Unlocking the Past Read online

  While it may be tempting to portray the conflict as between the evidence of fossils and that of molecules, it would be a false portrayal. Many of those studying the fossils have concluded that the details of their variability fit best within the recent ‘Out-of-Africa’ model. They also had the contentious molecular results at their disposal. Both sides persisted with the case, until one more piece of information was extracted from the fossil bones. The growing collection of almost human skulls from around the Old World had been scrutinized for ever finer details of form and structure. What was needed was for one of them, be it one of the south-east Asian Homo erectus fossils or a European Neanderthal, to yield up a clue about their own genetics. As fate would have it, it was the very first of these fossils to be recognized that would oblige.

  neanderthal genetics

  Allan Wilson, whose research group had been central to this story of exploration into the human molecular past, tragically died before its culmination. His colleague, Svante Pääbo, had recently moved to the Munich Institute of Zoology to take up a professorship. A few hours’ drive to the north-west of Pääbo’s new home was the cave above the River Dassel in which the remains of the first recognized Neanderthal had been unearthed. They were now kept in the Rheinisches Landes-museum at Bonn, where Ralf Schmitz and his colleagues were engaged in a new study of the Neanderthal specimen. Pääbo immediately opened negotiations to sample the specimen for ancient DNA. He had to be patient. The museum curators were very rightly cautious about the request not simply to study the bones, but to sample one of them destructively for a technique that was still very new to the scientific world. The age of these bones was still unclear. They were somewhere between 30,000 and 100,000 years old, which was clearly pushing DNA recovery to its limits. A likely outcome of cutting out a sizeable chunk from this precious specimen was a nil result. Balanced against this was the potential, for the very first time, to explore the genetics of a hominid other than ourselves. After several meetings, and the passage of a few years, the curators agreed that the work was sufficiently important to give it the green light. The meticulous investigation of Pääbo’s team demonstrates how far biomolecular archaeology had come by the mid 1990s. In place of a speculative dive into poorly understood ancient tissue, theirs was a careful analysis of biomolecular preservation of the bone as a whole, gradually homing in on the ancient DNA, followed by cross-checks and a critical phylogenetic consideration of the results.

  Pääbo’s team sawed into one of the long bones, removing a segment upon which the analyses could begin. They first looked at the state of the bone’s proteins, and of the proteins’ molecular building blocks, the amino acids. This was in order to get some sense of the general molecular survival within the fossil, before embarking on the target molecule, DNA. The levels of amino acid in the ancient bone were between one-quarter and three-quarters of the equivalent levels in a fresh bone. This was a very encouraging result, and they went on to examine the state of the amino acids in order to get a further idea of the conditions of molecular preservation. We saw in the last chapter how Hendrik Poinar had worked out how to use amino acid racemization as a measure of how dry the molecules had remained. They tried it now on the Neanderthal specimen. The level of racemization was low, indicating that the heart of the bone had remained almost completely dry.

  At first, this result may surprise. Why should a bone, for thousands of years in a fairly ordinary sediment, have stayed dry? Moreover, there are now a number of successful ancient DNA amplifications from bones recovered from waterlogged peats, which certainly were never dry. The truth is that the bone surface can remain moist, but islands of solid tissue within can remain dry. What matters for molecular preservation is not necessarily the general state of the tissue, but of the best conserved components of it. As molecular techniques have become fine-tuned to deal with smaller and smaller samples, so those conserved islands of molecular survival could also get smaller and smaller, yet still allow detection.

  The solidity of an ancient bone has a lot to do with the temperatures to which it has been exposed. At too high a temperature, the collagen, one of the molecules endowing the bone with strength, would turn to gelatine and dissolve, leaving a minutely porous structure open to breakdown. The Feldhof cave was well to the north of the Neanderthal range, close to the limits of glaciation during the cold spells of the Quaternary Epoch, and clearly a good place to start looking for molecules. Hendrik Poinar’s amino acid assays looked encouraging; the interior of the bone had remained dry. The team set about their hunt for ancient DNA.

  In a specimen so old, the DNA was bound to be heavily fragmented. The team needed to target a short length, but one with the right level of variability. The first hypervariable segment of the mitochondrial control region was clearly a good place to look, for the reasons discussed above. They chose a 105-base-pair segment of the first hypervariable segment at one end of the D-loop, and set to work designing primers. After a series of PCR cycles they separated out the amplified DNA and got a positive reading at the level corresponding to 105 base-pairs. A century and a half after these curious bones with their enlarged brow-ridges and sturdy limbs had first taken the world by surprise, those same bones were yielding up a short fragment of their genetic blueprint.

  After many checks and balances, it was clear the researchers had succeeded in amplifying a DNA strand that was similar to the equivalent strand in modern humans, but too different to be explained as contamination. To be doubly sure, Pääbo sent a sample of bone to his old colleague from the Berkeley days, Mark Stoneking, now at Penn State, to check the result in a different lab on the other side of the world from Munich. Stoneking had some difficulty with the full length that Pääbo’s lab had sequenced, but, targeting a shorter sequence within it, managed to corroborate Pääbo’s result. In this shorter 30-base-pair sequence, the labs on either side of the Atlantic displayed the same four deviations from the Anderson reference sequence. They were on to something.

  Reassured that this really was Neanderthal DNA, and not some contaminant or artefact, Pääbo’s team pressed on to a truly ambitious target. They planned to map the entire length of hypervariable segment I within the mitochondrial control region. What this entailed was building up, bit by bit, sequences of around 100 base-pairs long, to develop a rather longer master, in this case 379 base-pairs long. This was, in essence, to take the logic of Jurassic Park as far as it is technologically feasible to go. In the novel, this same patchwork procedure was employed on DNA from deposits millions of years old, to build an extinct composite sequence, billions of base-pairs long. Pääbo’s lab had, more modestly, taken DNA from a fossil tens of thousands of years old, to build an extinct composite sequence hundreds of base-pairs long. The other difference is that Pääbo’s team succeeded in the real world.

  This hypervariable segment lives up to its name. As we saw above, even its overall length can vary dramatically between different mammal taxa. Within a single, relatively young species such as humans, sequence differences vary from the Anderson sequence by eight substitutions on average. If we compare ourselves with our closest living relatives, the chimpanzees, the average number of differences is 55. The average deviation of the replicate Neanderthal sequences was estimated as 26.This measure of difference was three times greater than the internal measure for our species, and half the difference between chimps and ourselves. Furthermore, it was no closer to modern European sequences than it was to Asian or African sequences. In modern human terms, the Neanderthals were out on a limb.

  It was a dramatic finding that seemed to clinch the Out-of-Africa argument. Of all the living humans whose mitochondria had been sequenced, from throughout the world, none of them had anything like a Neanderthal anywhere in their maternal lineage. What Pääbo’s team had uncovered was instead a distant relative of modern Asians, Africans and Europeans. It was too far from any of them to be thought of as a close cousin, and with a distinct mitochondrial fingerprint that had never found its way int
o any modern human lineage. There was no sign of gene flow at all.

  These data also provided a basis for a new molecular clock to determine relative evolutionary time scales for chimps, humans and Neanderthals. Allan Wilson’s early use of a protein clock had suggested a common human-chimp ancestor around 5 million years ago, and this figure had not much changed. The most recent estimates placed it between 4 and 5 million years ago. Using that as a baseline, modern human ancestry would come out at 120,000-150,000 years ago, a figure consistent with that of Mitochondrial Eve, and the human-Neanderthal common ancestor lived 550,000-690,000 years ago. The first anatomically modern human that walked had had no relations with the Neanderthal line for half a million years.

  The findings were published in the prestigious journal Cell, and a news conference was held in London to launch the spectacular findings. The British press hailed the ‘coming of age’ of ancient DNA research. Chris Stringer compared the scientific importance to landing Pathfinder on Mars. Others, while admiring the research, were more circumspect, pointing out that of course this was only one specimen. At that stage it was argued that no ancient skulls of ‘modern’ form had been tested. Perhaps they too had a very different genotype. An interesting suggestion was put forward that the genetics of early modern humans and Neanderthals should be assessed in Israel, where they co-existed for a considerable time. An early modern form skull has since been assessed by Bryan Sykes in Oxford. It was from a 12,000-year-old deposit from Cheddar Gorge in south-west England. The amplified sequence carries only two deviations from the Anderson sequence, and thus tends to support the Pääbo model. Alas, the Israeli bones are unlikely to be suitable. At Oxford, Alan Cooper conducted a range of essays on Neanderthal and other bones from sites in various temperature zones. He succeeded in amplifying DNA from horse and mammoth bones of similar antiquity, but from Alaska and Siberia. Although the same methods were used, similarly ancient bone samples, including Neanderthal samples, from France, Croatia and Spain, produced a null result.

  The original Neanderthal specimen, however, has continued to yield genetic information from its ancient DNA. Two years after Matthias Krings and the Pääbo team published their findings from the first hypervariable segment of the control region, a further analysis appeared in print, this time of its second hypervariable segment. Once again they recorded a larger number of mutations than would be anticipated within our own species. Their earlier findings were further endorsed by a second section of the mitochondrial genome. More recently still, two other Neanderthal bodies, one from the northern Caucasus, the other from Croatia, have yielded up parts of their DNA sequence.

  Now these secrets have been so meticulously tapped, we have some insight into how different Neanderthals were in genetic terms, and what that means in terms of the fate of hominid species. While they were so very different, they by no means occupied different worlds. Their common world is something of which we can catch an occasional glimpse.

  a tale of two species

  It is almost impossible for us to conceive of the vast expanse of time that has elapsed since Palaeolithic hunters last roamed across a windswept frosty plain in pursuit of woolly mammoths, those long epochs during which farming, trade, urban society and the modern age all came into being. Yet for a period of time that was perhaps twice as long as this, two independent species of human coexisted in Europe. Their faces, the shape of their heads and bodies differed far more than humans today differ. They certainly would have seen each other, occupying the same regions and in some cases roaming across the same valleys and places of refuge. Both gathered around hearths to prepare and cook meat, using similar tools of wood and stone in its capture and preparation. Both adorned their bodies, the modern humans at least had language, and some have argued that the Neanderthals played music. Both cared for their elderly, sick and infirm, and buried their dead. The two groups had far more in common than humans share with any living primate, and both had large brains, the Neanderthals slightly larger. There is growing evidence that they watched one another and took ideas about toolkits, adornment, perhaps music and ritual. But they were different branches of the evolutionary bush with separate fates.

  It seems that for thousands of years these two distinct species of humans coexisted in Europe. We have no idea how cautious or hostile the two species were, but we now have evidence that they did not interbreed. Ideas passed between them, perhaps even artefacts. In itself, this does not imply a close bond. Today Coca-Cola, transistor radios and nuclear weapons can pass between modern human societies that are far from being on speaking terms with each other. Concepts and things could have passed between the big-brained Neanderthals and our own ancestors in a variety of ways, without them getting into bed with each other. Some Neanderthals did not adopt any traits from their modern human counterparts. Interestingly, these more conservative Neanderthals persisted for much longer than their more malleable relatives. They were still to be found in southern Spain 20,000 years ago, that is 10,000 years after the disappearance of the species from most parts of Europe, and 20,000 years after modern humans first moved into Europe.

  In Neanderthals, we see the typical fate of hominids, indeed the typical fate of any species. A genetic combination persists for a certain length of time, but not indefinitely. The Neanderthal had persisted for a few hundred thousand years. Some hominid species may persist for more than a million years, but not forever, and the same will probably be true of us. We are not part of an ongoing and unique surge towards human progress; we are finite components of a natural world that is changing and ephemeral.

  For the multi-regionalists, eager to cling to a more idealized view of human progress, the relationship is directly parallel to that between different ethnic groups today. Most reproduction is within the ethnic groups, but with a significant gene flow between them, creating a common species identity and trajectory. The Out-of-Africa model offers something rather harsher, and rather more resonant with the classic Darwinian view of nature red in tooth and claw. There was nothing sacred about human evolution, about the generation of self-consciousness, sympathy and creativity. The hominid species with the biggest brain lost out in the struggle for survival, finally dwindling and disappearing on the south-west perimeter of Europe as its more expansive cousin proved fitter for survival, at least for a while.

  Milford Wolpoff has yet to be convinced. He has praised the ancient DNA work on technical grounds, but wonders whether the conclusions are hastily drawn. He argues that just because a gene has disappeared, or a particular DNA sequence is no longer found, that does not necessarily amount to non-ancestral status. Chris Stringer naturally feels differently: ‘Of course this is only one specimen, but it fits so well with the view of one side of the argument about Neanderthals–that they are very distinct, that they are not our ancestors–that I think it goes a very long way toward resolving the Neanderthal problem’ (News Conference, Natural History Museum, 10 July 1997).

  This evidence has captured our own species in its youth, in a lifetime that may only have run a tenth of its course. Just as the archaeological record shows the Neanderthal population both expanding and shrinking, in our case it displays its expansion, out of Africa and across Asia and Europe. The molecules have played a central role in sharpening up that story, but as we move into the most recent 10,000-20,000 years, they play a more vital part. This is when molecular persistence becomes significant for a wide range of species and tissues. It is also in this last brief episode of human evolution, after Neanderthals have left the stage, that the archaeological record of past societies displays its greatest diversity by far.

  afterword

  Matthew Collins had suggested there might be nine Neanderthal individuals in a condition adequate to yield sequences of their DNA. In terms just of individuals for which published genetic information exists, that number has already trebled, and we in addition have a complete Neanderthal genome draft from Pääbo’s Leipzig lab. What is more, our curious cousins are now part of
hitherto unseen extended family, one of which came to be known through a single finger bone.

  When the Homo sapiens was extending its range beyond Africa and across the world, its extended family included two other species: H. neanderthalis and H. erectus. We can now extend that list to include H. denisova and H. floresiensis, and there are tantalizing hints of more relatives besides, including a certain H. naledi making the headlines as I write. The first ancient DNA analyses suggested that the known species were reproductively isolated; the last three pages of the chapter reviewed the ongoing debate and discussion of that issue. Fifteen years later, we have arrived at the knowledge that the reproduction isolation of sister hominin species was not as complete as those first analyses might suggest; a measurable amount of gene flow had taken place, prompting us to revisit what we consider to be the boundaries of ourselves as human beings and the larger family of nature of which we are part.

  Back in 2001, an excavation pit sunk into the deposits of the Indonesian cave of Liang Bua yielded a few bones of the Stegadon, an extinct elephant, alongside bones of rats and komodo dragons—interesting finds, providing an ecological glimpse of the small island of Flores about the time of the last glacial maximum and beyond. Two years later, the eminent palaeoanthropologist Peter Brown travelled to Jakarta to inspect a diminutive human skill from the same sediments. Within a few seconds of picking up a lower jaw, Brown realized he was holding something remarkable.