African populations crossbred with other extinct humans

It has been proved that African populations crossbred with other extinct humans
The San are one of the ethnic groups that constitute the Khoisan, one of the populations studied. Credit: Centre for Genomic Regulation

A new international study led by David Comas, principal investigator at UPFand at the Institute of Evolutionary Biology (IBE: CSIC-UPF), demonstrates for the first time using artificial intelligence that African populations hybridized with other extinct humans. The study is published today, 26 April, in the journal Genome Biology.

Until now it was known that some extinct populations, such as Neanderthals or Denisovans, had mixed with modern humans outside Africa. However, in African populations no crossbreeding had been consistently demonstrated. Now, they have identified the introgression of an extinct line of humans in the DNA of present-day African populations. "This totally unknown archaic mixed with the ancestors of Africans and their genes have been conserved in their until the present," explains David Comas, full professor of Biological Anthropology at the Department of Experimental and Health Sciences (DCEXS) at UPF.

This totally unknown archaic population mixed with the ancestors of Africans and their genes have been conserved in their genome until the present.

Belén Lorente-Galdos, one of the authors of the article says "the scenario we know in Africa of societies that mixed in a complex way during its recent history is just the tip of the iceberg of the evolutionary history of humans, and so it would appear complex from the beginning."

Artificial intelligence to study the DNA of African populations

The researchers conducted a study of modern genomes of different populations with a broad diversity of lifestyles, languages or geography in the African continent. By sequencing these current genomes they have demonstrated that some of them come from introgression. "By using tools and complete genomes we have been able to infer the general history of the evolution of African populations," saysÒscar Lao, principal investigator at the National Centre for Genome Analysis (CNAG-CRG), from the Centre for Genomic Regulation (CRG), also one of the authors of the study.

"What has surprised us is that in order to describe the genetic diversity found in African populations today, the presence must be taken into account of an extinct archaic African population, with whom anatomically modern humans would have mixed," he adds. This result indicates that not only were there archaic populations different from the sapiens lineage outside Africa (such as Neanderthals or Denisovans), but that within this continent there were sub-populations with which anatomically who remained in Africa had offspring.

By using artificial intelligence tools and complete genomes we have been able to infer the general history of the evolution of African populations.

"This finding challenges the observations made previously on the crossbreeding of Neanderthals or Denisovans with European or Asian ancestors because Africans have always been taken as a model of population without introgression," explains David Comas, head of the Human Genome Diversity group at the IBE. "Our research leads one to question some assumptions established today based on the premise that the African population did not have introgressions," he adds.

Belén Lorente-Galdos concludes, "our method has enabled clearly ruling out the prevalent model that does not consider archaic introgression in Africa. The new model we present has forced us, furthermore, to review the amount of DNA in people of Eurasian origin that comes from Neanderthals, which could be up to three times higher than had been estimated to date using the previous models."

The study involved researchers from the Yale School of Medicine, the University of Taibah (Saudi Arabia), the University of Jendouba (Tunisia), IDIBELL, the University of Helsinki (Finland), the University of Witwatersrand (South to Africa) and the Lebanese American University.

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Artificial intelligence applied to the genome identifies an unknown human ancestor

More information: Belen Lorente-Galdos et al. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations, Genome Biology (2019). DOI: 10.1186/s13059-019-1684-5
Journal information: Genome Biology

Provided by Centre for Genomic Regulation
Citation: African populations crossbred with other extinct humans (2019, April 26) retrieved 21 October 2019 from
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Apr 26, 2019
Her hair looks awesome.

I bet that inter breeding made some of their members very attractive as they carry genes that might be hard to find goodies.

Apr 27, 2019
An African introgression from other humans in Africa has long been an open question, the paper has several references. Nice to see it confirmed!

But the result is crazy nice! Same as earlier results the likelihood there was no introgression in Africa is virtually zero. And while they can exclude a Neanderthal ghost lineage, the one in Africa is about as old a lineage @ 528 ka as the Neanderthal/Denisovan ancestor @ 603 ka but it is also about as old as the latter split @ 426 ka, so effectively an archaic ghost.

Finally, the ghost that introgressed into the Denisovans turns up again, and it is crazy old in comparison @ 1.4 Ma (in the supplement; labeled Erectus; Dmanisi Eurasian Erectus @ 1.8 Ma) and crossed in crazy late (within the last 100 ka, while humans were in Asia). The introgressions into N/D are ~ 1 % while the introgressions into A are ~ 5 % (earlier underestimated), perhaps reflecting rates of successful couplings (we do procreate faster).

Apr 27, 2019
Perhaps I should add that the ghost populations were sizable, their Ne's were 20-30+ k as the other humans at the time. Especially the Erectus ghost fared well before it vanished.

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