The split appears to have occurred between 360,000 and a million years ago, say researchers at the University of California, Los Angeles. These ancient humans had babies with the ancestors of modern Africans, just as Neanderthals reproduced with the ancestors of modern Europeans, wrote geneticists Arun Durvasula and Sriram Sankararaman.
According to them, the DNA of this archaic population represents between 2% and 19% of the genetic ancestry of modern West Africans.
UCLA scientists overcame these challenges to find the "ghost" of the hominine tribe using computational modeling techniques in modern DNA.
They built "generic maps of archaic ancestry" in four West African ethnic populations living in three countries: Nigeria, Sierra Leone and Gambia.
The researchers compared 405 West African genomes with the Neanderthal and Denisovan genomes and found out whether there were crosses between an unknown hominine whose ancestors separated from the human family tree before the Neanderthals. The data suggest that this may have involved several populations.
Professor Joel D. Irish, a bioarchaeologist at John Moores University in Liverpool, told CNN that there are probably many ancient human populations.
"I think there have been all kinds of populations, with the genetics different enough to look a little different," he said.
"Everyone tends to mate with everyone. I think we're going to find more and more of these populations of 'ghosts' arriving."
Last month, researchers at the Lewis-Sigler Institute for Integrative Genomics at Princeton said they also detected Neanderthal ancestry in Africans for the first time.
Their data indicated that a wave of modern humans left Africa for Europe some 200,000 years ago and crossed with Neanderthals, before migrating back to Africa.
He called into question the widely held theory of human migration "outside Africa", which means that modern humans originated in Africa and dispersed to the rest of the world in a single wave between 60,000 and 80,000 years ago.
CNN's Katie Hunt contributed to this story.