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Thread: Error found in study of first ancient African genome ,Eurasian ancestry was mistaken

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    Error found in study of first ancient African genome ,Eurasian ancestry was mistaken

    Error found in study of first ancient African genome
    Finding that much of Africa has Eurasian ancestry was mistaken.


    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”.

    Nature doi:10.1038/nature.2016.19258

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    maybe that so called eurasian dna, is more of a general dna scattered throughout the world, making it useless for ethnicity estimates

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    I wonder how many times this has happened before and it has not been noticed

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    Quote Originally Posted by rock hunter View Post

    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.
    Yea, vestiges of Eurasian back-flow migration among the Mbuti pygmy and West-Africans seemed to be a bit of a stretch - I wonder how small of a trace they were inferring? If the paper suggested the gene-flow to be significant and fairly recent (3000 BP), you'd expect to see this widespread Eurasian affinity above noise level.
    As a personal anecdote, my immediate family has an Mbuti pygmy affinity that ranges from 2-12% and none of us have any notable traces of Eurasian ancestry (<1%) on any modern calculator.


    This diagram gives a nice visual of inferred proportions of ancestral clusters from an 09' Tishkoff paper, "The Genetic Structure and History of Africans and African Americans". It shows no significant recent Eurasian ancestry (in blue) among the Mbuti and none either among SSA West-Africans, apart from small detection among ethnic groups (e.g. Baggara, Fulani) with clearer ties to AA speakers:


     



    I recall first hearing about the Mota Cave genome from an Eritrean on 23andMe a year ago; I had started an L3x thread after not finding anyone in my haplogroup. The Eritrean of Tigranya descent, from my sister clade L3x2a, mentioned the remains found in Mota Cave was of his\her same subclade -- I thought that would be pretty cool of him\her to have as bragging rights as the first Ancient African genome.
    Last edited by Angoliga; 08-03-2016 at 04:22 AM.
    .... .. I have spoken."

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  7. #5
    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.


    West Eurasian haplogroups such as J and R1b can be found in East Africa at low to moderate frequencies as a result of ancient Arabian migrations to the region. For example, J1 and J2 make up 21.6% in Cushitic speakers in Ethiopia and the combined frequency of J haplotypes increases to 26.6% in Ethiopian Semitic speakers. R1b is absent in Ethiopia but 40% of the Hausa people in neighbouring Sudan belong to R1b-V88. The study's initial conclusion that a large migration from Western Eurasia to East Africa is not affected but the geographic impact of this migration was overestimated. West Eurasian components are mostly concentrated in East Africa and only a few populations outside East Africa show detectable levels (Fig. 2).



    The West Eurasian backflow mostly affected East Africa and only a few sub-Saharan populations. Llorente et al. (2015) further estimated that the proportion of West Eurasian ancestry is up to 50% in Amhara and Tygray peoples in Ethiopia (Fig. S6). The Mota individual is less than 3% West Eurasian because his generation of ancient Ethiopians missed the encounter with J people from the Arabian Peninsula by 1,500 years. Mota lived approximately 4,500 years ago in Ethiopia and the initial movement of West Eurasians to East Africa is dated approximately 3,000 years ago.



    Ethiopians, in particular highland Ethiopians, seem to me likely an ancient stabilized hybrid population between a population from Arabia, and a local Sub-Saharan population. This population seems unlikely to have been related to the peoples of West-Central Africa, who are associated with the Bantus across eastern and southern Africa. The Bantu agricultural toolkit runs into ecological constraints in various regions, and it is in those regions that non-Bantu populations have persisted. Ethiopia, with its unique climate and topography, naturally remains non-Bantu (as well as the Horn of Africa as a whole). The possible connections between Khoisan and Ethiopia may be a function of the fact that these areas harbor genetic variants which have disappeared in the intervening regions because of the Bantu expansion. I have a hard time accepting that the Bantu expansion was particular eliminationist, but I am starting to suspect that outside of Ethiopia population densities were very, very, low.

    The antiquity of this ancient hybridization event to me is attested by the fact that Ethiopians lack any of the other Middle Eastern components besides the one modal in Saudi Arabia. There is a great deal of intra-population variance in the Saudi data set. Why? Part of this must be the slave trade, as well as pilgrims who remained in places like Mecca. But, I think part of the untold story here is that there may have been a larger genetic impact on Arabia after the rise of Islam from the Levant than vice versa! Probably the gene flow precedes Islam, as Arabia was hooked into worldwide trade and population movements, which Ethiopia was relatively insulated from. The Saudi data set has several people who are “pure” Southwest Asian, but also several who have a great deal of West Asian + South European. These seem likely to be people who have some background in the Fertile Crescent.

    http://blogs.discovermagazine.com/gn.../#.V66Fdfl97IU

    Erratum to Gallego Llorente et al. 2015:

    http://biology-web.nmsu.edu/~houde/I...%20ERRATUM.pdf


    Also, you've got it mixed up with the Y-DNA J in the Horn of Africa.
    I was mixing up A3 (dark blue) with J2 (light blue) in the small haplogroup chart that I referenced and the errors have been fixed. It does not change the overall narrative that the Ethiopians are a hybrid population between an ancient migrant population from Arabia and a sub-Saharan African population. Moreover, 4-5% of Ethiopians also belong to Y-DNA haplogroup T, which has been found in two 7,500–6,800 ybp individuals from Karsdorf, Sachsen-Anhalt, Germany. T1a constitutes 22.2% of all ancient samples between 7,500 and 6,800 ybp in Germany. Llorente et al. (2015) argued that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier.
    Last edited by ThirdTerm; 08-15-2016 at 05:34 AM.
    Давайте вместе снова сделаем мир великий!

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    R1b in East Africa is nearly non-existant.

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    Quote Originally Posted by ThirdTerm View Post
    West Eurasian haplogroups such as J and R1b can be found in East Africa at low to moderate frequencies as a result of ancient Arab migrations to the region. For example, J2 makes up 13% in Cushite speakers in Ethiopia and it increases to 45% in Ethiopian Jews. R1b is absent in Ethiopia but 40% of the Hausa people in neighbouring Sudan belong to R1b-V88.
    I wouldn't use the term "Arab" when describing the West Eurasian ancestry carrying back-migrations responsible for these Y-DNA Haplogroups. "Arabs" as they are now, or were during the last ~2,000 years, did not exist when most of these Haplogroups were brought into Africa. Unless you're referring to the ancient predecessors of modern "Arabs"; but even, the use of the term is just odd.

    Also, you've got it mixed up with the Y-DNA J in the Horn of Africa. Y-DNA J2 is practically non-existent in the Horn (we so far just have some really miniscule frequencies among various ethnic groups across Ethiopia. See here). J1 is seems to be the main J marker in the Horn and it has a general frequency of about 10-25% among most Cushitic & Ethiopian Semitic speaking groups (see here). Ethiopian Jews also don't really show much J2 at all, and their most dominant Y-DNA Haplogroup (found at a frequency usually above 40%) actually tends to be A-M13 (see here).
    Last edited by Awale; 08-14-2016 at 02:18 PM.

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    Another article on out of Africa.

    "Genetic ‘trace’ in Papuan genomes suggests two expansions out of Africa"
    http://www.sciencedaily.com/releases...0921131119.htm

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