Scientists have found evidence for a mysterious “ghost population” of ancient humans that lived in Africa about half a million years ago and whose genes live on in people today.

Traces of the unknown ancestor emerged when researchers analysed genomes from west African populations and found that up to a fifth of their DNA appeared to have come from the missing relatives.

Geneticists suspect that the ancestors of modern west Africans interbred with the yet-to-be-discovered archaic humans tens of thousands of years ago, much as ancient Europeans once mated with Neanderthals.

“In the west Africans we looked at, all have ancestry from this unknown archaic population,” said Sriram Sankararaman, a computational biologist who led the research at the University of California in Los Angeles.

Unlike today, the world was once home to many related species or subspecies of human. And when they stumbled upon one another, mating was not out of the question. As a result, modern Europeans carry a smattering of Neanderthal genes, while indigenous Australians, Polynesians and Melanesians carry genes from Denisovans, another group of archaic humans.

Previous studies have hinted that other ancient humans once roamed Africa, but without any fossils or DNA to pore over, researchers have struggled to learn more about them.

Arun Durvasula and Sankararaman obtained 405 genomes from four west African populations and used statistical techniques to work out whether an influx of genes from interbreeding was likely to have happened in the distant past. The analysis suggested that it had in every case.

The scientists went on to scour the African genomes for chunks of DNA that looked different to modern human genes. This allowed them to pull out sequences that most probably came from an ancient relative. By comparing these with genes from Neanderthals and Denisovans, they concluded that the DNA had to come from an unknown group of archaic humans.

“They seem to have made a pretty substantial impact on the genomes of the present day individuals we studied,” Sankararaman said. “They account for 2% to 19% of their genetic ancestry.” The four populations studied came from three countries: two from Nigeria, and one each from Sierra Leone and the Gambia.

The findings are far from definitive, but according to the scientists’ best estimates, the ghost population split from the ancestors of Neanderthals and modern humans between 360,000 and 1m years ago. The group of perhaps 20,000 individuals then bred with the ancestors of modern west Africans at some point in the past 124,000 years.

But other explanations are possible, Sankararaman said. There may have been multiple waves of mating over many thousands of years. Or a number of different populations of so-far-unknown archaic human relatives. “It’s very likely that the true picture is much more complicated,” he said. Details of the work are published in Science Advances.

The researchers are now keen to delve into the ancient genes and work out what they do. One possibility is that west Africans retained the DNA because it helped them to survive and breed.

“It is always interesting and useful to see researchers applying new methods to try to get a better idea of what ancient populations might have been like,” said John Hawks, an anthropologist at the University of Wisconsin-Madison, who was not involved in the study.

“It’s an exciting moment because these studies open a window showing us that there is much more than we thought to learn about our ancestors. But actually knowing who those ancestors were, how they interacted, and where they existed is going to take fieldwork to find their fossil and archaeological remains.

“We do not know what this African population may have been. It is tempting to speculate. But I’ve got to say it is just too soon to know. We haven’t discovered enough fossils in most of Africa to say we know what was there.”