Four West African populations carry genes from what may be an undiscovered archaic hominin. This archaic group of humans seems likely to have diverged from the shared ancestor of Neanderthals, Denisovans and modern humans before these lineages split about 800,000 years ago.
Previous research has shown that Homo sapiens bred with Neanderthals and Denisovans after migrating from Africa, but little is known about the presence of genes from ancient hominins in people whose ancestors never left Africa, partly due to the difficulty of obtaining ancient DNA in hot climates where it can degrade.
To overcome these barriers, Sriram Sankararaman and Arun Durvasula at the University of California, Los Angeles, used computer modelling to compare gene variations in 405 West African genomes with those in Neanderthal and Denisovan genomes.
The team looked at both modern and ancient segments within the genomes of Yoruba people from Ibadan, Nigeria. They found more instances of genetic variation in the ancient segments than are seen in Neanderthal and Denisovan genes, suggesting that neither of these groups of ancient humans were the source of the genomic variance.
Similar patterns were seen in the genomes of Mende people in Sierra Leone, Esan people in Nigeria and those in western areas of Gambia. The four populations are estimated to derive between 2 and 19 per cent of their ancestry from an archaic group of genes.
We don’t know whether this archaic hominin is a “ghost”, for which we have no physical record, or one we have found traces of already, such as Homo heidelbergensis, which may have evolved around 700,000 years ago. “It’s a really intriguing question,” says Sankararaman.
This mystery hominin is most likely to have diverged from the ancestors of Neanderthals, Denisovans and modern humans before that lineage split into these groups, according to the researchers. They estimate this divergence took place at some point between 1 million and 360,000 years ago, and interbreeding between the archaic population and the ancestors of the modern populations occurred at some point in the past 124,000 years.
These findings complicate our understanding of human ancestry and the timing of when several branches evolved, much like the discovery of the Sima de los Huertos hominins in Spain, says Pontus Skoglund at the Francis Crick Institute in London. “Perhaps all this ties into something that we don’t fully understand, some complexity around the half-a-million year ago mark, or perhaps a bit more recently,” he says.
To discover more, we need more physical evidence, says Skoglund. “We might be able to find other hominins from Eurasia, where it is a bit colder with better DNA preservation, and they might let us understand the relationship between Neanderthals and modern humans in a better way.”
Science Advances DOI: 10.1126/sciadv.aax5097