1
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Bon C. [Palaeogenetics or the interest of genetic exploration of the past]. Med Sci (Paris) 2024; 40:556-559. [PMID: 38986102 DOI: 10.1051/medsci/2024084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024] Open
Affiliation(s)
- Céline Bon
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum national d'Histoire naturelle, Université Paris-Cité, Paris, France
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2
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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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3
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Mylopotamitaki D, Weiss M, Fewlass H, Zavala EI, Rougier H, Sümer AP, Hajdinjak M, Smith GM, Ruebens K, Sinet-Mathiot V, Pederzani S, Essel E, Harking FS, Xia H, Hansen J, Kirchner A, Lauer T, Stahlschmidt M, Hein M, Talamo S, Wacker L, Meller H, Dietl H, Orschiedt J, Olsen JV, Zeberg H, Prüfer K, Krause J, Meyer M, Welker F, McPherron SP, Schüler T, Hublin JJ. Homo sapiens reached the higher latitudes of Europe by 45,000 years ago. Nature 2024; 626:341-346. [PMID: 38297117 PMCID: PMC10849966 DOI: 10.1038/s41586-023-06923-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/30/2023] [Indexed: 02/02/2024]
Abstract
The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.
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Affiliation(s)
- Dorothea Mylopotamitaki
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany.
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London, UK
| | - Elena Irene Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | - Arev Pelin Sümer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Karen Ruebens
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, Bordeaux, France
| | - Sarah Pederzani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeological Micromorphology and Biomarker Lab, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Florian S Harking
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Huan Xia
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Jakob Hansen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - André Kirchner
- Department of Soil Protection and Soil Survey, State Authority for Mining, Energy and Geology of Lower Saxony (LBEG), Hannover, Germany
| | - Tobias Lauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Terrestrial Sedimentology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Mareike Stahlschmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology and Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Michael Hein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Ecology, Leuphana University, Lüneburg, Germany
- Historical Anthropospheres Working Group, Leipzig Lab, Leipzig University, Leipzig, Germany
| | - Sahra Talamo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Bologna University, Bologna, Italy
| | - Lukas Wacker
- Ion Beam Physics, ETH Zurich, Zurich, Switzerland
| | - Harald Meller
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Holger Dietl
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jesper V Olsen
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Jean-Jacques Hublin
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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4
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Fewlass H, Zavala EI, Fagault Y, Tuna T, Bard E, Hublin JJ, Hajdinjak M, Wilczyński J. Chronological and genetic analysis of an Upper Palaeolithic female infant burial from Borsuka Cave, Poland. iScience 2023; 26:108283. [PMID: 38047066 PMCID: PMC10690573 DOI: 10.1016/j.isci.2023.108283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 12/05/2023] Open
Abstract
Six infant human teeth and 112 animal tooth pendants from Borsuka Cave were identified as the oldest burial in Poland. However, uncertainties around the dating and the association of the teeth to the pendants have precluded their association with an Upper Palaeolithic archaeological industry. Using <67 mg per tooth, we combined dating and genetic analyses of two human teeth and six herbivore tooth pendants to address these questions. Our interdisciplinary approach yielded informative results despite limited sampling material, and high levels of degradation and contamination. Our results confirm the Palaeolithic origin of the human remains and herbivore pendants, and permit us to identify the infant as female and discuss the association of the assemblage with different Palaeolithic industries. This study exemplifies the progress that has been made toward minimally destructive methods and the benefits of integrating methods to maximize data retrieval from precious but highly degraded and contaminated prehistoric material.
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Affiliation(s)
- Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London NW1 1AT, UK
| | - Elena I. Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Cell and Molecular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Yoann Fagault
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Thibaut Tuna
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Edouard Bard
- CEREGE, Aix Marseille Université, CNRS, IRD, INRA, Collège de France, Technopôle de l’Arbois BP 80, 13545 Aix-en-Provence Cedex 4, France
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241 – U1050), Collège de France, 75231 Paris, France
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland
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5
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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6
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Duitama González C, Vicedomini R, Lemane T, Rascovan N, Richard H, Chikhi R. decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods. MICROBIOME 2023; 11:243. [PMID: 37926832 PMCID: PMC10626679 DOI: 10.1186/s40168-023-01670-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/13/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. RESULTS We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker. CONCLUSIONS decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.
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Affiliation(s)
- Camila Duitama González
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France.
| | - Riccardo Vicedomini
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France
- Université de Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Téo Lemane
- Université de Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Nicolas Rascovan
- Institut Pasteur, Université de Paris Cité, CNRS UMR 2000, Microbial Paleogenomics Unit, Paris, F-75015, France
| | - Hugues Richard
- Bioinformatics unit (MF1), Robert Koch Institute, Nordufer, 20, 13353, Berlin, Germany
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France
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7
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Creydt M, Fischer M. Artefact Profiling: Panomics Approaches for Understanding the Materiality of Written Artefacts. Molecules 2023; 28:4872. [PMID: 37375427 DOI: 10.3390/molecules28124872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
This review explains the strategies behind genomics, proteomics, metabolomics, metallomics and isotopolomics approaches and their applicability to written artefacts. The respective sub-chapters give an insight into the analytical procedure and the conclusions drawn from such analyses. A distinction is made between information that can be obtained from the materials used in the respective manuscript and meta-information that cannot be obtained from the manuscript itself, but from residues of organisms such as bacteria or the authors and readers. In addition, various sampling techniques are discussed in particular, which pose a special challenge in manuscripts. The focus is on high-resolution, non-targeted strategies that can be used to extract the maximum amount of information about ancient objects. The combination of the various omics disciplines (panomics) especially offers potential added value in terms of the best possible interpretations of the data received. The information obtained can be used to understand the production of ancient artefacts, to gain impressions of former living conditions, to prove their authenticity, to assess whether there is a toxic hazard in handling the manuscripts, and to be able to determine appropriate measures for their conservation and restoration.
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Affiliation(s)
- Marina Creydt
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany
| | - Markus Fischer
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany
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8
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Essel E, Zavala EI, Schulz-Kornas E, Kozlikin MB, Fewlass H, Vernot B, Shunkov MV, Derevianko AP, Douka K, Barnes I, Soulier MC, Schmidt A, Szymanski M, Tsanova T, Sirakov N, Endarova E, McPherron SP, Hublin JJ, Kelso J, Pääbo S, Hajdinjak M, Soressi M, Meyer M. Ancient human DNA recovered from a Palaeolithic pendant. Nature 2023:10.1038/s41586-023-06035-2. [PMID: 37138083 DOI: 10.1038/s41586-023-06035-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals1 who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited2-5. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.
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Affiliation(s)
- Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Biology, San Francisco State University, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ellen Schulz-Kornas
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS) Research Network, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, London, UK
| | - Marie-Cécile Soulier
- Maison de la Recherche, Université de Toulouse-Jean Jaurès, CNRS UMR 5608 TRACES, Toulouse, France
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Merlin Szymanski
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka Tsanova
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Nikolay Sirakov
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, Paris, France
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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9
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Guarino-Vignon P, Lefeuvre M, Chimènes A, Monnereau A, Guliyev F, Pecqueur L, Jovenet E, Lyonnet B, Bon C. Genome-wide analysis of a collective grave from Mentesh Tepe provides insight into the population structure of early neolithic population in the South Caucasus. Commun Biol 2023; 6:319. [PMID: 36966245 PMCID: PMC10039893 DOI: 10.1038/s42003-023-04681-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/08/2023] [Indexed: 03/27/2023] Open
Abstract
Despite the localisation of the southern Caucasus at the outskirt of the Fertile Crescent, the Neolithisation process started there only at the beginning of the sixth millennium with the Shomutepe-Shulaveri culture of yet unclear origins. We present here genomic data for three new individuals from Mentesh Tepe in Azerbaijan, dating back to the beginnings of the Shomutepe-Shulaveri culture. We evidence that two juveniles, buried embracing each other, were brothers. We show that the Mentesh Tepe Neolithic population is the product of a recent gene flow between the Anatolian farmer-related population and the Caucasus/Iranian population, demonstrating that population admixture was at the core of the development of agriculture in the South Caucasus. By comparing Bronze Age individuals from the South Caucasus with Neolithic individuals from the same region, including Mentesh Tepe, we evidence that gene flows between Pontic Steppe populations and Mentesh Tepe-related groups contributed to the makeup of the Late Bronze Age and modern Caucasian populations. Our results show that the high cultural diversity during the Neolithic period of the South Caucasus deserves close genetic analysis.
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Affiliation(s)
- Perle Guarino-Vignon
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France.
- UMR5288 CAGT, CNRS, Université Paul Sabatier, Toulouse, France.
| | - Maël Lefeuvre
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Amélie Chimènes
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Aurore Monnereau
- Department of Archaeology, University of York, BioArCh, Environment Building Wentworth Way Heslington, York, YO10 5NG, UK
| | - Farhad Guliyev
- Head of the Science Fund and the Museum Department of the Institute of Archeology, Ethnography and Anthropology, Azerbaijan National Academy of Science, Baku, Azerbaijan
| | - Laure Pecqueur
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
- Institut National de Recherches Archéologiques Préventives, Centre-île de France, Paris, France
| | - Elsa Jovenet
- Institut National de Recherches Archéologiques Préventives, Centre-île de France, Paris, France
| | - Bertille Lyonnet
- UMR7192 PROCLAC « Proche-Orient - Caucase: langues, archéologie, cultures », CNRS, Paris, France
| | - Céline Bon
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France.
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10
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Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean. Nat Ecol Evol 2023; 7:290-303. [PMID: 36646948 PMCID: PMC9911347 DOI: 10.1038/s41559-022-01952-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/11/2022] [Indexed: 01/18/2023]
Abstract
The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by 'eastern' gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.
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11
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Wang K, Bleasdale M, Le Moyne C, Freund C, Krause J, Boivin N, Schiffels S. 4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists. Sci Rep 2022; 12:20939. [PMID: 36463384 PMCID: PMC9719486 DOI: 10.1038/s41598-022-25384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/29/2022] [Indexed: 12/07/2022] Open
Abstract
Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.
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Affiliation(s)
- Ke Wang
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.8547.e0000 0001 0125 2443School of Life Sciences, Fudan University, Shanghai, China
| | - Madeleine Bleasdale
- grid.5685.e0000 0004 1936 9668Department of Archaeology, University of York, York, UK ,grid.469873.70000 0004 4914 1197Max Planck Institute for the Science of Human History, Jena, Germany
| | - Charles Le Moyne
- grid.469873.70000 0004 4914 1197Max Planck Institute for the Science of Human History, Jena, Germany ,grid.1003.20000 0000 9320 7537School of Social Science, The University of Queensland, Brisbane, Australia
| | - Cacilia Freund
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nicole Boivin
- grid.469873.70000 0004 4914 1197Max Planck Institute for the Science of Human History, Jena, Germany ,grid.1003.20000 0000 9320 7537School of Social Science, The University of Queensland, Brisbane, Australia
| | - Stephan Schiffels
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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12
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Guarino-Vignon P, Marchi N, Chimènes A, Monnereau A, Kroll S, Mashkour M, Lhuillier J, Bendezu-Sarmiento J, Heyer E, Bon C. Genetic analysis of a bronze age individual from Ulug-depe (Turkmenistan). Front Genet 2022; 13:884612. [PMID: 36072661 PMCID: PMC9441711 DOI: 10.3389/fgene.2022.884612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian–speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group.
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Affiliation(s)
- Perle Guarino-Vignon
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- CAGT, UMR 5288, CNRS, Université Paul Sabatier Toulouse III, Toulouse, France
- *Correspondence: Perle Guarino-Vignon, ; Céline Bon,
| | - Nina Marchi
- CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland
| | - Amélie Chimènes
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Aurore Monnereau
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Sonja Kroll
- Archéozoologie, Archéobotanique Sociétés, Pratiques et Environnements (AASPE), Muséum National D'Histoire Naturelle, CNRS, Paris, France
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique Sociétés, Pratiques et Environnements (AASPE), Muséum National D'Histoire Naturelle, CNRS, Paris, France
| | - Johanna Lhuillier
- Archéorient, Environnements et Sociétés de L'Orient Ancien, CNRS/Université Lyon 2, Lyon, France
| | - Julio Bendezu-Sarmiento
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Evelyne Heyer
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Céline Bon
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- *Correspondence: Perle Guarino-Vignon, ; Céline Bon,
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13
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Zhang X, Ji X, Li C, Yang T, Huang J, Zhao Y, Wu Y, Ma S, Pang Y, Huang Y, He Y, Su B. A Late Pleistocene human genome from Southwest China. Curr Biol 2022; 32:3095-3109.e5. [PMID: 35839766 DOI: 10.1016/j.cub.2022.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/27/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
Southern East Asia is the dispersal center regarding the prehistoric settlement and migrations of modern humans in Asia-Pacific regions. However, the settlement pattern and population structure of paleolithic humans in this region remain elusive, and ancient DNA can provide direct information. Here, we sequenced the genome of a Late Pleistocene hominin (MZR), dated ∼14.0 thousand years ago from Red Deer Cave located in Southwest China, which was previously reported possessing mosaic features of modern and archaic hominins. MZR is the first Late Pleistocene genome from southern East Asia. Our results indicate that MZR is a modern human who represents an early diversified lineage in East Asia. The mtDNA of MZR belongs to an extinct basal lineage of the M9 haplogroup, reflecting a rich matrilineal diversity in southern East Asia during the Late Pleistocene. Combined with the published data, we detected clear genetic stratification in ancient southern populations of East/Southeast Asia and some degree of south-versus-north divergency during the Late Pleistocene, and MZR was identified as a southern East Asian who exhibits genetic continuity to present day populations. Markedly, MZR is linked deeply to the East Asian ancestry that contributed to First Americans.
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Affiliation(s)
- Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xueping Ji
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China.
| | - Chunmei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Tingyu Yang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinhui Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wu
- Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; School of History, Wuhan University, Wuhan 430072, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China
| | - Shiwu Ma
- Mengzi Institute of Cultural Relics, Mengzi, Yunnan Province 661100, China
| | - Yuhong Pang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China.
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14
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Huang Y, Ringbauer H. hapCon: Estimating Contamination of Ancient Genomes by Copying from Reference Haplotypes. Bioinformatics 2022; 38:3768-3777. [PMID: 35695771 PMCID: PMC9344841 DOI: 10.1093/bioinformatics/btac390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
Motivation Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches. Results We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&Stephens haplotype copying model for haploid X chromosomes, with mismatches modeled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1× for SNP capture data (1240k) and 0.02× for whole genome sequencing data, substantially extending the coverage limit of previous male X chromosome-based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25–30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as ∼45 000 and various global ancestries. Availability and implementation We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
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15
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Population dynamics and genetic connectivity in recent chimpanzee history. CELL GENOMICS 2022; 2:None. [PMID: 35711737 PMCID: PMC9188271 DOI: 10.1016/j.xgen.2022.100133] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/29/2021] [Accepted: 04/15/2022] [Indexed: 11/22/2022]
Abstract
Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.
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16
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Heraclides A, Fernández-Domínguez E. Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods. Int J Mol Sci 2022; 23:4651. [PMID: 35563041 PMCID: PMC9104972 DOI: 10.3390/ijms23094651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 02/05/2023] Open
Abstract
Retrieving high-quality endogenous ancient DNA (aDNA) poses several challenges, including low molecular copy number, high rates of fragmentation, damage at read termini, and potential presence of exogenous contaminant DNA. All these factors complicate a reliable reconstruction of consensus aDNA sequences in reads from high-throughput sequencing platforms. Here, we report findings from a thorough evaluation of two alternative tools (ANGSD and schmutzi) aimed at overcoming these issues and constructing high-quality ancient mitogenomes. Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were reconstructed using different quality filters, with their accuracy measured and compared. Moreover, the influence of different sequence parameters (number of reads, sequenced bases, mean coverage, and rate of deamination and contamination) as predictors of derived sequence quality was evaluated. Complete mitogenomes were successfully reconstructed for all ancient samples, and for the majority of them, filtering substantially improved mtDNA consensus calling and haplogroup prediction. Overall, the schmutzi pipeline, which estimates and takes into consideration exogenous contamination, appeared to have the edge over the much faster and user-friendly alternative method (ANGSD) in moderate to high coverage samples (>1,000,000 reads). ANGSD, however, through its read termini trimming filter, showed better capabilities in calling the consensus sequence from low-quality samples. Among all the predictors of overall sample quality examined, the strongest correlation was found for the available number of sequence reads and bases. In the process, we report a previously unassigned haplogroup (U3b) for an Early Chalcolithic individual from Southern Anatolia/Northern Levant.
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Affiliation(s)
- Alexandros Heraclides
- Department of Health Sciences, European University Cyprus, Diogenis Str. 6, Nicosia 2404, Cyprus
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17
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Capo E, Monchamp ME, Coolen MJL, Domaizon I, Armbrecht L, Bertilsson S. Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential. Environ Microbiol 2022; 24:2201-2209. [PMID: 35049133 PMCID: PMC9304175 DOI: 10.1111/1462-2920.15913] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 11/30/2022]
Abstract
In‐depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo‐genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human‐induced global changes.
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Affiliation(s)
- Eric Capo
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Marie-Eve Monchamp
- Department of Biology, McGill University, Montréal, QC, H3A 1B1, Canada.,Groupe de recherche interuniversitaire en limnologie (GRIL)
| | - Marco J L Coolen
- Western Australia Organic and Isotope Geochemistry Centre (WA-OIGC), Curtin University, Bentley, 6102, Australia
| | - Isabelle Domaizon
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200 Thonon les Bains, France.,UMR CARRTEL, Pôle R&D ECLA, 74200 Thonon les Bains, France
| | - Linda Armbrecht
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia.,Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
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18
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Zavala EI, Thomas JT, Sturk-Andreaggi K, Daniels-Higginbotham J, Meyers KK, Barrit-Ross S, Aximu-Petri A, Richter J, Nickel B, Berg GE, McMahon TP, Meyer M, Marshall C. Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns. Genes (Basel) 2022; 13:genes13010129. [PMID: 35052469 PMCID: PMC8774965 DOI: 10.3390/genes13010129] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains.
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Affiliation(s)
- Elena I. Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
- Correspondence: (E.I.Z.); (C.M.)
| | - Jacqueline Tyler Thomas
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Jennifer Daniels-Higginbotham
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
| | - Kerriann K. Meyers
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
| | - Suzanne Barrit-Ross
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
| | - Julia Richter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
| | - Gregory E. Berg
- Defense Personnel Accounting Agency, Central Identification Laboratory, Hickam Air Force Base, Oahu, HI 96853, USA;
| | - Timothy P. McMahon
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
- Forensic Science Program, Pennsylvania State University, State College, PA 16802, USA
- Correspondence: (E.I.Z.); (C.M.)
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19
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Wang Y, Zhao B, Choi J, Lee EA. Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans. Mob DNA 2021; 12:22. [PMID: 34663455 PMCID: PMC8525043 DOI: 10.1186/s13100-021-00250-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational approaches, including cross-species comparative genomics and population genetic modeling, can be adapted for the study of the role of TEs in evolution. In particular, diverse ancient and archaic human genome sequences are increasingly available, allowing reconstruction of past human migration events and holding the promise of identifying and tracking TEs among other evolutionarily important genetic variants at an unprecedented spatiotemporal resolution. However, highly degraded short DNA templates and other unique challenges presented by ancient human DNA call for major changes in current experimental and computational procedures to enable the identification of evolutionarily important TEs. Ancient human genomes are valuable resources for investigating TEs in the evolutionary context, and efforts to explore ancient human genomes will potentially provide a novel perspective on the genetic mechanism of human brain evolution and inspire a variety of technological and methodological advances. In this review, we summarize computational and experimental approaches that can be adapted to identify and validate evolutionarily important TEs, especially for human brain evolution. We also highlight strategies that leverage ancient genomic data and discuss unique challenges in ancient transposon genomics.
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Affiliation(s)
- Yilan Wang
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Boxun Zhao
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Jaejoon Choi
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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20
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Maisano Delser P, Jones ER, Hovhannisyan A, Cassidy L, Pinhasi R, Manica A. A curated dataset of modern and ancient high-coverage shotgun human genomes. Sci Data 2021; 8:202. [PMID: 34349118 PMCID: PMC8338957 DOI: 10.1038/s41597-021-00980-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/10/2021] [Indexed: 11/09/2022] Open
Abstract
Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10-18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.
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Affiliation(s)
- Pierpaolo Maisano Delser
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland.
| | - Eppie R Jones
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- Genomics Medicine Ireland, Dublin, Ireland
| | - Anahit Hovhannisyan
- Institute of Molecular Biology, National Academy of Sciences, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | - Lara Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.
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21
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Ingman T, Eisenmann S, Skourtanioti E, Akar M, Ilgner J, Gnecchi Ruscone GA, le Roux P, Shafiq R, Neumann GU, Keller M, Freund C, Marzo S, Lucas M, Krause J, Roberts P, Yener KA, Stockhammer PW. Human mobility at Tell Atchana (Alalakh), Hatay, Turkey during the 2nd millennium BC: Integration of isotopic and genomic evidence. PLoS One 2021; 16:e0241883. [PMID: 34191795 PMCID: PMC8244877 DOI: 10.1371/journal.pone.0241883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/28/2021] [Indexed: 11/21/2022] Open
Abstract
The Middle and Late Bronze Age, a period roughly spanning the 2nd millennium BC (ca. 2000–1200 BC) in the Near East, is frequently referred to as the first ‘international age’, characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh, located in Hatay, Turkey), we explored the role of mobility at the capital of a regional kingdom, named Mukish during the Late Bronze Age, which spanned the Amuq Valley and some areas beyond. We generated strontium and oxygen isotope data from dental enamel for 53 individuals and 77 individuals, respectively, and added ancient DNA data of 10 newly sequenced individuals to a dataset of 27 individuals published in 2020. Additionally, we improved the DNA coverage of one individual from this 2020 dataset. The DNA data revealed a very homogeneous gene pool. This picture of an overwhelmingly local ancestry was consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be non-local. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana.
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Affiliation(s)
- Tara Ingman
- Koç University Research Center for Anatolian Civilizations (ANAMED), Koc University, Istanbul, Turkey
- * E-mail: (TI); (SE); (KAY); (PWS)
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- * E-mail: (TI); (SE); (KAY); (PWS)
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Murat Akar
- Department of Archaeology, Mustafa Kemal University, Alahan-Antakya, Hatay, Turkey
| | - Jana Ilgner
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Petrus le Roux
- Department of Geological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Rula Shafiq
- Anthropology Department, Yeditepe University, Istanbul, Turkey
| | - Gunnar U. Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cäcilia Freund
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sara Marzo
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Mary Lucas
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - K. Aslıhan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, United States of America
- * E-mail: (TI); (SE); (KAY); (PWS)
| | - Philipp W. Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Germany
- * E-mail: (TI); (SE); (KAY); (PWS)
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22
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Prüfer K, Posth C, Yu H, Stoessel A, Spyrou MA, Deviese T, Mattonai M, Ribechini E, Higham T, Velemínský P, Brůžek J, Krause J. A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nat Ecol Evol 2021; 5:820-825. [PMID: 33828249 PMCID: PMC8175239 DOI: 10.1038/s41559-021-01443-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/12/2021] [Indexed: 12/05/2022]
Abstract
Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2–3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000–5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust’-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa. The authors present the genome sequence of a >45,000-year-old female Homo sapiens individual from the site of Zlatý kůň, Czechia. Although radiometric dating of the human remains was inconclusive, the authors were able to use molecular methods to demonstrate that she was probably among the earliest Eurasian inhabitants following expansion out of Africa.
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Affiliation(s)
- Kay Prüfer
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
| | - He Yu
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Stoessel
- Max Planck Institute for the Science of Human History, Jena, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany
| | - Maria A Spyrou
- Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Thibaut Deviese
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford, UK.,Centre Européen de Recherche et d'Enseignement des Géosciences de l'Environnement (CEREGE), Aix-Marseille University, CNRS, IRD, INRAE, Collège de France, Aix-en-Provence, France
| | - Marco Mattonai
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Erika Ribechini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford, UK
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague, Czech Republic
| | - Jaroslav Brůžek
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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23
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Hajdinjak M, Mafessoni F, Skov L, Vernot B, Hübner A, Fu Q, Essel E, Nagel S, Nickel B, Richter J, Moldovan OT, Constantin S, Endarova E, Zahariev N, Spasov R, Welker F, Smith GM, Sinet-Mathiot V, Paskulin L, Fewlass H, Talamo S, Rezek Z, Sirakova S, Sirakov N, McPherron SP, Tsanova T, Hublin JJ, Peter BM, Meyer M, Skoglund P, Kelso J, Pääbo S. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature 2021; 592:253-257. [PMID: 33828320 PMCID: PMC8026394 DOI: 10.1038/s41586-021-03335-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/05/2021] [Indexed: 02/01/2023]
Abstract
Modern humans appeared in Europe by at least 45,000 years ago1-5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.
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Affiliation(s)
- Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Francis Crick Institute, London, UK.
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Laurits Skov
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Oana Teodora Moldovan
- Emil Racovita Institute of Speleology, Cluj Department, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Silviu Constantin
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucharest, Romania
- Centro Nacional de Investigación sobre la Evolución Humana, CENIEH, Burgos, Spain
| | | | - Nikolay Zahariev
- Archaeology Department, New Bulgarian University, Sofia, Bulgaria
| | - Rosen Spasov
- Archaeology Department, New Bulgarian University, Sofia, Bulgaria
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry 'G. Ciamician', University of Bologna, Bologna, Italy
| | - Zeljko Rezek
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of Pennsylvania Museum of Archaeology and Anthropology, University of Pennsylvania, Philadelphia, PA, USA
| | - Svoboda Sirakova
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nikolay Sirakov
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Shannon P McPherron
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka Tsanova
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, Paris, France
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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24
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Diroma MA, Modi A, Lari M, Sineo L, Caramelli D, Vai S. New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples. Front Genet 2021; 12:619950. [PMID: 33679884 PMCID: PMC7930628 DOI: 10.3389/fgene.2021.619950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.
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Affiliation(s)
- Maria Angela Diroma
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Alessandra Modi
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
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25
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Carlhoff S, Duli A, Nägele K, Nur M, Skov L, Sumantri I, Oktaviana AA, Hakim B, Burhan B, Syahdar FA, McGahan DP, Bulbeck D, Perston YL, Newman K, Saiful AM, Ririmasse M, Chia S, Hasanuddin, Pulubuhu DAT, Suryatman, Supriadi, Jeong C, Peter BM, Prüfer K, Powell A, Krause J, Posth C, Brumm A. Genome of a middle Holocene hunter-gatherer from Wallacea. Nature 2021; 596:543-547. [PMID: 34433944 PMCID: PMC8387238 DOI: 10.1038/s41586-021-03823-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.
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Affiliation(s)
- Selina Carlhoff
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Akin Duli
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Kathrin Nägele
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Muhammad Nur
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Laurits Skov
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Iwan Sumantri
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Adhi Agus Oktaviana
- grid.512005.30000 0001 2178 7840Pusat Penelitian Arkeologi Nasional (ARKENAS), Jakarta, Indonesia ,grid.1022.10000 0004 0437 5432Place, Evolution and Rock Art Heritage Unit, Griffith Centre for Social and Cultural Research, Griffith University, Gold Coast, Queensland Australia
| | - Budianto Hakim
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Basran Burhan
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | | | - David P. McGahan
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | - David Bulbeck
- grid.1001.00000 0001 2180 7477Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australian Capital Territory Australia
| | - Yinika L. Perston
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | - Kim Newman
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | | | - Marlon Ririmasse
- grid.512005.30000 0001 2178 7840Pusat Penelitian Arkeologi Nasional (ARKENAS), Jakarta, Indonesia
| | - Stephen Chia
- grid.11875.3a0000 0001 2294 3534Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Hasanuddin
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Dwia Aries Tina Pulubuhu
- grid.412001.60000 0000 8544 230XDepartemen Sosiologi, Fakultas Ilmu Sosial, Universitas Hasanuddin, Makassar, Indonesia
| | - Suryatman
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Supriadi
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Choongwon Jeong
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Benjamin M. Peter
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kay Prüfer
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam Powell
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.10392.390000 0001 2190 1447Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Adam Brumm
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
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