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There Was No Vast Migration of Eurasians Into Africa

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Last fall while at ASHG this paper came out, Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent:

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Turns out that there was a bioinformatics error which negates the magnitude of these results. 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 Sub-Saharan 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.

First, scientists are humans and mistakes happen. So respect that the authors owned up to it. On the other hand, the conclusion never smelled right to many people. I was confused by it. I asked Iosif Lazaridis at ASHG. He was confused by it. I asked Pontus Skoglund. He was confused by it.

Unfortunately the result from the bioinformatics error was emphasized on the abstract, and in the press. In The New York Times:

“The most astonishing thing is there’s quite a lot of backflow in all modern African populations,” Dr. Pinhasi said. He and his colleagues estimate that 7 percent of the genomes of the Yoruba people of Nigeria are of Eurasian origin. In the genomes of Mbuti pygmies who live in the rain forest in the Democratic Republic of Congo, 6 percent of the DNA comes from Eurasians.

Ryan L. Raaum, an anthropological geneticist at Lehman College, part of the City University of New York, called the new study “fantastic” but questioned its conclusions. If people from the Near East moved into Africa, he argued, a drastic shift in the archaeology of the region would logically follow. But no such shift occurred. It is also possible that Eurasian DNA moved into Africa earlier than 3,000 years ago, Dr. Raaum argued. Mota might have simply lived in an isolated community that never encountered people with those genes.

The best way to test the conclusions of Dr. Pinhasi and his colleagues, Dr. Raaum said, would be to gather more DNA from African fossils of the same age. If the researchers are right, they would also lack Eurasian DNA. “Then the argument starts to seem a lot more plausible,” Dr. Raaum said.

A rule of thumb in science is when you get a shocking and astonishing result, check to make sure you didn’t make some error along the sequence of analysis. That clearly did not happen here. The blame has to be distributed. Authors work with mentors and collaborators, and peer reviewers check to make sure things make sense. The idea of massive admixture across the whole of Africa just did not make sense.

If something like this happened to me I’d probably literally throw up. This is horrible. But then again, this paper made it into Science, and Nature wrote articles like this: First ancient African genome reveals vast Eurasian migration. The error has to be corrected.

 
• Category: Science • Tags: Ancient DNA, Genomics

17 Comments to "There Was No Vast Migration of Eurasians Into Africa"

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  1. Homo naledi and the braided stream of humanity. It’s miscegenation all the way down. | Praxtime by Nathan Taylor
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    […] [Update Jan 2016: Backmigration paper has bioinformatics error] […]

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  2. Hey Razib. Good post. Question.

    I was wondering if this applied to the Khoisan as well? It goes with the same period that the researchers say from the paper you linked.

    https://www.newscientist.com/article/dn24988-humanitys-forgotten-return-to-africa-revealed-in-dna/

    The same thing applies, correct?

    Thanks for your time.

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  3. Evidences (data) are the core of science thinking. Then with new corrected evidence, it was mostly out of Africa in term of human migration (up until recent colonial time). The beauty of science is willing to correct itself with new evidences.

    In Eurasia itself, we can see migration from north to south as your recent post of Britain genetics. In China, recent history has shown repeated sinicization of northern nomads/hunter-gatherers ( Xiongnu, Jie, Xianbei, Di, and Qiang) in northern agriculture region. Each time, it is mixture process with northern tribes. With right environment for agriculture (more productive than nomads steppe), every body become farmers as you can observe in USA, Peru ect. As I said before, the goal of human life is seeking wealth which is translated into survival advantage. As farm property owner, I can see why only bad land is used as pasture land. Agriculture is far more profitable. (corn field lease up to $400 per acre; pasture only $10 or less per acre in USA). After mixture, it is competition who is the best farmer no matter who is your ancestor. As land lord, I only offer my land to the farmer who can pay higher lease in a market. So incompetent farmer get selected out economically. Again survival of fittest at work in real time.

    Most recent one is Manchurian. The last emperor Fuyi even could not speak his ancestor language. This ethnic group only exist on paper. In reality, they are no different from Han anymore.

    So multidirectional migrations are true but not equal.

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  4. no, those results were robust. i happen to know the author, and he was confused so checked a lot of ways. and it’s been replicated, and, there is a good archeological peg for what’s going on (cattle arrived ahead of the bantu via east africans who brought eurasian ancestry).

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  5. Still a nice big piece of the puzzle.

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  6. The irony is that the paper would have been very big even without the extraordinary claim about West Eurasian admixture in other Africans. It is the first ancient DNA that old from Africa. Yet, because of this error that led to over reach, the whole paper has now become a net minus for the investigators involved.

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  7. It really shouldn’t be though. This is how things should work really. Everyone makes mistakes. What’s important is to rectify them as best you can and then move on.

    I recall reading about an engineer who, upon questioning from a grad student doing a project, realized his high rise could collapse in the face of a storm that had roughly a 1/10 chance of occurring in a given year. He had designed his structure to code, but the code didn’t contemplate the specific case at play here, and it was a pretty plausible scenario. So he reported the issue, and his insurance firm financed the repair work, which involved cutting open the interior finishes to weld additional material to major structural connections at significant cost.

    Thing is, when the work was complete, his insurance rates actually went down. The insurance company rightly figured that an engineer who is proactive about addressing issues even when not required to do so by code is far less of a risk than an engineer who just covers his or her butt.

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  8. Confirmation bias at work – significant back flow supports the idea that we are really all the same, so received less scrutiny.

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  9. i don’t know. i’d be curious. no one i talked to in the weeks after this paper came out really believed the topline result interpretation face value.

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  10. I think it’s great they owned up – definitely inspires confidence from us laycritters that this is real science, as opposed to eg Climate Change or Anthropology. >:)

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  11. The problem with this episode is a show of lack of basic competence in genomics by authors of the paper. It is misleading to claim it as an IT error. It is a step in converting data to PLINK-compatible format that every population geneticist should be aware of. This should be a retraction, not a correction since a main conclusion is invalidated.

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  12. I’ve always though there was a similarity to San and southern European rock art / cave paintings. Minoan art is similar too. I don’t know if the periods coincide.

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  13. I’m sure you could build a racist narrative around a back migration of Eurasian supermen too if you really wanted to.

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  14. Is there any reaction to this from Science? Will they publish the erratum? It seems a bit strange to see an erratum to a Science paper published anonymously via a Dropbox account.

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  15. To RaceRealist88′s point, the Western Eurasian ancestry detected in Southern Africa by Pickrell et al. 2014 was only observed among the historically semi-nomadic, pastoral Khoe-Kwadi group at a rate of 1-6.3% (a subset of their larger share of East African admixture, which was found at a rate of 6-25%), it was nearly absent in the traditionally hunter-gatherer Kx’a-Tuu or “San;” you already mentioned this but such admixture was likely transmitted not from SW Asian Neolithic farmers, or even South Cushitic pastoralists, but a population similar to the Sandawe, who share close genetic and possibly linguistic relations to the Khoe-Kwadi. Groups like the Nama, Khomani, and Karretjie aren’t really representative since they also possess an extra dose of “non-African” ancestry from their contacts with European settlers and the coloured community in historic times.

    Razib, I am not sure if you noticed but the revised statistics has resulted in a notable drop of Eurasian ancestry in East Africans and consequently populations with East African ancestry. For example, Pickrell detected WE admixture in the Khwe, GuiGhanaKgal, and Xuun at a rate of 1.2-4%, these new statistics comparing Mota/LBK only detect such ancestry at negative 0-0.37%. Also notice how the level of purported Western Eurasian ancestry in East Africa drops significantly by ~10% from the first run (with the Druze) to the second and third runs (using LBK); I wonder if you can point this out to some of your contacts? More ancient African genomes will reveal the full extent of Africa’s genetic sub-structure.

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  16. Ouch! I took the initial conclusion as the truth, an astonishing truth but the truth. Got some correcting to do.

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  17. It is important to remember that this error only affexts the admixture in the last 3000 years that is found mostly in East Africa. We still have no baseline for 0% Eurasian for older backflow (which certainly occurred to some extent).

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