THE CURIOUS CASE OF THE MISSING ANCESTOR
Recent archaeological discoveries cast new light on the origins of our species. ELIZABETH FINKEL examines these bones of contention.
Researchers have found the DNA, but so far the body is missing. ELIZABETH FINKEL reports on the technology transforming archaeological research and the hunt for Denisovans, which could redraw the evolutionary map.
It’s the biggest “whodunnit” in the mystery of human evolution. Who were the Denisovans? All they left behind were a few ancient fragments of bone and teeth. Human – clearly. But not enough to match anything in the fossil record.
Incredibly, some of those ancient bones provided DNA. Enough for an identikit: the perpetrator should be flat-headed with a sloping forehead and an exceptionally wide face and jaw – a bit like a Neanderthal, but different. We also know these guys bred with modern humans, because we carry their DNA, especially the indigenous populations of Oceania.
Now, a group of scientists have set out to find the perpetrator. They’re reminiscent of the detective Columbo, the streetwise, rumpled, trenchcoat-clad character of the long-running TV series – deftly circling, gathering a string of incriminating evidence.
In the beginning . . .
The story begins in 2010, a time when the “Out of Africa” (OOA) theory ruled –which provided the answer to the question of the origin of modern humans.
A hundred thousand years ago the planet was populated by a human menagerie – all members of the hominin family. Across Europe and Asia, we knew then of Neanderthals, Peking man, Java man and others. In contrast, Africa seems to have been mostly populated only by humans.
But by 30,000 years ago the hominin bush had been drastically pruned. Only modern humans existed around the globe. What happened? According to OOA, the planet was taken over by Africans who exterminated or outcompeted the other hominins in Europe and Asia. It was a theory underpinned by a marriage of genetics and anthropology – the geneticists led by Allan Wilson at the University of California at Berkeley, and the anthropologists by Chris Stringer at the British Natural History Museum (see box opposite).
But in 2010 that theory was challenged by the discovery of an ancient text. Ancient texts rewrite history, like the Rosetta Stone did for Egyptian history and the Dead Sea Scrolls for early Christianity.
The first evidence came from a Croatian cave, where three 40,000-year-old Neanderthal females delivered up their DNA. It turned out to be a little different from ours. Any two humans today have DNA code that differs by 0.1%, but between a Neanderthal and a modern human it’s 0.14%. Those extra differences may be small, but they can be spotted when reading through the entire three-billion-letter genome that specifies a modern human – letter by letter. Imagine reading through a modern edition of the English Bible to find archaic words that had slipped through from the King James edition, such as “anon” or “bewrayeth”. When geneticists scanned modern genomes for Neanderthal words, they found them. For all non-african
the hominin By 30,000 years ago, bush had been drastically humans pruned. Only modern existed. What happened?
populations, Neanderthal makes up about 2% of their DNA text, which means that at some point in time up to one in 50 ancestors was a Neanderthal.
This new text didn’t just rewrite history; it shook our understanding of what it is to be human. We weren’t entirely modern: we were streaked with ancient DNA. As modern Africans ventured into the Middle East and Europe, they interbred with Neanderthals who’d been roaming Eurasia for some 400,000 years. The descendants of these trysts went on to populate the rest of the world. By contrast, modern-day Africans carry less than 0.3% Neanderthal DNA, probably a result of the migration of Neanderthals into Africa.
The rewrite didn’t stop there: 2010 turned out to be a year of wonders. In Denisova Cave, located in a verdant valley at the foot of Siberia’s Altai mountains near the border with China, another hominin female was also offering up her DNA. Researchers couldn’t be quite sure what type of hominin she was: all that was left was a raisin-sized bone found in a pile of tiny bones in an archaeologist’s sieve. Some belonged to animals, but the raisin looked like it came from a human finger: a pinky, to be precise.
It proved to be a rich source of DNA. As researchers read it letter by letter, it became clear that its owner was neither a modern human, nor a Neanderthal. Who was our mystery female?
In the absence of a body, the new type was dubbed Denisovan, after the cave. It was the first time a new hominin species (or subspecies – taxonomists disagree) had been identified by DNA alone. Denisova Cave soon provided more DNA, from three oversized teeth – one a wisdom tooth so large and with such splayed roots it was initially thought to be from a cave bear. Emboldened, the scientists dug into a lower section of the cave to test the very sediments. Here too they detected shreds of Denisovan DNA. (See “Dirty DNA”, right.)
Columbo on the genetic case
Denisovans have not given us a body. But they’ve certainly delivered some enthralling leads. Guided by their ancient text, geneticists scrolled through the DNA of modern individuals searching for occasional Denisovan words. One might have thought the populations of Siberia would be the best candidates for carrying them, and they do carry tiny amounts – about 0.1%, just like other populations in Europe and Asia. But the population with the strongest traces of Denisovan DNA turned up in Oceania, a hemisphere away. The indigenous populations of New Guinea and Australia carry around 4% Denisovan DNA; some island populations, particularly the Mamanwa of the Philippines, carry up to 2%.
The surprise finding suggests that at least one of the trysts between modern humans and Denisovans might well have taken place on the islands of South
Dirty DNA
DNA been able to directly retrieve
Since 2003, scientists have from ancient signatures of everything from dirt – identifying the back with some soil samples dating mosses to woolly mammoths, of ways. It up in the soil in a number
400,000 years. DNA ends soup oozing out of a decomposing might be from the cellular very urine and faeces. Clays are animal or from a live creature’s
Alternatively, a piece of disintegrated good at binding up DNA. majority of the source. While the vast bone might have provided of are able to fish out the DNA soil DNA is microbial, researchers lures of matching DNA. Scientists the species they want using is ancient – that the source of the DNA also have tests to ensure chemically cytosine (C) has often been in ancient DNA, the letter
(T). altered into the letter thymine
East Asia (ISEA). To get to those islands – and particularly to Sahul, the ice-age continent made up of Australia and New Guinea that existed until about 10,000 years ago – they’d have had to trek across the Eurasian continent, then cross 100km stretches of open water.
Surely those trekking, sailing, amorous southern Denisovans must have left some remains.
Enter the scientific Columbos…
Southern jawbones and algorithms
Nine years after the discovery of the pinky bone in Denisova Cave, and 2800 km to the south in the high Tibetan plateau, another big clue surfaced. It was all thanks to a Tibetan monk who was partial to meditating in Baishiya Karst Cave. In a moment of distraction he spied a big jawbone embedded with two giant molars, which he gave to the sixth Gung-thang living Buddha, who consulted scholars and gave the jaw to Lanzhou University in 1980; the university anthropologists had no idea how to classify it.
Fast forward nearly four decades. Could the jaw be a Denisovan? The molars no longer preserved DNA, but their dentine preserved fragments of collagen, the hardy protein that comprises the framework of teeth. In 2019 it was enough for an ID: the 160,000-year-old jaw was confirmed as Denisovan. A year later sediments at the Baishiya Karst Cave yielded Denisovan DNA, confirming the cave had indeed once been a Denisovan stronghold.
While palaeoanthropologist were digging in Tibet, Murray Cox, a computational biologist at Massey University in New Zealand, was digging into the DNA of modern people. Previous genetic analyses of populations in Oceania suggested the Denisovans had made their way south. But how? Herawati Sudoyo at Eijkman Institute for Molecular Biology in Jakarta had painstakingly gathered samples from populations ranging from tiny islands to the remote highlands of PNG. Cox used these to drill down into the DNA codes of populations from the ISEA. Cox’s deep dive into this DNA detected relics of two different Denisovan populations. He could also estimate the dates for when these populations had interbred with people in ISEA.
The calculation relies on the fact that Denisovan text, like all DNA, gets broken and shuffled as the generations progress. The longer the length of unbroken text, the more recent the interbreeding event. A genome from a recent interbreeding might still preserve an entire phrase such as “The Lord is nigh unto them that are of a broken heart; and saveth such as be of a contrite spirit.” But a recent acquisition will likely be shuffled between modern and old versions so that it reads: “The Lord will mend a broken heart; and saveth such as be of a contrite spirit”.
While anthropologists have traditionally told the human origins story based on bones and stone tools, today’s population geneticists are adding chapters based on fossil DNA.
Cox’s narrative suggests that some of the Siberian Denisovans formed an offshoot group that travelled to east Asia and became geographically isolated around 363,000 years ago. Over time their DNA – like their language – would have become parochial. That new parochial signature eventually became incorporated into the DNA of modern Chinese people.
Another offshoot group then travelled from east Asia to Sahul, a journey involving multiple island crossings, that was not readily reversed. The offshoot group’s isolation here at around 283,000 years ago led to another new and unique parochial signature. Snippets of that signature appear to have made their way into the DNA of modern Papuans and Aboriginal Australians after they arrived between 65,000 to 50,000 years ago. The most striking finding of Cox’s