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Weigand A, Bücs SL, Deleva S, Lukić Bilela L, Nyssen P, Paragamian K, Ssymank A, Weigand H, Zakšek V, Zagmajster M, Balázs G, Barjadze S, Bürger K, Burn W, Cailhol D, Decrolière A, Didonna F, Doli A, Drazina T, Dreybrodt J, Ðud L, Egri C, Erhard M, Finžgar S, Fröhlich D, Gartrell G, Gazaryan S, Georges M, Godeau JF, Grunewald R, Gunn J, Hajenga J, Hofmann P, Knight L, Köble H, Kuharic N, Lüthi C, Munteanu C, Novak R, Ozols D, Petkovic M, Stoch F, Vogel B, Vukovic I, Hall Weberg M, Zaenker C, Zaenker S, Feit U, Thies JC. Current cave monitoring practices, their variation and recommendations for future improvement in Europe: A synopsis from the 6th EuroSpeleo Protection Symposium. RESEARCH IDEAS AND OUTCOMES 2022. [DOI: 10.3897/rio.8.e85859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This manuscript summarizes the outcomes of the 6th EuroSpeleo Protection Symposium. Special emphasis was laid on presenting and discussing monitoring activities under the umbrella of the Habitats Directive (EU Council Directive 92/43/EEC) for habitat type 8310 "Caves not open to the public" and the Emerald Network. The discussions revealed a high level of variation in the currently conducted underground monitoring activities: there is no uniform definition of what kind of underground environments the "cave" habitat should cover, how often a specific cave has to be monitored, and what parameters should be measured to evaluate the conservation status. The variation in spatial dimensions in national definitions of caves further affects the number of catalogued caves in a country and the number of caves to be monitored. Not always participants are aware of the complete national monitoring process and that data sets should be freely available or easily accessible. The discussions further showed an inherent dilemma between an anticipated uniform monitoring approach with a coherent assessment methodology and, on the contrary, the uniqueness of caves and subterranean biota to be assessed – combined with profound knowledge gaps and a lack of resources. Nevertheless, some good practices for future cave monitoring activities have been identified by the participants: (1) Cave monitoring should focus on bio- and geodiversity elements alike; (2) Local communities should be involved, and formal agreements envisaged; (3) Caves must be understood as windows into the subterranean realm; (4) Touristic caves should not be excluded ad-hoc from regular monitoring; (5) New digital tools and open FAIR data infrastructures should be implemented; (6) Cave biomonitoring should focus on a large(r) biological diversity; and (7) DNA-based tools should be integrated. Finally, the importance of the 'forgotten' Recommendation No. 36 from the Bern Convention as a guiding legal European document was highlighted.
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Massini Espino M, Mychajliw AM, Almonte JN, Allentoft ME, Van Dam AR. Raptor roosts as invasion archives: insights from the first black rat mitochondrial genome sequenced from the Caribbean. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02636-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Guimaraes S, Arbuckle BS, Peters J, Adcock SE, Buitenhuis H, Chazin H, Manaseryan N, Uerpmann HP, Grange T, Geigl EM. Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age. SCIENCE ADVANCES 2020; 6:eabb0030. [PMID: 32938680 PMCID: PMC7494339 DOI: 10.1126/sciadv.abb0030] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/31/2020] [Indexed: 05/12/2023]
Abstract
Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.
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Affiliation(s)
- Silvia Guimaraes
- Institut Jacques Monod, CNRS, University of Paris, Paris, France
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joris Peters
- ArchaeoBioCenter and Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication and the History of Veterinary Medicine, Ludwig Maximilian University Munich, Kaulbachstraße 37/111, 80539 Munich, Germany
- State Collection of Anthropology and Palaeoanatomy Munich, Bavarian Natural History Collections, Karolinenplatz 2a, 80333 Munich, Germany
| | - Sarah E Adcock
- Department of Anthropology, University of Chicago, 1126 East 59th Street, Chicago, IL 60637, USA
| | - Hijlke Buitenhuis
- Groningen Institute of Archaeology, University of Groningen, 9712 ER Groningen, Netherlands
| | - Hannah Chazin
- Department of Anthropology, Columbia University, 1200 Amsterdam Avenue, New York, NY 10031, USA
| | - Ninna Manaseryan
- Scientific Center of Zoology and Hydroecology, Institute of Zoology, National Academy of Sciences of the Republic of Armenia, 7 Paruyr Sevak Str., Yerevan 0014, Armenia
| | - Hans-Peter Uerpmann
- Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung für Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Universität Tübingen, Rümelinstraße 23, 72070 Tübingen, Germany
| | - Thierry Grange
- Institut Jacques Monod, CNRS, University of Paris, Paris, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, University of Paris, Paris, France.
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Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis. Mol Phylogenet Evol 2018; 125:188-195. [PMID: 29608962 DOI: 10.1016/j.ympev.2018.03.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 03/07/2018] [Accepted: 03/26/2018] [Indexed: 11/23/2022]
Abstract
The red-toothed shrews (Soricinae) are the most widespread subfamily of shrews, distributed from northern South America to North America and Eurasia. Within this subfamily, the tribe Nectogalini includes the fossil species Nesiotites hidalgo recorded from the Late Pleistocene to Holocene of the Balearic Islands (Western Mediterranean). Although there is a consensus about the close relationship between the extinct red-toothed shrew genera Nesiotites and Asoriculus based on morphology, molecular data are necessary to further evaluate the phylogenetic relationships of the Balearic fossils. We obtained a near complete mitochondrial genome of N. hidalgo, allowing the first molecular phylogenetic analysis of this species. Analyses based on 15,167 bp of the mitochondrial genome placed N. hidalgo as close relative to the extant Himalayan shrew (Soriculus nigrescens), and a combined analysis using molecular and morphological data confirm that N. hidalgo and Asoriculus gibberodon are sister-taxa with S. nigrescens as the immediate outgroup. Molecular clock and divergence estimates suggest that the split between N. hidalgo and its closest living relative occurred around 6.44 Ma, which is in agreement with the previously proposed colonisation of the Balearic Islands from mainland Europe by nectogaline shrews during the Messinian Salinity Crisis (5.97-5.33 My ago). Our results highlight that it is possible to retrieve genetic data from extinct small mammals from marginal environments for DNA preservation. Additional finds from the fossil record of Soricinae from the Eurasian Late Miocene/Early Pliocene are needed to shed further light on the still confusing taxonomy and paleobiogeography of this clade.
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Woods R, Marr MM, Brace S, Barnes I. The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species. Genes (Basel) 2017; 8:E312. [PMID: 29117125 PMCID: PMC5704225 DOI: 10.3390/genes8110312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 02/06/2023] Open
Abstract
The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.
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Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Melissa M Marr
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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Ottoni C, Van Neer W, De Cupere B, Daligault J, Guimaraes S, Peters J, Spassov N, Prendergast ME, Boivin N, Morales-Muñiz A, Bălăşescu A, Becker C, Benecke N, Boroneant A, Buitenhuis H, Chahoud J, Crowther A, Llorente L, Manaseryan N, Monchot H, Onar V, Osypińska M, Putelat O, Quintana Morales EM, Studer J, Wierer U, Decorte R, Grange T, Geigl EM. The palaeogenetics of cat dispersal in the ancient world. Nat Ecol Evol 2017. [DOI: 10.1038/s41559-017-0139] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse. Science 2017; 356:442-445. [DOI: 10.1126/science.aam5298] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Ancient genomics of horse domesticationThe domestication of the horse was a seminal event in human cultural evolution. Libradoet 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
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Affiliation(s)
- Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Charleen Gaunitz
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Mélanie Pruvost
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot, 75205 Paris cedex 13, France
| | - Anders Albrechtsen
- Bioinformatics Center, Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Naveed Khan
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | | | - Aitor Serres-Armero
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Lukas F. K. Kuderna
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Inna S. Povolotskaya
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- National High-Throughput DNA Sequencing Center, Copenhagen, Denmark
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum national d’histoire naturelle, Sorbonne Universités, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 55 rue Buffon, 75005 Paris, France
| | | | - Catherine Thèves
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed H. Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khaled Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, 1580 Avenches, Switzerland
| | - Zainolla Samashev
- Branch of Institute of Archaeology Margulan, Republic Avenue 24-405, 010000 Astana, Republic of Kazakhstan
| | - Henri-Paul Francfort
- CNRS, UMR 7041 Archéologie et Sciences de l’Antiquité, Archéologie de l'Asie Centrale, Maison René Ginouvès, 21 allée de l’Université, 92023 Nanterre, France
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany
| | - Christine Keyser
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bertrand Ludes
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut Médico-Légal, Université Paris Descartes, Paris, France
| | - Eric Crubézy
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
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Massilani D, Guimaraes S, Brugal JP, Bennett EA, Tokarska M, Arbogast RM, Baryshnikov G, Boeskorov G, Castel JC, Davydov S, Madelaine S, Putelat O, Spasskaya NN, Uerpmann HP, Grange T, Geigl EM. Past climate changes, population dynamics and the origin of Bison in Europe. BMC Biol 2016; 14:93. [PMID: 27769298 PMCID: PMC5075162 DOI: 10.1186/s12915-016-0317-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/11/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe's megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. RESULTS Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomes from throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus) and steppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmental changes. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modern wisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A population overlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave. Bayesian analyses of these complete ancient mitogenomes yielded new dates of the various branching events during the evolution of Bison and its radiation with Bos, which lead us to propose that the genetic affiliation between the wisent and cattle mitogenomes result from incomplete lineage sorting rather than post-speciation gene flow. CONCLUSION The paleogenetic analysis of bison remains from the last 50,000 years reveals the influence of climate changes on the dynamics of the various bison populations in Europe, only one of which survived into the Holocene, where it experienced severe reductions in its genetic diversity. The time depth and geographical scope of this study enables us to propose temperate Western Europe as a suitable biotope for the wisent compatible with its reintroduction.
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Affiliation(s)
- Diyendo Massilani
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Silvia Guimaraes
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Jean-Philip Brugal
- CNRS, USR 3336 IFRA (Institut Français de Recherche en Afrique), Nairobi, Kenya.,Aix-Marseille Université, UMR 7269 LAMPEA (Labo.Méd.de Préhistoire, Europe-Afrique) Maison Méditerranéenne des Sciences de l'Homme, BP 674, 13094, Aix-en-Provence, cedex 2, France
| | - E Andrew Bennett
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Malgorzata Tokarska
- Mammal Research Institute Polish Academy of Sciences, Genetics and Evolution Department, Waszkiewicza 1, 17-230, Bialowieza, Poland
| | - Rose-Marie Arbogast
- CNRS/UMR 7044/MISHA, 5 allée du Général Rouvillois, 67083, Strasbourg, France
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, 199034, Saint Petersburg, Russia
| | - Gennady Boeskorov
- Diamond and Precious Metal Geology Institute of the Siberian Branch of the RAS, Yakutsk, Russia
| | - Jean-Christophe Castel
- Muséum d'histoire naturelle de Genève (MHN), Département d'Archéozoologie, Route de Malagnou 1, 1208, Geneva, Switzerland
| | - Sergey Davydov
- North-East Science Station, Pacific Institute of Geography, Far East Branch, Russ. Ac. Sci., 678830, Cherskiy, Russia
| | - Stéphane Madelaine
- Musée national de Préhistoire, 24620, Les Eyzies de Tayac-Sireuil, France
| | - Olivier Putelat
- Archéologie Alsace, 11 rue Jean-François Champollion, 67600, Sélestat, France.,UMR 7041 ArScan - Archéologies environnementales - Maison de l'Archéologie et de l'Ethnologie, 92023, Nanterre, France
| | - Natalia N Spasskaya
- Zoological Museum of Moscow Lomonosow, State University, Bolshaya Nikitskaya Str. 6, Moscow, 125009, Russia
| | - Hans-Peter Uerpmann
- Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Rümelinstr. 23, 72070, Tübingen, Germany
| | - Thierry Grange
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France.
| | - Eva-Maria Geigl
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France.
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Côté NML, Daligault J, Pruvost M, Bennett EA, Gorgé O, Guimaraes S, Capelli N, Le Bailly M, Geigl EM, Grange T. A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites. PLoS One 2016; 11:e0146230. [PMID: 26752051 PMCID: PMC4709038 DOI: 10.1371/journal.pone.0146230] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/14/2015] [Indexed: 11/21/2022] Open
Abstract
Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.
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Affiliation(s)
- Nathalie M. L. Côté
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
- University of Bourgogne Franche-Comte, CNRS UMR 6249 Chrono-environment, 16 route de Gray, 25030, Besançon cedex, France
| | - Julien Daligault
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - Mélanie Pruvost
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - E. Andrew Bennett
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - Olivier Gorgé
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - Silvia Guimaraes
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
| | - Nicolas Capelli
- University of Bourgogne Franche-Comte, CNRS UMR 6249 Chrono-environment, 16 route de Gray, 25030, Besançon cedex, France
| | - Matthieu Le Bailly
- University of Bourgogne Franche-Comte, CNRS UMR 6249 Chrono-environment, 16 route de Gray, 25030, Besançon cedex, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
- * E-mail: (EMG); (TG)
| | - Thierry Grange
- Institut Jacques Monod, CNRS, University Paris Diderot, UMR 7592, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75205, Paris, Cedex 13, France
- * E-mail: (EMG); (TG)
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