated** sample.We extracted DNA from 151 mummified human remains and prepared double-stranded Illumina libraries with dual barcodes Nuclear DNA capture The non-UDG and UDG treated libraries were enriched by hybridization to probes targeting approximately 1.24 million genomic SNPs as described previously25. The target SNPs consist of panels 1 and 2 as described in Mathieson et al.41 and Fu et al.26 (see Supplementary Note 2 for details). Three samples were selected for down-stream analysis: JK2134, JK2888 and JK2911. In all three of these samples, contamination estimates were acceptable Nuclear data analysis: genotyping We called genotypes from the UDG treated data for the three individuals by sampling a random read per SNP in the SNP-capture panel, using a custom tool ‘pileupCaller’, available at Data availabilityThe mapped BAM files for the 90 mitochondrial samples and three nuclear samples are deposited in the European Nucleotide Archive (http://www.ebi.ac.uk/ena) with the study ID ERP017224. www.ebi.ac.uk/ena/data/search?query=ERP017224" "
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Post by djoser-xyyman on Mar 4, 2019 19:27:46 GMT -5
Ok. Here is a clean copy from Genesis @k2.
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Post by zarahan on Mar 4, 2019 20:43:30 GMT -5
Apparently they had a contamination issue.... Quotes: Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods Verena J. SchuenemannGeneration of nuclear data quote: "In order to analyse the nuclear DNA we selected 40 samples with high mtDNA coverage and low mtDNA contamination. Using in solution enrichment for 1.2 million genome-wide SNPs26, we obtained between 3,632 and 508,360 target SNPs per sample Overall, the nuclear DNA showed poor preservation compared to the mtDNA as depicted by a high mitochondrial/nuclear DNA ratio of on average around 18,000. In many samples, nuclear DNA damage was relatively low, indicating modern contamination. Three out of 40 samples fulfilling these criteria had acceptable nuclear contamination rates Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs. As shown below, to rule out any impact of potential contamination on our results, we analysed the three samples separately or **replicated results using only the least contaminated** sample.We extracted DNA from 151 mummified human remains and prepared double-stranded Illumina libraries with dual barcodes Nuclear DNA capture The non-UDG and UDG treated libraries were enriched by hybridization to probes targeting approximately 1.24 million genomic SNPs as described previously25. The target SNPs consist of panels 1 and 2 as described in Mathieson et al.41 and Fu et al.26 (see Supplementary Note 2 for details). Three samples were selected for down-stream analysis: JK2134, JK2888 and JK2911. In all three of these samples, contamination estimates were acceptable Oh, so it was a "contamination" issue, huh? and then they claim: Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods ^^ LOL, what Schuemann et al are trying to insinuate is that "Sub-Saharan" ancestry in Kemet is recent, a sly DNA version of the long debunked claim of Czech anthropologist Eugene Strouhal in the 1970s, about the "recent negro element." LMAO.. . Sheeeeyit.. SO called "sub-Saharan" elements have been in Egypt from Day 1, as Keita showed with the Badari, others with limb proportions, etc etc- we can fill 10 screen pages full of evidence.. Hell aside from the Badari skulls, we even have dental evidence via the "Bushman canine" dental feature.. This is ON TOP OF mounds of other evidence, DNA< limb proportion, material artifactual, religio/cultural, cranial etc.. Distinctive "Bushman canine" dental feature, found most frequently in sub-Saharan Africa, also appears among Ancient Egyptians. Dental data confirmed by DNA analysis showing Haplogroup L0f, a southern African marker, also appearing in Egyptians. Quote: "It is important to note that “SSA” influence may not be due to a slave trade, an overdone explanation; the green Sahara is to be considered as Egypt is actually in the eastern Sahara. SSA affinities of modern Egyptians from Abusir El-Meleq might be attributed to ancient early settlers as there is a notable frequency of the “Bushmen canine”- deemed a SSA trait in Predynastic samples dating to 4,000 BC9 from Adaima, Upper Egypt. Haplogroup L0f, usually associated with southern Africans, is present in living Egyptians in Adaima and could represent the product of an ancient “ghost population” from the Green Sahara that contributed widely. " [Crubézy, E. Le peuplement de la vallée du Nil. Archéo-Nil 20, 25-42 (2010).] --FROM: Ancient Egyptian Genomes from northern Egypt: Further discussion Gourdine1, Keita, Gourdine and Anselin. 2017 'Bushman canine' feature primarily African, and oft falsely reported in other populations. Quote: The mesial lingual ridge is an almost invariant feature of the upper canines while tuberculum dentale is polymorphic. In some cases, a large tuberculum dentate coalesces with the mesial lingual ridge to form what Morris (1975) calls the Bushman canine. This fact is most evident when one antimere exhibits the ‘Bushmen canine’ while the other exhibits a large free-standing tuberculum projection. This trait is most common in African populations, especially the Bushmen, but it has been observed in populations from other geographic areas, in some cases falsely so (Irish and Morris, 1996). -- Scott and Turner. 2000. The Anthropology of Modern Human Teeth: Dental Morphology and Its Variation.. p31-33 Africans have the highest ancestral dental diversity. Distinctive traits by SOME Africans are part of an INDIGENOUS range not stereotypical"Previous research by the first author revealed that, relative to other modern peoples, sub-Saharan Africans exhibit the highest frequencies of ancestral (or plesiomorphic) dental traits... The fact that sub-Saharan Africans express these apparently plesiomorphic characters, along with additional information on their affinity to other modern populations, evident intra-population heterogeneity, and a world-wide dental cline emanating from the sub-continent, provides further evidence that is consistent with an African origin model." (Irish JD, Guatelli-Steinberg D.(2003) Ancient teeth and modern human origins: an expanded comparison of African Plio-Pleistocene and recent world dental samples. Hum Evol. 2003 Aug;45(2):113-44. ) African populations have a broad range of characteristics- the most diverse in the world. Distinctive dental traits in one place do not mean ALL Africans are "supposed" to have the same thing, at all times, in all places. Nor does the absence of a unique trait in one area make the people "non-African". Some Africans have the feature, others do not, but all categories are still Africans. With these caveats noted against stereotypical claims that "only" Africans with said feature are true" Africans, the Bushman Canine feature registers notable frequencies in Africa and appears in Egypt, which too, is in Africa. "Because over one-third of Blacks manifest this condition, while it is rare in Whites and Asians, the presence of this feature supports an attribution of a skull to this ancestral group. The Bushman canine also is useful for attributing a skull to Black. In this trait, an additional cusp appears on the lingual side of the crown of the maxillary canine, making this tooth similar in configuration to a lower first premolar (Figure 7.1 lb). Because its frequency in Blacks is three times higher than other ancestral groups, the presence of this trait in the dentition of forensic remains generally implies Black ancestry." --By Steven N. Byers. Introduction to Forensic Anthropology. p. 141 "This range of variation is compatible with those obtained by genetic, craniometric, and odontometric data. Subsaharan Africans show the largest intra-regional diversity among the groups compared.. Regardless of different population structures in each geographic region, the gradients of the diversity presented herein indicate that geographic distance from subsaharan Africa is a significant and primary determinant of nonmetric dental variation observed on the vast Eurasian, Australian, and New World regions .. the geographic distance from subsaharan Africa along likely colonization routes is one of the strongly supported predictors for not only genetic but also phenotypic diversity of modern human populations. The pattern of decrease in dental variation with distance from East Africa is more or less smooth and provides no suggestion for major discontinuities that could be interpreted as evidence for a second or multiple origin(s) of modern human populations. Therefore, the globally distributed populations can be explained by an expansion from subSaharan Africa." --Tsunehiko Hanihara*. 2008. Morphological variation of major human populations based on nonmetric dental traits. AJPA 136:169–182
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Post by zarahan on Mar 4, 2019 20:50:59 GMT -5
I am glad Keita, Gourdine and Anselin below jumped down on some of the dubious stuff they were pushing. Aside from already published data debunking aspects of their spiel, heavyweights like Keita et al once again demonstrate, that is just not "random people on the Internet" or "wild-eyed Afrocentrists" calling them out.. Keita el al also cite DNA data, putting a spike in the hopes of those who tout DNA as something new and shiny in support of the old "true negro" whitewash. Turns out that the DNA supports the dental, cranial, limb proportion, relgio/cultural etc etc, mutually supporting lines of evidence confirming the African foundation and character of ancient Kemet. The regulars already know it- but to recap the DNA for newbies and web searchers who happen on the page: “Results that are likely reliable are from studies that analyzed short tandem repeats (STRs) from Amarna royal mummies5 (1,300 BC), and of Ramesses III (1,200 BC)6; Ramesses III had the Y chromosome haplogroup E1b1a, an old African lineage7. Our analysis of STRs from Amarna and Ramesside royal mummies with popAffiliator18 based on the same published data5,6 indicates a 41.7% to 93.9% probability of SSA affinities (see Table 1); most of the individuals had a greater probability of affiliation with “SSA” which is not the only way to be “African”- a point worth repeating.” FROM: -Gourdine JP, Keita SOY, Gourdine JL, Anselin A, 2018. Ancient Egyptian Genomes from northern Egypt------------------------------------------------------------------------------------------------------------ Credible peer-review scientists (Gourdine, Keita, Anselin) critique Abusir-El Meleq ancient DNA study for several flaws: (a) limited (3 samples) and skewed sampling excluding southern Egypt and other Africans like Nubians, (b) skewed on normal, full presentation of data and alternative explanations (such as using only Late Period samples excluding 3,000 years of prior Egyptian history, and (c) stereotypical conceptions of ‘Africans’ as only peoples ‘south’ of the Sahara. Study implied that ancient Egyptians came from the Asia, and that "sub-Saharan" Africans are recent due to the Islamic slave trades:QUOTES: “Schuenemann et al.1 seemingly suggest, based largely on the results of an ancient DNA study of later period remains from northern Egypt, that the ‘ancient Egyptians’ (AE) as an entity came from Asia (the Near East, NE), and that modern Egyptians “received additional sub-Saharan African (SSA) admixtures in recent times” after the latest period of the pharaonic era due to the “trans-Saharan slave trade and Islamic expansion..” There are alternative interpretations of the results but which were not presented as is traditionally done, with the exception of the admission that results from southern Egyptians may have been different. The alternative interpretations involve three major considerations: 1) sampling and methodology, 2) historiography and 3) definitions as they relate to populations, origins and evolution.”Tiny sample sizes: “The whole genome sample size is too small (n=3) to accurately permit a discussion of all Egyptian population history from north to south.” Other DNA data show substantial African affinity: “Results that are likely reliable are from studies that analyzed short tandem repeats (STRs) from Amarna royal mummies5 (1,300 BC), and of Ramesses III (1,200 BC)6; Ramesses III had the Y chromosome haplogroup E1b1a, an old African lineage7. Our analysis of STRs from Amarna and Ramesside royal mummies with popAffiliator18 based on the same published data5,6 indicates a 41.7% to 93.9% probability of SSA affinities (see Table 1); most of the individuals had a greater probability of affiliation with “SSA” which is not the only way to be “African”- a point worth repeating.” Arbitrary definition of some DNA haplogroups as ‘Asian’ problematic: “Conceptually what genetic markers are considered to be “African” or “Asian” .. For example, the E1b1b1 (M35/78) lineage found in one Abusir el-Meleq sample is found not only in northern Africa, but is also well represented in eastern Africa7 and perhaps was taken to Europe across the Mediterranean before the Holocene (Trombetta, personal communication). E lineages are found in high frequency (>70%) among living Egyptians in Adaima9. The authors define all mitochondrial M1 haplogroups as “Asian” which is problematic. M1 has been postulated to have emerged in Africa10, and there is no convincing evidence supporting an M1 ancestor in Asia: many M1 daughter haplogroups (M1a) are clearly African in origin and history10. The M1a1, M1a2a, M1a1i, M1a1e variants found in the Abusir el-Meleq samples1 predate Islam and are abundant in SSA groups10, particularly in East Africa.” So called “sub-Saharan” patterns in place from the beginning in Egypt and are not merely the product of the ‘slave trade.’ “Furthermore, SSA groups indicated to have contributed to modern Egypt do not match the Muslim trade routes that have been well documented11 as SSA groups from the great lakes and southern African regions were largely absent in the internal trading routes that went north to Egypt. It is important to note that “SSA” influence may not be due to a slave trade, an overdone explanation; the green Sahara is to be considered as Egypt is actually in the eastern Sahara. SSA affinities of modern Egyptians from Abusir El-Meleq might be attributed to ancient early settlers as there is a notable frequency of the “Bushmen canine”- deemed a SSA trait in Predynastic samples dating to 4,000 BC9 from Adaima, Upper Egypt. Haplogroup L0f, usually associated with southern Africans, is present in living Egyptians in Adaima9 and could represent the product of an ancient “ghost population” from the Green Sahara that contributed widely. Distributions and admixtures in the African past may not match current “SSA” groups12.” Definition of ‘African’ stereotypical, even as strangely, authors exclude many actual African samples near Egypt from the data“Schuenemann et al.1 seem to implicitly suggest that only SSA equals Africa and that there are no interconnections between the various regions of Africa not rooted in the slave trade, a favorite trope. It has to be noted too that that in the Islamic armies that entered Egypt that there were a notable number of eastern Africans. It is not clear why there is an emphasis on ‘sub-Saharan’ when no Saharan or supra-Saharan population samples--empirical or modelled are considered; furthermore, there is no one way to be “sub-Saharan.” In this study northern tropical Africans, such as lower and upper Nubians and adjacent southern Egyptians and Saharans were not included as comparison groups, as noted by the authors themselves.” FROM: -Gourdine JP, Keita SOY, Gourdine JL, Anselin A, 2018. Ancient Egyptian Genomes from northern Egypt
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Post by zarahan on Mar 4, 2019 21:11:48 GMT -5
Djoser XYZsays: Finally. My trek is over. So one Abusir jk2134 is non-African(contamination reading the preamble?) and the other two are pure Africans(red). More African than even Afro-barbados and Ethiopians. This is impossible. All 3 has to be African not just two!!!
Good work. Now to throw in a quick education piece, can you summarize the implications? WHat are 3 conclusions for example that can be drawn?
1)
2)
3)
and so on... If someone were to ask you, why is your analysis any better than Schuemann and co? WHat points would you lay on them in a nutshell?
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Post by djoser-xyyman on Mar 5, 2019 14:14:06 GMT -5
Let me see how I can answer your question. First off we need to understand the basics. Like..what is the genome and what is an SNP? There is no “better” than analysis. SNPs occur throughout the human genome—about one in every 300 nucleotide base pairs. This translates to about 10 million SNPs within the 3-billion-nucleotide human genome. learn.genetics.utah.edu/content/precision/snips/ For the Abusir only about 200,000-500,000 SNPs were recovered. Thinking about the human genome that is about 3% for the Abusir of recoverable SNPs and about 0.01% of the entire human genome. So they are making conclusions based upon 3% of the humans SNPs and 0.01% of the human genome. But let us look at what they recovered. Absolutely no CODIS STRs were recovered. That is highly unusual …to have zero CODIS STR unrecoverable. Keeping in mind the STRs are located across the entire human genome. It is hard to believe these were all “misses” for STRs.. I think they were deliberately removed or manipulated. There is no “better” than analysis. We have to compare apples and apples. Think of it as a car lot with 10 millions cars. Schuemann and co chose a section of the car lot with 300,000cars to ‘start’ her analysis. But she went further and selected yet a smaller sub-portion….not clear on how small because she did not state. In addition She chose her specific populations. She limited West Africa to YRI. I included a lot more west Africans and plus new world Africans like Barbados. I also included Henn et al and some University of Barcelona datasets. The populations you chose can skew the results in your favor or do the opposite. STR or some linkage D is the only way to go. BUT I have to also let you know that You can eye ball the results and come to conclusions. Eg That grey color seen in East Africans and North Africans and ‘some” Levant populations like Bedouins and Palestinian and not in Syrians and Khazars tells you the Bedouins are East African in origin and so to are the indigenous North Africans. The light blue component is therefore also African because it is found in East Africans , North Africans and the same Levantines. Schuemann and co stated that the Bedouins are the closest modern population to the Abusir so we can conclude that he Abusir are AEst Africans…..take it from there. Without CODIS STRs my analysis confirms that the Abusir (at least 2) are surely Africans. JK2134 is not even Khazar or Sysrian which makes me think jk2134 is contaminated. But I am working on LD analysis to further make my point. Djoser XYZsays: Finally. My trek is over. So one Abusir jk2134 is non-African(contamination reading the preamble?) and the other two are pure Africans(red). More African than even Afro-barbados and Ethiopians. This is impossible. All 3 has to be African not just two!!!Good work. Now to throw in a quick education piece, can you summarize the implications? WHat are 3 conclusions for example that can be drawn? 1) 2) 3) and so on... If someone were to ask you, why is your analysis any better than Schuemann and co? WHat points would you lay on them in a nutshell? whoops-xyz post
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Post by Tukuler al~Takruri on Mar 5, 2019 15:16:42 GMT -5
Thumbs up! Canya save images in png instead of jpg? Canya make vertical or slanted instead of horizontal labels? How much that customization cost me Mensa? Can't wait for your Mt Hora Girl runs mentioned elsewhere.
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Post by djoser-xyyman on Mar 5, 2019 16:07:47 GMT -5
On PNG vs jpg. I will try. PNG takes up so much more HD space although clearer than jpg.
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Post by zarahan on Mar 8, 2019 23:03:16 GMT -5
Let me see how I can answer your question. First off we need to understand the basics. Like..what is the genome and what is an SNP? There is no “better” than analysis. SNPs occur throughout the human genome—about one in every 300 nucleotide base pairs. This translates to about 10 million SNPs within the 3-billion-nucleotide human genome. learn.genetics.utah.edu/content/precision/snips/ For the Abusir only about 200,000-500,000 SNPs were recovered. Thinking about the human genome that is about 3% for the Abusir of recoverable SNPs and about 0.01% of the entire human genome. So they are making conclusions based upon 3% of the humans SNPs and 0.01% of the human genome. But let us look at what they recovered. Absolutely no CODIS STRs were recovered. That is highly unusual …to have zero CODIS STR unrecoverable. Keeping in mind the STRs are located across the entire human genome. It is hard to believe these were all “misses” for STRs.. I think they were deliberately removed or manipulated. There is no “better” than analysis. We have to compare apples and apples. Think of it as a car lot with 10 millions cars. Schuemann and co chose a section of the car lot with 300,000cars to ‘start’ her analysis. But she went further and selected yet a smaller sub-portion….not clear on how small because she did not state. In addition She chose her specific populations. She limited West Africa to YRI. I included a lot more west Africans and plus new world Africans like Barbados. I also included Henn et al and some University of Barcelona datasets. The populations you chose can skew the results in your favor or do the opposite. STR or some linkage D is the only way to go. BUT I have to also let you know that You can eye ball the results and come to conclusions. Eg That grey color seen in East Africans and North Africans and ‘some” Levant populations like Bedouins and Palestinian and not in Syrians and Khazars tells you the Bedouins are East African in origin and so to are the indigenous North Africans. The light blue component is therefore also African because it is found in East Africans , North Africans and the same Levantines. Schuemann and co stated that the Bedouins are the closest modern population to the Abusir so we can conclude that he Abusir are AEst Africans…..take it from there. Without CODIS STRs my analysis confirms that the Abusir (at least 2) are surely Africans. JK2134 is not even Khazar or Sysrian which makes me think jk2134 is contaminated. It is hard to believe these were all “misses” for STRs.. I think they were deliberately removed or manipulated. Yes and such manipulation would not be the first time like Keita shows below. You have done good work so people know what is going on with these studies..
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Post by djoser-xyyman on Mar 9, 2019 14:04:13 GMT -5
@ K5. Abusir are far from being related to West Asian. They are old Africans I will explain. . I will provide more plots but this is a sample. JK2134 is an older African bloodline
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Post by djoser-xyyman on Mar 9, 2019 17:43:26 GMT -5
I have finished running up to K10 with a sample set of about 2600 humans across the globe. All Abusirs looks African when compared to global populations.
The Cluster chart is huge. I can only post sections at time to the forum page. If I can upload the entire file I will but as of now I can only do small sections. Bottom line, Abusir are Africans and as can be seen above are not closely related to Bedouins of the Levant. The paper results were skewed because the reference panel used. A completely different set of variants shows the Abusir are closely related to older Africans. This means the migration OOA and population turnover was very recent. Surprising thing JK2134 is difinitely diffrentiated from other two but has "older" DNA. Like Americans.
Notice old Makrani is primarily "green". I will break it down ....with screen shots.
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Post by zarahan on Mar 9, 2019 18:17:17 GMT -5
I think back on ES you said that "back migration" was simply the movement of African variants back into Africa. If so can you expand on this a bit more, such as what sets the border of a genetic variant?
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Post by djoser-xyyman on Mar 9, 2019 20:21:09 GMT -5
You asked a good question in a prior post.(oh there was never a movement of humans back into Africa until the Ottoman Turks. There was no movement of variants back into Africa either. That type of gabble-gook comes from ElMeastro)
Anyways. To your question. Why is my analysis "better" than Schuenemann? Neither is better. Two different approaches. Schuenemann's is designed for deception.
quote from Schuenemann..."The non-UDG and UDG treated libraries were enriched by hybridization to probes targeting approximately 1.24 million genomic SNPs as described previously25. The target SNPs consist of panels 1 and 2 as described in Mathieson et al.41 and Fu et al.26 (see Supplementary Note 2 for details)."
What does it mean and what did she do? Schuenemann targeted specific SNPs in the human genome (panels 1 and 2). They were NOT randomly chosen or across the entire human genome. Why? This not rocket science. WhatI did was took what they gave us(variants/SNP) and compare it with a different global dataset ie population group. I included other populations besides those from HGDP/ I got some from Henn, University of Barcelona and Doron Behar Jews dataset. They showed a totally different outline than Scheuermann's. She stacked the deck to skew the results AWAY from SSA. Abusir are undoubtedly African. ALL OF THEM. Including JK2134. In fact JK2134 carry OLDER VAriants/SNP than the other two that is why it appears so different to the other two. I was surprised to find so much American ancestry in jk2134 but absent in the other two. That pink(and yellow) ancestry is NOT found in Bedouins!!!! Surprisingly yellow and pink is not found in Bedouins but found in Makrani. In fact Makrani carries even the "European" green along with pink and yellow and SSA blue. Makrani carry majority European green. This is most likely the Neolithic package. That left Africa and entered Eurasia
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