Unlocking the Past Read online

  From the hominid bones in the Liang Bua cave came a female of around a metre in height and with a brain around a third of the capacity of our own. The discovery would be much less surprising if the sediments were a few million years old, but these were a mere 18,000 years old. What is more, they were found in association with stone tools of a complexity typically associated with modern humans. In October of 2004, Nature was able to announce a new species of human, and christen it Homo floresiensis, though the popular press preferred the nickname ‘hobbit’.

  The nickname may be prescient. With some of the spirit of Tolkien’s fictional version, this hobbit has not proven easy prey for the molecular archaeologist. In 2003, two of the foremost research groups, Pääbo’s at Leipzig and Cooper’s at Adelaide, set to extracting DNA from the dentine in the hobbit’s teeth. By that time, 18,000 years was old, but far from the limits of DNA analysis, which in the same year had been persuasively pushed back 700 millennia by the Thistle Creek horse. Teeth seemed to offer ideal material; however, neither attempt was successful.

  It may be a problem of the drill speed, and perhaps the cementum may be a better source. At Adelaide, Christina Adler has stuck with the quest, and a lot more surprises may be in store for these diminutive cousins of ours. The hobbit has been featured much in the press; there is much ongoing debate and disagreements about the identity, ownership, and conservation of fragments of at least fourteen individuals sealed beneath volcanic ash in the Liang Bau cave. Those debates and disagreements among the living are conspicuous and ongoing. Meanwhile, the hobbits themselves are hanging on to most of their secrets.

  There is something of a striking contrast between the remains in the Liang Bua Cave in Flores, and those from the Denisova cave in the Altai Mountains. The number of hobbit individuals at Liang Bua runs into double figures. Although most of those individuals have left fragmentary evidence, one exists as an articulated skeleton, albeit poorly preserved. That is quite a cache for biomolecular analysis, but their genetics remain a mystery. The Denisova remains are twice as old, and comprises a finger bone, a toe bone, and two teeth. Yet from the finger bone alone, a story of profound richness and depth has unfolded, concerning not just a human species hitherto unknown, its physical characteristics and geographical spread, but also much about how the human genus has evolved and how different components of the larger human family have interacted. In the ever surprising world of ancient biomolecules, it has been perhaps the most remarkable story of all.

  The Denisova humans most likely form a sister branch to the Neanderthals, diverging around 640 millennia ago, around four-fifths of the time since the earlier divergence of our own species comprising of all living humans. After that genetic divergence, the fates of Neanderthals and Denisovans diverge in other ways. Neanderthals become prominent in Europe, where they interbred with our species, but also experienced significant selection from which derived a genetic bottleneck now observable in the range of ancient hominin DNA. Denisovans, by contrast, clearly expanded to the south and west, as Melanesia, where their legacy is to contribute up to 6 percent of the genome of contemporary Melanesian populations.

  Looking at this data together, we can infer ancient geographies much more expansive than envisaged from the physical remains alone. Neanderthals are known from their skeletal remains across Europe, and as far east as the site of Teshik Tash in Uzbekistan. The molecular evidence takes that range yet further east to the Altai mountains. Far more surprising is the range of the Denisova taxon. While only recorded in physical form at a single cave, their genetic imprint can be traced as far west as Spain, as far north as the Altai Mountains, and as far west as Melanesia. The fact that a significant amount of interbreeding has taken place causes us to revisit how we categorize and delineate the human family, and how old and diverse we perceive that family to be. At one level this is a taxonomic debate about what we actually mean today when we retain such units as ‘genus’ and ‘species’ to draw tight frontiers along boundaries that are actually porous. At another level, it challenges us to reflect on what we mean when trying to understand our world by means of a clear opposition between ‘ourselves’ and ‘the other.’

  The unfolding story is more complex still. Rather like a large family wedding, in which long-lost cousins are glimpsed at the back of the congregation, so in the more expansive human family that ancient DNA is revealing, alongside the obvious newcomers are glimpses of the more elusive family members.

  By a stroke of fortune, the Denisovans were not the only hominins to find shelter within the Denisova cave. Pääbo’s group also recovered a toe bone, whose DNA clearly attested to Neanderthal identity. But just as gene flow can be seen between modern humans and other hominins, so the Denisovan genome can be estimated to have up to 17 percent local Neanderthal DNA. But beyond that is another 4 percent of the Denisovan DNA, best accounted for by yet another human species, whose identity remains more mysterious still. Even as I write these words, newspapers and the airwaves bring news of yet another relative whose bones have been recovered from a deep cave system in the Gauteng province of South Africa. At this point we know very little about the age and affiliation of Homo naledi, who nonetheless serves to remind us the story is far from over.

  All the above relates to a single genus, Homo, but the fast pace of developments has also allowed us to look more closely at ourselves, and more broadly at our wider family. It has impacted both the understanding of our own particular species, and our more distant primate relatives. The Molecule Hunt was published while the Human Genome Project was well underway, and two years before it reached completion. Five years after that completion, it was followed by another large-scale cross-national effort, the Thousand Genome Project, which applied a battery of modern techniques to explore diversity within our species. This was no small undertaking; it aspired to sequencing ten billion base pairs a day over two years, and a new complete human genome every twelve hours.

  At the same time, the completion of the Human Genome Project was followed by parallel achievements with other primates. The chimpanzee genome was published in 2005, the macaque in 2007, the gorilla and bonobo in 2012. These achievements come together into a finely detailed genetic landscape, within which we can see who we are, what we look like and how we live our lives, how different we are and how much we share genes. In the 2014 issue of the journal Cell, Svante Pääbo, whose research groups have done so much to reveal this genetic landscape, summarized the known genetic landscape for Homo. He highlighted four branches (modern humans, Neanderthals, denisovans, and an additional mystery taxon). These could reasonably be thought of as separate species, but with measurable gene flow between them. Up to 8 percent of the mystery line DNA sequence (the only way we know of its existence), up to 5 percent of Denisovan, and up to 2 percent of Neanderthals crossed beyond their ‘species’ boundary into other hominids. Reproductive boundaries were clearly in place, but repeatedly breached. Alongside the leakiness of these species, Pääbo challenges us to reflect on our assumptions about patterns within our own species.

  Looking within modern humans, he reminds us that while we have clear perceptions of the physical difference between Africans and Asians, ‘not a single nucleotide difference distinguishes all Africans from all Eurasians, and only twelve positions carry differences where one allele is present in 95 percent or more of Africans and in 5 percent or less of Eurasians or vice versa.’

  A little later in the paper he comments:

  ‘When considering how modern humans may differ from Neandertals and Denisovans, it should not be forgotten that these archaic humans are so closely related to present-day humans that for about 90 percent of the genome, they fall within the present-day human variation, (i.e., for 90 percent of the genome, some humans today are more closely related to the Neandertals and Denisovans than to other present-day humans). In order to think about how modern humans may differ genetically from Neandertals and Denisovans, it may thus be useful to consider how present-day human groups d
iffer genetically among themselves’.

  These are challenging issues with implications that are not just scientific, but also philosophical and perhaps moral. The field began with a great deal of confidence in the phylogenetic trees. This chapter, and most of the subsequent ones had that tree in mind throughout. Back then, the branches were discrete with clear boundaries, joining at singular, identifiable branches points, which constituted ‘origins’, of humanity, of farming, or of particular ethnic entities. Now, those branches have become less distinct; they can even grow back into each other. Their boundaries are now more porous, and their branching points more complex. Those more complicated, nuanced trees no longer provide easy answers. They need to be addressed with specific questions, interrogated with the armory of bio-informatic techniques that has grown up alongside molecular science. So it is not just a shift in method, but also a shift in approach to knowledge that is taking place in the topics covered in each of the following chapters.

  4

  final traces of life

  burial

  We would be wrong to take the survival of ancient bones, or indeed any organic remains, for granted. Vestiges from the distant past are very variable indeed. Sometimes the search for archaeological remains takes us several metres below the surface. At other times, recognizable traces from some ancient epoch are found intact immediately below the modern topsoil. Rich patterns of ancient, unsuspected structures may be encountered with the removal of as little as a few centimetres of sediment. The fact that bio-archaeologists have anything at all to look at owes a great deal to the simple process of burial.

  Had those Neanderthal bones been left exposed on the surface of a fertile soil they would have vanished within weeks, or even days, the last bones stripped of meat and carried away by dogs and birds. Beneath the ground, and, in particular, buried within the sediments of the Feldhof Cave, the story is different. An army of insects, bacteria and fungi can dispatch the soft tissues without much difficulty. With the help of an acid medium around the body, they can also dispatch the bones.

  The micro-organisms of an alkaline soil can make much less impact upon sizeable dense organic objects like teeth and bones, and burial is sufficient to keep them intact. Burial also confers protection against the greatest ravages of frost or heat, or fluctuations between the two. There are one or two other organic tissues that burial can protect from destruction on its own. Charred plant remains and the shells of snails and other invertebrates are among these, though their apparent protection is often partial. Their seemingly intact appearance may be an illusion, and the molecules within may be in disarray. None the less, for many excavations, these are the core of the bio-archaeological record: teeth and bones, invertebrate shells and charred plant remains. On sites where the soil is acid, even the bones and shells will have gone. Such a pattern of limited preservation may persist however deep we dig. In some cases, however, it is radically transformed with depth, as it was beneath the Somerset field discussed in the opening chapter, and within the Florida sinkholes that yielded the remarkable pickled brains that figured prominently in an early episode of ancient DNA research.

  A striking feature of sites such as these is the permanent water table, the level below which water has never dropped since the archaeological layers were first buried. The whole character of the sediments below this permanent water table is quite distinct from what lies above. Unlike the aerated levels higher up, they have not been mixed or turned by soil animals. There are no earthworms or insects below this permanent water table–indeed, there are none of the soil organisms that need oxygen from the atmosphere. That cuts out the fungi and many bacteria, greatly reducing the pace and extent of decay. Massive fragments, such as pieces of wood, are the most obvious survivors in these pickling sediments, but, on closer inspection, these fragments can be seen to contain seeds, leaves, insects and other invertebrates. A microscope can reveal layer upon layer of intact pollen grains within them. If they were to be fully scrutinized, a single sample of one of these waterlogged sediments could absorb as much of a bio-archaeologist’s time and effort as an entire site on which the sediments had been permeated by air.

  Even in these submerged layers devoid of air pockets, there are many clues to the organic breakdown and decay that is still going on. One of these clues is the state of the waterlogged wood, and the manner in which it splits and flakes when lifted on to the grassy verge. Another clue is the state of some seeds. Although they were once hard compact objects, they are often found in waterlogged deposits reduced to empty sacs, their outer coating surviving but their innards gone. A third clue is the condition of some of the ‘bog-bodies’ that have been retrieved from peat deposits in several countries over the centuries. Their skin and their facial features may remain disconcertingly realistic, but many of their internal organs have gone. In most cases, they have lost their brains along with most other internal organs. All these clues point to partial breakdown, some components breaking down, and others not. What is happening is that a select band of anaerobic bacteria (those that can live in the absence of free oxygen) are gradually and incompletely continuing the process of decay. They have a more limited chemical repertoire than their aerobic counterparts, and cannot attack certain types of molecules. It is the tissues that are rich in such resilient molecules that can persist beneath the permanent water table.

  The sinkholes at Windover and Little Salt Spring in Florida preserve bodies in much the same way that the Somerset peats preserve the wooden trackways, by excluding most of the oxygen. In fact, there must be something else going on to protect even their brain tissues from decay–the bog bodies of the European peats are not preserved so well. Bill Hauswirth, who began the examination of DNA from the Windover group, suggests that the slight acidity and high mineral content of the water in the sinkhole might contribute to their longevity. The preservation of brain tissues is reflected by preservation of ancient DNA, and the Windover sinkhole has yielded one of North America’s large ancient genetic populations. Over 170 bodies have been recovered of which at least 91 retain soft tissue, presumably brain matter, within their skulls.

  If we could really dig deep within these waterlogged archaeological deposits, and many of these deposits do go down to a considerable depth, we might expect to encounter a level too inhospitable even for anaerobic bacteria. Such levels would surely provide the greatest wealth of organic residues and molecular survival. Archaeologists have, however, never reached far enough down to find such a level, but they have not been alone in looking. Another group of specialists, the Quaternary scientists, probe even deeper into the Earth’s surface to analyse ancient environments and climates. Their deepest probes penetrate the ocean floor.

  From the outside, the good ship JOIDES Resolution gives little clue to its unusual cargo and crew. That cargo comprises a vast assemblage of pipes, taking up much of the deck. Manoeuvring along the scant space around the stacked pipes is a group of eminent research scientists, whose goal it is to pass those tubes, each one connected to the next, down through the ocean floor. They will go down for hundreds, even thousands of metres, into ocean-bottom sediments that may have taken millions of years to accumulate. The interminable grey sausage they extract and transfer to a plastic tube will be taken to the several floors of laboratories above and below deck. It will provide a wealth of data about our planet’s recent history, and the minute fluctuations in its climate while those ocean-bottom sediments were being laid down. If the archaeologists digging on land have failed to reach sediments where biological activity has completely stopped, then surely here within these cores the ocean drillers would find it.

  Samples taken from these long grey cores were dispatched to John Parkes’s laboratory in Bristol. He found biological activity still present at the ocean bottom, and a few metres into the sediments. This he could show by culturing the samples in sterile conditions, bringing the slow-growing bacteria from this hostile world to life. This microbial activity continued as he sampled fu
rther and further down. Astonishingly, there were still viable bacterial moving through their life-cycles at an imperceptible pace, under the immense pressures within the sediments a full kilometre below the ocean floor. If biology was still at work at those remote depths, albeit incredibly slowly, there were certainly no sediments that archaeologists might dig that were sufficiently deep to bring biology to a complete halt. The best we could hope for would always be partial breakdown.

  high and dry

  Burial does two things. It excludes the larger beasts that have the power to reduce and digest even the densest of bones. Then, further down, with the help of the water table, it cuts off the oxygen supply and restricts the range of decay organisms to particular kinds of specialized bacteria. Oxygen is not the only major supply that can be cut off; many parts of the world are starved of the other major source of life, namely water.

  The two most spectacular forms of biological preservation that archaeologists encounter are thus found in extremes of wet and dry.Arid, water-free sites were to prove a magnet for the molecule hunters, drawing them, for example, to the dry banks of the Nile, where stems of sorghum have been excavated, neatly bound in their sheaths, their seed-heads still intact centuries after burial. The hunters also made their way to the intensely desiccated coast of South America above the Pacific Ocean, where, just under a century ago, the German scholar Max Uhle discovered a series of exceptionally well-preserved human bodies at a beach called Chinchorro. Their internal organs had been carefully removed, the resulting voids stuffed with hair or grass and the incisions stitched up. The stuffed bodies were painted and adorned with wigs. Since Uhle’s discovery, several hundred ‘Chinchorro mummies’ have come to light along that Pacific coast. The intricate mummification practices that preserved them have been traced back as far as 7000 BC, and continued for at least six millennia, providing the first generation of molecular archaeologists with a rich human data-set.