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1. Improving the extraction of ancient Yersinia pestis genomes from the dental pulp

Author

Pierre Clavel, Lexane Louis, Clio Der Sarkissian, Catherine Thèves, Claudia Gillet, Lorelei Chauvey, Gaétan Tressières, Stéphanie Schiavinato, Laure Calvière-Tonasso, Norbert Telmon, Benoît Clavel, Richard Jonvel, Stéfan Tzortzis, Laetitia Bouniol, Jean-Marc Fémolant, Jennifer Klunk, Hendrik Poinar, Michel Signoli, Caroline Costedoat, Maria A. Spyrou, Andaine Seguin-Orlando, and Ludovic Orlando

Subjects
Archeology, Biochemistry, Molecular biology, Science
Abstract

Summary: Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17th and 18th centuries Common Era.

Published
2023
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2. No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy

Author

Andaine Seguin-Orlando, Caroline Costedoat, Clio Der Sarkissian, Stéfan Tzortzis, Célia Kamel, Norbert Telmon, Love Dalén, Catherine Thèves, Michel Signoli, and Ludovic Orlando

Subjects
Paleontology, Genomics, Microbiology, Science
Abstract

Summary: The 17th century plague epidemic had a particularly strong demographic toll in Southern Europe, especially Italy, where it caused long-lasting economical damage. Whether this resulted from ineffective sanitation measures or more pathogenic Yersinia pestis strains remains unknown. DNA screening of 26 skeletons from the 1629-1630 plague cemetery of Lariey (French Alps) identified two teeth rich in plague genetic material. Further sequencing revealed two Y. pestis genomes phylogenetically closest to those from the 1636 outbreak of San Procolo a Naturno, Italy. They both belonged to a cluster extending from the Alps to Northern Germany that probably propagated during the Thirty Years war. Sequence variation did not support faster evolutionary rates in the Italian genomes and revealed only rare private non-synonymous mutations not affecting virulence genes. This, and the more heterogeneous spatial diffusion of the epidemic outside Italy, suggests environmental or social rather than biological causes for the severe Italian epidemic trajectory.

Published
2021
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4. Oral health status in historic population: Macroscopic and metagenomic evidence.

Author

Claire Willmann, Xavier Mata, Kristian Hanghoej, Laure Tonasso, Lenka Tisseyre, Céline Jeziorski, Elodie Cabot, Pierre Chevet, Eric Crubézy, Ludovic Orlando, Rémi Esclassan, and Catherine Thèves

Subjects
Medicine, Science
Abstract

Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.

Published
2018
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5. Tuberculosis epidemiology and selection in an autochthonous Siberian population from the 16th-19th century.

Author

Henri Dabernat, Catherine Thèves, Caroline Bouakaze, Dariya Nikolaeva, Christine Keyser, Igor Mokrousov, Annie Géraut, Sylvie Duchesne, Patrice Gérard, Anatoly N Alexeev, Eric Crubézy, and Bertrand Ludes

Subjects
Medicine, Science
Abstract

Tuberculosis is one of most ancient diseases affecting human populations. Although numerous studies have tried to detect pathogenic DNA in ancient skeletons, the successful identification of ancient tuberculosis strains remains rare. Here, we describe a study of 140 ancient subjects inhumed in Yakutia (Eastern Siberia) during a tuberculosis outbreak, dating from the 16(th)-19(th) century. For a long time, Yakut populations had remained isolated from European populations, and it was not until the beginning of the 17(th) century that first contacts were made with European settlers. Subsequently, tuberculosis spread throughout Yakutia, and the evolution of tuberculosis frequencies can be tracked until the 19(th) century. This study took a multidisciplinary approach, examining historical and paleo-epidemiological data to understand the impact of tuberculosis on ancient Yakut population. In addition, molecular identification of the ancient tuberculosis strain was realized to elucidate the natural history and host-pathogen co-evolution of human tuberculosis that was present in this population. This was achieved by the molecular detection of the IS6110 sequence and SNP genotyping by the SNaPshot technique. Results demonstrated that the strain belongs to cluster PGG2-SCG-5, evocating a European origin. Our study suggests that the Yakut population may have been shaped by selection pressures, exerted by several illnesses, including tuberculosis, over several centuries. This confirms the validity and necessity of using a multidisciplinary approach to understand the natural history of Mycobacterium tuberculosis infection and disease.

Published
2014
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6. Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.

Author

Catherine Thèves, Alice Senescau, Stefano Vanin, Christine Keyser, François Xavier Ricaut, Anatoly N Alekseev, Henri Dabernat, Bertrand Ludes, Richard Fabre, and Eric Crubézy

Subjects
Medicine, Science
Abstract

Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th) to the 19(th) century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th) century to the early 18(th) century.

Published
2011
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7. Hétérogénéité des ascendances mésolithiques et steppiques dans des génomes d’individus du Néolithique et du Campaniforme du territoire français

Author

Jean Guilaine, Jean-François Deleuze, John Southon, Love Dalén, Yaramila Tchérémissinoff, Andaine Seguin-Orlando, Beth Shapiro, Richard Donat, Ludovic Orlando, Claire Manen, Eric Crubézy, Clio Der Sarkissian, Catherine Thèves, Centre d'anthropologie et de génomique de Toulouse (CAGT), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), University of California [Irvine] (UC Irvine), University of California (UC), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire méditerranéen de préhistoire Europe-Afrique (LAMPEA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), University of California [Santa Cruz] (UC Santa Cruz), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre for Palaeogenetics, Collège de France (CdF (institution)), Institute for Advanced Study in Toulouse (IAST), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and ANR-17-CE12-0018,LifeChange,Déchiffrer les conséquences biologiques et pathogéniques liées à un changement majeur de mode de vie(2017)

Subjects
0301 basic medicine, Yamnaya, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Steppe, Human Migration, Population, Bell Beaker, Biology, General Biochemistry, Genetics and Molecular Biology, collective burial, 03 medical and health sciences, 0302 clinical medicine, Beaker, Bronze Age, Humans, DNA, Ancient, education, ancient DNA, Hunter-gatherer, Mesolithic, History, Ancient, ComputingMilieux_MISCELLANEOUS, geography, education.field_of_study, geography.geographical_feature_category, Genome, Human, Genomics, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Archaeology, methylomeoral microbiome, Europe, 030104 developmental biology, Ancient DNA, paleogenomics, Late Neolithic, admixture, France, General Agricultural and Biological Sciences, Mediterranean Islands, 030217 neurology & neurosurgery
Abstract

Summary The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe. 1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes 2 , 3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry. 4 , 5 , 6 , 7 , 8 This transition is documented through extensive ancient genomic data from present-day Britain, 9 , 10 Ireland, 11 , 12 Iberia, 13 Mediterranean islands, 14 , 15 and Germany. 8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63), 8 , 9 , 16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage. 16 This leaves the key transitional period covering ∼3,400–2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400–1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.

Published
2021
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8. Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides

Author

Odile Burlet-Schiltz, Mathilde Hourset, Catherine Mollereau, Rémi Esclassan, Nancy Sáenz-Oyhéréguy, Carine Froment, Claire Willmann, Clément Zanolli, Catherine Thèves, Emmanuelle Mouton-Barbosa, Richard Donat, Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Male, Proteomics, Sex Determination Analysis, [SDV]Life Sciences [q-bio], Biophysics, Single pair, Computational biology, Biology, Biochemistry, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Paleoproteomics, Humans, Database search engine, High potential, 030102 biochemistry & molecular biology, Amelogenin, Sex determination, Data dependent acquisition, Sex specific, Targeted proteomics, Parallel reaction monitoring, 030104 developmental biology, Proteome, Female, Peptides, Tooth
Abstract

International audience; The study demonstrates the high potential of MS-based proteomics coupled to an iterative database search strategy for the in-depth investigation of ancient proteomes. An efficient targeted PRM MS-based approach, although limited to the detection of a single pair of sex-specific amelogenin peptides, allowed confirming the sex of individuals in ancient dental remains, an essential information for paleoanthropologists facing the issue of sex determination and dimorphism.

Published
2019
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9. Ancient tooth proteomes

Author

Mathilde, Hourset, Froment, Carine, Zanolli, Clément, Nancy, Saenz, Claire, Willmann, Rémi, Esclassan, Catherine, Thèves, Burlet-Schiltz, Odile, Catherine, Mollereau, Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

10. Ancient tooth proteomes

Author

Froment, Carine, Hourset, Mathilde, Saenz, Nancy, Claire, Willmann, Stella, Alexandre, Mouton-Barbosa, Emmanuelle, Zanolli, Clément, Rémi, Esclassan, Catherine, Thèves, Burlet-Schiltz, Odile, Catherine, Mollereau, Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

11. Relationships between clans and genetic kin explain cultural similarities over vast distances: the case of Yakutia

Author

C Petit, L Romanova, V. Zvénigorosky, A. Alexeev, Bertrand Ludes, Eric Crubézy, A Riberon, N Kirianov, D Nikolaeva, V Pereda, S Kodolesnikov, O Meniltchuk, Jean Guilaine, C Keyser, A. Geraut, C Cannet, Jean-Luc Fausser, V Popov, Ludovic Orlando, M Petit, Catherine Thèves, Patrice Gerard, Xavier Mata, Sylvie Duchesne, and R Bravina

Subjects
Genetics, education.field_of_study, Population, Haplotype, Genetic data, Mitochondrial haplotypes, Population study, Clan, Biology, education, Genealogy
Abstract

Archaeological studies sample ancient human populations one site at a time, often limited to a fraction of the regions and periods occupied by a given group. While this bias is known and discussed in the literature, few model populations span areas as large and unforgiving as the Yakuts of Eastern Siberia. We systematically surveyed 31,000 square kilometres in the Sakha Republic (Yakutia) and completed the archaeological study of 174 frozen graves, assembled between the 15th and the 19th century. We analysed genetic data (autosomal genotypes, Y-chromosome haplotypes and mitochondrial haplotypes) for all ancient subjects and confronted these to data on 190 modern subjects from the same area and the same population. Ancient familial links were identified between graves up to 1500 km apart, as well as paternal clans. We provide new insights on the origins of the contemporary Yakut population and demonstrate that cultural similarities in the past were linked to (i) the expansion of specific paternal clans, (ii) preferential marriage among the elites and (iii) funeral choices that could constitute a bias in any ancient population study.

Published
2017
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12. Ancient genomic changes associated with domestication of the horse

Author

Christine Keyser, Inna S. Povolotskaya, Antoine Fages, Stefan Rieder, Zainolla Samashev, Ludovic Orlando, Pablo Librado, Markus Neuditschko, Lukas F. K. Kuderna, Bertrand Ludes, Clio Der Sarkissian, Vidhya Jagannathan, Tomas Marques-Bonet, Catherine Thèves, Eske Willerslev, Naveed Khan, Norbert Benecke, Henri-Paul Francfort, Arne Ludwig, Khaled A. S. Al-Rasheid, Saleh A. Alquraishi, Eric Crubézy, Mélanie Pruvost, Mikkel Schubert, Andaine Seguin-Orlando, Cristina Gamba, Tosso Leeb, Sébastien Lepetz, Michael Hofreiter, Ahmed H. Alfarhan, Charleen Gaunitz, Anders Albrechtsen, Aitor Serres-Armero, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Section of Biostatistics [Copenhagen], Department of Public Health [Copenhagen], Institute of Genetics, University of Bern, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Agroscope, Swiss National Stud Farm, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Swiss College of Agriculture, Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Natural Sciences, German Archaeological Institute (DAI), Department of Evolutianory Genetics, Max-Planck-Institut, Max-Planck-Institut-Leibniz Institute for Zoo and Wildlife Research Berlin (IZW), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, Departament de Ciencies Experimentals i de la Salut, Institut Cavanilles de Biodiverstitat i Biologia Evolutiva, University of Copenhagen = Københavns Universitet (KU), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), The German Archaeological Institute, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (UCPH)

Subjects
0301 basic medicine, Lineage (genetic), [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Breeding, Biology, Quantitative trait locus, DNA, Mitochondrial, Domestication, 03 medical and health sciences, Quantitative Trait, Heritable, Genetic variation, Animals, Horses, DNA, Ancient, Selection, Genetic, 610 Medicine & health, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, Institut für Biochemie und Biologie, Genetic diversity, Genome, Multidisciplinary, 630 Agriculture, Genetic Variation, 030104 developmental biology, Neural Crest, Evolutionary biology, Iron Age, 570 Life sciences, biology, 590 Animals (Zoology), Inbreeding
Abstract

Ancient genomics of horse domestication The domestication of the horse was a seminal event in human cultural evolution. Librado et al. obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestication process. They could also see evidence of admixture with archaic horses and the demography of the domestication process, which included the accumulation of deleterious variants. The horse appears to have undergone a different type of domestication process than animals that were domesticated simply for food. Science , this issue p. 442

Published
2017
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13. The genetics of kinship in remote human groups

Author

Vincent Zvénigorosky, Bertrand Ludes, Clémence Hollard, Angéla Gonzalez, Rozalia I. Bravina, Morgane Gibert, Eric Crubézy, Anatoly N. Alexeev, Sardana A. Fedorova, Christine Keyser, Catherine Thèves, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Fundacion Centro Tecnoloxico do Granito de Galicia, Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, 0301 basic medicine, Genotype, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population genetics, Biology, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Russia, Pathology and Forensic Medicine, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, Ethnicity, Genetics, Kinship, Humans, 030216 legal & forensic medicine, DNA, Ancient, Genotyping, ComputingMilieux_MISCELLANEOUS, Chromosomes, Human, Y, Genetic data, DNA Fingerprinting, Pedigree, Genetics, Population, 030104 developmental biology, Ancient DNA, Female, Forensic genetics, Microsatellite Repeats
Abstract

For fifteen years, part of the work of our research team has been focused on the study of parental links between individuals living hundreds or thousands of years ago, whose remains have been found in single graves or large funerary complexes. These studies have been undertaken using methods developed by forensic genetics to identify individuals, mainly based on the genotyping of autosomal STR (Short Tandem Repeats). Issues arose from this work, namely the limits of studying small numbers of subjects, originating from groups of finite sizes where kinships cannot be inferred a priori and for which reference allelic frequencies do not exist. Although ideal human populations are rare when undertaking such studies, the Yakuts of Eastern Siberia constitute a very advantageous model, with large numbers of small pastoral communities and well-preserved archaeological material. The study of kinship in the ancient Yakuts allowed us to highlight the difficulties in analysing genetic data from small ancient human groups and to develop a strategy to improve the accuracy of statistical computations. This work describes this strategy and possible solutions to the study of populations outside of the frame of reference of global meta-populations, due either to isolation, remoteness or antiquity.

Published
2016
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14. History of Smallpox and Its Spread in Human Populations

Author

Philippe Biagini, Catherine Thèves, Eric Crubézy, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
0301 basic medicine, Microbiology (medical), Paleopathology, Physiology, Human Migration, 030106 microbiology, Biology, Global Health, History, 18th Century, History, 17th Century, 03 medical and health sciences, Virology, Disease Transmission, Infectious, Genetics, medicine, Global health, Animals, Humans, Smallpox, Epidemics, History, Ancient, ComputingMilieux_MISCELLANEOUS, History, 15th Century, Travel, General Immunology and Microbiology, Ecology, Transmission (medicine), Human migration, business.industry, Poxviridae, History, 19th Century, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Cell Biology, History, 20th Century, medicine.disease, History, Medieval, 3. Good health, Natural history, Vaccination, 030104 developmental biology, Infectious Diseases, History, 16th Century, Ethnology, Variola virus, Lung tissue, business
Abstract

Smallpox is considered among the most devastating of human diseases. Its spread in populations, initiated for thousands of years following a probable transmission from an animal host, was concomitant with movements of people across regions and continents, trade and wars. Literature permitted to retrace the occurrence of epidemics from ancient times to recent human history, smallpox having affected all levels of past society including famous monarchs. The disease was officially declared eradicated in 1979 following intensive vaccination campaigns. Paleomicrobiology dedicated to variola virus is restricted to few studies, most unsuccessful, involving ancient material. Only one recent approach allowed the identification of viral DNA fragments from lung tissue of a 300-year-old body excavated from permafrost in Eastern Siberia; phylogenetic analysis revealed that this ancient strain was distinct from those described during the 20th century.

Published
2016
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15. About 42% of 154 remains from the 'Battle of Le Mans', France (1793) belong to women and children: Morphological and genetic evidence

Author

Pierre Chevet, Catherine Thèves, Elodie Cabot, Caroline Bouakaze, Patricia Balaresque, Eric Crubézy, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Adult, Male, 0301 basic medicine, Sex Determination Analysis, 010506 paleontology, Battle, Adolescent, Burial, media_common.quotation_subject, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Armed conflict, Exhumation, History, 18th Century, 01 natural sciences, Pathology and Forensic Medicine, Young Adult, 03 medical and health sciences, Humans, Medicine, DNA, Ancient, Young adult, Child, education, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, media_common, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, business.industry, Infant, Genetic data, Forensic anthropology, Armed Conflicts, Sex Determination by Skeleton, 16. Peace & justice, Civilian population, Archaeology, Body Remains, 030104 developmental biology, Child, Preschool, Forensic Anthropology, Female, France, Historical series, business, Law, Demography
Abstract

Mass graves were discovered in Le Mans and 154 skeletons were exhumed, representing a remarkable historical series of human remains from western France. We aimed to characterise the age-class and sex of these subjects, and to determine whether their profile fits with that of the Catholic and Royal Army of Vendee, who fought against the Republican Army during the Battle of Le Mans (12th-13th December, 1793). This atypical army was composed of male soldiers, but also of civilian people who followed the troops, including the elderly, children and women. In total 154 skeletons from nine mass graves were exhumed from 2009 to 2010. Two morphological methods were used to determine the sex of the subjects: the Probabilist Sexual Diagnosis (DSP) and Secondary Sexual Diagnosis (DSS) methods. Samples were handled cautiously to avoid any pre-laboratory contamination. Molecular genetic sex-typing using a recently developed assay was used to maximise sex-diagnosis of the ancient DNA samples, and 97 successful profiles including immatures were generated. Using morphological and genetic data combined, we successfully determined the sex of 93% of the subjects; 62% were male and 31% female. About 87% of subjects could be considered adults (>18 years old), 6% adolescents (15-19 years old) and 7% infants (

Published
2016
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16. Detection of the A189G mtDNA heteroplasmic mutation in relation to age in modern and ancient bones

Author

Eric Crubézy, Marie Lacan, Sylvain Amory, Bertrand Ludes, Norbert Telmon, Jean-Pierre Salles, Catherine Thèves, Christine Keyser, Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, Service de médecine légale, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Hôpital de Rangueil, CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Thèves, Catherine, Service Médecine légale et médecine pénitentiaire [CHU Toulouse], Pôle Santé publique et médecine publique [CHU Toulouse], and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)

Subjects
Adult, Male, Muscle tissue, Aging, Mitochondrial DNA, Adolescent, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Ribs, Biology, DNA, Mitochondrial, Polymerase Chain Reaction, DNA sequencing, Pathology and Forensic Medicine, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Point Mutation, 030216 legal & forensic medicine, Muscle, Skeletal, Aged, 030304 developmental biology, Aged, 80 and over, Genetics, 0303 health sciences, Point mutation, Infant, Sequence Analysis, DNA, Middle Aged, Heteroplasmy, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Blotting, Southern, medicine.anatomical_structure, Mutation (genetic algorithm), Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; The aim of this study was to demonstrate the presence of the A189G age-related point mutation on DNA extracted from bone. For this, a peptide nucleic acid (PNA)/DNA sequencing method which can determine an age threshold for the appearance of the mutation was used. Initially, work was done in muscle tissue in order to evaluate the sensitivity of the technique and afterwards in bone samples from the same individuals. This method was also applied to ancient bones from six well-preserved skeletal remains. The mutation was invariably found in muscle, and at a rate of up to 20% in individuals over 60 years old. In modern bones, the mutation was detected in individuals aged 38 years old or more, at a rate of up to 1%, but its occurrence was not systematic (only four out of ten of the individuals over 50 years old carried the heteroplasmy). For ancient bones, the mutation was also found in the oldest individuals according to osteologic markers. The study of this type of age-related mutation and a more complete understanding of its manifestation has potentially useful applications. Combined with traditional age markers, it could improve identification accuracy in forensic cases or in anthropological studies of ancient populations.

Published
2008
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17. Shotgun sequencing of the mitochondrial genome of the Aldabra giant tortoise (Aldabrachelys gigantea)

Author

Hélène Holota, Lucien M.A. Rakotozafy, Guillaume Besnard, Xavier Mata, Miguel Pedrono, Catherine Thèves, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Animal et gestion intégrée des risques (Cirad-Bios-UPR 22 AGIRs), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Animal et gestion intégrée des risques (UPR AGIRs), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0106 biological sciences, 0301 basic medicine, Mitochondrial DNA, Tortue terrestre, Phylogénie, Séquence nucléotidique, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Zoology, 010603 evolutionary biology, 01 natural sciences, Genome, DNA, Mitochondrial, 03 medical and health sciences, Phylogenetics, Genetics, Animals, 14. Life underwater, Aldabrachelys, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Phylogeny, Génome, Phylogenetic tree, biology, Shotgun sequencing, High-Throughput Nucleotide Sequencing, L60 - Taxonomie et géographie animales, DNA, Sequence Analysis, DNA, biology.organism_classification, L10 - Génétique et amélioration des animaux, Turtles, Aldabra giant tortoise, 030104 developmental biology, Ancient DNA, Testudinidae, Genome, Mitochondrial, L20 - Écologie animale, ADN mitochondrial
Abstract

The complete mitochondrial genome of the Aldabra giant tortoise [Aldabrachelys gigantea (Schweigger, 1812): Reptilia, Testudines, Testudinidae] was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA). This genome was 16 467 bp long and presents the typical organization found in vertebrates. The mean coverage of sequencing was 116×. A phylogenetic analysis of the Testudinidae confirms the placement of Aldabrachelys in an Indian Ocean group (including Madagascar). This mitogenome constitutes a reference for ancient DNA analyses of the extinct Madagascan lineages of Aldabrachelys.

Published
2016
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18. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

Author

Mikkel Schubert, Saleh A. Alquraishi, Andaine Seguin-Orlando, Clio Der Sarkissian, Tomas Marques-Bonet, Catherine Thèves, Eugenia S. Boulygina, Ruslan Popov, Cecilie Mortensen, Svetlana V. Tsygankova, Melinda A. Yang, Montgomery Slatkin, Eric Crubézy, Molly E. McCue, Alexei Tikhonov, Bent O. Petersen, Vidhya Jagannathan, Egor Prokhortchouk, Edward M. Rubin, Tosso Leeb, Markus Neuditschko, Matteo Fumagalli, Cristina Gamba, Anatoly N. Alekseev, Cindi A. Hoover, Rasmus Nielsen, Belen Lorente-Galdos, Juha Kantanen, Eske Willerslev, Semyon Grigoriev, Hakon Jonsson, Luca Ermini, Khaled A. S. Al-Rasheid, Pablo Librado, Stefan Rieder, Ludovic Orlando, Artem V. Nedoluzhko, Ahmed H. Alfarhan, Thomas Sicheritz-Pontén, Anders Albrechtsen, Danish Council for Independent Research, Danish National Research Foundation, European Commission, Université de Toulouse, German Research Foundation, King Abdulaziz University, King Saud University, Villum Fonden, Eurostat, Lundbeck Foundation, National Science Foundation (US), Human Frontier Science Program, National Institutes of Health (US), Academy of Finland, Ministère des Affaires étrangères (France), North-Eastern Federal University, Institut Polaire Français, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Bioinformatics Centre, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Department of Integrative Biology, National High-Throughput DNA Sequencing Centre, University of Copenhagen = Københavns Universitet (KU), Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark [Lyngby] (DTU), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Universitat Pompeu Fabra [Barcelona] (UPF), Centro Nacional de Análisis Genómico, National Research Centre Kurchatov Institute, Agroscope, Swiss National Stud Farm, Institute of Genetics, University of Bern, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), King Saud University [Riyadh] (KSU), Yakutian Research Institute of Agriculture, College of Veterinary Medicine, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Zoological Institute of Russian Academy of Sciences, Russian Academy of Sciences [Moscow] (RAS), Center for Theoretical Evolutionary Genomics [Berkeley] (CTEG), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California-University of California [Berkeley], University of California-University of California, Agrifood Research Finland, Department of Biology, University of Eastern Finland, and University of Eastern Finland

Subjects
Pleistocene, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population, Zoology, Population genetics, adaptation, Biology, Horse, regulatory changes, Evolution, Molecular, ancient genomics, Convergent evolution, MD Multidisciplinary, Animals, Horses, Adaptation, Domestication, education, education.field_of_study, Genome, Multidisciplinary, 630 Agriculture, Arctic Regions, Regulatory changes, Adaptation, Physiological, population discontinuity, horse, Cold Temperature, Siberia, Ancient genomics, Ancient DNA, PNAS Plus, Evolutionary developmental biology, 590 Animals (Zoology), 570 Life sciences, biology, Adaption, Population discontinuity
Abstract

Librado, Pablo et al., Yakutia is among the coldest regions in the Northern Hemisphere, showing ∼40% of its territory above the Arctic Circle. Native horses are particularly adapted to this environment, with body sizes and thick winter coats minimizing heat loss. We sequenced complete genomes of two ancient and nine present-day Yakutian horses to elucidate their evolutionary origins. We find that the contemporary population descends from domestic livestock, likely brought by early horse-riders who settled in the region a few centuries ago. The metabolic, anatomical, and physiological adaptations of these horses therefore emerged on very short evolutionary time scales. We show the relative importance of regulatory changes in the adaptive process and identify genes independently selected in cold-adapted human populations and woolly mammoths., This work was supported by the Danish Council for Independent Research, Natural Sciences (Grant 4002-00152B); the Danish National Research Foundation (Grant DNRF94); a Marie-Curie Career Integration grant (Grant FP7 CIG-293845); Initiative d'Excellence Chaires d'attractivité, Université de Toulouse (OURASI); and the International Research Group Program (Grant IRG14-08), Deanship of Scientific Research, King Saud University. P.L. was supported by a Villum Fonden Blokstipendier grant (primary investigator: L.O.); H.J. by a Marie-Curie Initial Training Network grant [EUROTAST (Exploring the History, Archeology, and New Genetics of the Transatlantic Slave Trade); Grant FP7 ITN-290344]; C.G. and L.E. by Marie-Curie Intra-European fellowships (FP7-IEF-328024 and FP7 IEF-302617); M. Schubert by a Lundbeck Foundation grant (Grant R52-A5062); M.A.Y. by a National Science Foundation Graduate Research fellowship; M.F. by a Human Frontier Science Program fellowship (LT000320/2014); A.A. by a Villum Fonden Blokstipendier grant; M. Schubert by an NIH grant (Grant R01-GM40282); and J.K. by the Academy of Finland (Grant 286040). Research work on the ancient Yakut population was supported by the French Archaeological Mission in Oriental Siberia (Ministry of Foreign and European Affairs, France), the North-Eastern Federal University (Yakutsk, Sakha Republic), and the Human Adaptation Program of the French Polar Institute Paul Emile Victor [HUMAD MAFSO (Missions Archéologiques Françaises en Sibérie Orientale) 1038].

Published
2015
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19. The rediscovery of smallpox

Author

Catherine Thèves, Eric Crubézy, Philippe Biagini, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), viruses, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Biology, History, 18th Century, complex mixtures, Virus, law.invention, History, 17th Century, 03 medical and health sciences, law, Immunity, Quarantine, evolution, medicine, Animals, Humans, Smallpox, Smallpox virus, 030304 developmental biology, 0303 health sciences, Ancient DNA, 030306 microbiology, virus diseases, History, 19th Century, Yakut population, Variola virus, General Medicine, History, 20th Century, palaeomicrobiology, medicine.disease, Biological Evolution, Virology, 3. Good health, Vaccination, smallpox, Infectious Diseases, History, 16th Century, Infectious disease (medical specialty), [SDE]Environmental Sciences
Abstract

International audience; Smallpox is an infectious disease that is unique to humans, caused by a poxvirus. It is one of the most lethal of diseases; the virus variant Variola major has a mortality rate of 30%. People surviving this disease have life-long consequences, but also assured immunity. Historically, smallpox was recognized early in human populations. This led to prevention attempts--variolation, quarantine, and the isolation of infected subjects--until Jenner's discovery of the first steps of vaccination in the 18th century. After vaccination campaigns throughout the 19th and 20th centuries, the WHO declared the eradication of smallpox in 1980. With the development of microscopy techniques, the structural characterization of the virus began in the early 20th century. In 1990, the genomes of different smallpox viruses were determined; viruses could be classified in order to investigate their origin, diffusion, and evolution. To study the evolution and possible re-emergence of this viral pathogen, however, researchers can only use viral genomes collected during the 20th century. Cases of smallpox in ancient periods are sometimes well documented, so palaeomicrobiology and, more precisely, the study of ancient smallpox viral strains could be an exceptional opportunity. The analysis of poxvirus fragmented genomes could give new insights into the genetic evolution of the poxvirus. Recently, small fragments of the poxvirus genome were detected. With the genetic information obtained, a new phylogeny of smallpox virus was described. The interest in conducting studies on ancient strains is discussed, in order to explore the natural history of this disease.

Published
2014
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20. Tuberculosis epidemiology and selection in an autochthonous Siberian population from the 16th-19th century

Author

Christine Keyser, Henri Dabernat, Caroline Bouakaze, Igor Mokrousov, Annie Geraut, Bertrand Ludes, Catherine Thèves, Eric Crubézy, Patrice Gerard, Anatoly N. Alexeev, Sylvie Duchesne, Dariya Nikolaeva, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut Pasteur de Saint-Pétersbourg, Réseau International des Instituts Pasteur (RIIP), Institut de Médecine Légale [Strasbourg], Siberian Branch of the Russian Academy of Sciences (SB RAS), Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Institute of Legal Medicine, Université Paris Descartes - Paris 5 (UPD5), Anthropologie Moléculaire et Imagerie de Synthèse ( AMIS ), PRES Université de Toulouse-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France ( IML ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ), Réseau International des Instituts Pasteur ( RIIP ) -Institut Pasteur de Saint-Pétersbourg, Anthropologie Moleculaire et Imagerie de Synthèse, IUT de Tarbes, Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique ( CNRS ), Siberian Branch of the Russian Academy of Sciences ( SB RAS ), Laboratoire d'Anthropobiologie ( LA ), École des hautes études en sciences sociales ( EHESS ) -Université Toulouse - Jean Jaurès ( UT2J ) -Université Toulouse III - Paul Sabatier ( UPS ), and Université Paris Descartes - Paris 5 ( UPD5 )

Subjects
Bacterial Diseases, Epidemiology, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, lcsh:Medicine, History of Tuberculosis, Social and Behavioral Sciences, History, 18th Century, Tuberculosis, Osteoarticular, [ SDE ] Environmental Sciences, Ethnicity, Cluster Analysis, lcsh:Science, Molecular Epidemiology, education.field_of_study, Multidisciplinary, biology, Paleogenetics, History, 19th Century, 3. Good health, Natural history, Infectious Diseases, History, 16th Century, [SDE]Environmental Sciences, Medicine, Ethnology, Research Article, Tuberculosis, Genotype, Population, Microbiology, Polymorphism, Single Nucleotide, History, 17th Century, Mycobacterium tuberculosis, Paleoanthropology, Genetics, medicine, Humans, Selection, Genetic, education, Biology, History of tuberculosis, Evolutionary Biology, Population Biology, lcsh:R, Paleontology, Outbreak, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, Siberia, Ancient DNA, Anthropology, [ SHS.ANTHRO-BIO ] Humanities and Social Sciences/Biological anthropology, lcsh:Q, Paleobiology
Abstract

International audience; Tuberculosis is one of most ancient diseases affecting human populations. Although numerous studies have tried to detect pathogenic DNA in ancient skeletons, the successful identification of ancient tuberculosis strains remains rare. Here, we describe a study of 140 ancient subjects inhumed in Yakutia (Eastern Siberia) during a tuberculosis outbreak, dating from the 16th-19th century. For a long time, Yakut populations had remained isolated from European populations, and it was not until the beginning of the 17th century that first contacts were made with European settlers. Subsequently, tuberculosis spread throughout Yakutia, and the evolution of tuberculosis frequencies can be tracked until the 19th century. This study took a multidisciplinary approach, examining historical and paleo-epidemiological data to understand the impact of tuberculosis on ancient Yakut population. In addition, molecular identification of the ancient tuberculosis strain was realized to elucidate the natural history and host-pathogen co-evolution of human tuberculosis that was present in this population. This was achieved by the molecular detection of the IS6110 sequence and SNP genotyping by the SNaPshot technique. Results demonstrated that the strain belongs to cluster PGG2-SCG-5, evocating a European origin. Our study suggests that the Yakut population may have been shaped by selection pressures, exerted by several illnesses, including tuberculosis, over several centuries. This confirms the validity and necessity of using a multidisciplinary approach to understand the natural history of Mycobacterium tuberculosis infection and disease.

Published
2014
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21. Close genetic relationships in vast territories: autosomal and X chromosome Alu diversity in Yakuts from Siberia

Author

Ares Rocañín-Arjó, Sardana A. Fedorova, Pedro Moral, Esther Esteban, Eric Crubézy, Morgane Gibert, Laura Rodríguez-Botigué, Larissa E. Evdokimova, Catherine Thèves, Seccio d'Antropologia, Universitat de Barcelona (UB), Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra [Barcelona] (UPF), Unitat d´Antropologia, Universitat de Barcelona (UB)-Departament de Biologia Animal, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Hospital of the Viljujsk, North-Eastern Federal University, Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), and Departament de Biologia Animal

Subjects
Male, Alu, media_common.quotation_subject, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Biology, X chromosome, 03 medical and health sciences, Alu Elements, Ethnicity, Humans, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, media_common, Genetics, Analysis of Variance, Chromosomes, Human, X, 0303 health sciences, education.field_of_study, Yakuts, 030305 genetics & heredity, Gene diversity, Genetic Variation, General Medicine, 3. Good health, Genetic differentiation, Siberia, Anthropology, [SDE]Environmental Sciences, Female, Animal Science and Zoology, Diversity (politics)
Abstract

Twelve autosomal and 8 X chromosome Alu markers were genotyped for the first time in 161 Central and West Yakuts to test their ability to reconstruct the genetic history of these populations, the northernmost Turkic-speaker ethnic group living in Siberia. Autosomal data revealed that both groups showed extremely close genetic distances to other populations of Siberian origins that occupied areas from Lake Baikal, the ancestral place of origin of Yakuts, to North Siberia, their current territories. Autosomal and X chromosome data revealed some discrepancies on the genetic differentiation and the effective sizes of Central and West Yakuts. Such discrepancies could be related to the patrilineal and occasionally polygamous structure of these populations. Autosomal and X Alu markers are informative markers to reconstruct population past demography and history, but their utility is limited by the available data. This study represents a contribution for further investigations on these populations. © 2013 E. Schweizerbart'sche Verlagsbuchhandlung, Stuttgart, Germany.

Published
2013

22. Variola virus in a 300-year-old Siberian mummy

Author

Patrice Gerard, Eric Crubézy, Dariya Nikolaeva, Eske Willerslev, Annie Geraut, Anatoly N. Alekseev, Philippe Biagini, Sylvie Duchesne, Bertrand Ludes, Philippe de Micco, Patricia Balaresque, Catherine Cannet, Catherine Thèves, Christine Keyser, Ludovic Orlando, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de Médecine Légale [Strasbourg], Université Louis Pasteur - Strasbourg I, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Center for Ancient Genetics, University of Copenhagen = Københavns Universitet (KU), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Siberian Branch of the Russian Academy of Sciences (SB RAS), Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0303 health sciences, Lineage (genetic), 030306 microbiology, business.industry, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, General Medicine, medicine.disease, Virology, 03 medical and health sciences, [SDE]Environmental Sciences, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Medicine, Smallpox, Variola virus, business, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

This letter describes a distant lineage of the variola virus (the agent of smallpox) that was identified in a mummy found buried in the Siberian permafrost.

Published
2012
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23. Detection of age-related duplications in mtDNA from human muscles and bones

Author

Christine Keyser, Audrey Farrugia, Eric Crubézy, Bertrand Ludes, Catherine Thèves, Jose-Pablo Baraybar, Marie Lacan, Laboratoire d'Anthropobiologie ( LA ), École des hautes études en sciences sociales ( EHESS ) -Université Toulouse - Jean Jaurès ( UT2J ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique ( CNRS ), Anthropologie Moléculaire et Imagerie de Synthèse ( AMIS ), PRES Université de Toulouse-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France ( IML ), Université Louis Pasteur - Strasbourg I, Institut de Médecine Légale [Strasbourg], Institute of Legal Medicine, Université Paris Descartes - Paris 5 ( UPD5 ), Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), and Université Paris Descartes - Paris 5 (UPD5)

Subjects
Muscle tissue, Adult, Male, Mitochondrial DNA, Aging, Adolescent, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Context (language use), Intercostal Muscles, Ribs, Biology, medicine.disease_cause, Bone tissue, DNA, Mitochondrial, Pathology and Forensic Medicine, [ SDE ] Environmental Sciences, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Gene duplication, medicine, Humans, Point Mutation, 030304 developmental biology, Aged, Genetics, Aged, 80 and over, 0303 health sciences, Mutation, Osteology, Point mutation, Middle Aged, 3. Good health, medicine.anatomical_structure, Child, Preschool, [ SHS.ANTHRO-BIO ] Humanities and Social Sciences/Biological anthropology, [SDE]Environmental Sciences, Female, 030217 neurology & neurosurgery
Abstract

International audience; Several studies have demonstrated the age-related accumulation of duplications in the D-loop of mitochondrial DNA (mtDNA) extracted from skeletal muscle. This kind of mutation had not yet been studied in bone. The detection of age-related mutations in bone tissue could help to estimate age at death within the context of legal medicine or/and anthropological identification procedures, when traditional osteological markers studied are absent or inefficient. As we detected an accumulation of a point mutation in mtDNA from an older individual's bones in a previous study, we tried here to identify if three reported duplications (150, 190, 260 bp) accumulate in this type of tissue. We developed a sensitive method which consists in the use of back-to-back primers during amplification followed by an electrophoresis capillary analysis. The aim of this study was to confirm that at least one duplication appears systematically in muscle tissue after the age of 20 and to evaluate the duplication age appearance in bones extracted from the same individuals. We found that the number of duplications increase from 38 years and that at least one duplicated fragment is present in 50% of cases after 70 years in this tissue. These results confirm that several age-related mutations can be detected in the D-loop of mtDNA and open the way for the use of molecular markers for age estimation in forensic and/or anthropological identification.

Published
2011
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24. Population genetics of 17 Y-chromosomal STR loci in Yakutia

Author

Patricia Balaresque, Anatoly N. Alekseev, Eric Crubézy, Catherine Thèves, André Sevin, Morgane Gibert, Innokentevich V. Timofeev, Larissa E. Evdokimova, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), laboratoire d'archéologie, Université de Yakutsk, Laboratoire d'Anthropobiologie (LA), and École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
Population sample, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population genetics, Biology, Polymerase Chain Reaction, Pathology and Forensic Medicine, 03 medical and health sciences, 0302 clinical medicine, Genetic variation, Genetics, Humans, 030216 legal & forensic medicine, education, Allele frequency, 030304 developmental biology, 0303 health sciences, education.field_of_study, Chromosomes, Human, Y, Haplotype, Genetic Variation, Siberia, Genetics, Population, Haplotypes, [SDE]Environmental Sciences, Str loci, Microsatellite
Abstract

Haplotype and allele frequencies of 17 Y-chromosomal short tandem repeat (Y-STR) markers in a population sample of 133 Yakut male volunteers from two regions: Central (n = 41) and Western Yakutia (n = 92) were determined using the AmpFlSTR Yfiler PCR Amplification Kit (Applied Biosystems). A total of 65 haplotypes were identified in the Yakut population, with 15 haplotypes in Central sample and 54 haplotypes in Western sample. Haplotype diversity values of 0.79 and 0.96, and average gene diversity values of 0.14 and 0.41 were calculated for Central and Western samples, respectively. The Fst distances between both our Yakut populations with other Russian, Siberian and Chinese populations were represented by MDS plot. The graphical view demonstrated close distances between most Yakut populations and differences with other Siberian populations. Crown Copyright (C) 2010 Published by Elsevier Ireland Ltd. All rights reserved.

Published
2010
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25. Apport de l'ADN ancien et moderne à la reconstitution du peuplement d'Asie centrale et de Sibérie orientale

Author

Morgane Gibert, Alekseev, Anatoly N., Sylvain Amory, Gérard, P., Christine Keyser, Jean-François Magnaval, Marc Perrucho, André Sevin, Catherine Thèves, Bertrand Ludes, Eric Crubézy, Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), laboratoire d'archéologie, Université de Yakutsk, Laboratoire d'anthropologie moléculaire (LAM), Université Louis Pasteur - Strasbourg I, Laboratoire d'anthropologie, FRE 2960, 39, allée Jules-Guesde, 31000 Toulouse, France, Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Institute of Legal Medicine, Université Paris Descartes - Paris 5 (UPD5), Laboratoire d'Anthropobiologie ( LA ), École des hautes études en sciences sociales ( EHESS ) -Université Toulouse - Jean Jaurès ( UT2J ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'anthropologie moléculaire ( LAM ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France ( IML ), Anthropologie Moléculaire et Imagerie de Synthèse ( AMIS ), PRES Université de Toulouse-Centre National de la Recherche Scientifique ( CNRS ), and Université Paris Descartes - Paris 5 ( UPD5 )

Subjects
[ SDE ] Environmental Sciences, [ SHS.ANTHRO-BIO ] Humanities and Social Sciences/Biological anthropology, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, [SDE]Environmental Sciences
Abstract

For anthropologists, Central Asia and Eastern Siberia represent a unique case study for two reasons. On one hand, Siberia is a key area for the understanding of the admixture between east eurasian and west eurasian populations through history, and for the reconstruction of the peopling of America and the Northern areas at different periods. On the other hand, the very harsh climatic conditions are favourable to the preservation of ancient DNA in skeletal remains. An interdisciplinary approach that compares past and modern populations in their two components, biology and culture, can therefore be considered. The present communication relates the studies we have carried out for the last 4 years in Yakutia and Buriatia. These studies are ongoing. Here we focus on the contribution of genetic data for the reconstruction of the history of past migrations and admixture of siberian populations.; L'Asie centrale et la Sibérie orientale constituent du point de vue anthropologique un terrain unique pour deux raisons. La première est qu'il s'agit d'une aire clé pour la compréhension de l'histoire des échanges entre populations eurasiatiques, et aussi pour la reconstruction de l'histoire du peuplement de l'Amérique et des régions du nord à différentes périodes. La seconde, c'est que les conditions climatiques exceptionnelles assurent une conservation remarquable de l'ADN dans les restes osseux. Il est alors possible de développer une approche pluridisciplinaire comparant les populations du passé et les populations vivantes dans leur double composante, " biologie et culture ". Nous proposons ici de présenter les travaux que nous menons depuis 4 ans en Yakoutie et en Bouriatie. Nous illustrerons ainsi l'apport des données de l'anthropologie génétique à la reconstitution de l'histoire des migrations et des échanges entre populations sibériennes.

Published
2006

26. Detection and quantification of the age-related point mutation A189G in the human mitochondrial DNA

Author

Bertrand Ludes, Norbert Telmon, Jean Pierre Salles, Eric Crubézy, Catherine Thèves, Christine Keyser-Tracqui, Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, Service de médecine légale, CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Hôpital de Rangueil, CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], Thèves, Catherine, Service Médecine légale et médecine pénitentiaire [CHU Toulouse], Pôle Santé publique et médecine publique [CHU Toulouse], and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)

Subjects
Peptide Nucleic Acids, Aging, forensic science, DNA Mutational Analysis, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, mitochondrial DNA, Polymerase Chain Reaction, "forensic science, 0302 clinical medicine, heteroplasmy, Mutation frequency, Child, Psoas Muscles, Aged, 80 and over, Genetics, 0303 health sciences, Hybridization probe, Middle Aged, Heteroplasmy, 3. Good health, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology, Child, Preschool, DNA Probes, Adult, Mitochondrial DNA, Adolescent, Biology, DNA, Mitochondrial, Human mitochondrial genetics, DNA sequencing, Pathology and Forensic Medicine, 03 medical and health sciences, Humans, Point Mutation, Aged, DNA Primers, 030304 developmental biology, Southern blot, Point mutation, Mouth Mucosa, age-related mutation, Infant, Sequence Analysis, DNA, Molecular biology, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, detection methods", detection methods, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery
Abstract

International audience; Mutation analysis in the mitochondrial DNA (mtDNA) control region is widely used in population genetic studies as well as in forensic medicine. Among the difficulties linked to the mtDNA analysis, one can find the detection of heteroplasmy, which can be inherited or somatic. Recently, age-related point mutation A189G was described in mtDNA and shown to accumulate with age in muscles. We carried out the detection of this 189 heteroplasmic point mutation using three technologies: automated DNA sequencing, Southern blot hybridization using a digoxigenin-labeled oligonucleotide probe, and peptide nucleic acid (PNA)/real-time PCR combined method on different biological samples. Our results give additional information on the increase in mutation frequency with age in muscle tissue and revealed that the PNA/real-time PCR is a largely more sensitive method than DNA sequencing for heteroplasmy detection. These investigations could be of interest in the detection and interpretation of mtDNA heteroplasmy in anthropological and forensic studies.

Published
2006
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27. EVOSHEEP Project. First zootechnical innovations in Southwest Asian societies (6th–1rst millennia B.C.): Origin and development of sheep breeds

Author

Emmanuelle Vila, Philippe Abrahami, Moussab Al Besso, Rémy Berthon, Frédéric Boyer, Catherine Breniquet, Dan Bradley, Jwana Chahoud, Thomas CUCCHI, Gilles Escarguel, Lionel Gourichon, Huangfu, W., Daniel Helmer, Jamet, H., Joséphine Lesur, Marjan Mashkour, Xavier Matta, Cécile Michel, Azadeh Mohaseb, Bruno Morandière, Ludovic Orlando, Stéphanie Pompanon F., Laure Tonasso-Calvière, Catherine Thèves, Manon Vuillien, ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), Archéologie des Sociétés Méditerranéennes (ASM), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Département Automatique, Productique et Informatique (IMT Atlantique - DAPI), IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre d'Histoire 'Espaces et Cultures' (CHEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Lebanese University [Beirut] (LU), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Gestion des ressources naturelles , environnements et sociétés (GReNES), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Département de Chimie Moléculaire - Chimie Inorganique Redox (DCM - CIRE ), Département de Chimie Moléculaire (DCM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Histoire et Archéologie de l'Orient Cunéiforme (HAROC), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE27-0004,EVOSHEEP,Exploration des premières innovations zootechniques dans les sociétés du sud-ouest asiatique (5e-1er millénaires av. J.-C.)(2017), Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UPVM)-Ministère de la Culture (MC), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Département de Chimie Moléculaire - Chimie Inorganique Redox Biomimétique (DCM - CIRE ), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Archéologie des Sociétés Méditerranéennes, Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Robotique Et Vivant (ReV), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques, Lebanese University [Beirut], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), GRENES, Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Département de Chimie Moléculaire - Chimie Inorganique Redox Biomimétique (DCM - CIRE), Université Joseph Fourier - Grenoble 1 (UJF)-Institut de Chimie Moléculaire de Grenoble (ICMG)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
breeds, 1rst, sheep, Asian, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, 6th, Southwend, B-C, innovations, Origin, societies, millennia, EVOSHEEP, zootechnical, First, development, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

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