by Martin Jones
Around the time of my initiation into archaeology in a Somerset field, another team was hunting down a series of earlier features that were immersed within the expanses of peat around us. Waterlogged wooden trackways had been stumbled upon by peat-cutters since the nineteenth century at least, but now they had attracted the attention of someone who recognized that they were prehistoric in date, and who would go on to commit much of his working career to tracing them and the ancient landscapes of which they were part. In 1973, a year after Clarke’s exciting paper, John Coles put together a research group of archaeologists, biologists and tree-ring specialists to unlock the treasury of bio-archaeological information contained within the peat. In the same year that the Somerset Levels Project began, a small number of ‘archaeological units’ were formed in Britain, to rescue archaeological information threatened by development projects. The general image of rescue archaeology at the time was of a cluster of itinerant diggers, working anxiously and rapidly in the shadow of an earthmover. A few of those units took the unusual step of putting the new bio-archaeological research at the forefront of their activities. As one of those itinerant diggers, but with a natural science degree, I became one of those bio-archaeologists in the Oxford Archaeological Unit. There weren’t any models for how we should work–we were in the delightful position of making it up as we went along. One of the main tasks facing the newly formed Oxford Unit was the remains of a series of farms and hamlets, contemporary with the Somerset villages discussed above, that were disappearing as the Thames gravels were quarried away. One thing we were clear about–we wanted to do a lot more than scrub and label fragments of pottery. We wanted to float and sieve for seeds, insects and bones, in order to gather the kind of biological data that could enrich the models of prehistory that David Clarke had begun to describe.
As the 1970s progressed, many excavations brought in sieving and flotation alongside the pickaxe and trowel, in order to capture some of that data. More and more organic fragments were found within archaeological sediments. Remains of food, fuel, bodies and building materials were augmented by the debris of wild plants and invertebrates that hinted at the living environments around those living settlements. Many of these required microscopic examination, and the high-power lens brought remarkable detail into view. Even where these organic fragments had been eroded, cooked, eaten away and discoloured, still, more often than not, cellular structure within them remained. In some cases even the nuclei and other sub-cellular structures were visible. Different archaeological scientists used this detail to rebuild environments, living conditions, and methods of food production and preparation.
from ancient tissues to ancient molecules
By the 1980s ‘bio-archaeology’ had come of age as a routine aspect of archaeological method. The arrow-laden maps of prehistoric cultures had given way to discussions of agricultural practice, house construction and the health and nutrition of ancient rural communities. Prehistoric people and their disappeared worlds were beginning to come to life. But it did not stop there–from the late 1980s another door opened on the archaeological record and what it was able to reveal to us.
The study of ancient people was increasingly concerned with the organic, living processes these new forms of evidence revealed. It was drawing closer to studies of the biological world. But biology too had been going through great changes. To get to the heart of the living world and how it operates, biologists too had expanded the range of their observations. For many years, they had looked within whole organisms to the cells and sub-cellular structures within that formed the mechanics of life. In more recent times, they moved one stage further to the molecules that made those structures work. These included the fatty substances and carbohydrates that fuelled living processes, the proteins that built living tissue and regulated biological pathways, and the molecules that encoded the instructions for all this, the DNA at the heart of each cell. By the time archaeologists were becoming proficient at digging up fragments of ancient organisms and recognizing their tissues, biologists had already progressed deep into the heart of cellular dynamics, to decipher the molecular basis of life.
Exploring the possibilities of bio-archaeology during the 1970s and 1980s, experimenting with some fairly primitive methods of flotation and sieving, and trying to make sense of countless blackened plant fragments from prehistory, we were conscious that the biology we were then introducing into archaeology was already lodged in the past. We were attempting comparative, whole-organism studies that had a lot in common with the kind of natural history that grew in the nineteenth century and blossomed in the early twentieth. They were proving extremely valuable in bringing the archaeological past to life, but at the same time what contemporary biologists were doing suggested that we could probe much deeper. What if there were molecular traces that allowed much greater precision in identification, even when the tissue was fragmented or had disappeared completely? What if these precise identifications could take us beyond species to close relatives, to individuals, even particular genes? All this was speculation, spurred on by what could be seen through our microscopes. Whatever ancient biological material we examined, it was clear that much cellular organization had survived the ravages of time. Perhaps secreted among those cells were intact biomolecules, minute time capsules each with their own record of a distant past.
Some of those biomolecules did persist in a relatively intact state. That much was clear from the organic objects within the peat–they had to be made of something. It was also already clear that the less conspicuously organic remains, such as pieces of pottery, retained some biomolecules. As early as the 1930s, a Boston scientist, Lyle Boyd, realized that the kind of antibodies that could attach themselves to blood proteins found throughout living tissue would also attach themselves to tissue taken from mummified bodies, and she went on to check the blood types of several hundred ancient Egyptians. By the 1970s various analytical chemists, such as Rolf Rottlander in Tubingen and John Evans in London, realized that methods of analysis in organic chemistry had reached levels of sensitivity that would allow slight traces of fatty/oily substances or ‘lipids’ to be detected inside ancient pots. They went on to use infra-red spectroscopy to track down the animal fats, plant oils, and even cooked eggs that once occupied some of the ancient pots unearthed by archaeologists.
Among the various molecules of which life is composed, we would anticipate the best survivors to be these ‘lipids’. The word is a generic term for organic substances that resist mixing with water, including fats, oils and waxes. Water is so important to disaggregation and decay below ground that failure to mix with water is bound to confer resilience. But lipids are not all that survives. During the 1980s, two developments were leading us to believe that a far wider range of biomolecules might be isolated from ancient deposits. The first of these developments was a change in palaeontology, the study of fossils. Like archaeology, it had started out by giving prominence to the most durable and visible of finds, such as the rock-solid silicified shells and bones chipped away from their matrix with a geological hammer.
Through time, awareness grew of the survival of much softer tissues, such as in the remarkably preserved soft-bodied specimens from the Burgess Shale over which Stephen Jay Gould enthused in his book Wonderful Life.
The second development involved much more recent fossils. During the early 1980s, two publications appeared, one involving an extinct zebra-like animal, the other an ancient Chinese corpse. In each case, researchers claimed to have detected fragments of ancient DNA, the molecule in which life was encoded. Alongside lipids and proteins, DNA could also be identified in specimens of archaeological age. With the isolation of the molecule central to life’s function, archaeology turned an important corner. It was difficult to put boundaries around the implications of recovering it from the past. The constraints on examining a living prehistory seemed to be falling away.
One of the first outcomes of these remarkable discoveries was that completely new brid
ges were hastily built between academic disciplines that had not hitherto had much to say to each other. Contact opened up between archaeologists, palaeontologists, molecular biologists, geochemists–specialists in widely different fields, who were beginning to sense a common interest. One of those meetings was between Terry Brown, a molecular scientist, Keri Brown, a prehistorian, Geoff Eglinton, an organic geochemist, and myself, by then a fully fledged bio-archaeologist. Born out of that meeting was a programme that the UK’s Natural Environmental Research Council put in place, in which 50 researchers around Britain put their minds to the problems, and their research efforts to solving them. For five years, the ‘Ancient Biomolecules Initiative’ found itself at the heart of a world-wide movement. Researchers in countless disciplines and countries became engaged in a molecule hunt that has, bit by bit, transformed our understanding of our own prehistory.
Looking back over three decades to my introduction to field archaeology, I can see that the change in our perception of what awaits discovery beneath our feet has been considerable. Those assiduously scrubbed pot fragments around which the whole exercise then revolved are seen now as the mere tip of a vast information ‘iceberg’. Lower down on the ‘iceberg’ was a vast residue of the living organic world that ancient people experienced around them, indeed of which they were a part. It was a messy residue, browned, fragmented and falling apart, but it was definitely there, and in no small quantity. What could be gleaned from this prolific organic database? Back in the 1960s, we had only fragmentary answers to that question. Gradually, over the last three decades, the various surviving elements of those past organic worlds have been dissected and understood. One by one, the surviving fragments of past living worlds have been identified. First the more visible elements–bones, teeth, seeds, and wood–became subject to rigorous analysis. The microscope has supplemented these with the less visible remnants–pollen grains, starch and silica bodies from inside plant cells, and the hard parts of insects and other invertebrates. Finally, molecular science has taken us one step deeper into this record. We can look within these fragmentary items to the molecules of which they are composed, and which determined their form and their biology. Some of these molecules are remarkably durable, surviving as evidence of living tissue that has otherwise completely dispersed. Other molecules take us to the very heart of life’s structure. At the core is the molecular blueprint of life, DNA. We now realize that fragments of this life-encoding molecule can survive on archaeological sites that are twenty times as old as that ancient village in Somerset.
Within a few years of biomolecular archaeology becoming a reality, many stories about the human past have been rewritten, and others, out of reach of the traditional evidence at our disposal, have been narrated for the first time. The main stimulus for this new swathe of stories has been a search for the one particular biomolecule to which all others ultimately owe their existence, DNA. In the following chapters, those new stories are recounted, after first exploring how that unusual search reached its goal.
afterword
In the final page of The Molecule Hunt’s opening chapter, I had estimated that fragments of DNA could survive in contexts that are twenty times as old as the Iron Age site at which I commenced my archaeological career in the Somerset Levels of South West England. Across the Atlantic in Canada’s Yukon Territory there are rather bleaker environments than may be encountered on the Somerset Levels, but which similarly preserve stratified organic silts beneath their surface. Over the past five years, findings from these deposits have demonstrated my estimate was out by at least a factor of thirty.
A braided stream called Thistle Creek winds its way through the forests, moors, and gold-bearing hills of Yukon Territory, far from modern city life. It lies within a larger region, spanning from Siberia, across the Bering Straits and reaching into North America and has proven to be of great significance for molecular archaeology. In these afterwords, I shall refer to that region as the ‘Northern Arc’. Thistle Creek has yielded up a horse bone, from which an entire genome has now been reconstructed of an animal that lived three-quarters of a million years ago.
Just a few months after The Molecule Hunt was published, a paper in Science led by Ian Barnes drew attention to this Northern Arc and to the extent of permafrost, the remote intact sedimentary sequences, and the intrinsic interest of the region bridging the planet’s greatest land masses. His senior author, Allan Cooper, had earlier set the stage with his work with Jennifer Leonard and Robert Wayne on Ice Age brown bears. Their paper now impressively demonstrated what could be learnt from the fossil remains of seventy-one brown bears, now one of many taxa for which the Northern Arc has offered up a wealth of informative ancient DNA.
The Arc is also of interest as the magnet for a second generation of molecular researchers, the work of a number of whose findings will feature in subsequent afterwords. Barnes and Cooper are among these. A third is a co-author on their Science paper, Beth Shapiro. Having preciously employed molecular methods to probe back into the extinct dodo’s own flighted ancestors, Shapiro now found herself dodging the swarming mosquitoes of the Northern Arc to persuade miners to let her stand close to their high-pressure water jets, blasting away the permafrost to reveal both precious ores and megafaunal bones.
Yet another figure attracted to the Arc had, at different stages in his career, been an ethnographic collector, Siberian fur trapper, and honorary member of Montana’s Crow Tribe. Around this time, Eske Willerslev was becoming interested in Yukon Territory’s Thistle Creek, better known as a focus of the Klondike Gold Rush a century or so earlier. In exposed sections, members of his group could pick out enduring ice wedges, bearing witness to sustained permafrost conditions. The antiquity of these profiles was revealed by analyses of volcanic ash contained within the sediments, connecting them with an eruption around 735,000 years BP. Some sediments were organic, comparable with those at the Somerset Levels, but 300 times as ancient. They contained bones with which the group was able to set a new timescale for the persistence of recognizable DNA sequences.
These remains did something else, beyond demonstrating how badly my earlier estimate was off. The basis of the molecular archaeology I wrote back then was a series of very small fragments of ancient biomolecules, analysed to hopefully reflect the larger whole. So, in the case of the pioneering work on the mitochondrial control region, the ratio in length between the DNA sequence analysed, and the mammalian genome sequence it aimed to reflect, was in the order of three million. Not only were the tiny, damaged DNA fragments from Thistle Creek to set a new timeframe for the analysis, important changes in DNA methodology (to which we shall return in the following afterword) enabled a far richer output from that analysis. Rather than a mitochondrial control region, or a stretch of DNA flanking a particular gene, the publication from Willerslev’s team discussed an entire genome. In many ways, the potential of whole genome research is of even greater significance than stretching the timeframe.
The focus on the whole genome connects with a recurrent theme in the changes of the last fifteen years that will be explored in these afterwords. Those changes are not just about molecules, or our ability to retrieve data from them. They are also about what we can do with this data, as a result of a parallel revolution that is taking place in the world of computing.
That parallel revolution has affected all aspects of our lives; take for example, our researchers’ journey to the Northern Arc. Their first trips may have involved finding a travel agent with some specialist knowledge, asking around amongst the mining and oil drilling community, and coming up with the fragments of information that at least allowed a field trip to be mounted. I have just this minute googled ‘travel accommodation Yukon Territory’. That single search led to 504,000 hits, including innumerable competitive suggestions for flight deals, pictures of a wide variety of accommodation options with a range of reviews, as well as prompting options for refining my search, should I wish to be near to the airport, enjoy a Jacuzzi, o
r bring my pets. The webpage also announced that the information was brought to my screen in 0.64 seconds.
That mirrors what has happened in many fields of study including DNA research. There has been a ‘genomics revolution’ that has transformed all aspects of that research. It has changed the way different taxa of living things are identified, considerably widened both the range of those taxa we can examine, and the range of genetic sequences we can explore within them. It has allowed us to move to a new level of sophistication in reconstructing evolutionary relationships, and connecting those relationships to the expression of genes and population histories. In our own lab, that genomic revolution has transformed our work on two Asian cereals, broomcorn and foxtail millet; we have been interested in how their genetics reflects the prehistoric spread of crops across the Old World. With the first cereal—broomcorn—my colleague Harriet Hunt began with twenty sequences from the GenBank database, trawled publications, undertook some laborious cloning options and considered several more, and finally acquired sixteen genetic markers from a Korean lab, that at least allowed some valuable phylogeographic research. With the second cereal—foxtail—we have worked on the plant’s complete genome and used modern sequencing technologies to generate tens of thousands of markers and identify genes to allow us to move ahead at an entirely different pace than had been possible with broomcorn. Much of this contrast between two episodes of research is the consequence of the broomcorn project commencing in 2004, and the foxtail project less than a decade later.
