An extinct branch of human ancestry has been discovered lurking inside the DNA of modern-day West Africans, which evolved around 500,000 years ago.
Although modern humans are now the only surviving lineage of humanity, others once lived on Earth. Some made their way out of Africa before we did, including the familiar Neanderthals in Eurasia and the newfound Denisovan lineages in Asia and Oceania. It isn’t completely clear whether these lineages would be considered species or subspecies, but the groups had identifiable genetic differences.
A team of researchers at the University of California has found evidence of “ghost” DNA in some modern West African people. In their paper published in the journal Science Advances, the group describes their study of genetic samples collected from the Yoruba and Mende groups and what they found.
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.
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.
Interestingly, this isn’t the first time ‘ghost’ species of unknown extinct ancestors have been found in modern DNA. Researchers looking at Eurasian DNA have previously found traces of at least three as-yet-undiscovered ancient hominins in modern human genomes. But this is a first for modern West African DNA.
In January, DNA discovered in four skeletons that belonged to children buried at a rock shelter at an archaeological site called Shum Laka in Cameroon also point to the existence of a long-lost ‘ghost’ branch of the human family tree.
Consequently, the most recent discovery, together with prior findings, complicates the picture of how modern human beings evolved.