February 2, 2016

Most Africans do not have significant Eurasian admixture

This is major news: the authors of the study on the ancient East African genome of Mota have recanted their conclusions. In a correction note echoed by Nature they say:

Erratum'to'Gallego'Llorente'et'al.'2015'

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ 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 Neanderthals 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. The conclusion of a large 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 SubUSaharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.

We thank Pontus Skoglund and David Reich for letting us know about this problem.

This makes much better sense admittedly. I strongly appreciate the willingness of Gallego, Jones et al. for publicly amending their wrong as quickly as possible. It's said that erring is human but correcting is only for the wise.

6 comments:

  1. Very commendable - not everybody would be honest enough to publicly admit and correct the error. More caution next time...

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  2. According to David, this paper is ''garbage''. What is your opinion?.

    http://www.eujournal.org/index.php/esj/article/viewFile/6837/6563

    R1A SUBCLADES AND BRONZE AGE
    MIGRATIONS ON THE EURASIAN STEPPES

    Csaba Barnabas Horvath, PhD
    Pátmány Péter Catholic University, Budapest, Hungary

    Abstract :
    Until recently, our knowledge of the prehistoric world has been blur
    in many aspects. It was unclear, whether if migrations, conquest, or merely
    cultural diffusion led from one culture to the other. By the beginning of the20th century, the introduction of genetics into the study of ancient historygave opportunity for a deeper insight to the prehistoric world. As more andmore genetic traces are explored, it becomes more and more possible toidentify the routes and time of prehistoric migrations. If we can decode the information hidden in genetic data, a turbulent picture of migrations andconquest between certain prehistoric cultures emerges in front of our eyes. This paper attempts to identify prehistoric migrations in Eastern Europe and Central Asia from the Neolithic to the Bronz Age, based on statistical data of genetic samples.

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    Replies
    1. When Davidski replies like that he acts like a fanatic religious person when his/her faith is challenged somehow. He does that often, sadly enough.

      Some of what Horvat says makes some sense. However my criticism would be when the author tries to include Z93 in the European scenario and I instead think that the internal structure of Z93 demands a separate Asian scenario, that when R1a migrated to Europe (maybe in the Neolithic), there was a leftover in Asia that expanded eastwards and northwards and that is Z93.

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    2. The Amount of Basal M-417 clades that are present in western Asia and the diversified structure of Z-93 makes it highly obvious that it originated around Iran.
      I mean by applying simple logic where is the Z-93 structure in Europe now?, seriously some Z-93* is enough?. Yes Poltavka is Z-94 from 3000 BC , but it also looks that it was the start of a kind of turnover from a R1b area to R1a. Now they hope that Ukrainian samples will have Z-93 which may be the ultimate source of Z-93 , but where is Z-93 in Ukraine now?.

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    3. Are you asking me? My only guess is that Davidski has found (in FTDNA?) one or two individuals derived with highly derived Samara/Central Asian Z93* but he never provided the reference so it's just a wild guess.

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  3. Nepal aDNA

    http://meeting.physanth.org/program/2016/session40/warinner-2016-long-term-genetic-stability-and-a-high-altitude-east-asian-origin-for-the-peoples-of-the-high-valleys-of-the-himalayan-arc.html

    "To investigate the peopling and early population history of this dynamic high altitude contact zone, we obtained low-coverage genome-wide sequences (0.04-0.65x, mean 0.25x) and high coverage mitochondrial sequences (20.8-77.8x, mean 46.4x) from eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3150-1250 BP. We demonstrate that the region is characterized by long-term stability of the population genetic make up despite marked changes in cultural remains. Genome-wide markers, mitochondrial haplotypes, and high altitude adaptive alleles suggest a high altitude East Asian origin for prehistoric Himalayan populations. "

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