Neanderthal Man

by Pbo, Svante

  It took Udo a few months to refine the mapping of all the fragments to each of the comparison genomes. The final mappings didn’t change the picture, and I became convinced that the Denisova girl was a member of a population that shared a common origin with Neanderthals, but that had lived separately from the Neanderthals for at least as long as Finns today have been separated from, say, the San in southern Africa. Denisova DNA sequences tended to be a bit closer to those of Eurasians than to Africans, but less so than were the Neanderthal DNA sequences. This was best explained by a common ancestry for the Denisova girl and Neanderthals so that when Neanderthals mixed with modern humans, Eurasian ancestors inherited DNA sequences that were somewhat similar to Denisova DNA sequences just because the Neanderthals were related to the Denisova girl.

  So it was clear that the population to which the Denisova girl belonged had separated from Neanderthals before they met modern humans. What would we call this population? We certainly didn’t want to give them a Latin name that would force us to label them a subspecies or a species. Since they were only about as different from the Neanderthals as I am from a San, this would be ridiculous. But we needed to call them something. We needed what taxonomists would call a trivial name, such as “Finn,” “San,” “German,” or “Chinese.” “Neanderthal” was such a trivial name, named for Neander Valley in Germany, Thal being an old spelling of the German word for “valley.” Following this example, I suggested that we call them “Denisovans.” Anatoly agreed, so we unceremoniously announced our decision in a phone meeting and, from then on, we referred to the population that included X-Woman and the individual with the unusually large molar as the Denisovans.

  One exciting issue remained: whether Nick’s finding, that the Denisovan girl shared more derived sequence variants (SNPs) with the Papuan individual than with the other four individuals we had sequenced, was a real discovery or instead due to some bug in a computer program or a quirk in the data. Over the next several weeks, we discussed different technical problems that could cause that data to look this way. But things remained ambiguous. There could, perhaps, be something special about the Papuan DNA sequences that made them appear to be slightly more similar to the Denisovan DNA sequences. To me, it seemed suspicious that we had seen no trace of this putative admixture in China since it would mean that Papuan ancestors could have met the Denisovans, who we knew existed in Siberia, without meeting the ancestors of the Chinese. Of course, maybe the Denisovans lived in other places beyond Siberia. We decided that the best way to address this was to sequence more present-day people. This slowed down our progress toward publication, but we didn’t want to make fools of ourselves by claiming something that would then turn out to be due to some technical oversight on our part. So we decided to sequence seven more people from around the world. We chose an African Mbuti and a European from Sardinia, two people we wouldn’t expect to have anything to do with the Denisovans. We also included a person from Mongolia in central Asia as a person who lived not too far from the Altai area; a Cambodian as someone on mainland Asia not too far from Papua; and a Karitiana from South America as a representative of Native Americans, whose ancestors had come from Asia and could perhaps have met Denisovans in the past. Finally, we decided to sequence two people from Melanesia and chose a second Papuan and a person from the island of Bougainville.

  With those sequences in hand, Nick and the others redid their analyses. Their results confirmed that the Denisovan genome had a special relationship with the people from Papua and Bougainville. In contrast, there was no extra sharing of derived SNPs whatsoever with the people from Cambodia, Mongolia, or South America.

  Martin also found another interesting thing. He detected an indication that the Denisovan genome carried slightly more ancestral (ape-like) sequence variants than the Neanderthal genome. This could indicate gene flow into Denisovan ancestors from some archaic human that could also have brought in the diverged mtDNA. But both Nick and Monty were still worried that we might be overlooking some artifact. Could it be risky to do detailed analyses with the Neanderthal and Denisovan genomes together? Since they were both ancient genomes they might share some errors that were the result of being deposited in the soil for thousands of years. There was even some discussion about whether the gene flow into Papuans might after all be due to some esoteric technical problem.

  By the end of May I was growing increasingly frustrated. After a long phone meeting with what seemed to me to be unnecessarily complicated discussions about possible technical problems, I wrote an e-mail to the consortium in a fit of bad temper, saying that I felt that our major contributions to the scientific community were the Denisovan genome sequence itself as well as the Denisovan tooth with its unusual morphology. So far, the world knew only about the Denisova mtDNA sequence and therefore thought that modern humans and Neanderthals were each other’s closest relatives and that the Denisova individual was a more distant relative. From the nuclear genome, we now knew that the real situation was that Denisovans and Neanderthals were closer to each other and that modern humans were their more distant relatives. We needed to tell this to the world as soon as possible and let other researchers have access to the genome we had sequenced. If we weren’t sure of whether or not there had been admixture with the Papuans, we simply didn’t need to discuss that issue in the paper. It could be addressed in a later paper when we had time to explore it more fully.

  This was a deliberately provocative suggestion, and many smart people in the consortium were opposed to it. Adrian wrote an e-mail saying “Surely publishing without the Papuan story risks the following: Someone will do their own analysis, find the Papuan admixture story, and publish it quickly. Why we didn’t mention it ourselves will then be interpreted as a) incompetence, b) rushing, c) political correctness. Isn’t that a problem?” Nick agreed, saying “We have to deal with the Papuan issue or we will look like fools or cowards.”

  So we continued to struggle with figuring out what technical issues might have caused this unexpected result. What finally turned the tide was that Nick analyzed the relationship of the Denisovan genome to another, publicly available data set. The Human Diversity Panel, available from a center in Paris, is a collection of cell lines and DNA from 938 humans from 53 populations from around the world. Each sample had been analyzed by a “gold standard” technology that shows with great accuracy which nucleotide is present at 642,690 variable sites in the genome. Nick looked at how often the Neanderthal and Denisovan genomes shared derived SNPs at places where we had good data for both ancient genomes. He found that all seventeen individuals from Papua New Guinea and all ten individuals from Bougainville stood out from all other individuals outside Africa in that they were closer to the Denisovan genome. This was in perfect agreement with what we had found when we analyzed the genomes we had sequenced. We were all now convinced that something special had indeed gone on between the Denisovans and the ancestors of the Papuans.

  Using the Denisova and Neanderthal genome data, David and Nick estimated that about 2.5 percent of the genomes of people outside Africa came from Neanderthals, and that later gene flow had brought about 4.8 percent of Denisovan DNA into the Papuans. Since Papuans also carried the Neanderthal component in their genome, this meant that approximately 7 percent of the genomes of Papuans came from earlier forms of humans. This was an amazing finding. We had studied two genomes from extinct human forms. In both cases we had found some gene flow into modern humans. Thus, low levels of mixing with earlier humans seemed to have been the rule rather than the exception when modern humans spread across the world. This meant that neither Neanderthals nor Denisovans were totally extinct. A little bit of them lived on in people today. It also meant that Denisovans must have been widespread in the past, although it is curious that they don’t seem to have mixed with modern humans in Mongolia, China, Cambodia, or anywhere else on mainland Asia. A plausible explanation was that we had found the traces of admixture between the first modern humans to have migrated o
ut of Africa, moving along the southern coast of Asia, before the rest of Asia was populated by modern humans. Many paleontologists and anthropologists have speculated about such an early coastal migration of modern humans from the Middle East to southern India, the Andaman Islands, Melanesia, and Australia. If these people met and mixed with Denisovans, perhaps in present-day Indonesia, then their descendants in Papua New Guinea and Bougainville, and presumably also Australian Aborigines, would all carry Denisovan DNA. Maybe we didn’t see evidence of admixture with Denisovans elsewhere in Asia because other modern human groups that later colonized mainland Asia followed more inland routes and so never mixed with Denisovans. Or maybe they didn’t even meet because Denisovans were already extinct by the time they arrived.

  Later on, after our paper describing the Denisovan genome had appeared, Mark Stoneking in our department together with David performed a much more detailed genetic survey of Southeast Asian populations and found Denisovan admixture in Melanesia, Polynesia, and Australia and in some populations in the Philippines, but not on the Andaman Islands, and nowhere else in the region. Thus, the idea that the early modern migrants out of Africa who came along a southern route met Denisovans and mixed with them somewhere on mainland Southeast Asia seems a plausible one.

  Monty Slatkin used all the DNA sequences we had generated to test various population models. As I expected, he found that the simplest model that explained all the data was admixture between Neanderthals and modern humans, followed by later admixture between Denisovans and Melanesian ancestors. But we still needed to explain the very strange Denisovan mtDNA. There were two possibilities. One was that the mtDNA lineage was introduced into Denisovan ancestors through admixture with another, more archaic hominin group. This was the idea I secretly favored. The other was that it was due to a process known as “incomplete lineage sorting.” This means simply that the population that was the common ancestor of Denisovans and Neanderthals as well as modern humans carried earlier versions of all three mtDNAs. Then, by chance, one mtDNA variant that carried a lot of differences from the other two became the one that survived in Denisovans whereas the other two, which were much more similar to each other, became the ones that survived in Neanderthals and modern humans, respectively. This was particularly likely to have occurred if the ancestral population of Denisovans, Neanderthals, and modern humans was large enough that many mtDNA lineages could have coexisted in it. Monty’s population models showed that the data could be explained either by a small amount of admixture from another unknown human group or by this “incomplete lineage sorting” scenario. Although that meant we couldn’t favor one explanation over another, admixture nonetheless seemed a more plausible explanation to me. After all, we had already detected two cases of mixture between archaic groups and modern humans, so I had become much more open to the possibility that mixing was a common feature during human evolution. Furthermore, if the Denisovans were willing to have sex with modern humans, it seemed plausible that they would have sex with other archaic groups as well. I had come to believe that although the big picture of modern human spread was one where the replacement crowd pushed other groups into extinction, this was not a total replacement. Rather, some DNA seemed to leak over into the groups that lived on, so much so that I started using a term I had picked up from somewhere to describe this process: “leaky replacement.” Perhaps, I thought, the spread of Denisovans had also been a “leaky” affair.

  In July, we started writing the paper. Since 70 percent of the DNA in the Denisovan bone was endogenous, the sequencing of the Denisovan genome was much less of a tour de force than sequencing the Neanderthal genome had been, but that meant we had been able to produce a better-quality genome sequence, with slightly higher coverage (1.9-fold instead of 1.3-fold) for the Denisovan sample. But more importantly, the removal of the deaminated C’s had reduced the numbers of errors in it so that they were about five times less frequent than in the Neanderthal genome. We submitted the paper to Nature in the middle of August. I felt it was an amazing paper. From a bone about one-quarter the size of a sugar cube, we had determined a genome sequence and used it to demonstrate that it came from a previously unknown human group. It showed that molecular biology could contribute fundamentally new and unexpected knowledge to paleontology.

  Nature again sent our paper out to four anonymous reviewers. The comments we received differed in quality, from the jealously quarrelsome to the insightfully critical. As with our earlier mtDNA paper, one of the reviewer’s comments ended up substantially improving our paper. He or she pointed out potential problems with the analyses where we had used the Neanderthal and Denisovan genomes together to suggest that archaic gene flow was likely to have contributed the mtDNA to the Denisovans. I felt that we had dealt with those problems adequately, but the reviewer made us take the safer route and avoid such analyses entirely. His or her review also made us do more work to show that the signals of gene flow into Melanesians could not be due to differences in DNA preservation, sequencing technology, or other differences in how the data were collected. When we resubmitted the paper after taking the comments into account, this reviewer graciously acknowledged our efforts, saying “often, when one raises concerns regarding the underlying analytical methodology used to arrive at a conclusion, . . . the concerns are explained away by the authors. . . . Here, the authors have done the opposite: they have taken my comments very seriously, investigated the issues I raised, and undertaken a substantive revision of their work to address my concerns.” I felt like a schoolboy being praised by his teacher. The reviewer even identified himself: it was Carlos Bustamante, a population geneticist at Stanford whom I had always respected.

  In late November 2010, Nature accepted our paper for publication. The editor suggested that we delay publication until mid-January in order to get more press coverage and attention than would be possible during the Christmas holidays. We discussed this in the consortium. Some agreed with the editor. I felt that if we had worked as fast as we could in view of the potential competition, then we shouldn’t delay the last step. Against what was perhaps a majority opinion I pushed for publication as soon as possible and the paper ended up appearing on December 23.{64} I’m sure this caused it to get less attention that it would have otherwise, but I felt good about the fact that it came out the same year as the Neanderthal genome.

  When Linda, Rune, and I drove up to our small house in snowy Sweden that Christmas, I felt that it had truly been an exceptional year. We had achieved even more than I had dreamt we would. But even though we had sequenced the Neanderthal genome and opened the door to the genomes of other extinct human groups, many mysteries remained. One big mystery was when the Denisovans had lived. Both the finger bone fragment and the tooth were too small to allow us to obtain radiocarbon dates. Instead, we had dated seven bone fragments, most with cut marks or other human modifications, found in the same layer in Denisova Cave. Four of the seven turned out to be older than 50,000 years, while three were between 16,000 and 30,000 years old. So it seemed there had been humans in the cave before 50,000 years ago and then again after 30,000 years ago. I tended to think that the older people were the Denisovans and the younger people modern humans, but we couldn’t be sure. Professor Shunkov and Anatoly had found amazingly sophisticated stone tools and a polished stone bracelet in what seemed to be the same layer as the finger bone. Could they have been made by the Denisovans? It was an outlandish idea but the archaeologists felt it was possible.

  Another big mystery was how far the Denisovans had ranged. We knew that they were in southern Siberia, but the fact that they had met and conceived children with the ancestors of Melanesians suggested that they had been much more widespread in the past. Perhaps they had roamed all over Southeast Asia, from temperate or even subarctic regions to the tropics. I thought we needed to look for Denisovan DNA in fossils from China. It would also be extremely exciting if Anatoly and his team could find more complete remains of Denisovans in the Altai Mountains. If thos
e bones had features that set Denisovans apart from other hominin groups, these features would perhaps allow us to identify other fossils elsewhere in Asia as Denisovans.

  My group and others have since gone on to work on these mysteries. Still other groups have begun to use ancient DNA to study past human epidemics and prehistoric civilizations. But that December I felt a satisfaction rare in my scientific career. What started as a secret hobby when I was a graduate student in my native Sweden over thirty years ago had resulted in a project that seemed like science fiction when we announced it a little over four years earlier. We had now brought this project to a successful conclusion. With my family in our cozy little Swedish hut, I was more relaxed over those Christmas holidays than I had been for a long time.