Neanderthal Man (30 page)

Figure 17.1. The consortium meeting in Dubrovnik, Croatia, in February 2009. Photo: S. Pääbo, MPI-EVA.

Thus, he inferred that all three bones came from female Neanderthals, and that the four Y chromosomal DNA fragments must have come from DNA contamination. This suggested that we had about 0.6 percent male contamination. This estimate was not perfect since we could detect only contaminating DNA from men, but it suggested that the level of contamination was low and similar to what we had estimated from the mtDNA.

We discussed other ways to estimate contamination. Philip Johnson from Monty’s group at Berkeley suggested an approach that relied on examining nucleotide positions where most people today have a derived allele but where a Neanderthal individual had the ancestral, ape-like allele. In cases where a different DNA fragment from the same or another Neanderthal individual didn’t turn out to carry the ancestral allele, Philip suggested that we take a mathematical approach and model the likelihood that this was due to either normal variation among Neanderthals, sequencing errors, or contamination from present-day humans. When Philip later implemented this, the extent of contamination again turned out to be below 1 percent. We finally had estimates of contamination that I trusted and which showed that the quality of our sequences was excellent!

Martin talked about the Illumina data, which we hadn’t yet mapped. It made up more than 80 percent of all the fragments sequenced, or almost 1 billion DNA fragments. Much of the discussion centered on the challenges Udo faced in modifying the computer algorithm so that it would map these fragments quickly on the computer cluster in Germany. Although the analysis of the whole genome would have to wait until Udo had mapped all the fragments, we nonetheless discussed how we would do it. The first question was how different the Neanderthal genome was from that of present-day humans. Answering this seemingly simple question was complicated by the errors in the Neanderthal sequences due either to modifications of nucleotides in the ancient DNA or to errors caused by the sequencing technology. Illumina generated up to one error in every hundred nucleotides. To compensate for this, we had sequenced each ancient molecule many times over. But we still estimated that the errors in the Neanderthal DNA sequences added up to about five times as many as in the “gold standard,” the human reference genome sequence. Therefore, if we simply counted how many nucleotides differed between the Neanderthal and human genomes, we would be counting mostly errors in our Neanderthal genome.

Ed had a way around this problem. It relied on disregarding all differences that were seen only in the Neanderthal fragments and instead scoring  what the Neanderthal carried at positions where the human genome had changed and now differed from the ape genomes. To do this, he simply found all the positions where the human genome differed from the chimpanzee and macaque genomes. He then checked whether the Neanderthal carried the modern human-like nucleotide or the ape-like nucleotide at those positions. If the Neanderthals carried the modern human-like nucleotide, the mutation that caused it was old and predated the split between the Neanderthal DNA fragment and the human reference genome. If the Neanderthals carried the ape-like nucleotide, the mutation was recent and happened in humans after they split from the Neanderthals. Thus, the percentage of substitutions where the Neanderthal was “ape-like” as a fraction of all substitutions along the human lineage gave an estimate of how far back along the human lineage the Neanderthal DNA sequences split from DNA sequences in humans today. The answer was 12.8 percent.

If we assume that our common ancestor with chimpanzees lived 6.5 million years ago, this would mean that the last men and women to transmit their DNA sequences both to people living today and to Neanderthals lived 830,000 years ago. When Ed did the same calculation for pairs of people living today, their common DNA ancestors were found to have lived about 500,000 years ago. So Neanderthals were clearly more distantly related to people living today than people today are to one another; in other words; the Neanderthals are about 65 percent more distantly related to me than I was to another person in the room in Dubrovnik. I could not stop myself from secretly peeking at some of my friends in the sun-lit room and imagine a Neanderthal sitting among us. For the first time I now had a direct genetic estimate of how much closer I was to one of them than to a Neanderthal.

The biggest question on everyone’s mind was whether or not Neanderthals and modern humans had interbred. This was David’s question to answer, and although he hadn’t been able to join us in Dubrovnik, he explained his analyses that suggested interbreeding over a speaker phone. We discussed his results not only in the sessions but throughout coffee breaks and long, lavish and delicious Mediterranean meals that our hosts had organized. The question even dominated the morning runs that Johannes and I took on the outskirts of Dubrovnik, distracting us from the city’s medieval beauty and the damage suffered during the recent Balkan war, although not so much that we failed to stick to the paved roads to avoid land mines. Our conversations invariably centered on the intimate relations that may have taken place between modern humans and Neanderthals, who until 30,000 years ago had lived in the very area where we were jogging.

One thing that worried us was that all of our admixture analyses relied on Nick’s count of nucleotide matches between the Neanderthal data and either African, European, or Chinese individuals. That left us vulnerable to error in Nick’s computer code, the products of which Nick himself was the first to stress that we needed to check. An error could come from some subtle but systematic differences in the techniques used to sequence the modern humans, or from the way Jim Mullikin had mapped them to the human reference genome to find SNPs. The effects of error could be great even if the errors were small; after all, we were talking about differences of only 1 or 2 percent.

During the sessions we collected a list of things to do to check Nick’s and David’s results. Jim would align his modern human sequences to the chimpanzee genome instead of the human genome to eliminate any bias that might come from the fact that the human reference genome came partly from a European and partly from an African individual. But we also felt that we needed to generate our own DNA sequences from present-day humans. By doing so, we could be certain that they were all produced and analyzed in exactly the same way. Accordingly, if there were systematic problems in our process, we could be certain that the sequences had the same types of errors in them. We decided to sequence the genomes from one person from Europe and one from Papua New Guinea. That might seem an odd choice, but it was prompted by the intriguing observation that we saw an admixture signal that was as strong in China as in Europe. Conventional wisdom had it that Neanderthals had never been in China, but I have always been ready to question paleontological conventional wisdom. Maybe there had been what I liked to call “Marco Polo Neanderthals” in China? After all, Johannes had shown in 2007 that Neanderthals—or at least humans carrying Neanderthal mtDNA—had lived in southern Siberia, some 2,000 kilometers further east of where paleontologists had thought they lived. Maybe some of them had made it to China? However, we were sure that there had never, ever been any Neanderthals in Papua New Guinea, so if we saw the admixture signal there, too, then Neanderthal genes had entered the ancestors of Papuans before they came to Papua, and presumably before Chinese and Europeans separated from each other. We also included a West African, a South African, and a Chinese person in our sequencing plans. With the genomes of these five individuals, we would then do all the analyses again to see if the results held up.

The Dubrovnik meeting ended with a culinary feast that lasted for hours and left us all full of excellent food and pleasantly inebriated. During my career I had been part of many collaborations but none had been as  good as this one. Still, I felt a sense of great urgency to bring the project to completion. During dinner, I impressed on everyone that we were now on a tight time schedule, both because the world was awaiting our results after the announcement at the AAAS meeting and because we didn’t know what Eddy Rubin was doing in Berkeley with the Neanderthal bones we knew he had collected. Although I hardly ever have bad dreams, I claimed in my improvised speech at the dinner that I had had nightmares about a paper from Berkeley appearing a week before ours with all the same insights we had found.

The next morning I slept on the plane back to Germany. Shortly after returning to Leipzig, I came down with a cold, which developed into a fever and then chest pains in sync with my breathing. I went to the hospital and was diagnosed with pneumonia and given a prescription for antibiotics. But shortly after I got home I received a call to return to the hospital immediately. The lab results suggested I had blood clots somewhere in my system. I soon found myself staring at a CT scan showing blood clots clogging large parts of my lungs. It was a rattling experience. If these clots had reached my lungs as one large clump instead of several smaller pieces, I would have died instantaneously. The doctors blamed the blood clots on too much flying and perhaps the long, cramped bus trip through the night from Split to Dubrovnik. I was prescribed anticoagulants for six months and began researching therapeutic alternatives with the intensity that only comes from being personally affected. To my amazement I stumbled upon references to my father’s work from 1943. He had elucidated the chemical structure of heparin, the drug the doctors had given me when I entered the hospital and which had perhaps saved my life. While I found this amusing, I was also quite shaken. It threw a stark light on my family background. I had grown up as the secret extramarital son of Sune Bergström, a well-known biochemist who had shared the Nobel Prize in 1982 for the discovery of prostaglandins, a group of natural compounds that have many important functions in our bodies. I had seen him only occasionally during my adulthood, and the fact that he had worked on the structure of heparin was just one of the innumerable things I did not know about him. The sadness I felt for not having known my father made me realize even more strongly that I wanted to be there when my own three-year-old son grew up. I wanted him to know me. And I wanted to see the Neanderthal project through to completion. It was too early for me to die.

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We began sequencing our five modern genomes in May 2009. The pristine DNA, free of the bacterial contamination and chemical damage that marred our Neanderthal samples, yielded about five times as many DNA sequences from each of the five people as we had generated from the Neanderthal. Only a year or two earlier, sequencing those genomes in Leipzig had been unimaginable, but the sequencing technologies such as those marketed by 454 and Illumina had now made it possible for small research groups like ours to sequence several complete human genomes in just a few weeks.

Using the approach he had described in Dubrovnik, Ed estimated how long ago the five present-day human genomes had shared common ancestors with the human reference genome. He found that the European, Papuan, and Chinese individuals shared common ancestors with the reference genome a little over 500,000 years ago. Adding the San from South Africa to the group pushed the point of divergence back to almost 700,000 years ago. The divergence between the San (and related groups) and other people in Africa and elsewhere was among the deepest seen between present-day people. This put the 830,000 year age estimate for the common ancestor of the Neanderthal and present day-human genomes in perspective: having diverged only 130,000 years earlier, Neanderthals were different from us, but not by a lot.

Such calculations must be treated carefully, as they give one single value for the age to a common ancestor as if that was true for the entire genome. Genomes are not inherited as units, however, which means that each part of an individual’s genome has its own history and therefore its own common ancestor with the genome of any other individual. This is because each person carries two copies of each chromosome and one of these is independently passed on to a child. So each chromosome has its own independent pattern of history—or its own genealogy, if you will. In addition, each chromosome pair exchanges pieces with each other in an  intricate molecular dance called recombination that takes place when egg cells and sperm are formed. Therefore, not only does each chromosome in a population have its own genealogy but each piece of each chromosome does, too. Thus, the ages that Ed had calculated for common ancestors with the reference human genome, 830,000 years for the Neanderthal and 700,000 years for the San, represent grand averages across all parts of the genome.

In fact, when we compared DNA regions from two present-day people with each other, we could easily find regions where they shared a common ancestor just a few tens of thousands of years ago but also regions where they last shared an ancestor 1.5 million years ago. The same was true in a comparison of present-day people with the Neanderthals. So if someone could take a walk down one of my chromosomes and compare it to both a Neanderthal and a reader of this book, that chromosomal pedestrian would find that sometimes I would be more similar to the Neanderthal than to the reader, sometimes the reader would be more similar to the Neanderthal, and sometimes the reader and I would be more similar to each other than to the Neanderthal. Ed’s average simply meant that there are slightly more regions of the genome where the reader and I are more similar to each other than either of us are to the Neanderthal.