Tightening the dragnet on Denisovans

Researchers have identified some prime suspects in the biggest ‘who done it’ mystery in human evolution: who were the Denisovans?

In a study published in Nature Ecology and Evolution, a team – led by population geneticist João Teixeira at the University of Adelaide in Australia – has attempted to nail down the identity of these enigmatic ancient humans by using AI to probe deep into the DNA of modern people of southeast Asia.

“Denisovans are making people rethink what they thought they knew,” says Teixeira, who collaborated with Murray Cox at Massey University, New Zealand; Guy Jacobs at the University of Cambridge, UK; Chris Stringer at London’s Natural History Museum; and Kris Helgen at the Australian Museum in Sydney.

Denisovans are known only from a few sparse remains, including DNA from 50,000-year-old Siberian finger bone and teeth, as well as collagen proteins from a 160,000-year-old jaw fragment in Tibet. Intriguingly, these bits of bone and teeth don’t match any of the known fossils in the human family tree.

In 2010, DNA extracted from the finger bone confirmed that this is a completely new species (or subspecies – taxonomists can’t agree). But Denisovans aren’t just some curious relic of our past – we still carry significant chunks of their DNA today, which suggests they interbred with modern humans as recently as 55,000–30,000 years ago. Genetic studies reveal very little Denisovan DNA in modern Europeans and Asians (less than 0.1%), but high percentages (around 4%) in New Guinea and Australia and the Mamanwa from the Philippines, people with ancestry from the traditional hunter-gatherers of the Asia-Pacific. (For comparison, Neanderthal DNA is found in all populations outside Africa at 1–3%.) This suggests the most recent trysts between Denisovans and modern humans took place in New Guinea and Australia.

So who exactly were these trans-Eurasian trekkers? And why haven’t we found their remains in south east Asia? Or is it possible we’ve misidentified existing fossil humans – and some might actually be the mystery “southern” Denisovans? The problem is, none of the key fossil suspects are forthcoming with their DNA: the tropics are unkind when it comes to preservation.

As a workaround, this new study deployed AI to sniff out cryptic signatures of ancient humans in the DNA of modern people of island southeast Asia (ISEA).

Until recently, the line-up of fossil Denisovan suspects in southeast Asia would have been limited to the hefty Homo erectus of Java, which had a brain size approaching that of modern humans, left Africa around 1.9 million years ago and roamed Java from 1.5 M years to 108,000 years ago. In 2004 the dwarf species H. floresiensis joined the line-up of suspects. Known to have lived on the island of Flores as recently as 60,000 years ago, individuals were a metre tall and had a brain capacity of 426 cubic centimetres, about one third that of a modern human. In 2019, the equally dwarfish H. luzonensis was added to the list; fossil remains from the island of Luzon in the Philippines reveal that this hominid stood around a metre tall and existed over a similar time span.

These three species are termed “super-archaics”. When it comes to their spot in the hominin family tree, most anthropologists place them on a branch that split from our line two million years ago.

To test if any of these super-archaics might be Denisovans, Teixeira and team trained an AI to use a Hidden Markov Model to “walk” along the DNA code, sniffing for two-million-year-old DNA. Thanks to the efforts of Herawati Sudoyo at the Eijkman Institute for Molecular Biology in Jakarta, who painstakingly gathered tissue samples from isolated populations ranging from tiny islands to the remote highlands of New Guinea, the AI was able to probe the genomes of 200 people from ISEA – populations that seem to have acquired their Denisovan DNA as recently as 30,000 years ago. This needle-in-a-haystack search method can detect traces of super-archaic code that represent 0.1% of the DNA – “one in a thousand ancestors”, emphasises Teixeira.

The first step was to mask off Neanderthal and Denisovan signatures, as well as any variant signatures also found in African populations. That sensitised the algorithm to see any new signatures that had arisen in ISEA.

The verdict?

Inconclusive.

A faint whiff of two-million-year-old super-archaic DNA was identified, but it wasn’t strong enough to convince the authors this was introduced by a hominin down under. It may have been a “methodological artefact”: a leftover signature from the mingling between Denisovans and a super-archaic in the northern hemisphere, possibly H. erectus – a finding which others like Cornell University’s Melissa Hubisz have reported.

Either way, the authors agree there is no conclusive evidence for a new super-archaic signature in people of ISEA.

University of Wisconsin anthropologist John Hawks, who was not involved in the study, finds it a convincing piece of work – especially since previous reports did suggest such signatures in Indian and Asian populations.

“The search for super-archaics is a rich target,” he says. “It took someone using more modern methods that are not easily tricked.”

But if this study was inconclusive, where does this leave the hunt for the Denisovans?

The authors are somewhat divided. Most say the evidence does not support the possibility that the island pygmies or hulking H. erectus are Denisovans. One suggestion is to keep searching the little-explored caves of ISEA for the remains of Denisovans. Sulawesi is the hot favourite. It has stone tools dating back 200,000–100,000 years ago, as well the world’s oldest cave paintings. 

A convincing fossil candidate should look more archaic than modern humans but not as archaic as the island hobbits – and it should have hung around till the moderns arrived about 50,000 years ago.

But others have not entirely let the line-up’s shady characters off the hook.

The ruling assumption was that the island hominins and H. erectus must all be super-archaic – in other words, their feature set is so ancient that they must have been travelling a separate track to modern humans for the past two million years. But that assumption could be flawed.

Perhaps the weird island hominids are not as super-archaic as they seem.

“Evolution goes crazy on islands,” says co-author Kris Helgen. Small founding populations and extreme conditions fire up the evolutionary engine – perhaps a mere 100,000 years ago Denisovans made their way to the island and not only shrank, but also produced throwbacks to a more ancestral state.

It’s possible that H. erectus evolved in unanticipated ways, too. Traditionally viewed as travelling a separate track to modern humans for over two million years, not everyone buys that theory. Previous research suggested that H. erectus in Java and China was modernising over its two-million-year stint in Asia through interbreeding with newer hominins roaming Eurasia.  

It’s possible that a modified form of H. erectus – like the 108,000-year-old population found buried in the banks of the Solo river near Ngandong, Java – might be Denisovans.

“We might have to rethink H. erectus,” say Teixeira.

Hawks agrees: “My hypothesis is that it’s Ngandong.”

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Related reading:

• Study puts Denisovans on roof of the world
• Denisovan DNA found in human genomes
• What Denisovans looked like