‘Ghost’ Ancestor Detected in DNA of Today’s West Africans

Yoruba and Mende have up to 19-percent genomic contribution from unidentified archaic human, who may have survived until recently. You might have a signal from it in your DNA too

Ruth Schuster
Ruth Schuster
Yoruba Magbo Helmet Mask. Southwest Nigeria
Yoruba masksCredit: Ismoon, Wikimedia Commons
Ruth Schuster
Ruth Schuster

An unknown hominin made a substantial contribution to the genome of modern West Africans, a new study has demonstrated. The genetic signal of this unknown ancestral species has been identified in four groups of West Africans, report Arun Durvasula and Sriram Sankararaman of the University of California, Los Angeles.

In fact, you may have a trace of this unknown archaic human as well. “Our study shows that some of this ancestry is also present in non-African populations,” Sankararaman tells Haaretz – it’s just less pronounced than in the West African groups.

He and Durvasula are in the process of testing other populations around Africa for the signal, he shares.

The interbreeding event in West Africa may have been quite recent in evolutionary terms, even though this new unknown species split off from the Homo line well over half a million years ago, before the split between Neanderthals and Homo sapiens, they reported Wednesday in Science Advances.

Yoruba Obatala priests in their temple in Ife
Yoruba Obatala priests in their temple in Ife Credit: Dierk Lange, Wikimedia Commons

Specifically, by comparing the genomes of 405 West Africans with Neanderthal and Denisovan genomes and applying computer modeling, Durvasula and Sankararaman have discovered that contemporary Yoruba and Mende people derive between 2 to 19 percent of their genomes from this mysterious archaic hominin. In terms of averages, 6.6 percent of the Yoruba and 7 percent of Mende genome sequences are archaic, they calculate.

Their revelation comes years after the discovery that non-Africans contain genetic signals from Neanderthals and Denisovans. But in this case, the authors demonstrate by statistical methods that these sequences cannot have originated in Neanderthals, Denisovans or African populations such as the southern African Khoisan or central African pygmies.

Asked if Neanderthals might have had it too, Sankararaman explains that we can’t know at this stage. “Our methods require substantial sample sizes to detect this ghost population,” he says – and there is very little Neanderthal DNA around to work with, which is a challenge.

But who might it have been? Could this mysterious ghost have been a hominin not ancestral to Homo sapiens: a line that split off, but before going extinct, introgressed with the modern humans in West Africa? “That’s a very likely model,” Sankararaman answers.

Prehistoric liaisons dangereuses

We have long since debunked the assumption that our evolution was a linear progression from tree rat to monkey to ape to us, with only one species in the Homo line at a time. Not so. Only Homo sapiens ultimately survived. But throughout all our history until the last 30,000 years or so (maybe less), there were multiple coexisting humanoid species on the Homo tree.

For example, at least four types of australopithecines overlapped 4 to 2 million years ago, and the less said about our understanding of Homo erectus’ spread and lineages the better

It has also become clear that hominins weren’t too choosy about their love interests. In Eurasia, after Homo sapiens left Africa, they met and mixed with Neanderthals and Denisovans, many times. Neanderthals and Denisovans had a common ancestor, but after they split they also interbred: extraordinarily, a first-generation hybrid teenage girl resulting from just such a mix was found in Siberia. Remains of hybrid Neanderthal-Homo sapiens have been found in Israel.

This is why all non-Africans have some Neanderthal genes, typically between 1 to 2 percent. Many non-Africans – chiefly Melanesians, but in fact Asians in general (and the earliest Americans who came from Eurasia) – have Denisovan heritage too. Oceanic people have as much as 6 percent Denisovan contribution in their DNA.

Also: Hundreds of thousands of years ago, the shared ancestor of Neanderthals and Denisovans interbred with a “superarchaic” hominin that had separated from the Homo line about 2 million years ago.

San gathering foods in Botswana
San gathering foods in BotswanaCredit: Andy Maano, Wikimedia commons
Infographic shows interbreeding between different types of species of hominins, including both archaic and modern
Interbreeding between human species: Latest relevation shows ties between a ghost hominin and modern humans in Africa

More? Well, recent research found that after Neanderthals and Homo sapiens mixed in Europe, some hybrid Homo sapiens-Neanderthals went back to Africa and mixed with the Africans, resulting in a faint Neanderthal signal in them too. However, if in non-Africans the Neanderthal signal is usually around 1 to 2 percent of the genome, in the tested African populations the Neanderthal signal is about 0.3 percent.

On top of all this, several studies had indicated contributions from “deep lineages” to the ancestry of today’s Africans. But the extreme rarity of hominin fossils and the even more extreme difficulty in obtaining DNA from anything that died more than a week ago had hampered the research. Now the researchers have found the smoking DNA of a strange ancestor in the Yoruba and Mende, where the signal is loud and strong, and in some non-Africans, where the signal is weaker.

Once upon a time in West Africa

When might this mixing have happened? It likely was quite recent, also indicated by the fact that some West Africans have as much as 19 percent genomic contribution from this enigmatic ancestor.

Durvasula and Sankararaman estimate that the introgression event was about 43,000 years ago – though the potential margin of error is tens of thousands of years.

Therefore, the archaic may have survived, living contemporaneously with modern humans until recently, Sankararaman confirms.

“Alternately, it may have interbred earlier with a modern human population, which then interbred with the ancestors of present-day West Africans,” he tells Haaretz. There could have been a single interbreeding event, but a more realistic model would include low levels of gene flow over an extended period of time, they say.

San, in Namibia, southern Africa
San, in Namibia, southern AfricaCredit: Reuters

Durvasula and Sankararaman deduce that the mystery hominin split from the Homo line about 625,000 years ago (mean), though their margin of error is again stupefyingly wide: 340,000 years to 1.02 million years.

Just to make the messy ancestry even more confusing, fossils evincing strange morphological combinations of archaic and modern features can be found from times as recent as 35,000 years ago in sub-Saharan Africa – at Iwo Eleru, Nigeria, and Ishango in the Democratic Republic of Congo – and the Middle East, says the two-man team.

The bottom line is that people who were something other than “Homo sapiens sapiens” may have persisted much, much later than we usually assume.

San hunter, Botswana
San hunter, BotswanaCredit: Andy Maano, Wikimedia Commons

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