People in West Africa carry mysterious genes that may belong to another species of hominin. The finding hints that primitive hominins lingered in Africa until fairly recently.
Our species repeatedly interbred with other hominins, in particular the Neanderthals and a less well-known species called the Denisovans. This happened after some members of our species first left our African homeland, probably within the last 100,000 years. As a result, all non-African people carry some Neanderthal DNA, and some Asian people also have Denisovan DNA.
What about people whose ancestors never left Africa? They might also carry DNA from other species, but it is harder to spot because we do not have DNA from any extinct African hominins to compare: the hotter and wetter climate there tends to destroy any preserved DNA.
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To get around this problem, and at the University of California, Los Angeles devised a statistical method to identify out-of-place DNA in the human genome, without the need for the genome of the hominin from which it came. The model was able to correctly identify the known Neanderthal DNA in human genomes.
They applied it to 50 Yoruba people from West Africa, who had had their DNA sequenced for the 1000 Genomes Project. On average, 8 per cent of their genome was from an archaic population. The mystery DNA was not Neanderthal, and nor did it match modern Pygmies who might plausibly have interbred with the Yoruba.
Ghost lineage
It appears the ancestors of modern Yoruba interbred with members of a distinct population, but it’s not clear what this “ghost lineage” was. It might have been a group of Homo sapiens that remained isolated from the rest of the population for thousands of years, or it may have been another hominin species altogether.
As with the Neanderthal interbreeding, many of the archaic genes in the Yoruba have been strongly selected against – suggesting that the hybrid children from these mysterious matings were only just viable. However some parts of the Yoruba genome, notably a tumour suppressor gene, still carry archaic DNA – hinting that these fragments were somehow advantageous.
So who did the Yoruba’s ancestors interbreed with?
The Neanderthals and Denisovans are not in the frame, as there is no record of them living in Africa. The recently-discovered Homo naledi was present in South Africa around 250,000 years ago, so it overlapped with our species, but it seems unlikely humans would have mated with them. They had small brains compared to ours, and may well have been too different from us to breed successfully. “I would be amazed if there was anything of them in us,” says of University College London in the UK.
A better candidate is Homo heidelbergensis, which was present in Africa until around 200,000 years ago. It was a fairly big-brained, advanced hominin, and has been proposed as the common ancestor of modern humans and Neanderthals. A small population of H. heidelbergensis may have lived on in the forests of west Africa until relatively recently, suggests of the University of Oxford, UK.
There is also archaeological evidence that relatively primitive hominins lingered in west Africa for a long time after fully modern humans had emerged elsewhere.
Scerri says stone tools have been found in west Africa that are just 12,000 years old, but look like they could be 300,000 years old. “We’re finding it in the forests,” she says. Similarly, a partial skull found at Iwo Eleru in Nigeria seems to belong to a very early Homo sapiens, but .
The study is a reminder that our species did not emerge from a single founding population, says Thomas. Instead, there were many populations scattered across Africa, many of which remained isolated and evolved on their own for thousands of years before coming back together with their neighbours.
Reference: bioRxiv, DOI:
