Why Researchers found an error in, Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa , by M. GALLEGO LLORENTE

Researchers found an error in,  Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa 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 SCIENCE13 NOV 2015 : 820-822. This was an important article because it maintained that there was extensive Eurasian admixture in Africa. 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”. See: http://www.nature.com/news/error-found-in-study-of-first-ancient-african-genome-1.19258 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.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. As you can see from the case of Mota man, analysis of aDNA from Africans can upset the status quo. It destroys the protocols of Structure and Admixture programs that maintain Africans and Eurasians only came in contact after 1492 due to the Atlantic slave trade. References 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. K. Prufer et al (2014).The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014 Jan 2;505(7481):43-9. doi: 10.1038/nature12886. Epub 2013 Dec 18. ...