Distant human relative mixed with our cousins

A map of human prehistory is starting to look more like a tangled web than a family tree. First, we heard that our own ancestors – early modern humans – got it on with the Neanderthals. Then we learned that the Denisovans, another ancient but extinct human, interbred with both Neanderthals and our own forebears. Now, a team of researchers from the University of Utah has come to the conclusion that an older line of “superarchaic” humans interbred with both Denisovans and the common ancestor of the Neanderthals and Denisovans – a group they call the “neandersovans”.

The study, published in the journal Science Advances, is just the latest in a string of papers to highlight how fluid the early human gene pool was.

The new model suggests the superarchaic human split from the common ancestor of modern humans, Neanderthals and Denisovans around two million years ago, close to the time when the Homo line first appeared.  

The ancestors of modern humans then split with the ancestor of Neanderthals and Denisovans – the ‘neandersovans’ – and Neanderthals and Denisovans split from each other by approximately 700,000 years ago.

This superarchaic population interbred with the neandersovans and then later with the Denisovans.

When they interbred, the superarchaic humans and neandersovans would have been separated for 1.2 million years. The superarchaics were even more distantly related to the Denisovans they mated with.

Later still, early modern humans split into an African and a Eurasian line, with groups in the Eurasian line intermingling with Neanderthals and Denisovans.

In the latest study, the team looked for shared sequences in genome data from Neanderthals from the Altai Mountains of Siberia and the Vindija Cave in Croatia, as well as from modern Europeans, then used a computational method to determine which of several scenarios best fit the data.  

Several simpler scenarios for how history might have played out have been proposed over recent years, but according to population geneticist Alan Rogers, who led the current modelling effort, “everybody’s model fit the data poorly. So that was an indication that something had been left out of the model.”

The missing piece, according to the new model, is the superarchaic human.

The results resolve some thorny questions that had existed with previous work. For example, one proposal based on genetics estimated that Neanderthals and Denisovans split around 381,000 years ago, yet Neanderthal remains found in the Spanish Sima de los Huesos, or pit of bones, predates this split. The bones have been dated to 600,000 years ago.

“That was a real discrepancy between the genetic estimate and the fossil estimate,” says Rogers.

The new model fixes this discrepancy.

It also fits with a fairly simple narrative of early human migrations. A first wave of migration out of Africa occurred around two million years ago. Fossils in Dmanisi in Georgia that date to 1.85 million years ago attest to that migration.

The superarchaics likely descended from this initial Eurasian settlement. 

Around 700,000 years ago, a second wave of migration from Africa occurred. This was the neandersovans, who largely replaced the resident superarchaics and went on to form Neanderthals in the west and Denisovans in the east.

Later still – around 50,000 years ago – the ancestors of modern humans made the trek out of Africa, eventually replacing the Neanderthals and Denisovans from Eurasia.

Not everyone is convinced. Computational geneticist Kay Prüfer from the Max Planck Institute for the Science of Human History says he is sceptical about the approach used. But, he says, “Disagreement in science isn’t a drama. We’ll eventually sort out what explanation fits better. Often with better data.”

Who were these superarchaic humans?

Nobody knows for sure, says Rogers, but Homo erectus and Homo antecessor are contenders. But, he says, “it could have been some other population that we don’t know about.”

Just last week, researchers sifting through the genomes of modern-day West Africans discovered the signal of a dalliance with an ancient “ghost” hominin.

Whether the ghost hominin from West Africa and the superarchaic hominin that Rogers and his colleagues found are one and the same is unclear, but Rogers is keen to find out.