1
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Oberreiter V, Gelabert P, Brück F, Franz S, Zelger E, Szedlacsek S, Cheronet O, Cano FT, Exler F, Zagorc B, Karavanić I, Banda M, Gasparyan B, Straus LG, Gonzalez Morales MR, Kappelman J, Stahlschmidt M, Rattei T, Kraemer SM, Sawyer S, Pinhasi R. Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach. Sci Rep 2024; 14:19388. [PMID: 39169089 PMCID: PMC11339378 DOI: 10.1038/s41598-024-69741-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.
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Affiliation(s)
- Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - Florian Brück
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stefan Franz
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Evelyn Zelger
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Sophie Szedlacsek
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | | | - Florian Exler
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Ivor Karavanić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Marko Banda
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, USA
- EvoAdapta Group Universidad de Cantabria, Santander, Spain
| | - Manuel R Gonzalez Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Gobierno de Cantabria, Banco Santander, Spain
| | - John Kappelman
- Department of Anthropology and Department of Earth and Planetary Sciences, The University of Texas, Austin, TX, USA
| | - Mareike Stahlschmidt
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephan M Kraemer
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institut für Analytische Chemie, University of Vienna, Vienna, Austria
- Forschungsverbund Umwelt und Klima, University of Vienna, Vienna, Austria
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
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2
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Özdoğan KT, Gelabert P, Hammers N, Altınışık NE, de Groot A, Plets G. Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past. ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES 2024; 16:108. [PMID: 38948161 PMCID: PMC11213777 DOI: 10.1007/s12520-024-01999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/20/2024] [Indexed: 07/02/2024]
Abstract
Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds significant potential in addressing key archaeological questions concerning the origins, lifestyles, and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool, thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the archaeological workflow.
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Affiliation(s)
- Kadir Toykan Özdoğan
- Department of History and Art History, Utrecht University, Drift 6, Utrecht, 3512 BS Netherlands
- Animal Ecology, Wageningen Environmental Research, P.O box 47, Wageningen, Gelderland 6700 AA The Netherlands
| | - Pere Gelabert
- Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, Vienna, 1030 Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, Vienna, 1030 Austria
| | - Neeke Hammers
- Environmental Archaeology, ADC ArcheoProjecten, Nijverheidsweg-Noord 114, Amersfoort, Utrecht, 3812 PN Netherlands
| | - N. Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, Ankara, 06800 Türkiye
| | - Arjen de Groot
- Animal Ecology, Wageningen Environmental Research, P.O box 47, Wageningen, Gelderland 6700 AA The Netherlands
| | - Gertjan Plets
- Department of History and Art History, Utrecht University, Drift 6, Utrecht, 3512 BS Netherlands
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3
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Aldeias V, Stahlschmidt MC. Sediment DNA can revolutionize archaeology-if it is used the right way. Proc Natl Acad Sci U S A 2024; 121:e2317042121. [PMID: 38900796 PMCID: PMC11214044 DOI: 10.1073/pnas.2317042121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Affiliation(s)
- Vera Aldeias
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, Universidade do Algarve, Faro8005-139, Portugal
| | - Mareike C. Stahlschmidt
- Department of Evolutionary Anthropology, University of Vienna, Vienna1010, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna1010, Austria
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4
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Smith GM, Ruebens K, Zavala EI, Sinet-Mathiot V, Fewlass H, Pederzani S, Jaouen K, Mylopotamitaki D, Britton K, Rougier H, Stahlschmidt M, Meyer M, Meller H, Dietl H, Orschiedt J, Krause J, Schüler T, McPherron SP, Weiss M, Hublin JJ, Welker F. The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany. Nat Ecol Evol 2024; 8:564-577. [PMID: 38297138 PMCID: PMC10927544 DOI: 10.1038/s41559-023-02303-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Recent excavations at Ranis (Germany) identified an early dispersal of Homo sapiens into the higher latitudes of Europe by 45,000 years ago. Here we integrate results from zooarchaeology, palaeoproteomics, sediment DNA and stable isotopes to characterize the ecology, subsistence and diet of these early H. sapiens. We assessed all bone remains (n = 1,754) from the 2016-2022 excavations through morphology (n = 1,218) or palaeoproteomics (zooarchaeology by mass spectrometry (n = 536) and species by proteome investigation (n = 212)). Dominant taxa include reindeer, cave bear, woolly rhinoceros and horse, indicating cold climatic conditions. Numerous carnivore modifications, alongside sparse cut-marked and burnt bones, illustrate a predominant use of the site by hibernating cave bears and denning hyaenas, coupled with a fluctuating human presence. Faunal diversity and high carnivore input were further supported by ancient mammalian DNA recovered from 26 sediment samples. Bulk collagen carbon and nitrogen stable isotope data from 52 animal and 10 human remains confirm a cold steppe/tundra setting and indicate a homogenous human diet based on large terrestrial mammals. This lower-density archaeological signature matches other Lincombian-Ranisian-Jerzmanowician sites and is best explained by expedient visits of short duration by small, mobile groups of pioneer H. sapiens.
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Affiliation(s)
- Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- School of Anthropology and Conservation, University of Kent, Kent, UK.
| | - Karen Ruebens
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Elena Irene Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Evolutionary Genetics, 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, Pessac, France
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London, UK
| | - 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
| | - Klervia Jaouen
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Géosciences Environnement Toulouse (GET), Observatoire Midi-Pyrénées (OMP), Toulouse, France
| | - Dorothea Mylopotamitaki
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Kate Britton
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, Scotland
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | - Mareike Stahlschmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Holger Dietl
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Jörg Orschiedt
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Shannon P McPherron
- Department of Human Origins, 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
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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6
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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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Parfitt SA, Bello SM. Bone tools, carnivore chewing and heavy percussion: assessing conflicting interpretations of Lower and Upper Palaeolithic bone assemblages. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231163. [PMID: 38179084 PMCID: PMC10762443 DOI: 10.1098/rsos.231163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
The use of bone tools by early humans has provided valuable insights into their technology, behaviour and cognitive abilities. However, identifying minimally modified or unshaped Palaeolithic osseous tools can be challenging, particularly when they are mixed with bones altered by natural taphonomic processes. This has hampered the study of key technical innovations, such as the use of bones, antlers and teeth as hammers or pressure-flakers to work (knap) stone tools. Bones chewed by carnivores can resemble osseous knapping tools and have sometimes been mistaken for them. In this paper, we review recent advances in the study of osseous knapping tools with a focus on two Palaeolithic sites in the UK, the Acheulean Horse Butchery Site at Boxgrove and the Magdalenian site of Gough's Cave, where knapping tools were mis-attributed to carnivore chewing. These osseous knapping tools are investigated using microscopy, high-resolution imaging and comparisons with experimental knapping tools. This allows for new insights into human behaviour at these sites and opens fresh avenues for future research.
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Affiliation(s)
- Simon A. Parfitt
- Institute of Archaeology, University College London, 31–34 Gordon Square, London WC1H 0PY, UK
- Centre of Human Evolution Research, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Silvia M. Bello
- Centre of Human Evolution Research, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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8
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Urban L, Miller AK, Eason D, Vercoe D, Shaffer M, Wilkinson SP, Jeunen GJ, Gemmell NJ, Digby A. Non-invasive real-time genomic monitoring of the critically endangered kākāpō. eLife 2023; 12:RP84553. [PMID: 38153986 PMCID: PMC10754495 DOI: 10.7554/elife.84553] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023] Open
Abstract
We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered kākāpō (Strigops habroptilus). We first established an environmental DNA metabarcoding protocol to identify the distribution of kākāpō and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality kākāpō reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the kākāpō population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on kākāpō distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.
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Affiliation(s)
- Lara Urban
- Department of Anatomy, University of OtagoDunedinNew Zealand
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Technical University of Munich, School of Life SciencesFreisingGermany
| | | | - Daryl Eason
- Kākāpō Recovery Programme, Department of ConservationInvercargillNew Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of ConservationInvercargillNew Zealand
| | | | | | - Gert-Jan Jeunen
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Andrew Digby
- Kākāpō Recovery Programme, Department of ConservationInvercargillNew Zealand
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9
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Wang N, Xu Y, Tang Z, He C, Hu X, Cui Y, Douka K. Large-scale application of palaeoproteomics (Zooarchaeology by Mass Spectrometry; ZooMS) in two Palaeolithic faunal assemblages from China. Proc Biol Sci 2023; 290:20231129. [PMID: 37876197 PMCID: PMC10598447 DOI: 10.1098/rspb.2023.1129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The application of Zooarchaeology by Mass Spectrometry (ZooMS) on Pleistocene sites in Europe and northern Asia has resulted in the discovery of important new hominin fossils and has expanded the range of identified fauna. However, no systematic, large-scale application of ZooMS on Palaeolithic sites in East Asia has been attempted thus far. Here, we analyse 866 morphologically non-diagnostic bones from Jinsitai Cave in northeast China and Yumidong Cave in South China, from archaeological horizons dating to 150-10 ka BP. Bones from both sites revealed a high degree of collagen preservation and potentially time-related deamidation patterns, despite being located in very distinct environmental settings. At Jinsitai, we identified 31 camel bones, five of which were radiocarbon dated to 37-20 ka BP. All dated specimens correspond to colder periods of Marine Isotope Stages 3 and 2. We regard the presence of camels at Jinsitai as evidence of wild camels being a megafauna taxon targeted, most likely by early modern humans, during their expansion across northeast Asia. This large-scale application of ZooMS in China highlights the potential of the method for furthering our knowledge of the palaeoanthropological and zooarchaeological records of East Asia.
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Affiliation(s)
- Naihui Wang
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, 72070 Tübingen, Germany
| | - Yang Xu
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Zhuowei Tang
- School of Archaeology, Jilin University, 130012 Changchun, People's Republic of China
| | - Cunding He
- China-Central Asia ‘the Belt and Road’ Joint Laboratory on Human and Environment Research, 710127 Xi'an, People's Republic of China
- School of Cultural Heritage, Northwest University, 710127 Xi'an, People's Republic of China
| | - Xin Hu
- Chongqing China Three Gorges Museum, 400013 Chongqing, People's Republic of China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Katerina Douka
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
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10
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Pochon Z, Bergfeldt N, Kırdök E, Vicente M, Naidoo T, van der Valk T, Altınışık NE, Krzewińska M, Dalén L, Götherström A, Mirabello C, Unneberg P, Oskolkov N. aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow. Genome Biol 2023; 24:242. [PMID: 37872569 PMCID: PMC10591440 DOI: 10.1186/s13059-023-03083-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
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Affiliation(s)
- Zoé Pochon
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Mário Vicente
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Uppsala, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - N Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800, Beytepe, Ankara, Turkey
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Claudio Mirabello
- Department of Physics, Chemistry and Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Department of Cell and Molecular Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Nikolay Oskolkov
- Department of Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden.
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11
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Dalén L, Heintzman PD, Kapp JD, Shapiro B. Deep-time paleogenomics and the limits of DNA survival. Science 2023; 382:48-53. [PMID: 37797036 PMCID: PMC10586222 DOI: 10.1126/science.adh7943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.
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Affiliation(s)
- Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE- 10405 Stockholm, Sweden
| | - Peter D. Heintzman
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden
- Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Joshua D. Kapp
- Department of Biomolecular Engineering, University of California Santa Cruz; Santa Cruz, California, 95064, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz; Santa Cruz, California, 95064, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz; Santa Cruz, California, 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz; Santa Cruz, California, 95064, USA
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12
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Bacon AM, Bourgon N, Dufour E, Demeter F, Zanolli C, Westaway KE, Joannes-Boyau R, Duringer P, Ponche JL, Morley MW, Suzzoni E, Frangeul S, Boesch Q, Antoine PO, Boualaphane S, Sichanthongtip P, Sihanam D, Huong NTM, Tuan NA, Fiorillo D, Tombret O, Patole-Edoumba E, Zachwieja A, Luangkhoth T, Souksavatdy V, Dunn TE, Shackelford L, Hublin JJ. Palaeoenvironments and hominin evolutionary dynamics in southeast Asia. Sci Rep 2023; 13:16165. [PMID: 37758744 PMCID: PMC10533506 DOI: 10.1038/s41598-023-43011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Secure environmental contexts are crucial for hominin interpretation and comparison. The discovery of a Denisovan individual and associated fauna at Tam Ngu Hao 2 (Cobra) Cave, Laos, dating back to 164-131 ka, allows for environmental comparisons between this (sub)tropical site and the Palearctic Denisovan sites of Denisova Cave (Russia) and Baishiya Karst Cave (China). Denisovans from northern latitudes foraged in a mix of forested and open landscapes, including tundra and steppe. Using stable isotope values from the Cobra Cave assemblage, we demonstrate that, despite the presence of nearby canopy forests, the Denisovan individual from Cobra Cave primarily consumed plants and/or animals from open forests and savannah. Using faunal evidence and proxy indicators of climates, results herein highlight a local expansion of rainforest at ~ 130 ka, raising questions about how Denisovans responded to this local climate change. Comparing the diet and habitat of the archaic hominin from Cobra Cave with those of early Homo sapiens from Tam Pà Ling Cave (46-43 ka), Laos, it appears that only our species was able to exploit rainforest resources.
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Affiliation(s)
- Anne-Marie Bacon
- Université Paris Cité, CNRS, BABEL UMR 8045, 75012, Paris, France.
| | - Nicolas Bourgon
- IsoTROPIC Research Group, Max Planck Institute for Geoanthropology, 07745, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, 04103, Leipzig, Germany
| | - Elise Dufour
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), MNHN, CNRS, Université Paris Cité, Musée de l'Homme, 75016, Paris, France
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600, Pessac, France
| | - Kira E Westaway
- 'Traps' Luminescence Dating Facility, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group (GARG), Southern Cross University, Lismore, NSW, Australia
| | - Philippe Duringer
- Ecole et Observatoire des Sciences de la Terre, Institut de Physique du Globe de Strasbourg, UMR 7516 CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Luc Ponche
- Laboratoire Image, Ville Environnement, UMR 7362 UdS CNRS, Université de Strasbourg, Strasbourg, France
| | - Mike W Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Sturt Road, Bedford Park, Adelaide, SA, 5042, Australia
| | - Eric Suzzoni
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle en Vercors, France
| | - Sébastien Frangeul
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle en Vercors, France
| | - Quentin Boesch
- Ecole et Observatoire des Sciences de la Terre, Institut de Physique du Globe de Strasbourg, UMR 7516 CNRS, Université de Strasbourg, Strasbourg, France
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France
| | | | | | - Daovee Sihanam
- Ministry of Information, Culture and Tourism, Vientiane, Lao PDR
| | | | | | - Denis Fiorillo
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Olivier Tombret
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Elise Patole-Edoumba
- Muséum d'histoire naturelle de La Rochelle, UMRU 24140 Dynamiques, interactions, interculturalité asiatiques (UBM, LRUniv), La Rochelle, France
| | - Alexandra Zachwieja
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, USA
| | | | | | - Tyler E Dunn
- Anatomical Sciences Education Center, Oregon Health & Sciences University, Portland, OR, USA
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, 04103, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
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13
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Wegner CE, Stahl R, Velsko I, Hübner A, Fagernäs Z, Warinner C, Lehmann R, Ritschel T, Totsche KU, Küsel K. A glimpse of the paleome in endolithic microbial communities. MICROBIOME 2023; 11:210. [PMID: 37749660 PMCID: PMC10518947 DOI: 10.1186/s40168-023-01647-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/09/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards. RESULTS By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past. CONCLUSIONS Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.
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Affiliation(s)
- Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Irina Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Alex Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Thomas Ritschel
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
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14
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Essel E. Releasing secrets bound to ancient remains with modern DNA extraction techniques: an interview with Elena Essel. Biotechniques 2023; 75:42-46. [PMID: 37589132 DOI: 10.2144/btn-2023-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Elena Essel (Msc) spoke to Ebony Torrington, Managing Editor of BioTechniques. Essel is a molecular biologist in Matthias Meyer's Advanced DNA Sequencing Techniques group at the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany). Essel studied biology at University of Erlangen-Nuremberg (Erlangen, Germany) for her bachelor's and in Martin-Luther-University Halle-Wittenberg (Halle an der Saale, Germany) for her master's. Essel worked in Meyer's group on DNA extraction of very degraded material for her master's thesis. Meyer is an expert in developing new cutting-edge methods for researching ancient DNA, with a focus on skeletal remains, and more recently on sediment remains. Essel now focusses on DNA sampling and extraction aspects of the pipeline at Meyer's lab for the ancient DNA workflow.
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Affiliation(s)
- Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103 Leipzig, Germany
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15
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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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16
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Antón SC, Middleton ER. Making meaning from fragmentary fossils: Early Homo in the Early to early Middle Pleistocene. J Hum Evol 2023; 179:103307. [PMID: 37030994 DOI: 10.1016/j.jhevol.2022.103307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 11/16/2022] [Accepted: 11/27/2022] [Indexed: 04/10/2023]
Abstract
In celebration of the 50th anniversary of the Journal of Human Evolution, we re-evaluate the fossil record for early Homo (principally Homo erectus, Homo habilis, and Homo rudolfensis) from early diversification and dispersal in the Early Pleistocene to the ultimate demise of H. erectus in the early Middle Pleistocene. The mid-1990s marked an important historical turning point in our understanding of early Homo with the redating of key H. erectus localities, the discovery of small H. erectus in Asia, and the recovery of an even earlier presence of early Homo in Africa. As such, we compare our understanding of early Homo before and after this time and discuss how the order of fossil discovery and a focus on anchor specimens has shaped, and in many ways biased, our interpretations of early Homo species and the fossils allocated to them. Fragmentary specimens may counter conventional wisdom but are often overlooked in broad narratives. We recognize at least three different cranial and two or three pelvic morphotypes of early Homo. Just one postcranial morph aligns with any certainty to a cranial species, highlighting the importance of explicitly identifying how we link specimens together and to species; we offer two ways of visualizing these connections. Chronologically and morphologically H. erectus is a member of early Homo, not a temporally more recent species necessarily evolved from either H. habilis or H. rudolfensis. Nonetheless, an ancestral-descendant notion of their evolution influences expectations around the anatomy of missing elements, especially the foot. Weak support for long-held notions of postcranial modernity in H. erectus raises the possibility of alternative drivers of dispersal. New observations suggest that the dearth of faces in later H. erectus may mask taxonomic diversity in Asia and suggest various later mid-Pleistocene populations could derive from either Asia or Africa. Future advances will rest on the development of nuanced ways to affiliate fossils, greater transparency of implicit assumptions, and attention to detailed life history information for comparative collections; all critical pursuits for future research given the great potential they have to enrich our evolutionary reconstructions for the next fifty years and beyond.
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Affiliation(s)
- Susan C Antón
- Center for the Study of Human Origins, Department of Anthropology, New York University, NY, NY 10003, USA.
| | - Emily R Middleton
- Department of Anthropology, University of Wisconsin-Milwaukee, WI 53211, USA
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17
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Ghasidian E, Kafash A, Kehl M, Yousefi M, Heydari-Guran S. Modelling Neanderthals' dispersal routes from Caucasus towards east. PLoS One 2023; 18:e0281978. [PMID: 36821540 PMCID: PMC9949648 DOI: 10.1371/journal.pone.0281978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/05/2023] [Indexed: 02/24/2023] Open
Abstract
The study of the cultural materials associated with the Neanderthal physical remains from the sites in the Caucasus, Central Asia and Siberian Altai and adjacent areas documents two distinct techno-complexes of Micoquian and Mousterian. These findings potentially outline two dispersal routes for the Neanderthals out of Europe. Using data on topography and Palaeoclimate, we generated computer-based least-cost-path modelling for the Neanderthal dispersal routes from Caucasus towards the east. In this regard, two dispersal routes have been identified: A northern route from Greater Caucasus associated with Micoquian techno-complex towards Siberian Altai and a southern route from Lesser Caucasus associated with Mousterian towards Siberian Altai via the Southern Caspian Corridor. Based on archaeological, bio- and physio-geographical data, our model hypothesises that during climatic deterioration phases (e.g. MIS 4) the connection between Greater and Lesser Caucasus was limited. This issue perhaps resulted in the separate development and spread of two cultural groups of Micoquian and Mousterian with an input from two different population sources of Neanderthal influxes: eastern and southern Europe refugia for these two northern and southern dispersal routes respectively. Of these two, we focus on the southern dispersal route, for it comprises a 'rapid dispersal route' towards east. The significant location of the Southern Caspian corridor between high mountains of Alborz and the Caspian Sea, provided a special biogeographical zone and a refugium. This exceptional physio-geographic condition brings forward the Southern Caspian corridor as a potential place of admixture of different hominin species including Neanderthals and homo sapiens.
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Affiliation(s)
- Elham Ghasidian
- Neanderthal Museum, Mettmann, Germany
- DiyarMehr Institute for Palaeolithic Research, Kermanshah, Iran
- Institute for Prehistoric Archaeology, University of Cologne, Koln, Germany
- Institute of Geography, University of Cologne, Cologne, Germany
| | - Anooshe Kafash
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | - Martin Kehl
- Institute for Prehistoric Archaeology, University of Cologne, Koln, Germany
- Institute of Geography, University of Cologne, Cologne, Germany
| | - Masoud Yousefi
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | - Saman Heydari-Guran
- Neanderthal Museum, Mettmann, Germany
- DiyarMehr Institute for Palaeolithic Research, Kermanshah, Iran
- Institute for Prehistoric Archaeology, University of Cologne, Koln, Germany
- Institute of Geography, University of Cologne, Cologne, Germany
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18
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Li H, Zhang H, Chang F, Liu Q, Zhang Y, Liu F, Zhang X. Sedimentary DNA for tracking the long-term changes in biodiversity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17039-17050. [PMID: 36622608 DOI: 10.1007/s11356-023-25130-5] [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: 05/25/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Yang Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Fengwen Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
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19
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de March CA, Matsunami H, Abe M, Cobb M, Hoover KC. Genetic and functional odorant receptor variation in the Homo lineage. iScience 2022; 26:105908. [PMID: 36691623 PMCID: PMC9860384 DOI: 10.1016/j.isci.2022.105908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/07/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.
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Affiliation(s)
- Claire A. de March
- Institut de Chimie des Substances Naturelles, UPR2301 CNRS, Université Paris-Saclay, Gif-sur-Yvette 91190, France,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA,Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA,Corresponding author
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA,Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA
| | - Masashi Abe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Matthew Cobb
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Kara C. Hoover
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA,Corresponding author
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20
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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21
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ter Schure AT, Bruch AA, Kandel AW, Gasparyan B, Bussmann RW, Brysting AK, de Boer HJ, Boessenkool S. Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia. J Hum Evol 2022; 172:103258. [DOI: 10.1016/j.jhevol.2022.103258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/15/2022]
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22
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Dating the Paleolithic: Trapped charge methods and amino acid geochronology. Proc Natl Acad Sci U S A 2022; 119:e2109324119. [PMID: 36252044 PMCID: PMC9618083 DOI: 10.1073/pnas.2109324119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the vast array of different geochronological tools available, dating the Paleolithic remains one of the discipline’s greatest challenges. This review focuses on two different dating approaches: trapped charge and amino acid geochronology. While differing in their fundamental principles, both exploit time-dependent changes in signals found within crystals to generate a chronology for the material dated and hence, the associated deposits. Within each method, there is a diverse range of signals that can be analyzed, each covering different time ranges, applicable to different materials and suitable for different paleoenvironmental and archaeological contexts. This multiplicity of signals can at first sight appear confusing, but it is a fundamental strength of the techniques, allowing internal checks for consistency and providing more information than simply a chronology. For each technique, we present an overview of the basis for the time-dependent signals and the types of material that can be analyzed, with examples of their archaeological application, as well as their future potential.
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23
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Finestone EM, Breeze PS, Breitenbach SFM, Drake N, Bergmann L, Maksudov F, Muhammadiyev A, Scott P, Cai Y, Khatsenovich AM, Rybin EP, Nehrke G, Boivin N, Petraglia M. Paleolithic occupation of arid Central Asia in the Middle Pleistocene. PLoS One 2022; 17:e0273984. [PMID: 36269723 PMCID: PMC9586385 DOI: 10.1371/journal.pone.0273984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/19/2022] [Indexed: 11/07/2022] Open
Abstract
Central Asia is positioned at a crossroads linking several zones important to hominin dispersal during the Middle Pleistocene. However, the scarcity of stratified and dated archaeological material and paleoclimate records makes it difficult to understand dispersal and occupation dynamics during this time period, especially in arid zones. Here we compile and analyze paleoclimatic and archaeological data from Pleistocene Central Asia, including examination of a new layer-counted speleothem-based multiproxy record of hydrological changes in southern Uzbekistan at the end of MIS 11. Our findings indicate that Lower Palaeolithic sites in the steppe, semi-arid, and desert zones of Central Asia may have served as key areas for the dispersal of hominins into Eurasia during the Middle Pleistocene. In agreement with previous studies, we find that bifaces occur across these zones at higher latitudes and in lower altitudes relative to the other Paleolithic assemblages. We argue that arid Central Asia would have been intermittently habitable during the Middle Pleistocene when long warm interglacial phases coincided with periods when the Caspian Sea was experiencing consistently high water levels, resulting in greater moisture availability and more temperate conditions in otherwise arid regions. During periodic intervals in the Middle Pleistocene, the local environment of arid Central Asia was likely a favorable habitat for paleolithic hominins and was frequented by Lower Paleolithic toolmakers producing bifaces.
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Affiliation(s)
- Emma M. Finestone
- Department of Anthropology, The Cleveland Museum of Natural History, Cleveland, OH, United States of America
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- * E-mail:
| | - Paul S. Breeze
- Department of Geography, Kings College London, London, United Kingdom
| | - Sebastian F. M. Breitenbach
- Department of Geography and Environmental Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Nick Drake
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Geography, Kings College London, London, United Kingdom
| | - Laura Bergmann
- Department of Physical Geography, Catholic University of Eichstätt-Ingolstadt, Eichstätt, Germany
| | - Farhod Maksudov
- National Center of Archaeology, Uzbekistan Academy of Sciences, Tashkent, Uzbekistan
| | - Akmal Muhammadiyev
- National Center of Archaeology, Uzbekistan Academy of Sciences, Tashkent, Uzbekistan
| | - Pete Scott
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Yanjun Cai
- Institute of Global Environmental Change, Xi’an Jiaotong University, Xi’an, China
| | - Arina M. Khatsenovich
- Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeny P. Rybin
- Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Gernot Nehrke
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, University of Queensland, Brisbane, Australia
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, University of Queensland, Brisbane, Australia
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, Australia
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24
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Skov L, Peyrégne S, Popli D, Iasi LNM, Devièse T, Slon V, Zavala EI, Hajdinjak M, Sümer AP, Grote S, Bossoms Mesa A, López Herráez D, Nickel B, Nagel S, Richter J, Essel E, Gansauge M, Schmidt A, Korlević P, Comeskey D, Derevianko AP, Kharevich A, Markin SV, Talamo S, Douka K, Krajcarz MT, Roberts RG, Higham T, Viola B, Krivoshapkin AI, Kolobova KA, Kelso J, Meyer M, Pääbo S, Peter BM. Genetic insights into the social organization of Neanderthals. Nature 2022; 610:519-525. [PMID: 36261548 PMCID: PMC9581778 DOI: 10.1038/s41586-022-05283-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022]
Abstract
Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans1-8, but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave9,10 and 2 from Okladnikov Cave11-making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father-daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals' genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.
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Affiliation(s)
- Laurits Skov
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Divyaratan Popli
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Leonardo N M Iasi
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thibaut Devièse
- European Centre for Research and Education in Environmental Geosciences (CEREGE), Aix-Marseille University, CNRS, IRD, INRAE, Collège de France, Aix-en-Provence, France
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology Sackler, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elena I Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- The Francis Crick Institute, London, UK
| | - Arev P Sümer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Steffi Grote
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alba Bossoms Mesa
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David López Herráez
- 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
| | - Sarah Nagel
- 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
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Petra Korlević
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Wellcome Sanger Institute, Hinxton, UK
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Aliona Kharevich
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey V Markin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria
| | - Maciej T Krajcarz
- Institute of Geological Sciences, Polish Academy of Sciences, Warsaw, Poland
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Thomas Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Andrey I Krivoshapkin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Kseniya A Kolobova
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Janet Kelso
- 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
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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25
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Andreeva TV, Malyarchuk AB, Soshkina AD, Dudko NA, Plotnikova MY, Rogaev EI. Methodologies for Ancient DNA Extraction from Bones for Genomic Analysis: Approaches and Guidelines. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel. Sci Rep 2022; 12:14528. [PMID: 36008437 PMCID: PMC9411205 DOI: 10.1038/s41598-022-17399-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.
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27
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Andreeva TV, Manakhov AD, Gusev FE, Patrikeev AD, Golovanova LV, Doronichev VB, Shirobokov IG, Rogaev EI. Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations. Sci Rep 2022; 12:13016. [PMID: 35906446 PMCID: PMC9338269 DOI: 10.1038/s41598-022-16164-9] [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: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 11/09/2022] Open
Abstract
The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal’s branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.
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Affiliation(s)
- Tatiana V Andreeva
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192.
| | - Andrey D Manakhov
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Fedor E Gusev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Anton D Patrikeev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333
| | | | | | - Ivan G Shirobokov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg, Russia, 199034
| | - Evgeny I Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192. .,Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01604, USA.
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28
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Phosphate Record in Pleistocene-Holocene Sediments from Denisova Cave: Formation Mechanisms and Archaeological Implications. MINERALS 2022. [DOI: 10.3390/min12050553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The distribution of authigenic phosphates in the sedimentary sequence of prehistoric Denisova Cave (Altai, South Siberia) has important archeological implications. The sampled Late Pleistocene–Early Holocene sedimentary sequence in the East Chamber of the cave consists of argilo-sandy-phosphatic sediments intercalated with guano layers of insectivorous bats. The sediments bear partially degraded N-rich organic matter (OM); chitin fragments enriched in S, P, Zn, and Cu; and a set of phosphates. The guano layers record at least three prolonged episodes of cave occupation by colonies of insectivorous bats between 10 kyr and 5 kyr BP, after people had left the cave or visited it rarely in small groups. The formation of phosphates follows the OM biodegradation pathways, with acidic leaching and gradual neutralization of P-rich solutions. The depth profile of authigenic phosphates shows a suite of mineral assemblages that mark a trend from acidic to slightly alkaline pH conditions of guano degradation (from top to bottom): ardealite, taranakite, and leucophosphite corresponding to acidic environments; whitlockite, brushite, and hydroxylapatite, which are stable under slightly acidic and neutral conditions; and hydroxylapatite in coexistence with calcite and stable at the bottom of the leaching profile under alkaline conditions. Authigenic phosphates can be used as reliable indicators of human non-occupation (abandonment) periods of Denisova Cave. Acidic leaching is responsible for disturbance and/or elimination of archaeological and paleontological materials in Late Pleistocene–Early Holocene sediments that were exposed to at least three “acidic waves”.
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29
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Malyarchuk AB, Andreeva TV, Kuznetsova IL, Kunizheva SS, Protasova MS, Uralsky LI, Tyazhelova TV, Gusev FE, Manakhov AD, Rogaev EI. Genomics of Ancient Pathogens: First Advances and Prospects. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:242-258. [PMID: 35526849 PMCID: PMC8916790 DOI: 10.1134/s0006297922030051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/08/2022] [Accepted: 01/21/2022] [Indexed: 11/23/2022]
Abstract
Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.
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Affiliation(s)
- Alexandra B Malyarchuk
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Tatiana V Andreeva
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Irina L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Svetlana S Kunizheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Maria S Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Lev I Uralsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Tatiana V Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Fedor E Gusev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Andrey D Manakhov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Evgeny I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia.
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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30
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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: 16] [Impact Index Per Article: 8.0] [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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Murchie TJ, Karpinski E, Eaton K, Duggan AT, Baleka S, Zazula G, MacPhee RDE, Froese D, Poinar HN. Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments. Curr Biol 2022; 32:851-860.e7. [PMID: 35016010 DOI: 10.1016/j.cub.2021.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022]
Abstract
Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Sina Baleka
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Box 2703, Whitehorse, YT Y1A 2C6, Canada; Collections and Research, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, ON K1P 6P4, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; CIFAR, Humans and the Microbiome Program, MaRS Centre, West Tower, 661 University Avenue, Suite 505, Toronto, ON M5G 1M1, Canada.
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32
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Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments. Proc Natl Acad Sci U S A 2022; 119:2113666118. [PMID: 34969841 PMCID: PMC8740756 DOI: 10.1073/pnas.2113666118] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/26/2023] Open
Abstract
DNA preserved in sediments has emerged as an important source of information about past ecosystems, independent of the discovery of skeletal remains. However, little is known about the sources of sediment DNA, the factors affecting its long-term preservation, and the extent to which it may be translocated after deposition. Here, we show that impregnated blocks of intact sediment are excellent archives of DNA. DNA distribution is highly heterogeneous at the microscale in the cave sediment we studied, suggesting that postdepositional movement of DNA is unlikely to be a common phenomenon in cases where the stratigraphy is undisturbed. Combining micromorphological analysis with microstratigraphic retrieval of ancient DNA therefore allows genetic information to be associated with the detailed archaeological and ecological record preserved in sediments. Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.
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33
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Brown S, Massilani D, Kozlikin MB, Shunkov MV, Derevianko AP, Stoessel A, Jope-Street B, Meyer M, Kelso J, Pääbo S, Higham T, Douka K. The earliest Denisovans and their cultural adaptation. Nat Ecol Evol 2022; 6:28-35. [PMID: 34824388 PMCID: PMC7612221 DOI: 10.1038/s41559-021-01581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 09/23/2021] [Indexed: 11/15/2022]
Abstract
Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave's sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205-192 ka at 68.2% or 217-187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.
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Affiliation(s)
- Samantha Brown
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Scientific Archaeology, University of Tübingen, Tübingen, Germany.
| | - Diyendo Massilani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Maxim B. Kozlikin
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V. Shunkov
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P. Derevianko
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Stoessel
- Max Planck Institute for the Science of Human History, Jena, Germany,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany,Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany
| | - Blair Jope-Street
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, UK,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Austria
| | - Katerina Douka
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
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Abstract
Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.
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35
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Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021; 288:20211252. [PMID: 34428961 PMCID: PMC8385357 DOI: 10.1098/rspb.2021.1252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Petter Larsson
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Špela Lemež
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana N Meleg
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,'Emil Racoviță' Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.,Emil. G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johannes Måsviken
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Ancient DNA Unit, SciLifeLab, Stockholm and Uppsala, Sweden
| | - Jovanka Studerus
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Mário Vicente
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Peter D Heintzman
- The Arctic University Museum of Norway, The Arctic University of Norway, 9037 Tromsø, Norway
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