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The Mota article has been found to be in error.
quote: Error found in study of first ancient African genome Finding that much of Africa has Eurasian ancestry was mistaken.
Ewen Callaway 29 January 2016 Article toolsRights & Permissions
Kathryn and John Arthur This rocky area in Mota cave held bones that yielded the first ancient African genome. An error has forced researchers to go back on their claim that humans across the whole of Africa carry DNA inherited from Eurasian immigrants.
This week the authors issued a note explaining the mistake in their October 2015 Science paper on the genome of a 4,500-year-old man from Ethiopia1 — the first complete ancient human genome from Africa. The man was named after Mota Cave, where his remains were found.
Although the first humans left Africa some 100,000 years ago, a study published in 2013 found that some came back again around 3,000 years ago; this reverse migration has left its trace in African genomes.
In the Science paper, researchers confirmed this finding. The paper also suggested that populations across the continent still harbour significant ancestry from the Middle Eastern farmers who were behind the back-migration. Populations in East Africa, including Ethiopian highlanders who live near Mota Cave, carried the highest levels of Eurasian ancestry. But the team also found vestiges of the ‘backflow’ migration in West Africans and in a pygmy group in Central Africa, the Mbuti.
Andrea Manica, a population geneticist at the University of Cambridge, UK, who co-led the study, says the team made a mistake in its conclusion that the backflow reached western and central Africa. “The movement 3,000 years ago, or thereabouts, was limited to eastern Africa,” he says.
Incompatible software Manica says that the error occurred when his team compared genetic variants in the ancient Ethiopian man with those in the reference human genome. Incompatibility between the two software packages used caused some variants that the Ethiopian man shared with Europeans (whose DNA forms a large chunk of the human reference sequence) to be removed from the analysis. This made Mota man seem less closely related to modern European populations than he actually was — and in turn made contemporary African populations appear more closely related to Europeans. The researchers did have a script that they could have run to harmonize the two software packages, says Manica, but someone forgot to run it.
Pontus Skoglund, a population geneticist at Harvard Medical School in Boston, Massachusetts, says that he was surprised by the claim that as much as 6–7% of the ancestry of West and Central African groups came from the Eurasian migrants. But after obtaining the Mota man’s genome from Manica’s team, he and his colleague David Reich carried out their own comparison and found no evidence for that conclusion. They informed Manica’s team, who then discovered the processing error. “Almost all of us agree there was some back-to-Africa gene flow, and it was a pretty big migration into East Africa,” says Skoglund. “But it did not reach West and Central Africa, at least not in a detectable way.” The error also undermines the paper’s original conclusion that many Africans carry Neanderthal DNA (inherited from Eurasians whose ancestors had interbred with the group).
Skoglund praised the paper — “the genome itself is just fantastic,” he says — and the researchers’ willingness to share their data and issue a speedy note about the error: they posted it online on 25 January. When asked to confirm whether and when it would publish the researchers' update, a representative for Science said the journal couldn't yet comment.
Manica is not yet sure if Science will change the title of the paper, ‘Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent’. But if the team had caught the error earlier, he says, “I’m sure we would have phrased things differently”.
If you read the paper above we learn two things that made it necessary to dispute this paper.
Firstly, this paper made it clear that Mota man's evidence of Eurasian genes was deliberately blocked. As a result, it indicated that Ethiopians were carry Eurasian genes long before their is evidence of of Eurasians migrating into Africa.
Any researcher worth his salt, could flip the script and show that the so-called Eurasian genes found in Mota man prove the African origin of many so-called Middle Eastern caucasian haplogroups.
Secondly, the researchers of MOta man reported that he carried Neanderthal DNA. This finding could not be allowed to stand. Because it confirmed the finding of Prufer 2013 of a relationship between Altaic Neanderthals and Africans. The idea that Mota man was related to the Neanderthals had to be reversed, because this finding disputed the myth that only Eurasians carried Neanderthal genes, and that Eurasians were a unique AMH because Africans did not carry Neanderthal genes.
An exception to this norm are the Khoisan who share a phylogenic relationship with Altai Neanderthals (Prufer, et al, 2013). Many researchers claim that Africans have no relationship to the Neanderthals.But Prufer et al (2013) share more alleles with Altaic Neanderthal than Denisova.
In the Supplemental section of Prufer et al (2013) there is considerable discussion of the relationship between Neanderthal and Khoisan. In relation to the Altaic Neanderthal the non-Africans have a lower divergence rate than Africans between 10-20%. Prufer et al (2013) note little statistical difference between non-African and African divergence.
Researchers have observered a relationship between the Neanderthals, the Khoisan and Yoruba. Prufer et al (2013) detected a relationship between the Neanderthal and Mandekan. It is interesting to note that Yoruba traditions place them in Mande-speaking areas (Prufer et al,2013).
There is interesting information in Figure S7.1. In Figure S7.1 the maximum likelihood tree of bonobo, Denisova and Neanderthal, the closest present-day hmans are Africans, not Europeans. Reading the Tree Chart Graph, the neighbor joining tree of archaic and present day human individuals has the Khoisan following the Denisova.
As you can see from the case of Mota man, analysis of aDNA from Africans can upset the status quo. It will destroy the protocols of Structure and Admixture programs that maintain Africans and Eurasians only came in contact after 1492 due to the Atlantic slave trade.
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posted
These points were major reasons why the Mota paper had to be found in error. But the most important reason for the disavowal of the Mota article was the finding that as much as 6–7% of the ancestry of West and Central African groups came from the Eurasian migrants.
This finding had to be eliminated because there is no evidence that Eurasians made their way to West and Central Africa. Since Eurasians were not in West and Central Africa, the so-called Eurasian admixture among these groups reflected the fact that the Eurasian genome, is really West and Central African not Eurasian.
The discovery of Eurasian "admixture" among West Africans is not a recent discovery. Pickrell et al (2014) found that the Mande people carry 2% Eurasian admixture. This supports the claim of the authors of the Mota article. .
. If it has been known since 2014 that West Africans were carrying Eurasian admixture the findings of, the authors of the Mota article that as much as 6–7% of the ancestry of West and Central African groups was "Eurasian" was not an error.
But like R1-V88, the "Eurasian" admixture, found among the West Africans in East, Central, West and South Africa is in reality African genomes passed onto the Eurasians when the Kushites migrated into Eurasia after the Great Flood. Other "Eurasian" genomes of African origin were deposited in Eurasia first by the Khoisan and later the Anu (Pygmies) that ruled Eurasia up to the Great Flood.
Reference:
Joseph K. Pickrell, Nick Patterson, Po-Ru Loh, Mark Lipson, Bonnie Berger, Mark Stoneking, Brigitte Pakendorf, and David Reich.(2014). Ancient west Eurasian ancestry in southern and eastern Africa. PNAS 2014 111 (7) 2632-2637.
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Science. 2016 Feb 19;351(6275). pii: aaf3945. doi: 10.1126/science.aaf3945.
Erratum for the Report "Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa"
(previously titled "Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent")
by M. Gallego Llorente, E. R. Jones, A. Eriksson, V. Siska, K. W. Arthur, J. W. Arthur, M. C. Curtis, J. T. Stock, M. Coltorti, P. Pieruccini, S. Stretton, F. Brock, T. Higham, Y. Park, M. Hofreiter, D. G. Bradley, J. Bhak, R. Pinhasi, A. Manica.
[No authors listed] Abstract In the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa,” the results were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neandertals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. These changes are reflected in the corrected Fig. 2B, fig. S6, and table S5. Tables S6 and S7 have been removed from the corrected Supplementary Material, because there is no detectable Western Eurasian component in Yoruba and Mbuti. The conclusion of a migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: The Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota. Hence, the title and abstract of the published paper did not accurately represent the geographical extent of the admixture, and both have been corrected accordingly. The authors acknowledge Pontus Skoglund and David Reich for detecting these problems. Erratum for Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. [Science. 2015]
posted
^The claim that the amount of "Eurasian" ancestry can be correlated to so-called Neanderthal-DNA is outrageous rubbish. And that case has been proven already.
quote:Originally posted by the lioness,: Mota man had no Neanderthal DNA so your comment doesn't make sense
If I recall correctly, they rectified the paper one year later correct? Based on what...again? lol
What doesn't make sense is the claim that no Neanderthal-DNA was found, yet all over Africa there are supposed back migrations of "Eurasian ancestry". Mr PHd. lol
That stuff was one of the most funniest errors in the history of "science"-fiction.
[ 11. June 2017, 01:42 AM: Message edited by: the lioness, ]
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by the lioness,: No insults please
quote:This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes.
—Fernando L. et al.
The Divergence of Neandertal and Modern Human Y Chromosomes - april2016
quote:Genotyping of a DNA sample that was submitted to a commercial genetic-testing facility demonstrated that the Y chromosome of this African American individual carried the ancestral state of all known Y chromosome SNPs. To further characterize this lineage, which we dubbed A00 (see Figure S1, available online, for proposed nomenclature), we sequenced multiple regions (totaling ∼240 kb) of the X-degenerate portion of this chromosome, as well as a subset of these regions (∼180 kb) on a chromosome belonging to the previously known basal lineage A1b (which we rename here as A0).
—Michael F. Hammer Fernando L. Mendez et al.
An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by Ish Gebor: If I recall correctly, they rectified the paper one year later correct? Based on what...again?
No, it was a few months later. The paper was published Oct 8 2015 and the error was acknowledged on Jan 25 2016, with the official erratum published in February.
The results did not really make sense in the first place, and this is not entirely hindsight talking. We were so used to surprising aDNA results that at first people mostly accepted them, but doubts rapidly set in. Maju, gihanga.rwanda, and I discussed this: how could it be that Dinka, Yoruba, San, Mbuti, and other distinct and widely separated groups with entirely different histories, different uniparental markers, and so forth not only had this recent West Eurasian admixture, but more importantly all had approximately the same amount? That would be a heck of a coincidence - what fits instead is approximately zero, inflated by some constant amount. We were scratching our heads trying to come up with an explanation involving archaic African ancestry, or African gene flow into China or something, but we never thought of simple software error. But actual geneticists were not so trusting of the results of other geneticists.
The original authors simply screwed up - they forgot to run a program that was needed to format the data properly and as a result a whole lot of Mota's SNPs were missing from the analysis. Reich and Skoglund asked for the raw data and tried to replicate the results and could not. The original authors then looked for the discrepancy and discovered their mistake. Very embarassing as it was such a high profile paper, but scientists are human too.
Clyde's explanation needless to say makes no sense and cannot even get the simplest facts right.
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posted
All and all, a desperate attempt to revive Seligman's Hamitic Hypothesis. Those so-called "Eurasian genes" are in reality African genotypes that spread out to cover the Eurasian continent. Not the other way round--i.e. the Eurocentric hypothesis.
Recall in another context, Breasted's Dynastic race hypothesis.
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quote:Originally posted by lamin: All and all, a desperate attempt to revive Seligman's Hamitic Hypothesis. Those so-called "Eurasian genes" are in reality African genotypes that spread out to cover the Eurasian continent. Not the other way round--i.e. the Eurocentric hypothesis.
Recall in another context, Breasted's Dynastic race hypothesis.
So would it be correct to say that there is no such thing as a haplgroup that originated in Europe, Asia or the Middle East? That there are no mutations unique to these areas?
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posted
There is such a thing as a haplogroup that originated in situ in different areas. The contentious issue is that when there is a haplogroup and its derivations that appears both in Europe and Africa, the Eurocentric tendency has been to ascribe its source to Europe.
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quote:Originally posted by lamin: There is such a thing as a haplogroup that originated in situ in different areas. The contentious issue is that when there is a haplogroup and its derivations that appears both in Europe and Africa, the Eurocentric tendency has been to ascribe its source to Europe.
What is the afrocentric tendency?
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posted
So it is possible for a haplogroup that appears in both Africa and Europe/Asia to originate outside of African and that is not necessarily endorsement of the Hamitic hypothesis?
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No major haplogroups originated outside Africa!!!! yDNA Q can be found even in Western Africa and Italy. Significance? Q is a supposed Native American marker. yDNA P is found in pygmies. Significance.
Point? - OOA is very recent and the Hamitic hypothesis is dead!
There is no such thing as "Eurasian" markers or genes.
"Eurasian" is used in lieu of Caucasians is used to steal African history and genes. To make Europeans feel important. Ancient Eurasian are closely genetically matched to Hunter gatherers of Africa and NOT Neolithic Africans such as YRI. That is why Natufians carry no Neanderthal Ancestry and very little La Brana and other ancient Eurasian ancestry.
This is not rocket science.
quote:Originally posted by the lioness,: So it is possible for a haplogroup that appears in both Africa and Europe/Asia to originate outside of African and that is not necessarily endorsement of the Hamitic hypothesis?
-------------------- 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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quote:Originally posted by xyyman: No major haplogroups originated outside Africa!!!! yDNA Q can be found even in Western Africa and Italy. Significance?
quote:Originally posted by the lioness,: So it is possible for a haplogroup that appears in both Africa and Europe/Asia to originate outside of African and that is not necessarily endorsement of the Hamitic hypothesis?
So if any haplgroup is found in Africa not matter how low the frequency or how low the diversity it therefore originated in Africa
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quote:Originally posted by xyyman: No major haplogroups originated outside Africa!!!! yDNA Q can be found even in Western Africa and Italy. Significance? Q is a supposed Native American marker. yDNA P is found in pygmies. Significance.
Point? - OOA is very recent and the Hamitic hypothesis is dead!
There is no such thing as "Eurasian" markers or genes.
"Eurasian" is used in lieu of Caucasians is used to steal African history and genes. To make Europeans feel important. Ancient Eurasian are closely genetically matched to Hunter gatherers of Africa and NOT Neolithic Africans such as YRI. That is why Natufians carry no Neanderthal Ancestry and very little La Brana and other ancient Eurasian ancestry.
This is not rocket science.
quote:Originally posted by the lioness,: So it is possible for a haplogroup that appears in both Africa and Europe/Asia to originate outside of African and that is not necessarily endorsement of the Hamitic hypothesis?
What are the papers that discuss hg Q in West Africa?
.
-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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quote:So it is possible for a haplogroup that appears in both Africa and Europe/Asia to originate outside of African and that is not necessarily endorsement of the Hamitic hypothesis?
.
It all depends on whether the evidence is both theoretically and empirically strongly supportable.
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quote:So it is possible for a haplogroup that appears in both Africa and Europe/Asia to originate outside of African and that is not necessarily endorsement of the Hamitic hypothesis?
.
It all depends on whether the evidence is both theoretically and empirically strongly supportable.
So does diversity and frequency of basal haplogroup R theoretically and empirically suggest a Eurasian or African origin?
Haplogroup J and M same question
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quote:So it is possible for a haplogroup that appears in both Africa and Europe/Asia to originate outside of African and that is not necessarily endorsement of the Hamitic hypothesis?
.
It all depends on whether the evidence is both theoretically and empirically strongly supportable.
So does diversity and frequency of basal haplogroup R theoretically and empirically suggest a Eurasian or African origin?
Haplogroup J and M same question
African origin!!!!!!!!! Now go dry your white supremacy tears.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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