Denisovans are diverse (Introduction)

by David Turell , Monday, March 22, 2021, 23:02 (1341 days ago) @ David Turell

Traces of DNA pops up everywhere, but real fossils are hard to find:

https://cosmosmagazine.com/history/palaeontology/tightening-the-dragnet-on-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.

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"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.

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"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.

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"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.

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"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.

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"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."

Comment: Denisovans sure got around. Fossils must be in some unexplored cave waiting to be discovered.