Various DNA / Technology
Human ancient DNA analysis within The Genographic Project: a project update and preliminary results from two powerful multiplex SBE typing methods
Wolfgang Haak1, Juan J Sanchez2, Clio Der Sarkissian1, Christina Adler1 & Alan Cooper1
1 The Australian Centre of Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia
2 National Institute of Toxicology and Forensic Science, Canary Islands Delegation, 38320 Tenerife, Spain.
The Australian Centre of Ancient DNA (ACAD) is one of 11 Regional Centres of The Genographic Project (TGP), and the only centre dedicated solely to ancient human DNA analyses. Our aim is to provide a temporal perspective to the movements and presence of prehistoric and historic populations through ancient DNA, and establish a time depth to the detailed genetic landscape being generated from the largescale modern human population data of TGP. We will present an update on the current activities and an overview of the protocols and strategies used in the ACAD. The retrieval of authentic human ancient DNA is plagued by methodological problems, and to deal with these we are relying on state-of-the-art methods ranging from sample collection through to data generation. We are using SPEX and multiplex PCR assays followed by SBE typing to analyse both mtDNA coding region markers and nuclear NRY markers. New multiplex assays were designed to amplify highly degraded DNA with an average amplicon length of 60-80bp, targeting 22 mtDNA SNPs and 25 NRY SNPs - to match the core marker panel used within TGP. Preliminary results show that the SBE typing protocols are robust and prove to be highly efficient in targeting minute amounts of suriving aDNA. In addition, the main advantage of SBE has proven to be the detecting power of omnipresent (background) contamination. We conclude that the mtDNA and NRY SBE assays, in combination with sequence data from the mtDNA control region (backed up by cloning and SPEX), and specialised sample collecting systems, provide a powerful means to effectively generate largescale (pre-)historic population data from ancient human samples.
What colour was Attila the Hun’s horse?: genetic signatures of phenotypic traits in archaeological materials
Mim A. Bower1, Michael G. Campana2, Diane Lister1, Mark Whitten3, Kathy M. Dominy4, Angela M. Murphy5, Paula Jenkins6, Richard Sabin6, Michael Akam7, Robert Asher7 & Matthew Binns5.
1 McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK.
2 Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK.
3 Comparative Population Linguistics Group, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
4Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, SE1 9RT, UK.
5Department of Veterinary Basic Sciences, the Royal Veterinary College, Royal College Street, London, NW1 0TU, UK.
6 Department of Zoology, Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK
7Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
Studying the phenotype, i.e. what a plant or animal looked or behaved like, is perhaps the next “Holy Grail” in ancient DNA research. If we could trace the genes responsible for particular characters in archaeological specimens, it would open the door to some highly relevant and interesting questions in archaeology; the least of which may be the elusive “domestication gene”, but could cover more basic questions, such as: did people in mediaeval Europe prefer cows that had a tendency to lay down fat or muscle? When and where did a particular genetic disorder enter a domestic population? Was the spread of agriculture influenced by adverse environmental conditions? Or what colour was Attila the Hun’s horse? We could begin to understand past approaches to animal and plant husbandry, the expression of past human choice and selection, and past understanding of biological processes such as heredity. Fortunately, molecular biology is fast uncovering the genes responsible for particular phenotypic traits – the only problem, and a significant one perhaps, is looking for these genetic signatures in ancient DNA, known to be a recalcitrant material for analysis.
Greece & Italy
Aristophanes and Stable Isotopes: Comparing literary and isotopic evidence of diet in Classical Thebes, Greece.
Efrossini Vika 1,2, Mike Richards3,4, Holger Schutkowski2 and Vassilis Aravantinos5
1 School of Conservation Sciences, Bournemouth University, BH12 5BB, UK
2 Division of Archaeological, Geographical and Environmental Sciences, University of Bradford, BD7 1DP, UK
3 Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, DE
4 Department of Archaeology, Durham University, DH1 3LE, UK
5 IX Ephorate of Prehistoric and Classical Antiquities, Thebes 60200, GR
The greatest advantage for an archaeologist working with historically dated material is the existence of literary sources, which can complement scientific analyses in archaeology. The present study compiles a dietary profile for the inhabitants of Classical Thebes, using δ13C and δ15N isotope analysis, comparing this evidence with information on diet as presented in Aristophanes’ comedies (Acharnians, Plutus, Wasps).
Aristophanes’ work is abundant in satirical scenes, which emphasize personal attributes and local characteristics. Within this realm, it is possible to extract information on dietary habits, trade and economy in the Classical times. Merchants from Thebes oftentimes appear in his work, reflecting the city’s wealth. Among the goods deriving from this region, eels feature prominently, and are praised as an exceptional delicacy.
Stable isotope analyses of bone collagen were carried out for individuals from the Classical burials of the Northeastern cemetery of Thebes. Results show a remarkable increase of the nitrogen values relative to the previous periods, which is not accompanied by an analogous enrichment of the carbon values. This profile can partly be explained by an increased consumption of freshwater sources in Thebes during the Classical times, such as Aristophanes’ famous eels.The results demonstrate how the integration of isotopic and literary evidence can provide novel information about Classical society in Thebes.
Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, UK
The Greek Bronze Age is the time of the Homeric legends and the Greek myths. The work of Schliemann, Tsountas, Wace and others revealed the material remains of the Mycenaean civilisation that was dominant in the Aegean during the 17th to 12th centuries BC, these remains including human skeletons, some buried with rich grave goods. Biomolecular archaeologists have been attracted to the Greek Bronze Age because there are interesting kinship questions for the burials at several sites, and because aDNA could throw light on the impact of diseases such as malaria on these societies. Addressing these questions clearly requires that aDNA is preserved in the relevant material, and our conclusion after ten years of work is that largely it is not. We have found no indication of aDNA at Lerna, Antron Grave Circles A and B and Mycenae Grave Circle A. At Mycenae Grave Circle B, we detected mitochondrial aDNA in just four of the 22 skeletons that we studied. Only at Kouphovouno have we have obtained sufficient aDNA results to attempt any kind of archaeologically relevant study. The distinguishing feature of Kouphovouno is that we obtained skeletal samples immediately after their excavation. We used optimised PCR systems in order to maximise our chances of detecting aDNA if it was present, but we also used a high containment facility and took scrupulous care to remove surface contamination from the bone samples and to prevent cross-contamination with PCR products from previous experiments. We also confirmed that our negative results were not due to inhibition of PCRs by substances co-purifying with aDNA. Negative results tend not to get widely publicised – we would have preferred positive ones but not if they lead to new Greek myths.
Late Bronze Age Diet in the Greek Peloponnese
E.I.Petroutsa1 & M.P.Richards2
1.20 Koundouriotou str., Exarcheia, 10683 Athens, Greece
2.Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
In this paper we present the results of an isotopic study of bone collagen samples from four Late Bronze Age cemeteries from the Northern Peloponnese in Greece: Voudeni, Aghia Triada, Almyri and Kritika. Through isotope analyses we sought to characterise the general diets in these four sites, especially the amounts of marine protein, as well as animal vs. plant proteins in diets. We also compared the isotopic results from these sites with other Bronze Age sites, including Mycenae. Despite the coastal location of most of the sites we could not find evidence of any significant consumption of marine foods. Instead, most human diets are based on a mixture of plant and animal protein, from C3 terrestrial resources.
Preliminary results of C and N isotope analyses and 14C dating of prehistoric humans and animals from the Mesolithic-Neolithic site of Grotta dell’Uzzo, Sicily, Italy
Marcello A. Mannino1, Sahra Talamo1, Rosaria Di Salvo2, Vittoria Schimmenti2, Marcello Piperno3, Sebastiano Tusa4, Antonio Tagliacozzo5, Michael P. Richards1,6
(1) Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig (Germany)
(2) Museo Archeologico Regionale ‘Antonino Salinas’, Via Bara all’Olivella 24, 90133 Palermo (Italy)
(3) Dipartimento di Scienze Storiche, Archeologiche ed Antropologiche dell’Antichità, Sezione di Paletnologia, Università di Roma ‘La Sapienza’, Via Palestro 63, 00185 Roma (Italy)
(4) Soprintendenza del Mare, Palazzetto Mirto, Via Lungarini 9, 90133 Palermo (Italy)
(5) Museo Nazionale Preistorico Etnografico ‘L. Pigorini’, Piazzale Guglielmo Marconi 14, 00144 Roma E.U.R. (Italy)
(6) Department of Archaeology, University of Durham, South Road, DH1 3LE Durham (United Kingdom)
Grotta dell’Uzzo is one of the key sites in the Mediterranean for the study of the changes in subsistence that took place in the transition from hunter-gatherer (Mesolithic) to agro-pastoral (Neolithic) economies. The cave is also important because 13 Mesolithic humans have been unearthed from 11 burials excavated within it. In order to study the diets of these humans, C and N isotope analyses were undertaken on skeletal remains recovered in the burials and from different trenches excavated at the cave. The preliminary results of these analyses suggest that the main sources of dietary protein were terrestrial and probably originated from the consumption of mammalian herbivores such as red deer (the most commonly exploited animal for much of the cave’s occupation). The contribution of marine resources to human diet at Grotta dell’Uzzo was probably not very significant in absolute terms. This finding might appear to be in contrast with the results of the archaeozoological studies, which have demonstrated that there was an intensification in shellfish collecting and in fishing from the end of the Mesolithic to the inception of the Neolithic. However, given that on the basis of the chronological data currently available the burials predate the end of the Mesolithic, the results of the isotope analyses are in line with the findings of the archaeozoological studies and of the seasonality studies, which have shown that marine resources (mainly represented by shellfish) were not exploited throughout the year before the final stages of the Mesolithic.
Phylogeographic analysis of barley (Hordeum vulgare) landraces shows that the distribution of lineages retains an imprint from the initial patterns of agricultural spread through Europe.
Huw Jones1, James Cockram1, Lydia M Smith1, Ian MacKay1, Robin G Allaby2, Terrence A Brown3, Wayne Powell1
1 National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE
2 Warwick HRI , Wellesbourne, Warwick , CV35 9EF
3 Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN
In the 8000 years since barley was first introduced into the continent of Europe, the evolution of this crop species has been subject to selection under biotic and abiotic pressures. European farmers will have influenced the distribution of barley ecotypes by the movements of early farmers and by their selection of preferred types. The evolution of barley in Europe will also reflect the differing environments in which it has been grown. Modern barley cultivars from across Europe can be seen to differ in their morphology and growth habits. We have attempted to dissect the origins of these different forms by examining the landraces and assess the relative importance of human and environmental selection on modern barley lineages.
We have sampled barley landraces from Europe and discovered their population structure by microsatellite genotyping and statistical analysis. We have used passport data from germplasm collections to characterise the 2-row / 6-row head morphology, hulled / naked grain morphology and the spring / winter growth habit of these sub-populations. The genetic variation underlying key adaptive traits controlling flowering time has been explored by re-sequencing the photoperiod response gene Ppd-H1 and by haplotype analysis at the spring / winter vernalisation genes Vrn-H1 and Vrn-H2. These studies were designed to run alongside analysis of ancient DNA and historic DNA from barley and emmer wheat collected from across Europe.
The population structure we have discovered divides barley landraces into a number of sub-populations each with a distinct geographic distribution. Our genetic data for key adaptive traits allows us to understand the environmental influence on the geographic distribution of each lineage. Where lineages with a similar adaptive profile have distinct geographic distributions we see the imprint of early dispersal by ancient farmers.
Stable isotope evidence for the consumption of millet in Bronze Age Italy
Mary Anne Tafuri1, Oliver Craig2 & Alessandro Canci2
1 Dipartimento di Biologia Animale e dell’Uomo, Sapienza Università di Roma, P.le A. Moro, 5, 00185 Roma. Italy – email: firstname.lastname@example.org
2 Department of Archaeology, University of York, BioArch Biology, S Block PO Box 373 York YO10 5YW, UK
3 Dipartimento di Storia e Tutela dei Beni Culturali, Università degli Studi di Udine, Via Palladio, 8, 33100 Udine. Italy
This study presents, via carbon and nitrogen stable isotope analysis on human and animal bone collagen, new data on diet and subsistence strategies at northern and southern Italy Early and Middle Bronze Age sites, which clearly indicate the direct or indirect consumption of C4 plants. On the basis of paleobotanic data available and as suggested by previous similar studies, we argue here that the isotopic signal obtained can be associated with the consumption of millet (P. miliaceum and Setaria italica). If such an interpretation were true, while we wait for further paleobotanical and isotopic studies, we should consider the results obtained as the earliest evidence of millet consumption in prehistoric Europe. We thus suggest a possible pattern of distribution in the Peninsula of the practice of production and consumption of millet, while setting a new agenda on food security and subsistence strategies in prehistoric Italy
Cattle & Goats
A PCR system free of contaminating DNA for the amplification of bovine DNA from bovine fossils
Camille Berthelot, Sophie Champlot, Marie Liouville, Thierry Grange, Eva-Maria Geigl
Institut Jacques Monod CNRS UMR 7592, Universités Paris 6 et 7, Tour 43, 2, Place Jussieu, 75251 Paris cedex 05, France
Palaeogenetic analyses of bovine bone remains from many Neolithic sites in Europe and in Southwest Asia suffer from poor DNA preservation in these bones that increases the risk of amplification of contaminating modern bovine DNA. Indeed, trace amounts of contaminating bovine DNA occur ubiquitously. In particular, they can be found at low quantities in biochemical reagents used to extract and amplify DNA. These contaminating molecules mimic ancient DNA molecules. Indeed, the contamination rate often resembles the success rate of ancient DNA studies from bovine remains and the length of the contaminating DNA fragments is often comparable to ancient DNA fragments. We elaborated a decontamination protocol for PCR reagents combining various treatments to reduce contamination towards zero. This system significantly increases the reliability of ancient DNA results from bone remains of domesticated animals.
Detecting selection in ancient cattle remains: Pre industrial selection in Bos Taurus and SNP typing in medieval cattle remains
Emma Svensson1, Anders Götherström1
1 Evolutionary Biology, Evolution Genomics & Systematics, Uppsala University, 752 36 Uppsala, Sweden
Historic and prehistoric animal breeding is an enigmatic topic, complicated to approach with conventional genetics and osteology. Questions like when it started, and how strict it was, are of general interest, but it is also complicated to generate a suitable dataset for such questions. By tracing changes in genetic diversity with serial data we can find out how cattle has changed since the domestication of the aurochs to become the array of breeds seen today. Cattle are likely to have been subjected to selection predating the 18th century but the information is scarce. Using a 12plex SNP stream system alongside pyrosequencing we typed up to eight coding and six neutral SNPs in 142 ancient and 216 modern Bos Taurus from Northern Europe. We found a significant decrease in total heterozygosity over time for the coding SNPs which are presumably associated with phenotypic traits such as milk quality and coat colour while neutral markers on the other hand don’t show any significant change over time. This suggests that the decline in diversity is caused by artificial selection and not other genetic processes. The medieval period was a dynamic time in northern European history. The society was moving toward a higher degree of specialization in general, and a number of towns based on trade arouse in Scandinavia. Our findings of early selection fit well with the more sophisticated farming and higher degree of animal breeding that likely occurred at this time.
Using new and old approaches to study bovid systematics and evolution across Eurasia
Alan Cooper1, Kefei Chen1, Beth Shapiro2
1 The Australian Centre of Ancient DNA, School of Earth & Environmental Sciences, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia
2 Department of Biology, The Pennsylvania State University, 326 Mueller Laboratory, University Park PA 16802, USA
Ancient DNA studies of bovid remains from Europe have detected four main taxa: Bison bonasus (the European Bison); Bison priscus (Steppe bison), Bos primigenius (Aurochs); and early Bos taurus (Daisy). Studies of bones recovered from caves in the Urals and Caucasus, and from material dredged from the North Sea, have revealed a fifth European bovid – the Caucasus bison. Previously recognised only as a sub-species of European bison, this taxon appears to represent a separate species, with more genetic diversity than Beringian populations of Bison priscus, suggesting a long evolutionary history and stable population size. It has changed ecological dominance with Bison priscus at several points in the Pleistocene, which appear to be related to climatic and environmental change.We have been using emulsion PCR and high-throughput hybridisation-based SNP screening systems that can simultaneously analyse 50,000 bovid SNPs to explore the genomic evolution of ancient bovids during the Pleistocene and subsequent domestication. We have been concentrating on pre-domestic Bos taurus specimens, as well as representatives of the other Pleistocene bovid species. This approach holds enormous promise for fine-scale temporal analyses of evolution in response to climate and environmental change, as well as archaeology and domestication.
The process of cattle domestication during the Neolithic as revealed by a large-scale palaeogenetic study
Eva-Maria Geigl, Mélanie Pruvost, Marie Liouville, Camille Berthelot, Reinhard Schwarz, Sophie Champlot, Thierry Grange, Virginia Bessa-Correia, Hans-Peter Uerpmann, Lamys Hachem, Hitomi Hongo, Séverine Braguier
Institut Jacques Monod CNRS UMR 7592, Universités Paris 6 et 7, Tour 43, 2, Place Jussieu, 75251 Paris cedex 05, France
Cattle domestication and the troublesome aurochs
Cecilia Anderung1, Jurgita Baubliene2, Daniel Makowiecki3, José Miguel Carratero4, Linas Daugnora2, Juan Luis Arsuaga5 and Anders Götherström6
1Palaeontology Department, Natural History Museum, Cromwell road, London SW7 5BD, Great Britain.
2Department of Anatomy and Histology, Lithuanian Veterinary Academy, Tilžes str. 18, LT-3022, Kaunas, Lithuania
3Institute of Archaeology, Nicolaus Copernicus University, Podmurna 9/11 87-100 Toruń, Poland
4Laboratorio de Evolución Humana, Departamento Ciencias Históricas y Geografía Edificio I+D+I Plaza de Misael Bañuelos s/n, 09001, Burgos, Spain
5Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos c/ Sinesio Delgado Nº 4 Pabellón 14, 28029 Madrid, Spain
6Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
A number of genetic studies relating to the origin of modern cattle have been published recently. In particular the extinct European aurochs (Bos primigenius), progenitor of the modern domesticated form, has attracted a lot of attention. European aurochs bones that have yielded mitochondrial DNA are genetically clearly different from modern cattle. This genetic data, in combination with the genetic patterns observed in modern cattle, has led to the suggestion that modern cattle have a single origin in the Near East, and that the European aurochs population had little to do with their domestication.
However, we ask the question: could this picture of European cattle domestication be too simple?
Here we present results from an investigation of published and novel aurochs sequences from Lithuania, Spain, Poland, and Britain, giving special attention to the Spanish sequences. We looked at the mitochondrial DNA variation in Iberian aurochs remains and searched for aurochs sequences in a domestic context. We find that cattle and aurochs mitochondrial sequences from Iberia deviate from the pattern observed in sequences from Central and Eastern Europe.
In the light of this data, we discuss the possibility of local aurochs domestication events in Europe.
High mtDNA diversity among cattle and goats from the earliest Neolithic settlements on the European continent
Amelie Scheu1,2, Norbert Benecke2 and Joachim Burger1
1 AG Palaeogenetik, Institut für Anthropologie, Johannes Gutenberg-Universität, 55099 Mainz, Germany
2 Deutsches Archäologisches Institut, Eurasienabteilung, 14195 Berlin, Germany
The process of domestication includes a decline in genetic variability. Additional homogenisation occurs due to subsequent colonisation events, such as the Neolithisation of Europe. Our previous studies have shown genetic uniformity even among early Neolithic European cattle (Bollongino et al. 2006). But modern goats also share more than 90% of the same mtDNA haplogroup.
To find out exactly when and where this genetic bottleneck arose during the Neolithisation of Central Europe, we investigated remains of early domesticates on the border between Asia and Europe, i.e. at the origin of the trans-Danubian route of Neolithisation. That region, particularly the area around the Bosphorus and the transit country of Bulgaria, plays a crucial role.
We found higher mtDNA diversity among Neolithic and Bronze Age domesticated cattle East and West of the Black Sea (haplogroups T, T2 and T3) than in Central European populations. Among goats, we found the two different mtDNA haplogroups A and G. G had previously been found among modern goats only near the Fertile Crescent (Naderi et al. 2007).
Our results argue for large and genetically more diverse herds imported to this area and/or for intense trade. Furthermore, they indicate that a second wave of expansion in the direction of Central Europe is responsible for the final loss of mtDNA diversity.
Ice man Schnidi’s trousers: insight into prehistoric goat diversity
1 Institute of Prehistory and Archaeological Science, University of Basel, Spalenring 145, 4055 Basel, Switzerland
2 Gentle Craft, Rue du Rôtillion, 10, 1001 Lausanne, Switzerland
3 Gentle Craft, Rue du Rôtillion, 10, 1001 Lausanne, Switzerland
4 Institute of Prehistory and Archaeological Science, University of Basel, Spalenring 145, 4055 Basel, Switzerland
5 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland
6 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland
7 Archaeological Service of the Canton Bern, Brünnenstrasse 66, 3001 Bern, Switzerland
Since 2003 more than 300 prehistoric remains were discovered in the vicinity of a melting ice patch of the Schnidejoch (2750 m; Bernese Alps, Switzerland), paralleling the finds accompanying the Iceman from the Tisenjoch (Oetztal Alps, Italy/Austria; “Oetzi”). One leg of a Neolithic leather trouser was found and 14C dated to 2900 – 2600 BC. The morphological identification of the animal skin was ambiguous because of the bad preservation of diagnostic features. Based on grain patterns of the skin the leather was made either from sheep or goat.
Because of the importance of the object, a genetic identification of the animal species was attempted. After DNA extraction with QiAmp DNA Mini Kit a 70bp fragment of the mitochondrial cytochrome b gene was amplified in the diluted extract. The leather was made of goat skin (Capra hircus). Six geographically broadly distributed goat lineages are recognized based on mitochondrial d-loop variation, of these lineage A and C were identified by others in prehistoric goat bones from France. The “trouser’s goat” however, belongs to lineage B, which is common in Asia, but extremely rare in Europe today.
An Ancient DNA study from The Farm Beneath the Sand
Martin Bay Hebsgaard1
1 Dept. of Biology, University of Copenhagen, Universitetsparken 15, Denmark
Applying ancient DNA techniques on samples from the archaeological site “The Farm Beneath the Sand” (GUS) near Nuuk in Southwest Greenland is the first attempt to extract DNA from these relative young but novel samples. The sample site highlight the dramatic landscape changes that resulted in floodplain aggradations that eventual buried the site fixing the site under perma-frozen conditions.
The Farm beneath the Sand is situated on a plain surrounded by low mountains ca. 80 km east of Nuuk. When the building remains were found they were overlain by ca. 1,5 m thick layers of sand and gravel, and today the plain in front of the farmhouse appears as a sandy dessert intersected by meandering watercourses that are draining off the icecap.
All together the samples yielded DNA from humans, cattle, sheep, goat and reindeer. Quantification shows approximately 16 times more DNA from cattle than from sheep. Goat DNA was undetectable using Quantitative PCR. The amount of cattle DNA declines over time while sheep DNA probably reflects background variation.
Thanks to thick layers of sand and gravel that may have protected the DNA in the anthropogenic layers ancient DNA is usable in an archaeological context in the reconstruction of the past. In this example ancient DNA research has helped to refine and define archaeological interpretations of the Norse life by adding information not seen by the naked eye. In the future ancient DNA have the capacity to be used more vigorously to investigate the diet of the Norse and show what function specific farms may have had during the settlement. As in this study the future research is not limited to animal DNA but DNA from plant and humans can be used to address different questions.
Pleistocene Horses genetics before and after the last glacial maximum
Sebastian Lippold1 and Michael Hofreiter1
1 Dept. Evolutionary Genetics, MPI for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
We are investigating how the last glacial period affected the genetic composition of populations, particularly the horse (Equus spec.). Vast climatic changes that occurred between 30,000 and 12,000 years BP resulted in dynamic mammalian population structures. Restriction and expansion events during this period influenced both the genetic distribution and variability of a variety of mammals. We focus on western European horse populations, and try to characterize their genetic diversity and phylogeographic patterns both before and after the last glacial maximum. We sequence 600 bp of mtDNA from the mitochondrial D-Loop of different individuals obtained from different locations. Our initial results indicate tremendous genetic diversity, but no phylogeographic pattern within this marker. The genetic distribution of these ancient samples also falls within the broad diversity range apparent in recent horses. Because of this finding, we started screening the DNA samples for additional nuclear markers. Our comparison of these different markers has enabled us to reconstruct several scenarios for horse population dynamics during this period.
Investigating Eneolithic horse exploitation in northern Kazakhstan, via compound-specific stable carbon and deuterium isotope analysis of pottery.
Natalie A. Stear1, David Chivall1, Alan K. Outram2 and Richard P. Evershed1
1Organic Geochemistry Unit, School of Chemistry, University of Bristol, Clifton, BS8 1TS,
2 Department of Archaeology, SoGAER, University of Exeter,Laver Building,
The Eneolithic site of Botai in northern Kazakhstan has been the centre of much debate regarding its role in early horse domestication (Levine, 1999; Olsen, 2003). The faunal assemblage from this remarkable site was almost entirely comprised of horse (99%); however it has remained unknown whether any of these horses were domesticated. Horse domestication is extremely difficult to detect morphologically from skeletal remains and consequently it is necessary to establish a reliable proxy for detecting ancient domestic horse populations.
Fermented mare’s milk (Kumyss) is commonly consumed in rural communities in Kazakhstan, a tradition dating back to prehistory. It is not clear if the milking of horses began (i) in the Eneolithic, during the height of the horse centred communities of the Botai culture; (ii) in the Bronze Age, in response to the milking of ruminants or, (iii) much later. If mare’s milk were identified in ancient pottery it would serve as conclusive evidence for the presence of domestic horses and enable a chronology of horse exploitation to be established.
Equine fat residues can be identified in potsherds using compound-specific stable carbon isotope analysis, but unlike ruminant fats, equine milk and adipose fats are indistinguishable from one another based on δ13C values. However, we show that it is possible to further classify equine fats as either milk or adipose, based upon the δD values of their C16:0 and C18:0 fatty acids which are determined using GC-thermal conversion-IRMS (GC-TC-IRMS). This new proxy has been applied to organic residues extracted from potsherds from Botai as part of a large scale investigation of Eneolithic and Bronze Age pottery from sites in northern Kazakhstan. Using the δ13C and δD values obtained from the Botai residues we have been able to detect equine milk residues preserved within the pottery and consequently, we provide the first direct evidence for the presence of domestic horses at Botai during the Eneolithic.
Detecting dairying with stable calcium isotope ratios (δ44/42Ca) of bones and teeth
Linda M. Reynard1,2, Robert E.M. Hedges1 & Gideon M. Henderson2
1 Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, United Kingdom
2 Department of Earth Sciences, University of Oxford, Parks Road, Oxford, OX1 3PR, United Kingdom
The use of dairy products in antiquity is an important part of the development of agriculture and pastoralism in Eurasia. They offer advantages of more efficient land use, improved nutrition, and more reliable and constant access to protein. Understanding the adoption of dairy, its timing, and geographical spread is relevant to developing a fuller understanding of changes in subsistence from the Neolithic.
An investigation into origins of individuals from a mass grave in Roman Gloucester, UK: strontium and stable isotope evidence
Carolyn Chenery1,2, Gundula Müldner1, Jane Evans2, Louise Loe3, Nicholas Márquez Grant3, Hella Eckardt1 Stephanie Leach1, Mary Lewis1
1 Department of Archaeology, University of Reading, Reading, Berkshire.
2 NERC Isotope Geoscience Laboratory, British Geological Survey, Keyworth, Nottingham.
3 Oxford Archaeological Unit Ltd, Janus House, Osney Mead, Oxford.
Contrary to popular assumptions, Britain under Rome was truly multi-cultural, with historical and epigraphic evidence recording the voluntary and forced migration of Gaulish, Germanic and North African individuals into the British provinces refs. This paper presents the results an isotopic investigation of population diversity in 1st to the 4th century Roman Gloucester; focusing on individuals found in a late 2nd century mass burial pit and comparing them to those found in single graves.The results suggest that the majority of the individuals buried in the London Road Cemetery were from areas within the UK. However, the isotope data has identified a number of individuals whose origins lay in a region with a warmer climate than the UK. Whether these were soldiers, their followers or merchants cannot be determined.
On Rome’s Northern Frontier: Multi-isotopic investigations into cultural diversity in Roman York
Gundula Müldner1, Carolyn Chenery1,2, Stephany Leach1, Mary Lewis1 & Hella Eckardt1
1 Department of Archaeology, University of Reading, Whiteknights, PO Box 227, Reading RG6 6AB, England
2 NERC Isotope Geoscience Laboratory, British Geological Survey, Keyworth, Nottingham, NG12 5GG, England
Britain under Rome was a multi-cultural society, with historical and epigraphic evidence attesting to the presence of migrants from continental Europe, North Africa and the Middle East. Here, we combine isotope analysis for the reconstruction of diet (C,N) and mobility (Sr, O) with skeletal (craniomorphometric) and archaeological data, in order to investigate diversity in Roman York, the political, military and administrative centre of the North. The results show a heterogenous population and highlight the varied life-histories of individuals in the northernmost provincial capital of the Empire; however, they also show that skeletal and isotopic evidence are not always easily correlated. It is suggested that a diet high in marine protein was used to demonstrate a “Roman” identity.
Investigating Marine Food Consumption in Prehistoric Humans via the δ13C values of Collagen Amino Acids
Philip Dunn1, Richard P. Evershed1 & C. Joshua Pollard2
1 School of Chemistry, University of Bristol, Organic Geochemistry Unit, School of Chemistry, Cantock's Close, Bristol, BS8 1TS, UK
2 Department of Archaeology and Anthropology, 43 Woodland Road, Clifton, Bristol BS8 1UU, UK
The current debate concerning the importance of marine foods in the diets of prehistoric peoples has stimulated interest in refining analytical approaches based on stable isotopes. An alternative to the widely bulk collagen approach is to investigate the stable carbon isotope composition of human bone collagen at the amino acid level. Our investigations of prehistoric humans from the Western Cape, South Africa, have shown that the Δ13CGlycine-Phenylalanine values for bone collagen amino acids correlate strongly with bulk δ15N values and provide a new proxy for marine food consumption. We are currently applying this new approach to human skeletal remains from northern Europe.
The tomb at Isbister lies on the south west coast of South Ronaldsay and is one of a number of Neolithic cairns found in the Orkney Islands. During excavation in 1976, the stalled main chamber and three side chambers were found to contain some 16,000 human bones and bone fragments deriving from a minimum of 341 individuals along with a wide range of faunal remains. Previous analyses of bone collagen from the human remains have shown that the tomb was in use from 4,500 to 3,800 BP and bulk collagen stable isotope values for 5 individuals lay in the range -19.9 to -21.2 ‰ indicating a predominantly terrestrial diet, which is surprising for people that lived so close to the coast.
We have now employed the recently introduced LC-IRMS technique to determine the δ13C values of bone collagen amino acids from 22 individuals from Isbister. The results will be compared to those obtained by GC/C/IRMS. The derived Δ13CGlycine-Phenylalanine values give enhanced insights into the dietary habits of the people of Isbister.
Large-scale FLX-sequencing and the Swedish Neolithic
Helena Malmström1,2, Anna Linderholm3, M. Thomas P. Gilbert2, Mikael Brandström1, Jan Storå4, Petra Molnar4, Christian Bendixen5, Gunilla Holmlund6, Kerstin Lidén6, Anders Götherström1, Eske Willerslev2
1Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
2Ancient DNA and Evolution Group, Biological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark
3Archeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
4Osteoarchaeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
5Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences Research Centre Foulum, K25 PO Box 50, DK-8830 Tjele, Denmark
6National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology, Artillerigatan 12, SE-587 58 Linköping, Sweden
The relationship between the contemporary hunter-gatherer Pitted Ware Culture (PWC) and the farming Funnel Beaker Culture (TRB) in Middle Neolithic (3300-2500 B.C.) Sweden has been debated for more than a century. We approach this issue by determining the genetic signatures of skeletal remains from both complexes. Initially, we generated large amounts of “cloned” ancient mitochondrial DNA (mtDNA) PCR amplicons using a single run of the Genome Sequencher FLX System, and a recently described primer tagging protocol. Our data set consisted of Hypervariable Region I (HVRI) amplicons derived from bleach pre-treated powdered bone from Neolithic humans as well as from a large number of negative controls (animal samples, extraction and PCR blanks). We compared the ‘clone’ data with sample quality indicators, such as the number of PCR starting template molecules and the degradation ratio of DNA in the sample (number of long/short fragments). The data shows distinct patterns that differ between high and low quality extracts. After establishing the efficacy of the large scale sequencing approach, additional high-quality PWC and TRB samples (based on collagen preservation) were sequenced in a second FLX run. The compiled data yielded unambiguous HVRI sequences for approximately 40 Neolithic human samples, each compiled from cloned, duplicate PCR amplicons derived from overlapping HVRI fragments. F-statistics and AMOVA revealed significant genetic differences between the PWC and TRB samples, indicating that they indeed comprise of two distinct groups.
Allele frequencies of the lactase gene in Scandinavian Neolithic populations, hunter-gatherers vs. farmers
Anna Linderholm1, Helena Malmström2, 5, Love Dalén3, Kerstin Lidén1, Jan Storå4, Petra Molnar4, M. Thomas P. Gilbert5, Eske Willerslev5, Gunilla Holmlund6, Anders Götherström2
1Archeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
2Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
3Marie Curie Fellow, School of Biological Sciences, University of London, United Kingdom
4Osteoarchaeological Research Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
5Ancient DNA and Evolution Group, Biological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark
6National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology,Artillerigatan 12, SE-587 58 Linköping, Sweden
Genetics and culture are believed to interact, but it has been difficult to find direct evidence for the process. One example that has been put forward as a candidate is lactase persistance in adulthood, i.e. the ability to continue drinking milk. This genetic trait is believed to have evolved within a short space of time in connection with the emergence of farming cultures. Here we investigate certain Scandinavian Neolithic populations and their allele status with respect to the gene responsible for lactase persistance. We find that the allele responsible for lactase persistance was common and not significantly different from modern Swedish populations among Neolithic farmers, whereas Neolithic hunter-gatherers had a lower frequency of the allele.
aDNA analysis of human population samples from the Danish past – what have we learned?
L.C. Melchior1, N. Lynnerup2 and J.Dissing1.
1Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, Denmark, 2Laboratory of Biological Anthropology, Institute of Forensic Medicine, University of Copenhagen, Denmark.
During an ongoing survey of the Danish genetic past we analyzed mtDNA from teeth from human remains from a range of burial sites from medieval times to the Stone Age. To ensure the highest possible degree of reliability generally accepted authentication criteria (including sequencing of multiple clones and replication by different researchers) as well as additional precautions (e.g. testing of laboratory performance) were observed.
Unequivocal assignment of mtDNA haplotypes was possible for more than 50 ancient subjects; however, the success rate varies substantially between sites. The highest success rate (11 out 11) was obtained with freshly excavated Viking Age subjects (ca AD 1,000), but good results were also obtained for recently excavated Iron Age sites (AD 0-400). Poor results were found with highly manipulated subjects (contamination) and with most of the Stone Age samples (4,500-5,000 YBP).
While laboratory related contamination can effectively be prevented by the abovementioned precautions, the most serious challenge to authenticity is caused by pre-lab contamination. This problem was tackled using several approaches including analysis of DNA damage patterns, haplotyping of archaeologists, phylogenetic testing and as the most efficient measure, sampling from the ancient subjects during exhumation. We show that reliable retrieval and analysis of DNA from ancient humans is indeed a possible undertaking.
A high degree of nucleotide diversity was observed in the ancient populations, and at four out of six locations the diversity was considerable higher than among modern Danes. Also, we observed a consistently higher abundance of Hg I (10-20%) than among modern Danes (~3%).The effect of the Black Death has been suggested as a possible explanation for a similar decline in the English genetic diversity. Interestingly, we found the highest genetic diversity in a 15th century population sample long after the major outbreak in the14th century.
Henryk W. Witas1, Magdalena Kołodziejczak1, Paweł P. Liberski2
1 Dept. of Molecular Biology, Medical University of Lodz, 91-738 Lodz, Sporna 36/50, Poland
2 Dept. of Molecular Pathology and Neuropathology, Medical University of Lodz, 92-216 Łódź, Pomorska 251, Poland
Although precise biological role of prion proteins (PrPC) is still a subject of extensive study and debate, a few suggestions of their involvement in cellular processes have been described, including involvement in biology of synapse, short-term memory formation and long-term memory consolidation. Prion proteins became commonly recognizable as a cause of some human transmissible spongiform encephalopathies (TSE). Among a number of SNPs, A385G / Met129Val is assumed as a factor involved in the pathogenesis of TSEs (e.g. kuru) and a marker of memory efficiency as well. Although frequency of Met129Val alleles are precisely characterised for modern populations and its significance discussed, no data for historic and prehistoric populations to compare are available.
Specimens came from seven medieval cemeteries located throughout today’s Poland, and have been excavated recently. Teeth stored at low temperature underwent procedures generally accepted for aDNA isolation, performed automatically (MagNa Pure, Roche) at least two times on different teeth of each individual. Only the samples represented by collagen quantity above 2% dry weight, negative result of appropriate mock controls throughout isolation and amplification procedures, with successfully cloned (Amersham) and sequenced (AB 310) PCR products have been considered as authentic ancient templates. Moreover, we have applied NspI restriction analysis as a method for recognition and retrieval of undamaged ancient sequences.
The results show rapid increase in PRNP allele A frequency (Met 129) since the beginning of the Second Millennium (0.51 v. 0.65), accompanied by slight drop in heterozygotes (0.49 v. 0.39) and significant rise in Met homozygotes (0.27 v. 0.45).
As compared to present Polish as well as present European PRNP alleles frequency, medieval specimens provided the data which suggest altered mode of PRNP alleles transmission within last 35-40 generations. Although the nature of mechanism leading to observed changes is unclear, the impact of demographic factors is probably the most pronounced one affecting the process of local fluctuations of Met allele spreading out. However, the effect of selection processes should also be considered. This work is being supported by grant from Ministry of Science and Higher Education
Mice and Vikings
1 Department of Biology, University of York, Heslington, YO10 5DD, United Kingdom
Originally native to the northern Indian subcontinent and the Middle East, house mice (Mus musculus) have spread to their current near global distribution by exploiting a commensal niche with humans, originally in agrarian settlements. Mice also owe their current distribution pattern to human movements: they have reached the areas they now inhabit by being accidentally transported with grain and livestock foods. This close association between mice and humans means we can use information from the current genetic distribution of house mice to make inferences about past human colonisations and cultural linkages. In this study, we used mitochondrial DNA sequences from modern house mice in Great Britain, France, Ireland, Iceland, the Faeroe Islands and Norway to identify patterns in the their distribution, and tie these in to historic human migrations. The mice appear to be telling us about Norse Viking colonisations, and add a useful source of information to complement archaeological and historical data.
East Asia & Pacific
Genetic relationship of Human Skeletal Remains from an archaeological cemetery
Sang Hyun Jee 1, Yun Ji Kim 1, Yong Jae Chung1 & Min Seok Seo 1
1 Conservation Science Division, National Research Institute of Cultural Heritage, 472 Munji-dong, Yuseong-gu, Daejeon, 305-380, South Korea
We carried out genetic analyses of human skeletal remains from cemetery of a historic site, Myeong-arm-ri of Asan in South Korea. According to archaeological evidences, this site had been constructed from the Neolithic Age to the Joseon Dynasty. Twenty one human skeletons excavated from thirty pit tombs that have outer coffin build up into plaster dated to the Joseon Dynasty (14-19th century). To identify the genealogy and traditional burial pattern were assessed using mitochondrial DNA (mtDNA) and Y chromosomal STRs. We take cautious to avoid erroneous recombination by the segmental and modern contaminations were derived from researchers and all experimental stages. We sequenced the segmental amplicons of the hyper variable regions (HVRs) of mtDNA, and appointed relevant haplogroups according to the sequence polymorphism using the known mtDNA database. We also applied variable short tandem repeat (STR) marker in Y chromosome to understand paternal lineage and kinship among the burials. Especially, we interested in the four burying together and examined genetic relationship more closely between two individuals.
Not quite in the bag: A systematic bioarchaeological approach to the question of South American chickens origins
1 Dept. of Archaeology, Durham University, South Road, DH1 3LE, UK
Though chickens were undoubtedly introduced into the American continents by the Spanish after their arrival in the 15th century, there is an ongoing debate as to the possible that Polynesians traveling across the Pacific introduced chickens to South America before Europeans did so. A recent publication concluded on the basis of ancient DNA extracted from an archaeological Chilean chicken bone that domestic fowl were present in a pre-Columbian context and that those chickens possessed a Polynesian genetic signature. In order to test this hypothesis, we generated mitochondrial DNA control region sequences from 41 modern, native Chilean specimens and analyzed them within a database consisting of both the published ancient DNA sequences and ~1,000 globally distributed modern domestic chicken sequences. Our modern Chilean sequences cluster closely with haplotypes predominantly distributed amongst European, Indian, and Southeast Asian chickens, consistent with a European genetic origin. The previously published, apparently pre-Columbian, Chilean specimen and seven pre-European Polynesian specimens, also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing, at this stage, no support for a Polynesian introduction of chickens to South America. Ancient DNA sequences from two archaeological sites on Easter Island, however, cluster with chickens found in Island Southeast Asia, and may represent a genetic signature of an early Polynesian dispersal as far as Easter Island. Lastly, we modeled the potential marine carbon contribution to the Chilean archaeological specimen (thus revising the derived date of the specimen) which cast doubt on the pre-Columbian age of the chicken remains. Definitive proof of a pre-Columbian introduction will require excavating more chicken bones, and further analyses of ancient DNA and radiocarbon data from Chilean and Polynesian archaeological excavations.
A New Bioarchaeological Clue for the DongHu Nationality
ZHANG Quan-chao, CHANG E，ZHU Hong
( Research Center f or Chinese Frontier A rchaeology , Jilin University , Changchun , Jilin , 130012 , China)
Obtaining population genetics data via non-destructive means: a three-dimensional analysis of human craniofacial morphology
Sabrina B. Sholts1, Sebastian Wärmländer2, & Phillip L. Walker3
1 Department of Anthropology, University of California at Santa Barbara, Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
2 Division of Biophysics, Arrhenius Laboratories for Natural Science, Stockholm University, 10691 Stockholm, Sweden
3 Department of Anthropology, University of California at Santa Barbara, Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
In this study, shapes extracted from the human craniofacial skeleton were used to investigate the genetic heritabilities of morphological traits. Three-dimensional point data was collected from human crania with a 3D laser scanner and used to render complete 3D surface models of the original skeletal material. 3D data analysis software was used to digitally slice the cranial models with geometric planes defined by traditional craniometric landmarks. The cross-sections produced by these planes yielded contours of cranial outlines for different craniofacial features. Using elliptical Fourier transforms, the contours were parametrized into series of Fourier coefficients, which, due to their inherent orthogonality, form suitable input parameters for statistical analysis. Principal components analysis (PCA) was employed to differentiate population groups based on shape differences in various aspects of cranio-facial skeletal morphology. This method can yield population genetics data and information on probable ancestral affinity using non-destructive analysis of human remains and with greater accuracy than with traditional craniometric studies of metric and non-metric traits. The application of this method to human skeletal collections can elucidate genetic relationships in past populations and improve our understanding of their archaeological contexts. This non-invasive method also offers a viable alternative for determining ancestral affinities between groups and individuals in cases where DNA testing is not possible, due to either the necessary destruction of bone required for DNA analysis or the degraded condition of the material.