Unlocking the Past

by Martin Jones

  Cano and Borucki waited for three years of further tests before publishing their findings in Science. DNA sequencing demonstrated that the bacterium was distinct from any modern species, but its closest living relatives were gut flora bacteria. Both these points supported the notion of the spores being from the ancient insect’s gut flora. By the time they had the confidence to publish in Science, they had sufficient results to embark on exploiting them in a unique way. Cano set up a company, Ambergene, that was devoted to reviving these ancient organisms, and he patented the process of revival. Ambergene has since claimed to have revived species by the thousand, some from over 100 million years of dormancy in amber. Jurassic Park might just be possible for bacteria, if not for dinosaurs.

  A large question mark now hangs over the recovery of highly fragmentary DNA within amber-entombed insects. One might imagine that the recovery of viable bacteria within those same insects’ bodies was equally problematic. It would involve the survival of complete DNA sequences, not just the tiny fragments normally recovered as ancient DNA. This, however, is not as crazy as it seems. Many who have queried the insect DNA have reserved judgement on the more ambitious claim for bacterial DNA. This is for two reasons. First, the bacterial spore is a remarkable DNA survival capsule, which could well display a molecular resilience not shared by the surrounding host. Second, we are becoming increasingly familiar with other bacterial ‘prisons’, in which some combination of dormancy and ultra-slow metabolism allows bacteria to persist entrapped for millions of years. Researchers boring into the sea floor have found viable bacteria beneath a kilometre of sediment, and others have found ancient bacteria in the heart of geological rock salt, still viable within tiny saline vacuoles in the salt. These survivals are both well attested, so why not also within an amber-entombed host?

  Cano is not alone in claiming to have revived ancient bacteria. From rather younger samples, another group found evidence of bacteria in the gut of one of North America’s extinct megafauna, the elephant-like mastodon. Specimens of this beast had been recovered from a couple of late Pleistocene ponds in Ohio and Michigan. Within their massive frames were lumps of what looked like the preserved remnants of their large and small intestines. Here, too, bacteria were encountered that could apparently be brought back to life.

  beyond amber

  We do not yet know how long these spores can remain viable, but even when they fragment and their contents disappear, there are still biomolecular features from within these least visible components of the living world that outlast all others. Franco Rollo’s work has demonstrated bacterial DNA persisting outside the spores for thousands of years, and Angela Gernaey’s research has shown that the lipids around the bacterial cell can also persist. Within the lipids of the cell coat in many bacteria can be found one of the most durable biomolecules of all. These belong to a family of molecules known as the hopanes, made up of five interlinked carbon rings with a long-chain strand projecting from them. These chains will fragment with time, but the characteristic set of rings and part of the attached chain can persist indefinitely. They have been found in rocks that are billions of years old, providing evidence of some of the earliest life on earth. These seemingly indestructible hopanoid molecules are widespread as traces within petroleum deposits. Here they retain some of the characteristic structure of the ancient bacteria that millions, or billions, of years ago formed part of the living worlds from which these deposits derive. Ian Head and his colleagues at Newcastle are currently attempting to decode the hopanoid signatures from deep within the Earth’s crust, this most enduring legacy of all the world’s ancient microbial populations.

  These characteristic molecules, whose age is of the same order as the Earth itself, epitomize the transformation underway in the molecular approach to the past. A generation ago, many plants and animals remained archaeologically invisible. We had not yet learnt how to seek out and identify the scattered fragments of tissue they left behind. The seeking out of microbes was far beyond the aspirations of the first generation of bio-archaeologists. The molecule hunt has turned that around. What seemed at first to be the least accessible organisms from the past can now be seen to leave lipid and DNA signatures as clear as anything from a more conspicuous organism. Furthermore, these signatures cling tenaciously, first to life itself, and then to the molecular traces of life, for periods of time during which every other component of life has been broken down and recycled millions of times over.

  afterword

  A theme that has already recurred is the shift in focus from the archaeological ‘object’ itself, to the stuff ‘cleaned’ off it by generations of well-meaning archaeologists and curators. Possibly conscious of their own oral hygiene, a number of our predecessors had thus been quite active in removing from museum skulls what is now seen as a gold mine of information about ‘enemies within’.

  Back in the 1970s and 1980s, closer observation was already revealing the internal structure of dental calculus, and the fact that minute contents related to the diets and daily lives of the owners of that dentition. Down the lens of an optical microscope, pollen grains, animal hairs, even whole bacteria could be discerned. In 2011, Oslo pharmacologist Hans Preus established that the calcareous matrix of dental calculus was also a suitable host for ancient bacterial DNA. In the early days of the field, when the better established matrices such as seeds and bones were similarly shown to be suitable hosts, the methodological armoury at our disposal was entirely different. Today, rather than moving laboriously and meticulously through the minefields of sequence fragmentation, contamination and slow computing, as was the case in the 1990s, it only required two years to elapse for Christina Adler to follow Preus’ paper by publishing a series of detailed inferences. With the help of high throughput sequencing and metagenomic methodologies, the bacterial ecosystem of the human mouth was charted over eight millennia, revealing much about diet, health and disease. Adler’s paper marked a new phase of biomolecular archaeology, in which it seemed, in terms of the untapped source, of evidence of the past, that the buildup of lime around our teeth might be the most dramatic of all.

  Disease is only one element of the mouth flora, but it remains a most important and revealing one. Over the last fifteen years a whole series of different pathogens have been the topic of ancient DNA study. The list of such pathogens now includes: typhus, cholera, malaria and brucellosis. Moreover, a wide range of these studies has given us a much better sense of how these diseases work as organisms, and how they interact with their host organisms.

  Take the example of the wide range of diseases thought to have proliferated from the time of the beginnings of farming, when settled communities brought more people and more animals together. Some of the pioneering research into ancient pathogen DNA quickly demonstrated a deeper time story for some of these, most notably when Old World pathogens were found in mummies and skeletons unearthed from pre-Columbian sites in the New World. These must have travelled on the journey across the Bering Straits, no longer crossable at the time of agricultural origins.

  Agriculture is still clearly important, particularly in the case of the ‘crowd diseases’, caused by highly virulent pathogens that require very high density host populations in order to simultaneously flourish and avoid boom-bust extinction. One of the diseases associated with Neolithic farmers has those characteristics, but also another contrasting set of characteristics that connects with its detection in pre-Columbian mummies. Tuberculosis is also subject to chronic progression, latency and reactivation, features that connect with a more ancient style of human life.

  Back in 1993, Mark Spigelman’s pioneering work drew inferences from a single 123-base-pair fragment. Twenty years later, Inaki Comas explored the same bacterium, but this time drawing inferences from over 34,000 SNPs dispersed across the entire genome. With human data gathered in similar intensity, Comas and colleagues were able to compare their results with human trees inferred from almost 6,000 mitochondrial genomes. With computing power un
imagined by Spigelman, these data revealed a rich history of the ‘white death’ to connect with an equally rich history of its human host. The meticulous trees arising from the two massive datasets showed an impressive match in pattern, right back to their shared African origins. Our modern human species and the bacterium that foreshortened so many of their lives were together from the very start.

  Several of the host species of pathogenic bacteria have now yielded up their complete genomes to new methodologies; the same is true of the pathogens themselves. When The Molecule Hunt was written, work had just started on that most brutal predator that haunted Medieval Europe and did more to shape the continent’s cultural and political history than any other invertebrate species. Yersinia pestis DNA had already been detected in the dental pulp from six plague pit skeletons. A decade or so later, Kirsten Bos and colleagues have done something similar using dental pulp from a burial ground established in London precisely at the time of the peak of the Black Death, and drawing on the possibilities of new sequencing technologies, were able to publish this notorious pathogen’s draft genome in 2011.

  The cemetery at East Smithfield had been created to take London’s plague victims. Each day as the plague raged, hundreds of bodies were interred, stacked five high. These have occasionally been unearthed in advanced of rescue excavation, and have provided a source of dental pulp for Bos and her colleagues to do something similar to what has been noted in earlier afterwords, using new sequencing methodologies to complete the jigsaw puzzle of complete genome analysis. That complete genome could then be compared both with extant human and rodent strains, as well the putative ancestor of them all, a soil-dwelling bacterium labelled Yersinia pseudotuberculosis. From all this a great deal can be told.

  First of all, the Smithfield victims’ genomes are able to account for the known modern genetic range of the disease. Extinct Yersinia pestis can all track back to its Black Death predecessor. That puts its earlier counterpart, the Justinian Plague, somewhat out on a limb. That limb is conjecturally found in a branching event in the generated tree estimated to belong to the later first millennium AD. Another branch in the tree connects with accessions from China, hinting perhaps at an Asian origin for the Black Death pathogen. As well as sketching out the larger Yersinia tree, Bos’s analysis can home in on microevolutionary patterns within the population, and there is enough such variation for the exciting inference that evolution is being observed in process.

  Does all this suggest the ebullient microevolutionary crucible can account for the dramatic virulence of the pathogen at the time of the Black Death? Bos thinks probably not. For all the hints of mutability, comparisons with extant genomes revealed no unique derived positions in the Medieval organism. To return to a question left open in the original writing of this chapter, the odds are now stacked in favour of the changing social, ecological, and climatic environment of the pathogen, rather than the pathogen itself, as driving the greatest reduction in life expectancy in recorded European history.

  11

  the hunt goes on

  a molecular spotlight

  The roots of biomolecular archaeology can be traced back many years–at least as far as Lyle Boyd’s search for blood groups of ancient mummies in the 1930s. Today, the number of ancient bodies assayed for ancient DNA runs into four figures, and molecular traces have been identified from seeds and animal bones, from inside pots and from the surface of tools of stone. The time has come to ask how many of the early hopes and aspirations have been realized.

  What always follows the excitement of the opening up of a new avenue of science is the realization of its pragmatic limitations, and here the limitations are to how much those ancient biomolecules can reveal. However well preserved, they never actually cease breaking down. The more tattered and fragmentary they become, the less easy it is to make sense of them and to deal with such issues as contamination and the demands of fine-resolution analysis. Space, time and context all impose limits on what is possible. Within those limits, we have learnt a great deal about the Neanderthal question, about human migrations and the development of farming, about cooking and about ancient disease. At the same time, these limits still leave many targets beyond our reach, at least for the moment. Many new avenues of scientific research come up against such a boundary. Two other limitations upon the new science are rather different, and reveal something about the limits of what is in principle knowable about the human past.

  In several instances, successful biomolecular projects have shone a spotlight on a particular community caught up in one of our grand narratives of the past. These could be narratives about progress, social structure, revolutionary change or population movement, each in some way translatable into patterns of lineage and kinship. Our first expectation is for that spotlight to reveal evidence that either supports or disputes that narrative. What it has revealed instead is that life tends to be more complicated than that. Where one major journey was under the molecular spotlight, a complex of subsidiary journeys began to appear. Where a single domestication was sought, a double or triple domestication was found. The situation seems to me to resemble another, much earlier, transformation in the scale of our observations. When, three centuries ago, van Leeuwenhoek first looked through a microscope at water from a pond, what seemed like clear transparent fluid erupted under his lens into a welter of life on a hitherto unobserved scale. Microscopy has since dramatically demonstrated how patterns that seem to be simple at one level, at a finer scale of resolution resolve into patterns that are more complex. Then, at yet finer levels, they again break up into patterns of greater or lesser complexity. Neither in society nor in nature is the microcosm simply a more detailed snapshot of the macrocosm. In society, the distinctiveness of the microcosm is further enhanced by a particular attribute of being human, the nature of human action.

  The sharper the focus of the molecular spotlight upon particular events and individuals in the past, the more directly it will illuminate the freedom of human action. There may be broader patterns, relationships and cultural rules, but we humans by our very nature are constantly reworking patterns, renegotiating relationships and breaking rules. This is where biomolecular applications in archaeology come very close to those in forensic science, which is all about the analysis of broken rules. As we rebuild a particular human episode from the past, with the precision that biomolecular science allows, then the complexity that arises from a constellation of individual lives will be far more evident than it is in the patterns from a distance that inform the grand narratives.

  The projects featured in the preceding pages have tended to blur the edges of many of the simpler narratives of the human past, and instead reveal the diversity of the lives that cluster around those narratives. In the case of the origins and spread of agriculture, for example, waves of migrating farmers are gradually being superseded in our accounts by meetings within a diverse world. This is a world in which roots, tubers and leaves are as much a part of the story as cereals. It encompasses regions and time scales lying well outside those enshrined in stories of the Fertile Crescent. At the same time as such patterns of complexity and diversity fall under the molecular spotlight, a beam is also cast upon a new generation of narratives emerging from the molecular sciences themselves.

  Biomolecular archaeology came about as a result of two different disciplines moving forward in tandem. Biology was gaining knowledge and control of its own molecular architecture, at a considerable pace. At the same time, archaeology was reaching out to explore a different range of ancient materials beneath the ground. Through luck and circumstance the two converged. It was less a case of dredging up some tried and tested scientific tools for archaeological application, and more the meeting of two independent research frontiers, uncertainly coming together on what emerged as shared questions. This uncertain convergence is still going on, perhaps most obviously in the studies of human genetic diversity. Upon the groundwork laid by Luca Cavalli-Sforza, the mapping of the human genome a
nd its variation is continuing apace. As more and more DNA data from living humans becomes available, it comes rich in hints about early episodes in the human past. Much as the intense mapping of the mitochondrial genome resulted in a new treasure chest of data on the human family tree, so the study of hot spots along the Y chromosome is having a similar effect, and other chromosomes will follow suit. As patterns of variation emerge, so resonances are sought with the various principal components of Cavalli-Sforza’s gene maps. In addition, entirely new spatial patterns are coming to light. As a first approximation, the overworked molecular clock places these patterns in some broad time frame, in line with hypotheses about how the human past was shaped. To an archaeologist this rapid expansion of the genetic database is reminiscent of an earlier growth in the evidence of human variation. It is similar to the blossoming of the world-wide archaeological record in the mid-twentieth century. That too depended on an over-stretched clock, derived from sequences of artefact styles. It was rationalized and corrected by much tighter chronological controls from carbon dating and other radiometric chronologies. The same needs to happen with the wealth of new genetic patterns and ancient DNA. Fragments of genetic information from well-dated, secure contexts in the archaeological record are what will anchor the broader modern pattern in time as well as space.