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Ancient molecules and human prehistory*
Analysts and archaelogists
Diets and use of animals
Construction, jewellery and trade
Problems with molecules
Chemical transformations
Working from fossils
Theoretical models
What did they die of?
Ancient agriculture and animal husbandry
Movements of people
Molecular genetics is controversial
The New World
The Pacific
Summary
DNA and other molecules found in ancient remains are yielding new information about the origins, spread, interaction and culture of early humans. Molecules of animal fats preserved in archaeological pottery have shown that people living in medieval times ate non-ruminant animals such as pigs but burned tallow from ruminants such as sheep and cattle. Geochemical analysis of bitumen in the Middle East has documented ancient trade routes. Studies of molecular genetic diversity have shed light on when and how cattle were domesticated. Analysis of human hair from remains up to 5200 years old has revealed the diets of those ancient people. DNA recovered from other remains has also given researchers evidence for theories about the origins and spread of agriculture, and human migration into the Pacific.
Analysts and archaeologists
The research is a joint effort between disciplines which have not traditionally worked together: archaeologists, molecular biologists, geneticists and geochemists. Professor Geoffrey Eglinton of the Department of Earth Sciences at the University of Bristol, outlined the contribution analysts can make to archaeology. Molecules are identifiable through their structures. Archaeological samples will contain different molecules in different amounts, and their abundance patterns are called molecular fingerprints. These can be used to distinguish between residues left by different organisms and environments. In addition to molecules' structures, their chirality (or handedness) and their isotopic composition (the proportions of the different sorts of atoms of nitrogen, carbon, hydrogen and oxygen they contain) also yield information about compounds. Analysts are interested not only in DNA but in a wide range of molecules which can give information about human prehistory.
Diets and use of animals
Unglazed pottery from Neolithic times (4500 years ago) has preserved in its porous structure molecules from ancient meals cooked in the pots. These have been analysed by Dr Richard Evershed from the Organic Geochemistry Unit at the University of Bristol, and have turned out to be a variety of lipids: animal fats, plant oils, waxes and resins. Their structures, distributions and stable isotope values mean they can be related to particular plant and animal groups.
One lipid material extracted from an early medieval pot was a plant leaf wax identical to that in modern cabbage. The concentration of the lipids was higher at the top of the pot than the bottom, suggesting that the cabbage was boiled. An analysis of other lipids in two sorts of vessels - dripping dishes, which are presumed to have caught fat from animals as they roasted, and lamps - shows that different types of animals were used for different purposes. Fats from ruminants such as sheep and cattle were used for the oil of the lamps, but only non-ruminant animals such as pigs were eaten. This sort of information is valuable in adding to archaeologists' knowledge of the diets and cultures of Neolithic peoples, especially when there are few preserved remains of animals or plants from those times.
It is often difficult to analyse ancient bones - a subject we will return to. One of the problems with bone is that its isotopic composition may change as the bone deteriorates. Dr Stephen Macko from the Department of Environmental Sciences at the University of Virginia, USA, prefers to analyse hair, whose isotopic composition seems to remain constant. This makes it ideal for looking at diet. Macko presented results comparing analyses of hair of modern people with known diets, showing there is wide diversity in carbon, sulphur and nitrogen isotopes found between vegans, vegetarians and omnivores. Seafood, corn-fed beef and grains result in different isotope compositions too.
Similar analyses can be done on hair from ancient populations, and inferences made about their diets. The Ice Man found in 1991 in the Italian/Austrian alps showed an isotopic composition the same as modern vegans. A curious result perhaps, as he was also found with a bow and arrow and a hatchet! But perhaps, Macko suggested, he did not eat much of what he caught. Hair from Coptics from Egypt in 700 AD showed that a huge range of food was available and different types of vegetation figured in their diet. In contrast, some Egyptian mummies from the Middle Kingdom, who lived thousands of years before the Coptics, showed a far narrower range of foods. They were the aristocracy of their time and their diet was rich in meat and corn, millet and sorghum which leave a specific value for the isotopic ratio of carbon. Chinchorro mummies which go back to 7000 BC at Arica, on the dry west coast of Chile, also have hair preserved. It showed that the proportion of seafoods in their diet decreased the further they lived from the coast.
Construction, jewellery and trade
Another light on ancient cultures is being shed by the molecular analysis of bitumen. Dr Jacques Connan of Elf Exploration Production in France explained that the analytical techniques of petroleum geochemistry (gas chromatography, mass spectrometry, isotopic chemistry) have distinguished between the geological origins of bitumen from different archaeological sites. Bitumen-coated flint implements as old as 40,000 years have proved that Neanderthal people in the Syrian desert used it to fix handles to their tools. Ancient people in northern Iraq, south-west Iran and the Dead Sea area used bitumen as mortar in the construction of palaces, temples and ziggurats (eg the tower of Babel in Babylon), terraces (the hanging gardens of Babylon) and even - again in Babylon - for coating roads. Since the Neolithic period bitumen has been used to waterproof containers, seal sarcophagi, glue ceramics and jewellery. Examples of artefacts have been excavated from the Royal tomb at Ur, and are on display at the British Museum. Analysis of bitumen has documented trade routes in the Middle East and the Arabo-Persian Gulf between 5800 and 3500 BC. Characterisations of the bitumen imported into Tell el ÔOueili in South Mesopotamia show that between 5800 and 4550 BC it came from Luristan and Khizistan in Iran. Between 4550 and 3700 BC supplies came from northern Iraq; then trade switched to Hit and Abu Jir in present-day Iraq. These different supply lines fit with the cultural and geopolitical changes taking place in the region during these periods.
Problems with molecules
Chemical transformations
The whole area of research depends on the preservation of molecules and techniques that can extract and identify them reliably. Professor Derek Briggs of the Department of Earth Sciences at the University of Bristol gave an overview of what happens to different molecules as they decay. It is the hard parts of animals and plants that survive after the death of the organism: the bones, shells, teeth and cuticles (protective shells) of animals resist decay whereas the DNA does not. Briggs and his colleagues are particularly interested in the chemical changes that occur in the cuticles of animals in the fossil record. The cuticles are made up of protein and chitin, which is the second most abundant organic chemical on earth (after cellulose). They analysed cuticles of various ages: present-day mantis shrimps as they decayed in the laboratory; fossils of 20,000 year old beetles from tar pits at La Brea in California; and fossils older than 3 million years. The protein components of the cuticle break down quickly but chitin lasts much longer and they found components of it in fossils up to 25 million years old. Older than this, the cuticles had no protein or chitin left. In these ancient fossils, the cuticles had been chemically transformed into hydrocarbon-type material that forms oil when heated. Plants have long been recognised as forming oil, but not animals; and there is no obvious chemical process that could account for this change. The Bristol team is pursuing research to try to discover how it happens.
Working from fossils
It is amino acids and the possible persistence of DNA that interest Professor Jeffrey Bada of the Scripps Institution of Oceanography at the University of California at San Diego. His approach makes use of the fact that some amino acids (-amino acids) change their chemical composition over time in a process called racemisation. This involves chirality: the "handedness" of all organic molecules. These -amino acids in living tissues are left-handed, but over time they convert to right-handedness, finally arriving at an equilibrium mixture of left and right. The rate at which this happens depends on temperature and other variables, and the proportion of left-handedness to right-handedness at any given time can be used to predict the survival of other molecules such as DNA.
By testing fossils of modern and Pleistocene ostrich eggshells and mammalian bones, Bada has developed a model for the racemisation of amino acids in fossil specimens. He predicts that practically all amino acids will be totally racemised in less than 5 million years in most environments on Earth. Most bone samples of interest to the development of modern humans will be too old to contain any DNA; however skeletons from between 13,000 and 33,000 years ago found in caves at Zhoukoudian in China may have some. Bones from the Neander Valley contain Neanderthal DNA, whereas other skeletons from France, Spain and the Middle East probably do not. Ancient fossils such as dinosaur specimens and insects entombed in amber should contain a small amount of amino acids in left and right equilibrium. However, both have been shown to contain intact amino acids. Those in dinosaur bones have probably been contaminants; but those in entombed insects may be genuine, preserved because the amber has protected the insect from water and has thus retarded racemisation. This holds out the prospect of extracting DNA from entombed insects. Although researchers at the Natural History Museum in London have discounted this as a realistic possibility, Bada held out hope that it might still be done.
Theoretical models
Rather than working with excavated artefacts, Dr Matthew Collins of the Fossil Fuels and Environmental Geochemistry Unit at the University of Newcastle is developing a theory of how bones decay under different circumstances. He hopes to be able to point archaeologists in the direction of sites where they might find well-preserved bone, and to distinguish between better- and less-well preserved bones at any site. As Shakespeare wrote: "..water is a sore decayer of your whoreson dead body"; and Collins' description concentrates on the effect of water on collagen which makes up 90% of the protein found in bone and teeth.
The work is producing results but also has problems. It has shown that the way the bone sample is currently prepared (by grinding it up) will affect the state of the collagen and needs to be changed. Grinding may cause much of the collagen to change from its normal insoluble form to gelatin which cannot be used in carbon-dating or isotopic analysis. Grinding also increases the rate of racemisation which is a problem when racemisation is itself used as a measure of ageing in bone. A major problem with the work is that as yet its data refer to high temperatures but most of the remains of interest to archaeologists will have been preserved at low temperatures. Nevertheless, it predicts that remains will be of a quality worth looking for in the UK, where collagen residues should still be found after 300,000 years. Good specimens should also exist in northern Europe, the African rift valley (a high-altitude region), southern South Africa, Tunisia and Morocco. African hominid samples have in fact generally come from the places in which collagen would be expected to survive longest. In the hotter climates of northern Australia and eastern South America, however, the work predicts that much of the collagen will have been degraded into gelatin.
What did they die of?
Some of the practical problems of using molecular analysis to learn more about ancient cultures were described by Professor Franco Rollo of the University of Camerino in Italy. Ancient human remains yield not only bones and hair but also bacteria, fungi and yeasts. Rollo studies the DNA in these ancient microbiota in order to understand the spread of disease, the natural mummification process and the effects of diets on historical human populations. DNA fragments of pathogenic bacteria including Mycobacterium tuberculosis, Yersinia pestis (which causes plague) and Treponema pallidum (syphilis) have been amplified. But the methodological difficulties in extracting and identifying ancient DNA can lead to false conclusions, as when analysis of the mummy of Maria of Aragon seemingly showed that she died of syphilis. In fact, the bacterium T. pallidum was not present at all.
The case study of a 20 year old female mummy from the Andes, aged between 1000 and 600 years old, again showed potential pitfalls of analysis. There is more chance of zeroing in on ancient DNA if the target sequence of base pairs is kept as short as possible. When this was done, the DNA of the prevailing microflora in the mummy's large bowel appeared to be that of Clostridium botulinum (which causes botulism): a most unexpected result. However, better identification is made using a longer sequence of base pairs; and this showed no botulinum at all, rather Clostridium algidicarnis which developed on frozen meats, and another Clostridium (intestinalis) which is typical of the mammalian bowel. The trick must be to strike a balance between a short sequence likely to remain in ancient DNA and a longer one which is better for identification but which will be much less abundant. Rollo suggested such a compromise (about 200 base pairs).
Ancient agriculture and animal husbandry
Ancient DNA can also help in understanding the origins and spread of agriculture. Dr Terry Brown, a molecular biologist from the University of Manchester Institute of Science and Technology, explained that the transition from hunting and gathering to agriculture occurred about 10,000 years ago. It happened in parallel in different parts of the world, and was centred around rice in the Far East, maize in Central America and, in the Fertile Crescent, around wheat, barley, peas and lentils. Technology then spread from each of these centres, for example, reaching Europe (by way of Africa from the Fertile Crescent) by 5000 BC.
Genetic analysis of modern plants is beginning to answer questions about how many times a crop was domesticated and the geographical location of individual domestications. Conclusions drawn from this work are, however, risky, because it is trying to predict the past from limited information. Also, many of the wheats whose genotypes are of interest have disappeared. Researchers have therefore turned to ancient DNA in an attempt to sample some of these extinct populations. Archaeological sites yield desiccated seeds, charred grains and stones that were used in producing flour, and DNA from these sources is throwing light on the spread of particular cultivars and the genetic diversity of ancient crops.
One of the earliest types of wheat to be grown was emmer wheat. It has evolved into durum wheat and bread wheat which predominates today. The work has tried to understand the evolution of emmer since its domestication and to link that in with human events and pre-history. It has found that one of the Bronze Age wheats from Assiros in northern Greece contains a gene (dubbed the "Mother's Pride gene") which makes good, springy bread: a surprise, because we had no prior knowledge of targeted breeding for particular qualities. A study of the genetic composition of modern wheats has enabled researchers to trace the evolution of the genomes of these wheats, and has shown that there are two distinct lineages of cultivated emmer wheat which diverged about 2 million years ago - long before agriculture began. One type is found everywhere emmer is now grown, in Asia, Africa and Europe; but the other occurs only in Central Europe, Italy, the Balkans, one in Turkey and one in Azerbaijan. This may mean that emmer cultivation has expanded twice from its origins in the Middle East, possibly with the more limited type stalling in Central Europe and later being overtaken by the ubiquitous type.
Cattle were first domesticated about 8000 years ago, and Dr David MacHugh of the Department of Genetics, Trinity College, Dublin, has been using genetic analysis to tease out the relationships between cattle populations in Europe, Asia and Africa. The idea is to build up a picture of the migrations and movements of cattle and people since that time. Part of the task is to decide whether all domesticated cattle came originally from the Fertile Crescent, or whether they were domesticated independently in different places. Genetic analysis has concentrated on zebu cattle (those with humps and dewlaps, now found in India) and taurine cattle (the humpless variety that were the original indigenous inhabitants of Africa, and which are now found in south-west Africa and Europe). Analysis of the genetic make-up of the Indian zebu population and the taurine animals in Africa and Europe shows they are different, providing strong support for the hypothesis that these cattle were domesticated independently by two different Neolithic cultures. Similar analyses show that the Middle Eastern populations gave rise to European cattle, and that it and perhaps north Africa were the centres that gave rise to genetic diversity in cattle.
Movements of people
Molecular genetics is controversial
The use of molecular genetics to track the migrations of people is a development that traditional population geneticists find hard to swallow. The long-standing research in this field has drawn up population trees based on the frequency of different gene types (blood groups is a simple example) amongst different groups of people. According to Professor Bryan Sykes from the Institute of Molecular Medicine at the University of Oxford these trees have mistakenly been interpreted as though they explain something about evolution. Researchers whose work depends on such trees greeted a recent paper from Sykes' group (Richards, M et al (1996), Palaeolithic and Neolithic lineages in the European mitochondrial gene pool, Am J Hum Genet 59, 185-203) with outrage. This paper related an analysis of mitochondrial DNA within Europe to that in the Middle East, and suggested that the contribution of Neolithic arrivals to the modern-day gene pool was less than had been generally accepted. Mitochondrial DNA (mtDNA) has many advantages for analysis over nuclear DNA. It is maternally inherited and transmitted intact from generation to generation without being recombined with paternal DNA; and it mutates at a high rate which gives the researcher a greater chance of distinguishing between two different people.
The disputed paper on Europe divided mtDNA in European populations into five groups on the basis of genetic similarities. It then estimated the mutation rates these groups would have been subject to and calculated how long ago they would all have arisen from a common ancestor. This date was well before the Neolithic, which began 8-10,000 years ago and which resulted in a big population increase with the spread of agriculture. Sykes dealt with the criticisms of the paper: the mutation rate, which some said could be ten times as fast as the paper suggested; the robustness of the five groups of genetic similarities; and the time the groups took to develop their diversity in Europe (as opposed to before they arrived in Europe). Having reanalysed and broadened the data, he has refined the picture to conclude that the population which had the most dramatic effect on the modern gene pool in Europe, contributing about 70%, spread out from southern European latitudes to colonise northern Europe about 13-14,000 years ago - after the last ice age 18-20,000 years ago. This still puts it before the Neolithic, which was 8-10,000 years ago. The Neolithic contribution to the modern gene pool stands at around 20%: more than estimated by the 1996 paper but still less than pre-Neolithic genes.
The New World
Some of the big questions in anthropology are being approached by advances in genetics. Dr Andrew Merriwether of the Department of Anthropology at the University of Michigan is asking how the New World and the Pacific were populated. He used mtDNA to trace lineages. The samples he used were taken from Yanomami Indians in Venezuela and Brazil between 1967 and 1977 and stored in liquid nitrogen (hence the title of his talk: "Freezer Anthropology"). By amplifying the DNA and identifying patterns within it, he was able to see which individuals were related to which. The findings from this area have shown that native Americans fall into four genetically-distinct groups. The distribution of the groups suggests to Merriwether that people migrated from Asia into the New World (via Siberia, across the Bering Straight into Alaska, Canada and down into the Americas) and separately from Asia into the Pacific. He doubts whether there is any connection between the people of the two migrations. He also thinks that the New World was peopled in one single migration rather than three different waves, as some researchers have suggested. Merriwether uses ancient DNA to test hypotheses generated from modern DNA, for example to look for lineages that have become extinct in the New World and look at the relationship between extant and extinct populations. He has confirmed the presence of four of the genetically-distinct groups in samples 1500 years old from North and South America.
Professor Mark Stoneking from the Department of Anthropology at Pennsylvania State University has analysed the mt and nuclear DNA of prehistoric remains 6-700 years old buried in an Amerindian cemetery in the Illinois River Valley, between Chicago and St Louis. The cemetery and the village site next to it are part of the Oneota tradition, which is thought to have been a cultural intrusion into the area. About one third of the 260 well-preserved skeletons in the cemetery show death due to violence: scalping, clubbing, arrow and spear wounds. There are four clusters of lineages in Amerindians, but reduced diversity in contemporary Indians. Analysis of DNA from the skeletons showed that this was because of a reduction in diversity during the initial Amerindian colonisation of the New World, rather than from the European conquest which decimated the Indian population and could conceivably have reduced its genetic variation. Further DNA analysis suggested that there could be another genetic lineage to add to the four already known, to which nearly all Amerindians belong. It also showed that the Europeans may have had some effect on the DNA variation, perhaps pruning some of the rare types in modern populations.
The Pacific
The last large area of the world to be settled by anatomically modern humans was the Pacific, and it was this area that Dr Erika Hagelberg of the Department of Genetics at the University of Cambridge described. For the last 2000 years or so the Polynesians have occupied a huge triangle of the eastern Pacific which takes in Hawaii at its northern angle, New Zealand at its bottom left angle and Easter Island at its bottom right. The Polynesians have spread all over the eastern Pacific, and there is no doubt that they came originally from island South-East Asia. However, there is still some debate on the time and route of their expansion into the Pacific. Hagelberg has worked in coastal New Guinea and island Melanesia (the central Pacific region to the west of Polynesia which takes in islands off the east coast of Australia: the Solomon Islands, Tuvalu, Fiji). There have been two hypotheses about where the proto-Polynesian colonizers came from. One idea is that people migrated directly from South-East Asia; the other, that the Lapita culture, which was a maritime culture taking in New Guinea and Fiji, expanded from Melanesia into Polynesia. She cannot really answer the question of the route of the Polynesian migrations, but her results suggest there have been recent (about 1000 years ago) migrations from east to west from Polynesia, resettling parts of the Pacific like New Guinea and Vanuatu. Her analyses of Lapita bones suggest that the people at those sites were not like the Polynesians but were genetically rather like the Melanesians. This caused some surprise because many scholars have associated Lapita with Polynesia. Hagelberg's results, however limited, would suggest that the Lapita culture expanded into the central Pacific before the arrival of the Polynesians.
Wendy Barnaby
ABSW
December 1998
Contacts
Professor Geoffrey Eglinton FRS
Department of Earth Sciences, University of Bristol
Tel 0117 968 3833 Fax 0117 962 6065
Dr Richard Evershed
School of Chemistry, University of Bristol
Tel 0117 928 7671 Fax 0117 928 1295
Dr Stephen Macko
Department of Environmental Sciences, University of Virginia, USA
Tel 00 1 804 924 6849 Fax 00 1 804 982 2137
Dr Jacques Connan
Elf Exploration Production, France
Tel 00 33 5 5983 6201 Fax 00 33 5 5983 4369
Professor Derek Briggs
Department of Earth Sciences, University of Bristol
Tel 0117 928 7793 Fax 0117 925 3385
Professor Jeffrey Bada
Scripps Institution of Oceanography, University of California, USA
Tel 00 1 619 534 4258 Fax 00 1 619 534 2674
Dr Matthew Collins
Fossil Fuels and Environmental Geochem, University of Newcastle
Tel 0191 222 6855/6605 Fax 0191 222 5431
Professor Franco Rollo
University of Camerion, Italy
Tel 00 39 737 403219 Fax 00 39 737 636216
Dr Terry Brown
Department of Biomolecular Sciences, UMIST
Tel 0161 200 4173 Fax 0161 236 0409
Dr David MacHugh
Department of Genetics, Trinity College, Dublin
Tel 00 353 1 608 1088 Fax 00 353 1 679 8558
Dr Bryan Sykes
Institute of Molecular Medicine, University of Oxford
Tel 01865 222404 Fax 01865 222498
Dr Andrew Merriwether
Department of Anthropology, University of Michigan, USA
Tel 00 1 313 647 6777 Fax 00 1 313 763 6077
Professor Mark Stoneking
Department of Anthropology, Pennsylvania State University, USA
Tel 00 1 814 863 1078 Fax 00 1 814 863 1474
Dr Erika Hagelberg
Department of Genetics, University of Cambridge
Tel 0223 334465 Fax 0223 335460
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