Discovering Denny

As I write, we are in total lockdown in New Zealand. I haven’t been beyond the front path for days, but thankfully the internet is still going strong, bringing me news from the outside world. Excavations worldwide have been cancelled, there are no seminars, and no lectures. Looking back to just a few weeks ago, it seems like another world. In 1946, Dr William Evans left in his will, funds to provide for visiting fellows to come to Otago, which was the world’s most southerly university until the Chilean Government founded the National University of Tierra del Fuego. This year, Otago offered the fellowship to my son, Tom, who directs the radiocarbon dating laboratory at Oxford. Our Department in Otago is engaged in fieldwork across a wide area from New Zealand up to China, New Guinea, and the Solomon Islands, while we have a strong bioarchaeology group in the Medical School with similarly broad coverage. For the past five years, Tom has directed the PalaeoChron Project at Oxford, very generously funded by the European Research Council. And when Tom came, there was the double bonus as his wife Katerina, who is also funded by the ERC, gave lectures too.

I have, of course, been well aware of their regular research trips to remote sites stretching from Spain to Siberia, but their visit was a chance for all we archaeologists in Otago to catch up with some really amazing discoveries. One of these began at Denisova Cave in the remote Altai. Just to get there entails an arduous ten hour drive from Novosibirsk, the main city in Siberia. Denisova is one of those caves with a deep buildup of occupation layers covering an immense timespan. My own work involves about 3000 years of cultural change, but Denisova takes one back about 300,000 years with occupation yielding a myriad of bone and stone tools. One problem is that the cave attracted not only human residents, but also hyaenas, the latter having the irritating habit of crunching up and eating bones and littering the cavern with half-digested chips.

In 2008, one bone was found intact, a tiny human finger bone. The constant cold of the cave interior at Denisova has a massive bonus: ancient DNA survives well. A lentil-sized piece of the finger bone was sent to the Leipzig Max Planck laboratory of Svante Pääbo for analysis and what began as a routine DNA analysis turned into one of the most stunning discoveries in the prehistory of our human past. A recent graduate student, Johannes Krause, managed to extract mitochondrial DNA that matched neither that of a modern human, nor a Neanderthal. It slowly dawned on him that this could only be a new human. He called Svante, who was stunned, and dashed back to Leipzig from a conference to find out more. Their paper describing an unknown hominin from southern Siberia was published in the journal Nature in March 2010, and Tom described in one of his lectures here, how he was completely dumfounded when he read this news. My diary recalls how he emailed me at once and I replied that I would immediately incorporate this in my lectures to first year students. Later that year, another paper appeared in Nature with David Reich as lead author. They announced that nuclear DNA had been extracted from this bone, and that modern Melanesians could count the mysterious Denisovans among their remote ancestors.

Let’s just pause here to take in the significance of all this. Traditionally, we have recognized three types of hominin occupying Eurasia between half a million and 50,000 years ago. Homo erectus was recognized years ago in Java and China. The Neanderthals lived in Europe and the Near East. Modern humans, following the African Eve model, emerged out of Africa and spread over Europe and the rest of the Old World and then, into the New. In doing so, Neanderthals disappeared, and Homo erectus might have died out before they even reached the Far East. Already, Tom and his team at PalaeoChron had shown that there was at least a 10,000 year overlap with the Neanderthals and they also interbred with modern humans in Europe. Now, we have another ancient human from the wide expanses and hunting grounds of Siberia. Not only that, but the ancestors of the Australian Aborigines and the Negritos of the Philippines had met and interbred with them.

Let me digress again. As every excavator knows, bones are a vital source of information. They tell us what species prehistoric people hunted or tended. One can track the timing and location of domestication, and, from the age structure of a bone sample, ancient husbandry. But the vast majority of bones survive as unidentifiable chips, that were fractured in antiquity, or at Denisova, crunched by hyaenas. Without the recognizable form of an articular surface, chips are pretty useless. Or are they? Quite recently there was a fuss in the press over Romanian horse meat mysteriously appearing via Ireland into British sausages. How do we know a bit of meat comes from a horse rather than a cow? By means of a cunning technique called peptide fingerprinting. Animal species have different protein sequences in their collagen. This has turned the identification of archaeological bone fragments on its head, for the technique known as ZooMS, or Zooarchaeology by Mass Spectrometry, can now identify even tiny bone fragments to genus or species level.

Broadening the family tree

Naturally, after the discovery of the tiny finger bone, the hunt was on for more. We didn’t, and indeed still don’t, know what a Denisovan looked like. It must be remembered that East and Southeast Asia is a vast territory, hardly touched archaeologically, particularly when compared with Western Europe. Tom and Katerina described how they flew out to Siberia to talk to Academician Anatoly Derevianko, leader of the Denisova team. They returned with bags of bone chips to Oxford and one of Tom’s graduate students, Samantha Brown, volunteered to undertake the long laboratory procedure of sampling every single one. Over the ensuing months, working with Mike Buckley at the University of Manchester, results accumulated: there were hyaena, horse, deer, and bear bones by the hundred, but no humans. Then, in June 2015, they discovered the needle in the haystack, a human fragment. Tom describes the finding as ‘one of the great moments of my life’, And indeed, it was a fragment, just 2.4cm long and weighing 1.6 grams, but 120,000 years old. Here is a very important lesson: never throw away what you have excavated. You never know what new scientific breakthroughs are just round the corner. This potential of DNA is a clear example. A few years ago, for example, I received out of the blue, an email from the Director General of the Thai Fine Arts Department, requiring immediate return of the dog bones from the site of Ban Chiang, that I studied 40 years ago. Long forgotten by me, I read on. His Majesty the King wished to subject them to DNA extraction. Panicking, I dashed down to the Department store and with an outpouring of relief, found them and had them in the courier’s hands within the hour.

Imagine the hushed audience as Tom talked us through this moment of discovery. The sliver of bone was dispatched to Leipzig for DNA extraction, followed by a long wait. The first results showed that the bone had mitochondrial DNA of the Neanderthal type. Later, when the full nuclear genome was sequenced, however, it showed something truly astonishing. The tiny fragment was from a young woman born of a Neanderthal mother and a Denisovan father. For the first time in the history of our species, the team had identified a first generation human hybrid.
On 22 August 2018, a paper drawing on input from the entire team of researchers was published in Nature with a dramatic cover for the journal showing clasping human hands entwined with DNA, which was produced by the graphic designer Annette Günzel.

This monumental discovery is still only the beginning. Just to think that we now have at least six different humans emerging from Siberia to Australia, with the 65,000 year old Homo luzonensis, the Hobbit, Homo erectus, Denisovans, and Neanderthals, as well as ourselves. Mapping their spread can now proceed with no human remains or artefacts, for DNA can be extracted from soil.

The Corona lockdown has spawned a multitude of online meetings, but lets us hope that normal service will be resumed as soon as possible, because as the William Evans visiting fellowships have shown time and again, there is nothing quite like the human touch. Denisovans and Neanderthals appreciated this as well.