Ancient "ghost" DNA identified in living humans

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Ancient human fossilsare often found in Africa, but ancient human DNA is scarce.

Intense heat and humidity destroy DNA, so ancient fossil DNA is rarely found on the continenthumans came from. But in a new study, researchers reveal that the genomes of living West Africans may hold clues to a mysterious, ancient hominin — a "ghost" human species that currently can't be identified.

The data add another layer of complexity to the story of human history. They also add to our growing understanding of which ancient human species' genetic signatures remain in present-day African genes — just as modern-day Europeans carry Neanderthal DNA.

“We hope that this will lead to exploration of complex models of human history that account for these interactions,” study co-author Sriram Sankararamantells Inverse.

“The fact that segments of archaic ancestry are present in African genomes leads us to wonder how archaic DNA is impacting human biology," he says.

The results were published Wednesday in the journal Science Advances.

The hunt for strange genes

Sankaraman and Arun Durvasula, both affiliated with the University of California, Los Angeles, examined genomes of 405 West Africans currently living in Nigeria, Gambia, and Sierra Leone. The DNA was collected as part of the 1,000 Genomesproject.

They compared these genomes to the genomes of Neanderthals and Denisovans using a novel method with an “improved sensitivity” to finding archaic genomes without a reference point, Sankaram says. This method uses the fact that we have genomes from many present-day people, and identifies segments that look “different” from a typical modern human, he says.

The analysis reveals a substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations. On average, some 2 to 19 percent of these populations' genetic ancestry came from an ancient human, the results suggest. This ancient predecessor likely diverged from our family tree before the split of Neanderthals and modern humans, the authors say.

Complicating human history

These genes may have entered the modern West African genome recently, or it the process may have involved multiple populations of archaic humans, which mixed over generations, the researchers say. From the data, the most-likely time interbreeding between our own species and this "ghost" hominin would be around 43,000 years ago — with a fairly wide confidence interval, Sankaraman says. There just is not enough data to say for sure.

The study assumes modern West Africans do not have any Neanderthal or Denisovan ancestry, but instead may include some other hominin as a part of their ancient history. It's a big assumption: A studyreleased in January 2020 concludes that living Africans can have fragments of Neanderthal DNA — a result of Neanderthal-human interbreedingand migration back to Africa.

It is likely African populations have ancestry from both Neanderthals and from this other archaic population — which, according to this study, is not related to Neanderthals, Sankaraman says.

“The picture is one of complex interbreeding across divergent populations,” he says. In other words, it is not so simple.

The new study jibes with previous research, which also suggests the presence of “ghost” hominins in the genetic material of modern-day Africans. In a 2017 study, researchers examined the saliva of people from sub-Saharan Africa, finding that the sample carried genetic evidence of an as-yet-unknown ancestor.

When that study was released, lead author Omer Gokcumentold Inverse that the findings were proof that Homo sapiens“absorbed different populations that lived around us."

Human history, he said, is not “as simple as we previously thought.”