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Found in Study of First Ancient African Genome Scientific American
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2/3/2016 Error Found in Study of First Ancient African Genome Scientific American
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 4,500yearold man from Ethiopia—the
first complete ancient human genome from Africa. The man was named after
Mota Cave, where his remains were found (For more about the initial findings,
please read the following article: “First Ancient African Genome Reveals Vast
Eurasian Migration”).
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 coled 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
http://www.scientificamerican.com/article/errorfoundinstudyoffirstancientafricangenome/ 3/8
2/3/2016 Error Found in Study of First Ancient African Genome Scientific American
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 backtoAfrica 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 January 25. 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”.
http://www.scientificamerican.com/article/errorfoundinstudyoffirstancientafricangenome/ 4/8
2/3/2016 Error Found in Study of First Ancient African Genome Scientific American
This article is reproduced with permission and was first published on January
29, 2016.
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Ewen Callaway
Ewen Callaway works for Nature magazine.
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