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Human skeleton, Abingdon: These are skeletons at the medieval cemetery in Abingdon, Oxforshire. Courtesy of Erika Hagelberg.
Satellite meeting organised by Professor Erika Hagelberg, Professor Michael Hofreiter and Professor Christine Keyser
In this satellite meeting we aim to bring together an international group of scientists to discuss the most exciting, technically challenging and contentious area of ancient DNA research, the analysis of DNA from old human remains and its application to the study of human evolution, migrations and past diseases.
Final programme available here
This is a residential conference, which allows for increased discussion and networking. It is free to attend, however participants need to cover their accommodation and catering costs if required.
Participants are also encouraged to attend the related scientific discussion meeting Ancient DNA: the first three decades which immediately precedes this event.
Enquiries: Contact the events team
Professor Erika Hagelberg, University of Oslo, NorwayOrganiser and Chair
Professor Michael Hofreiter, University of York, UKOrganiser and Chair
Professor Michi Hofreiter studied biology in Munich, and completed his diploma with Svante Paabo on DNA from ground sloth feces to reconstruct vegetation changes during the Pleistocene. He then moved to the Max Plank Institute for Evolutionary Anthropology in Leipzig, completing his PhD in 2002 on cave bear population genetics and ancient DNA damage, and a post doc in 2005 working on various aspects of ancient DNA including population analyses of Pleistocene species, DNA extraction methods, palaeogenomics. From 2005 he ran an independent research group at the MPI looking at mammoth and mastodon phylogenetics, functional ancient DNA analyses, and adapting Next Generation Sequencing for work with ancient DNA and multiple samples. Since April 2009 he has been Professor of Evolutionary Biology and Ecology at the University of York.
Professor Christine Keyser, Université de Strasbourg, France Organiser
Christine Keyser currently is Full Professor at the University of Strasbourg (France). In 1996, she received her PhD in Molecular and Cellular Biology and in 2007 her Habilitation in Genetics, both from the University of Strasbourg. She has taught as an Assistant Professor from 2003 to 2011. In 2001, she was appointed legal expert by the Court of Appeal of Colmar and in 2002 she was accredited to proceed to the genetic identification of persons. Until recently, she worked as forensic DNA expert for the French Ministry of Justice to identify living or deceased persons. She has both teaching and research duties, mainly in the fields of population genetics, forensic genetics, and molecular anthropology. Her research, conducted within the Institute of Legal Medicine of Strasbourg (AMIS laboratory), has been pioneer, in France, in the use of molecular techniques applied to forensic human identification for the study of ancient human remains.
Her research area covers many aspects of ancient DNA works such as the study of the kinship relations within a necropolis, the migration patterns of a population, the phenotypic traits and bio-geographic ancestry of ancient specimens or the disease of past human populations. At this time, herresearch projects are conductedmainly in four regions of the world: Central Asia, Siberia, Southern America, and Europe.
Dr Paula F Campos, Natural History Museum, DenmarkPleistocene humans in the Americas/ East Asia and their environment
Paula F. Campos graduated in Biology by the University of Porto, gained a Marie Curie early training grant and completed a PhD in Biology – ancient DNA and Evolution in 2009, at University of Copenhagen, focusing on Pleistocene musk ox population dynamics. In 2011 she was appointed curator of Zoology in the Science Museum, University of Coimbra, Portugal, and is since March 2013 an Assistant Professor at the Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen. Her research interests focus on megafauna population dynamics in the late Pleistocene and Holocene and early human migrations into the New World.
The timing, route and origin of the first human migration into the Americas are still heavily debated. The most widely accepted dates of occupation are still the ones related to the Clovis complex, ~11,000 to 10,800 14C years before the present (yr B.P.) (13.2–13.1 to 12.9–12.8 ka), a distinct culture that appears to have originated and spread throughout North America in as little as 200 to 300 years, and that has been blamed for the extinction of several genera of megafaunal mammals approximately 10,000 years before present.
However, human mitochondrial DNA recovered from coprolites found at the Paisley 5 Mile Point Caves, in south-central Oregon, suggest human presence as early as 12,300 14C years B.P (coprolites were directly dated by accelerator mass spectrometry). Here we present genetic, archaeological and stratigraphical data that further confirm these results.
Professor Anne Stone, Arizona State University, USAImpacts of colonization in the Americas
Anne Stone is Professor in the School of Human Evolution and Social Change at the Arizona State University. Her specialization and main area of interest is anthropological genetics. Currently, her research focuses on population history and understanding how humans and the great apes have adapted to their environments, including their disease and dietary environments. This has three main strands: (a) Native American population history, (b) the evolutionary history of the Great Apes, and (c) understanding the co-evolutionary history of mycobacteria (specifically Mycobacterium tuberculosis and M. leprae, the causative agents of tuberculosis and leprosy, respectively) with human and non-human primates. She has been a Fulbright Fellow (1992-93) and a Kavli Scholar (2007), and in 2011 she was elected a fellow of the American Association for the Advancement of Science. She has served on the editorial boards of the American Journal of Physical Anthropology and the Journal of Human Evolution, and currently serves as a senior editor of Molecular Biology and Evolution.
European contact in the Americas resulted in major social changes to Native American societies. In addition, biological impacts, including changes in population size and patterns of diversity, admixture, and disease introduction, have left lasting signatures today. Genetic analyses of ancient populations (both pre and post contact) can provide insight into these changes. Here, we will present mitochondrial DNA data obtained from people from pre-contact archaeological sites, including Norris Farms in the Midwestern United States and Chen Chen in southern Peru, as well as at a contact period mission site in southern Argentina in order to highlight aspects of population diversity and continuity as well as, more recently, admixture. In addition, we will report initial results from attempts to characterize ancient disease strains including mycobacterial strains from cases of disseminated bone TB and Leishmania strains from facial lesions in order to understand the phylogenetic relationships between strains of these pathogens prior to and after contact.
Marie-France Deguilloux, Université Bordeaux 1Where are the Caribs ? Ancient DNA from ceramic period human remains in the Lesser Antilles.
In charge of the palaeogenetic approach in the UMR PACEA (Team Anthropology of Past and Present Populations), I develop various projects using aDNA to better understand the evolution of past human populations and their migrations. In close collaboration with anthropologists and archaeologists, the characterisation of past human gene pools permit us to reconstruct the peopling dynamics of past human populations in various regions (in Polynesia, Lesser Antilles or Europe), or to better understand the funerary practices of ancient human groups (Neolithic, Medieval periods).
When Europeans reached the Caribbean archipelago, in the late 15th century, they described four distinct human groups: Ciboneys and Tainos in Greater Antilles, Arawaks and Caribs in Lesser Antilles. Genetic analyses of extant populations from the Caribbean region have clearly confirmed high levels of genetic admixture with West African populations, and illustrated the limitations of working with modern Caribbean populations to unravel ancient populations’ origin and dynamics. We therefore developed a palaeogenetic project aiming to characterize the gene pool of the extinct Caribs, in order to ascertain the genetic affinities between Caribbean extinct populations. Carib human remains, originating from Guadeloupe, Marie-Galante and La Désirade were analysed for mtDNA and Y chromosome variation. The results obtained provide persuasive arguments concerning the origin of this human group in South America. They also permit to point out clear genetic differentiation between human groups from Greater and Lesser Antilles, furthermore clearly differentiated in front of social organization and archaeological cultures. Nevertheless, we also highlight the necessity to investigate the identity of individuals under study in palaeogenetic analyses (assessed through different funerary practices in our case), to propose reliable evolutionary scenarios for ancient populations. This task necessitates a real collaboration between archaeology and ancient DNA research.
Professor Yinqiu Cui, Jilin University, ChinaKinship analysis of ancient human remains based on Y-chromosomal, autosomal and mitochondrial DNA.
Professor Yinqiu Cui received her Ph.D. at Jilin University in 2002, studying patterns of genetic diversity among contemporary and ancient populations in northwestern China? She then continued as a postdoctoral fellow in the department of Microbiology at University of Queensland. After her postdoctoral training, Dr. Cui joined the faculty at the Jilin University in August of 2003. Her research interests include reconstructing genetic structure of ancient populations and molecular forensic anthropology, such as sex identification, kinship reconstruction, and individual identification. Previous and on-going projects involve the whole mitochondrial genome study of a prehistoric Xinjiang population using next generation sequencing technique, DNA identification of archaeological human remains, and forensic species identification of degraded biological samples.
The Yuan dynasty was the first foreign dynasty to rule all of China, and lasted more than 200 years. The Mongol rulers were a minority among the Han majority, and most of the cemeteries that have been discovered belong to the Han. Cemeteries belonging to Mongolian nobles have been rarely found, due to the special burial customs and absence of historical records.
Archaeological excavations in Shuzhuanglou at Hebei province of China led to the discovery of 13 skeletons in 6 separate tombs, currently assumed to be of Mongol nobles or Korgis. A multidisciplinary approach including archaeology, anthropology, isotope analysis and ancient DNA methods was applied to confirm the identity of the cemetery owners, and resolve the kin relationships between individuals. Data from autosomal, mitochondrial, and Y-chromosomal markers permitted the identification of genetic kin relationships between some of the individuals. A combination of archaeological information, stable isotope data and molecular evidence allowed the cemetery owners to be tentatively identified. We demonstrate that a multidisciplinary approach is useful for the identification of individuals and kinship relationships using bone specimens from old historic sites
Dr Anders Götherström, Uppsala University, SwedenChair
Biography not available
Dr Agnar Helgason, deCODE Genetics, University of IcelandAssessing the authenticity of clonal sequence reads from ancient samples: A case study from Iceland
Agnar Helgason completed his undergraduate training in Anthropology at the University of Iceland in 1992, after which he obtained a research-based Masters degree in social anthropology in 1995 at the same institution. In 1996 Agnar graduated from the University of Cambridge with an MPhil in Biological Anthropology and with a D.Phil in the same subject from the University of Oxford in 2001. In 2000 he joined deCODE Genetics where he is currently a senior research scientist in biological anthropology and population genetics as well as being a research professor at the Department of Anthropology at the University of Iceland.
Agnar’s research areas include the genetic history of the Icelanders and the Inuit, the use of genealogical data in population genetics, the mutation rate, the identification of patterns of natural selection at loci associated with complex diseases and traits such as pigmentation, the impact of population structure on association studies, and statistical analyses of ancient DNA. Agnar is an author of more than 50 articles in peer-reviewed scientific journals.
The Viking age witnessed the expansion of Norse invaders across much of Northwestern Europe, with a particularly long-lasting cultural and genetic impact on the populations in the North Atlantic –particularly in Iceland and the Faroes, where there were no pre-existing human populations. In my talk, I will summarize the outcome of ancient DNA research that helps shed some light on the origin of the Icelandic population and the activities of the Norse invaders in the North Atlantic region
Pontus Skoglund, Uppsala University, Sweden Genomic analysis of prehistoric populations in Europe: authentication and population history
An evolutionary geneticist at Uppsala University, Pontus Skoglund's main research interests are population genetic analysis of ancient and modern genomes. He defended his MSc thesis in 2009, which focused on exploring population genetic approaches for low-coverage shotgun sequencing of ancient genomes. Building on ideas from his MSc, he and researchers in Uppsala and Denmark used the low-coverage shotgun approach to publish the first study of prehistoric modern humans at the population level in 2012, pioneering analysis methods for low-coverage ancient population genomics and providing evidence for a major migration associated with the spread of farming in Europe. He is also a primary author of recent high-profile studies on differences in archaic ancestry across Eurasia and the population genetics of southern African hunter-gatherers, an analysis that also provided novel evidence of evolutionary processes in the ancestors of modern humans. His continuing focus involves applying statistical methods for obtaining and analyzing reliable genomic data directly from ancient populations to address outstanding questions in archaeology and human evolution.
One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. I will describe a novel statistical framework for isolating endogenous ancient DNA sequences from contaminating sequences using postmortem degradation patterns, and demonstrate using both published and novel large-scale sequence data that this approach is able to reduce high contamination fractions to negligible levels. This approach thus opens up the possibility of authenticating genome-wide sequence data from human remains. In an application for this, we have generated ancient genomic sequence data from several Scandinavian individuals associated with foraging and agricultural groups. We show that the Neolithic Scandinavian individuals show remarkable population structure corresponding to their cultural association, and that comparison with southern European ancient individuals as well as modern-day variation suggests a model where initial colonization by agricultural populations was followed by later admixture with hunter-gatherer populations and/or gene flow from other regions.
Professor Concepción de la Rúa, University of the Basque Country, SpainThe Neolithic transition in the Cantabrian fringe (Peninsula Iberica)
Concepción de la Rúa, graduate in Biology as well as in Medicine, is currently Full Professor at the University of the Basque Country (UPV/EHU) in Bilbao. She has both teaching and research duties, in the field of human evolutionary biology as well as in forensic human identification in the Balcans. Her ancient DNA group has been pioneering in Spain in the analysis of DNA from ancient human remains from the Cantabrian fringe. Her research focus is on investigating evolutionary processes in pre-historic human groups mainly the transition from Paleolithic foraging to Neolithic farming societies from Iberian Peninsula.
The variability of mitochondrial DNA from different prehistoric populations of the Northern Iberian Peninsula (from the Magdalenian to the Bronze Age) was analyzed. The results obtained were validated using the authentication criteria proposed by the scientific community. The analysis of the mitochondrial variability in this study together with the ancient and present-day populations studied so far, indicates the differentiation of the hunter-gatherer groups regarding both Neolithic and present populations. As for Neolithic European groups, within the heterogeneity observed two groupings can be appreciated: on one side, the Neolithic sites that present haplogroup N (proposed as a marker for the spread of the Neolithic in Central Europe) and on the other side those lacking such haplogroup (Mediterranean sites and sites from the Cantabrian fringe). DNA analysis from ancient groups indicates that the diffusion of the Neolithic had different genetic impact in different European prehistoric populations, highlighting the complex biological patterns resulting from Neolithization in contrast with the simpler and more evident cultural patterns.
Dr Claudio Ottoni, Center for Archaeological Sciences, KU Leuven, BelgiumHuman ancient DNA from the ancient city of Sagalassos (Turkey): a diachronic view of mtDNA variation from Roman to Byzantine time.
Claudio Ottoni obtained his degree in Biological Sciences at the University of Rome “Tor Vergata” in 2004. Since then, he focused his research on the study of human evolution, with particular attention to population genetics and aDNA studies. In 2008 he completed his PhD in Evolutionary Biology, in the group of Molecular Anthropology of Tor Vergata university, thereby addressing his research on the study of ancient (Pastoral and Garamantian civilizations) and modern (Tuareg) populations from Northern Africa. During his PhD he also explored the preservation of aDNA in animal cooked bones, in collaboration with the Bioarch group of York, and in 2007-2008 he moved to Mainz, in the Paleogenetic group of the Gutenberg University, where he took part in a project about aDNA in skeletons from plague mass graves.
Since 2009 he is a post-doctoral research fellow at the University of Leuven, in the Center for Archaeological Sciences. In 2011 he was a visiting researcher in the Palaeogenomic group of the Institute Jacques Monod, in Paris. His current research focuses on the study of aDNA to unravel questions around animal domestication (pigs and cats) and the human peopling of the ancient city of Sagalassos, in Turkey.
More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of an ancient urban settlement in all its features. The rise of the ancient city of Sagalassos can be likely placed at the end of 5th BC. At the crossroad between Europe and Southwest Asia, over the centuries the study region of Sagalassos experienced the domination and the influence of several empires and civilizations (Phrygians, Persians and Romans just to mention some). The city was eventually abandoned in the mid Byzantine time (13th century AD), after the Seljuk invasion.
The main goal of our study is to describe the maternal genetic variation in Sagalassos across a wide temporal frame of its human occupation and to reconstruct potential demographic dynamics in relation to historical events documented in the Anatolia region (e.g. a plague epidemic in the 6th century AD). For this purpose, we have analysed bone and teeth samples of 45 skeletons dated to the Classic-Hellenistic up to Roman Imperial times. By means of coalescence simulations and multivariate analyses, the novel mtDNA sequences will be compared with Byzantine (12th-13th century AD) sequences previously analysed in order to detect potential significant changes in the maternal genetic pools of Sagalassos dwellers across time and to envisage demographic scenarios which may have affected the region.
Co-authors: Rita Rasteiro, Dept of Genetics, School of History, University of Leicester, UK
Reyhan Yaka, METU Department of Biological Sciences, Turkey
Katrien Van de Vijver, Center for Archaeological Sciences, University of Leuven, Belgium
Rinse Willet, Sagalassos Archaeological Research Project, University of Leuven, Belgium
Jeroen Poblome, Sagalassos Archaeological Research Project, University of Leuven, Belgium
Lounés Chikhi, Laboratoire Evolution et Diversité, Biologique (UMR 5174, CNRS/UPS), University Paul Sabatier, Toulouse, France & Instituto Gulbenkian de Ciência, Oerias, Portugal
Dr Eva-Maria Geigl, Université Paris Diderot/CNRS, France Palaeogenomic analysis of ancient humans: methodological issues
After a university training in chemistry and biology at the University of Munich (LMU), Germany, Dr. Eva-Maria Geigl obtained a PhD in molecular radiation biology from the LMU. During her postdoctoral work at the University of Stanford, Medical Center, she was involved in the Human Genome Project focusing on the physical mapping of chromosomes and on endogenous retroviral sequences. She then joined the Jacques Monod Institute in Paris where she investigated the architecture and evolution of human chromosomes. Later she became interested in using the palaeogenetic approach to study the evolution of genomes and species, developed projects in this area and set up a high containment laboratory in which to carry out this work. She proposed that ancient DNA is preserved in bones in molecular niches and demonstrated the importance of post-excavation treatments of archaeological bones for ancient DNA preservation. She is now head of research at the French National Research Center CNRS and runs a research group at the Jacques Monod Institute in Paris. The main research lines of her group are the study of the evolution of genomes, the analysis of the domestication of animals, the study of extinct and endangered animals, parasites and pathogens, the methodological development in palaeogenetics and –genomics, and taphonomic approaches to better understand DNA preservation.
The analysis of genomes retrieved from archaeological material offers unprecedented new and detailed views of human evolution and the history of ancient human populations, as recent research has demonstrated. So far, however, these analyses were possible only in the cases of exceptionally well preserved specimens, ie either preserved in the permafrost or under particularly favorable taphonomic conditions in caves. To access the genomes of the majority of anthropologically important specimens where DNA is only poorly preserved, our approach to DNA retrieval and sequencing methods must be improved and fine tuned. Genomic analysis of this material, even when aseptically excavated and handled, is also particularly prone to contamination with modern DNA originating either from reagents and oligos or from previous analyses. We will show which lessons can be learned from our NGS experiments on human and animal bones and teeth.
Co-authors: E. Andrew Bennett and Thierry Grange, Institut Jacques Monod, CNRS, University Paris Diderot, Paris, France
Professor Erika Hagelberg, University of Oslo, Norway Shall we still worry about contamination?
Erika Hagelberg gained a PhD in biochemistry from Cambridge University, and a master in history and philosophy of science from University College London. From 1987 to 1992, she worked at the then Institute of Molecular Medicine, University of Oxford, on the analysis of DNA from ancient bone. While in Oxford, she pioneered the earliest applications of bone DNA typing in forensic identification and human evolutionary history. After holding teaching positions at Cambridge University and at the University of Otago, New Zealand, in 2002 she was appointed professor of evolutionary biology at the University of Oslo, Norway. Her main research interests are in the fields of ancient DNA and the human settlement of the Pacific.
For many years, studies on ancient human DNA were haunted by the spectre of contamination, and some of the most contentious discussions in the field concerned contamination and the authenticity of DNA sequences from human remains. Studies on human DNA were even held to be impossible by some researchers, and standards were imposed to try to weed out “suspect” research. It is interesting to note, however, that despite the prominent role of DNA contamination, none of the studies presented at this meeting on ancient human DNA focuses chiefly on contamination. This is a heartening development, and suggests researchers are now more interested in the outcome of research than in the obstacles to research. A few questions remain: do the standards for ancient DNA research still stand, shall we still worry about contamination with the advent of next generation sequencing, and how shall we address the issues of contamination constructively as a research community?
Dr Odile Loreille, American Registry of Pathology, USANext generation sequencing solutions to unidentified human remains cases
Dr Odile Loreille studied molecular Biology and evolution in Paris and obtained her PhD from the University of Claude Bernard in Lyon, France. She then went to Germany (Göttingen and Mainz) for two post doctoral studies on ancient DNA. In 2004 she left Europe to join the Forensics community at the Armed Forces DNA Identification Laboratory (AFDIL) in the USA. She did three years of postdoctoral work on Human identification before being hired as a senior research scientific by the American registry of Pathology (contractors supporting the AFDIL). She belongs to the emerging technologies section and develops new protocols for the case work sections. Her main project deals with the identification of unknown American soldiers killed during the Korean War whose remains have been extensively degraded by Formaldehyde. She became a member of the International Society for Forensic Genetics in 2007 and was awarded the "identification techniques advancement award" by the AFDIL in 2008.
One of the missions of the Armed Forces DNA Identification Laboratory (AFDIL) is to assist the Joint POW/MIA Accounting Command in the identification of missing service members from past military conflicts. Until recently, specimens submitted for testing from a specific set of 800 service members buried as unknowns have been surprisingly recalcitrant to the standard DNA identification methods employed by AFDIL. The reason for this lies in the extensive post-mortem treatment performed on these remains which included, among other things, immersion in formaldehyde for a several days. These aggressive mortuary practices caused severe damage to the endogenous DNA, generally leaving fragments of only 80 bp or less.
Using Illumina technology paired with hybridization capture, we are now able to produce sequence data for these highly degraded specimens. The first phase of our study has focused on individuals who were identified based on physical and circumstantial evidence and for whom “known” DNA from a maternal relative is available. The reference sequences are being employed to authenticate data, optimize bioinformatics parameters, and characterize the features of the NGS sequences generated from the degraded specimens. Most importantly, the reference samples are serving to demonstrate that the NGS methods being applied are indeed yielding authentic sequence data from these particularly recalcitrant specimens, and that these methods have the potential to aid in the identification of missing U.S. service members.
Co-authors: Alice Chung, Suzanne Barritt-Ross, Jodi Irwin, Timothy McMahon
Dr Matthias Meyer, Max Planck Institute for Evolutionary Anthropology, GermanyIncreasing the resolution - new molecular methods improve access to archaic human DNA
Matthias Meyer gained a diploma in biochemistry at Leipzig University in 2005. In 2009 he completed his PhD in Michael Hofreiter's group at the Max Planck Institute for Evolutionary Anthropology in Leipzig, and then stayed at the Max Planck Institute to become a postdoc in Svante Pääbo's group.
Since 2013 he has lead a research group on "advanced DNA sequencing techniques". Matthias Meyer has developed many methods to improve the scope of DNA sequencing in evolutionary studies, a work that has recently enabled the generation of high-quality genome sequences from two extinct archaic human groups, Denisovans and Neanderthals.
Improvements to ancient DNA extraction and library preparation techniques have enabled the reconstruction of genome sequences from Late Pleistocene archaic human groups at an unprecedented level of resolution, most prominently those of Neanderthals and Denisovans. Recent success in sequencing Middle Pleistocene animal remains indicates that these methods may also make it possible to retrieve DNA sequences from human fossils of much greater age in the future. However, if DNA is present in such fossils, it is even more degraded and present in smaller quantities than in any other ancient human fossil that has produced meaningful genetic data to date. My presentation will summarize the progress of our work on extremely poorly preserved ancient human DNA and the technical difficulties that are faced, both in the laboratory and with sequence analysis.
Professor Sir Paul Mellars, University of Cambridge, UKChair
Paul Mellars is Professor Emeritus of Prehistory and Human Evolution at the University of Cambridge, Professional Fellow in Archaeology at the University of Edinburgh and a Fellow of Corpus Christi College. He took his initial doctorate at Cambridge in 1967 (specialising in the behaviour and organization of Neanderthal populations in Europe), and taught for ten years at Sheffield University before returning to Cambridge in 1981. His recent research has focused on the cultural and cognitive origins of Homo sapiens populations in Africa, and their subsequent dispersal to other parts of the world, based on a close integration between the DNA and archaeological evidence for modern human dispersals, with publications in Nature, Science and elsewhere.
His books include The Neanderthal Legacy (1996), Modelling the Early Human Mind (1996), Rethinking the Human Revolution (2007) and reports on excavations of later prehistoric (Mesolithic) sites in northern England and Scotland. He is a member of the Academia Europaea, an 'Officier dans l'Ordre des Palmes Academiques', and a recipient of the British Academy Grahame Clark Medal for Prehistory (2008). He was awarded a knighthood for 'services to scholarship' in the 2010 New Year's honours list.
Dr Carles Lalueza-Fox, Instituto de Biología Evolutiva (CSIC-UPF), Spain Paleogenomics and the Mesolithic-Neolithic transition in Europe
Carles Lalueza-Fox (Barcelona, 1965) is a researcher at the Institute of Evolutionary Biology (CSIC-UPF) in Barcelona. He did the first PhD on ancient DNA in Spain (1995, University of Bacelona), subsequently being a postdoctoral researcher at the University of Cambridge (1997) and Oxford (1998). He has contributed to numerous works on ancient DNA, including the first complete mitochondrial genome from an extinct species, the first Cro-Magnon DNA, the first functional analysis of an ancient gene or the first Mesolithic human genomic data. Since 2004, he has focused especially on Neandertal genomics, mainly working with a Neandertal family group from El Sidrón site in Asturias (Spain). He has been pioneer in retrieving specific nuclear genes from Neandertals, including hair pigmentation, language and blood group genes. He has collaborated in the Neandertal Genome Project, directed by Svante Pääbo, from the Max Planck Institute at Leipzig. Beyond his research, he has published several popular science books, winning for this task different awards in Spain.
Neandertal remains at El Sidrón cave (Asturias, North Western Spain) were accidentally discovered in 1994 by cave explorers. The systematic excavations started in the year 2000 and have continued ever since. The remains of thirteen Neadertal individuals have been retrieved with a pioneer excavation protocol designed to prevent contamination of the remains with modern human DNA; moreover, the stable and cold temperatures within the cave have favoured endogenous DNA to be preserved for all the specimens. Different archaeological and geological evidences indicate that El Sidrón is a synchronic assemblage of a Neandertal family group cannibalized in the surface by other Neandertals and thus offer a unique opportunity to study intragroup genetic diversity, mating behaviour and kinship structure in these archaic humans. Since 2005, different paleogenetic studies -some of them in collaboration with the Max Planck Institute at Leipzig- have uncovered crucial phenotypic aspects of these individuals, including information about the hair pigmentation, the language and the ABO blood group. Moreover, new technological approaches have started unraveling patterns of genomic diversity among the individuals of this unique site
Professor David Reich, Harvard Medical School, USAThe landscape of Neandertal ancestry in present-day humans
David Reich received his undergraduate degree in physics from Harvard University in 1996. He received his doctorate from the Department of Zoology at the University of Oxford in 1999, working with Professor David Goldstein. He did his post-doctoral work at the Whitehead Institute/MIT Center for Genome Research from 1999-2003 working with Professor Eric Lander on statistical analysis of human evolutionary history with applications to disease gene mapping. He has been on the faculty at the Harvard Medical School Department of Genetics since 2003, where he has focused on studying population mixture both in terms of its role in human history and in terms of its implications for disease. Since 2007 he has been collaborating with Professor Svante Paabo at the Max Planck Institute for Evolutionary Anthropology in Leipzig Germany, working on studying how the ancient human genomes that Professor Paabo has been generating are related to modern genomes.
We inferred the locations of DNA sequences that derive from Neandertals in 1,004 present-day humans. We find regions of millions of base pairs that are nearly devoid of Neandertal ancestry and that are significantly enriched in functional elements showing that they owe their origin in part to rapid selection to remove Neandertal-derived gene material. The Neandertal-devoid regions are significantly enriched in genes expressed in testis compared with other tissues, and the greatest deficiency of Neandertal ancestry in the genome is on chromosome X where it is about a fifth of that on the autosomes; these two patterns can be parsimoniously explained if Neandertals carried alleles that conferred hybrid sterility when moved to a modern human genetic background. Neandertal alleles continue to shape human biology. We find 24 regions in Europeans and 22 in East Asians that harbor more Neandertal ancestry than can be explained by genetic drift. We also find that regions of high Neandertal ancestry are significantly enriched for genes affecting keratin filaments, sugar metabolism, oocyte meiosis, and vascular smooth muscle contraction, suggesting that mutations in these biological pathways may have helped modern humans to adapt to non-African environments. Finally, we show that multiple alleles that affect risk for disease entered present-day humans from Neandertals.
Elena Gigli, University of Florence, ItalyAncient DNA studies: new perspectives on old samples
Elena Gigli gained a PhD in Biomedicine and a master in Biomedicine Research from Pompeu Fabra University (Barcelona, Spain). Since 2012 she has been a postdoctoral researcher in Professor David Caramelli’s lab at University of Florence. During her PhD she focused on Neandertal genome collaborating in retrieving of two important nuclear genes that provide specific information on aspects of the Neandertal phenotype and adaptation. She also became interested in modern human contamination in old samples developing novel PCR method, based on the use of blocking primers. Currently she is involved in a research project regarding genetic relationship between Cro magnon type human and Neanderthals in the Italian Peninsula
Twenty years ago an exceptionally preserved archaic human skeleton was discovered inside a karstic cave (Lamalunga Cave) in the Altamura countryside in Southern Italy (Bari, Apulia). First observations, pointed out that the remains belonged to “Anteneanderthals”; with the exception of some photographic documentations, no direct examinations were carried out on the skeleton, until 2009 when in a new survey in the cave we remove a skeletal fragment to be used for high-quality investigations. In this study, we report the first results obtained from dating, paleogenetic and morphometric analyses. Overall, our data show that the skeleton from Altamura belonged to a Neanderthal, with some interesting peculiar features. Dating results show that Altamura skeleton is the most ancient Neanderthal from which endogenous DNA has been retrieved so far. Due to the very special conditions of preservation, it may be considered a good candidate for genome-wide analyses
Dr Barbara Bramanti, University of Oslo, Norway Evolutionary consequences of the past pandemics
Since 1997, I have worked exclusively with ancient DNA techniques on human remains for different projects and in different institutions. During the time in the Palaeogenetics Group at the Institute of Anthropology in Mainz, Germany, I have started to work independently with a close group of assistants and with active co-operations from all over the world. The major goals of my investigations in the last ten years were: uncovering the process of Neolithisation in Central Europe, the determination of genetic evolution mechanisms in human populations of the past driven by host-pathogens interactions and the retrieval of Yersinia pestis, the etiological agent of plague,in human skeletons from the first (6th century) and the second pandemic with the Black Death (14th-18th centuries). Since 2013, I am working at the Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, as PI of a project about ancient Y. pestis awarded with an ERC-advanced grant".
In historical times epidemics and pandemics killed large proportions of the European population, with likely consequences for the human genome as a result of positive selection acting on protective alleles. Pathophysiological evidence has suggested, for example, that cystic fibrosis mutations may confer resistance to cholera or other chloride-secreting diarrhoeas, whereas a high incidence of the CCR5-Delta32 mutation, which nowadays plays a substantial role in immunity against HIV-I infection, has been proposed to have provided some immunity against plague.
To test these and other hypotheses of selection directly on ancient DNA from cholera and plague victims of the past we developed a multilocus analysis, which simultaneously assays up to 17 genetic loci for single nucleotide polymorphisms (SNPs) or deletions, by means of minisequencing or NGS analysis. Beyond polymorphisms hypothesised to be under selection, we investigated simultaneously five neutral SNPs which enable the individualisation of each analysed skeleton and the identification of contamination. Here we presented some preliminary results obtained from the analyses of about 300 skeletons.
Co-authors: Stephanie Hänsch, Magdalena Bogus, Anja Meister, Claudio Ottoni, Antonella Lannino, Joachim Burger, Mark G. Thomas
Public lecture 5 Dec
Conference 11 Dec
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