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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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2
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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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3
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Noel HL, George RL, Bintz B, Hickman MP, West F. Utilization of qPCR to Determine Duration and Environmental Drivers Contributing to the Persistence of Human DNA in Soil. Genes (Basel) 2024; 15:741. [PMID: 38927677 PMCID: PMC11202937 DOI: 10.3390/genes15060741] [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: 05/15/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Little is known about the underlying mechanisms that contribute to the persistence and degradation of DNA within soil. The goals of this study are to determine the duration of mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) persistence in soils enriched by surface-level human decomposition and to better understand the contribution of environmental factors. The surface-level decomposition of three human cadavers was documented over 11 weeks. Based on quantitative PCR results, we found nuDNA to persist in soils six weeks post-placement, while mtDNA was recoverable for the entire 11-week decomposition period. Principle components analyses and Spearman's rank correlations revealed that (1) time, (2) total body score, and (3) weekly average air temperature were significantly correlated with concentrations of nuDNA and mtDNA in soil, suggesting these factors play a role in the degradation of DNA in soils.
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Affiliation(s)
- Hannah L. Noel
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rebecca L. George
- Department of Anthropology and Sociology, Western Carolina University, Cullowhee, NC 29723, USA;
| | - Brittania Bintz
- Department of Chemistry and Physics, Forensic Science Program, Western Carolina University, Cullowhee, NC 29723, USA;
| | | | - Frankie West
- Department of Chemistry and Physics, Forensic Science Program, Western Carolina University, Cullowhee, NC 29723, USA;
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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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5
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [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: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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6
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Kırdök E, Kashuba N, Damlien H, Manninen MA, Nordqvist B, Kjellström A, Jakobsson M, Lindberg AM, Storå J, Persson P, Andersson B, Aravena A, Götherström A. Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals. Sci Rep 2024; 13:22125. [PMID: 38238372 PMCID: PMC10796427 DOI: 10.1038/s41598-023-48762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/30/2023] [Indexed: 01/22/2024] Open
Abstract
Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
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Affiliation(s)
- Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin, Turkey.
| | - Natalija Kashuba
- Department of Archaeology and Ancient History, Uppsala University, Engelska Parken, Thunbergsvägen 3H Box 626, 751 26, Uppsala, Sweden
| | - Hege Damlien
- Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway
| | - Mikael A Manninen
- PAES, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science, University of Helsinki, Viikinkaari 1, P.O. Box 65, Helsinki, Finland
| | - Bengt Nordqvist
- Foundation War-Booty Site Finnestorp, Klarinettvägen 75, 434 75, Kungsbacka, Sweden
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Uppsala University, Evolutionsbiologiskt Centrum EBC Norbyvägen 18 A, Uppsala, Sweden
| | - A Michael Lindberg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Hus Vita, 44018, Kalmar, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Per Persson
- Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Insitutet, P.O. Box 285, 171 77, Stockholm, Sweden
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden
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7
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Morley MW, Moffat I, Kotarba-Morley AM, Hernandez VC, Zerboni A, Herries AIR, Joannes-Boyau R, Westaway K. Why the geosciences are becoming increasingly vital to the interpretation of the human evolutionary record. Nat Ecol Evol 2023; 7:1971-1977. [PMID: 38036632 DOI: 10.1038/s41559-023-02215-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/08/2023] [Indexed: 12/02/2023]
Abstract
Advanced geoscience techniques are essential to contextualize fossils, artefacts and other archaeologically important material accurately and effectively. Their appropriate use will increase confidence in new interpretations of the fossil and archaeological record, providing important information about the life and depositional history of these materials and so should form an integral component of all human evolutionary studies. Many of the most remarkable recent finds that have transformed the field of human evolution are small and scarce, ranging in size from teeth to strands of DNA, recovered from complex sedimentary environments. Nevertheless, if properly analysed, they hold immense potential to rewrite what we know about the evolution of our species and our closest hominin ancestors.
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Affiliation(s)
- Mike W Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, Australia.
| | - Ian Moffat
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Anna M Kotarba-Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, Australia
- School of Humanities, University of Adelaide, Adelaide, South Australia, Australia
| | - Vito C Hernandez
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra 'A. Desio', Università degli Studi di Milano, Milano, Italy
| | - Andy I R Herries
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria, Australia
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group, Southern Cross University, Lismore, New South Wales, Australia
| | - Kira Westaway
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
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8
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Ficetola GF, Taberlet P. Towards exhaustive community ecology via DNA metabarcoding. Mol Ecol 2023; 32:6320-6329. [PMID: 36762839 DOI: 10.1111/mec.16881] [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] [Received: 10/08/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and to evaluate impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability to perform biodiversity inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority of metabarcoding studies published in the last years used just one or two markers and analysed a limited number of taxonomic groups. Here, we provide an overview of emerging approaches that can allow all-taxa biological inventories. Exhaustive biodiversity assessments can be attempted by combining a large number of specific primers, by exploiting the power of universal primers, or by combining specific and universal primers to obtain good information on key taxa while limiting the overlooked biodiversity. Multiplexes of primers, shotgun sequencing and capture enrichment may provide a better coverage of biodiversity compared to standard metabarcoding, but still require major methodological advances. Here, we identify the strengths and limitations of different approaches, and suggest new development lines that might improve broad scale biodiversity analyses in the near future. More holistic reconstructions of ecological communities can greatly increase the value of metabarcoding studies, improving understanding of the consequences of ongoing environmental changes on the multiple components of biodiversity.
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Affiliation(s)
- Gentile Francesco Ficetola
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
- University Grenoble Alpes, University Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Écologie Alpine, Grenoble, France
| | - Pierre Taberlet
- University Grenoble Alpes, University Savoie Mont Blanc, CNRS, LECA, Laboratoire d'Écologie Alpine, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
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9
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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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10
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Pollen AA, Kilik U, Lowe CB, Camp JG. Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. Nat Rev Genet 2023; 24:687-711. [PMID: 36737647 PMCID: PMC9897628 DOI: 10.1038/s41576-022-00568-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/05/2023]
Abstract
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches - including cell atlases and organoids - are enabling exploration of the candidate causal factors that underlie human-specific traits.
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Affiliation(s)
- Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Umut Kilik
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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11
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Żarczyńska M, Żarczyński P, Tomsia M. Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics. Genes (Basel) 2023; 14:1643. [PMID: 37628694 PMCID: PMC10454188 DOI: 10.3390/genes14081643] [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: 07/13/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.
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Affiliation(s)
- Małgorzata Żarczyńska
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Piotr Żarczyński
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Marcin Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland
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12
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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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13
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Vassallo A, Modi A, Quagliariello A, Bacci G, Faddetta T, Gallo M, Provenzano A, La Barbera A, Lombardo G, Maggini V, Firenzuoli F, Zaccaroni M, Gallo G, Caramelli D, Aleo Nero C, Baldi F, Fani R, Palumbo Piccionello A, Pucciarelli S, Puglia AM, Sineo L. Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy). Microbiol Spectr 2023; 11:e0437422. [PMID: 37071008 PMCID: PMC10269861 DOI: 10.1128/spectrum.04374-22] [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: 10/26/2022] [Accepted: 03/26/2023] [Indexed: 04/19/2023] Open
Abstract
The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.
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Affiliation(s)
- Alberto Vassallo
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Michele Gallo
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre (VE), Italy
| | - Aldesia Provenzano
- Department of Clinical and Experimental Biomedical Sciences “Mario Serio,” University of Florence, Florence (FI), Italy
| | - Andrea La Barbera
- Unit of Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genoa (GE), Italy
| | - Giovanna Lombardo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Valentina Maggini
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, Florence (FI), Italy
| | - Fabio Firenzuoli
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, Florence (FI), Italy
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Carla Aleo Nero
- Soprintendenza ai Beni culturali e ambientali di Palermo, Palermo (PA), Italy
| | - Franco Baldi
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre (VE), Italy
| | - Renato Fani
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Luca Sineo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
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14
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Baumann M, Plisson H, Maury S, Renou S, Coqueugniot H, Vanderesse N, Kolobova K, Shnaider S, Rots V, Guérin G, Rendu W. On the Quina side: A Neanderthal bone industry at Chez-Pinaud site, France. PLoS One 2023; 18:e0284081. [PMID: 37315040 DOI: 10.1371/journal.pone.0284081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/23/2023] [Indexed: 06/16/2023] Open
Abstract
Did Neanderthal produce a bone industry? The recent discovery of a large bone tool assemblage at the Neanderthal site of Chagyrskaya (Altai, Siberia, Russia) and the increasing discoveries of isolated finds of bone tools in various Mousterian sites across Eurasia stimulate the debate. Assuming that the isolate finds may be the tip of the iceberg and that the Siberian occurrence did not result from a local adaptation of easternmost Neanderthals, we looked for evidence of a similar industry in the Western side of their spread area. We assessed the bone tool potential of the Quina bone-bed level currently under excavation at chez Pinaud site (Jonzac, Charente-Maritime, France) and found as many bone tools as flint ones: not only the well-known retouchers but also beveled tools, retouched artifacts and a smooth-ended rib. Their diversity opens a window on a range of activities not expected in a butchering site and not documented by the flint tools, all involved in the carcass processing. The re-use of 20% of the bone blanks, which are mainly from large ungulates among faunal remains largely dominated by reindeer, raises the question of blank procurement and management. From the Altai to the Atlantic shore, through a multitude of sites where only a few objects have been reported so far, evidence of a Neanderthal bone industry is emerging which provides new insights on Middle Paleolithic subsistence strategies.
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Affiliation(s)
| | - Hugues Plisson
- PACEA UMR 5199, CNRS, University of Bordeaux, Pessac, France
| | | | | | - Hélène Coqueugniot
- PACEA UMR 5199, CNRS, University of Bordeaux, Pessac, France
- Ecole Pratique des Hautes Etudes-PSL University, Paris, France
| | | | - Ksenyia Kolobova
- Paleolithic Department, Institute of archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Svetlana Shnaider
- ZooSCAN, International Research Laboratory 2013, CNRS, Novosibirsk, Russian Federation
| | | | - Guillaume Guérin
- Géosciences Rennes UMR 6118, CNRS, University of Rennes, Rennes, France
| | - William Rendu
- ZooSCAN, International Research Laboratory 2013, CNRS, Novosibirsk, Russian Federation
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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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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535797. [PMID: 37066305 PMCID: PMC10104067 DOI: 10.1101/2023.04.06.535797] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases since it first was made available and crossed the threshold of >10,000 ancient individuals with genome-wide data at the end of 2022. This note is intended as a citable description of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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17
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Zimmermann HH, Stoof-Leichsenring KR, Dinkel V, Harms L, Schulte L, Hütt MT, Nürnberg D, Tiedemann R, Herzschuh U. Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing. Nat Commun 2023; 14:1650. [PMID: 36964154 PMCID: PMC10039020 DOI: 10.1038/s41467-023-36845-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.
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Affiliation(s)
- Heike H Zimmermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland (GEUS), DK-1350, Copenhagen, Denmark
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
| | - Viktor Dinkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
- Constructor University Bremen, Computational Systems Biology, Bremen, D-28759, Germany
| | - Lars Harms
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Data Science Support, D-27568, Bremerhaven, Germany
| | - Luise Schulte
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
| | - Marc-Thorsten Hütt
- Constructor University Bremen, Computational Systems Biology, Bremen, D-28759, Germany
| | - Dirk Nürnberg
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Ocean circulation and climate dynamics, D-24148, Kiel, Germany
| | - Ralf Tiedemann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Marine Geology, D-27568, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, D-28334, Bremen, Germany
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany.
- University of Potsdam, Institute of Biochemistry and Biology, D-14476, Potsdam, Germany.
- University of Potsdam, Institute of Environmental Sciences and Geography, D-14476, Potsdam, Germany.
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18
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Min-Shan Ko A. The 2022 nobel prize in physiology or medicine awarded for the decoding of the complete ancient human genome. Biomed J 2023; 46:100584. [PMID: 36796758 DOI: 10.1016/j.bj.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Since the publication of the first ancient DNA sequence in 1984, experimental methods used to recover ancient DNA have advanced greatly, illuminating previously unknown branches of the human family tree and opening up several promising new avenues for future studies of human evolution. The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his work on ancient DNA and human evolution. On his first day back at work, he was thrown in the pond as part of his institute's tradition of celebrating award winners.
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Affiliation(s)
- Albert Min-Shan Ko
- Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan; Cardiovascular Department, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Healthy Aging Research Center, Chang Gung University, Taoyuan, Taiwan.
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19
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Johnson MD, Freeland JR, Parducci L, Evans DM, Meyer RS, Molano-Flores B, Davis MA. Environmental DNA as an emerging tool in botanical research. AMERICAN JOURNAL OF BOTANY 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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Affiliation(s)
- Mark D Johnson
- Engineering Research and Development Center, Construction Engineering Research Laboratory (CERL), Champaign, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joanna R Freeland
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brenda Molano-Flores
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mark A Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
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20
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Everett R, Cribdon B. MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.888421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.
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21
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Harvati K, Reyes-Centeno H. Evolution of Homo in the Middle and Late Pleistocene. J Hum Evol 2022; 173:103279. [PMID: 36375244 PMCID: PMC9703123 DOI: 10.1016/j.jhevol.2022.103279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022]
Abstract
The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.
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Affiliation(s)
- Katerina Harvati
- Paleoanthropology, Institute for Archaeological Sciences and Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Rümelinstrasse 19-23, Tübingen 72070, Germany; DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past', Rümelinstrasse 19-23, Tübingen 72070, Germany.
| | - Hugo Reyes-Centeno
- Department of Anthropology, University of Kentucky, 211 Lafferty Hall, Lexington, KY 40506, USA; William S. Webb Museum of Anthropology, University of Kentucky, 1020 Export St, Lexington, KY 40504, USA
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22
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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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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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Harvati K, Ackermann RR. Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins. Nat Ecol Evol 2022; 6:1573-1585. [PMID: 36064759 DOI: 10.1038/s41559-022-01875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.
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Affiliation(s)
- K Harvati
- Paleoanthropology section, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - R R Ackermann
- Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa.
- Department of Archaeology, University of Cape Town, Cape Town, South Africa.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
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25
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Reilly PF, Tjahjadi A, Miller SL, Akey JM, Tucci S. The contribution of Neanderthal introgression to modern human traits. Curr Biol 2022; 32:R970-R983. [PMID: 36167050 PMCID: PMC9741939 DOI: 10.1016/j.cub.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.
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Affiliation(s)
| | - Audrey Tjahjadi
- Department of Anthropology, Yale University, New Haven, CT, USA
| | | | - Joshua M Akey
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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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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Pérez V, Liu Y, Hengst MB, Weyrich LS. A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples. Microorganisms 2022; 10:microorganisms10081623. [PMID: 36014039 PMCID: PMC9414430 DOI: 10.3390/microorganisms10081623] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022] Open
Abstract
High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.
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Affiliation(s)
- Vilma Pérez
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence:
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Martha B. Hengst
- Laboratorio de Ecología Molecular y Microbiología Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1270300, Chile
| | - Laura S. Weyrich
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Anthropology and Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA 16802, USA
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28
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De Sanctis B, Money D, Pedersen MW, Durbin R. A theoretical analysis of taxonomic binning accuracy. Mol Ecol Resour 2022; 22:2208-2219. [PMID: 35285150 DOI: 10.1111/1755-0998.13608] [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: 05/25/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/28/2022]
Abstract
Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate which depends both on the assignment algorithm and on underlying population genetic and database parameters. In particular, as we move towards using environmental DNA to study eukaryotic taxa subject to regular recombination, we must take into account issues concerning gene tree discordance. Though accuracy is often compared across algorithms using a fixed data set, the relative impact of these population genetic and database parameters on accuracy has not yet been quantified. Here, we develop both a theoretical and simulation framework in the simplified case of two reference species, and compute binning accuracy over a wide range of parameters, including sequence length, species-query divergence time, divergence times of the reference species, reference database completeness, sample age and effective population size. We consider two assignment methods and contextualize our results using parameters from a recent ancient environmental DNA study, comparing them to the commonly used discriminative k-mer-based method Clark (Current Biology, 31, 2021, 2728; BMC Genomics, 16, 2015, 1). Our results quantify the degradation in assignment accuracy as the samples diverge from their closest reference sequence, and with incompleteness of reference sequences. We also provide a framework in which others can compute expected accuracy for their particular method or parameter set. Code is available at https://github.com/bdesanctis/binning-accuracy.
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Affiliation(s)
- Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Daniel Money
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
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29
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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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30
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Liu Y, Bennett EA, Fu Q. Evolving ancient DNA techniques and the future of human history. Cell 2022; 185:2632-2635. [PMID: 35868268 DOI: 10.1016/j.cell.2022.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/28/2022]
Abstract
Ancient DNA (aDNA) techniques applied to human genomics have significantly advanced in the past decade, enabling large-scale aDNA research, sometimes independent of human remains. This commentary reviews the major milestones of aDNA techniques and explores future directions to expand the scope of aDNA research and insights into present-day human health.
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Affiliation(s)
- Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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31
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Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
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32
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Lunghi E, Valle B, Guerrieri A, Bonin A, Cianferoni F, Manenti R, Ficetola GF. Environmental DNA of insects and springtails from caves reveals complex processes of eDNA transfer in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154022. [PMID: 35202680 DOI: 10.1016/j.scitotenv.2022.154022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/01/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Subterranean environments host a substantial amount of biodiversity, however assessing the distribution of species living underground is still extremely challenging. Environmental DNA (eDNA) metabarcoding is a powerful tool to estimate biodiversity in poorly known environments and has excellent performance for soil organisms. Here, we tested 1) whether eDNA metabarcoding from cave soils/sediments allows to successfully detect springtails (Hexapoda: Collembola) and insects (Hexapoda: Insecta); 2) whether eDNA mostly represents autochthonous (cave-dwelling) organisms or it also incorporates information from species living in surface environments; 3) whether eDNA detection probability changes across taxa with different ecology. Environmental DNA metabarcoding analyses detected a large number of Molecular Operational Taxonomic Units (MOTUs) for both insects and springtails. For springtails, detection probability was high, with a substantial proportion of hypogean species, suggesting that eDNA provides good information on the distribution of these organisms in caves. Conversely, for insects most of MOTUs represented taxa living outside caves, and the majority of them represented taxa/organisms living in freshwater environments (Ephemeroptera, Plecoptera and Trichoptera). The eDNA of freshwater insects was particularly abundant in deep sectors of caves, far from the entrance. Furthermore, average detection probability of insects was significantly lower than the one of springtails. This suggests that cave soils/sediments act as "conveyer belts of biodiversity information", possibly because percolating water lead to the accumulation of eDNA of organisms living in nearby areas. Cave soils hold a complex mix of autochthonous and allochthonous eDNA. eDNA provided unprecedented information on the understudied subterranean cave organisms; analyses of detection probability and occupancy can help teasing apart local eDNA from the eDNA representing spatially-integrated biodiversity for whole landscape.
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Affiliation(s)
- Enrico Lunghi
- Division of Molecular Biology Ruđer Bošković Institute, Zagreb, Croatia; Natural Oasis, Prato, Italy.
| | - Barbara Valle
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy; Unità di Climatologia ed Ecologia, MUSE-Museo delle Scienze di Trento, Italy
| | - Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Aurélie Bonin
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Fabio Cianferoni
- Istituto di Ricerca sugli Ecosistemi Terrestri (IRET), Consiglio Nazionale delle Ricerche (CNR), Sesto Fiorentino (Firenze), Italy; Zoologia, La Specola, Museo di Storia Naturale, Università degli Studi di Firenze, Firenze, Italy
| | - Raoul Manenti
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy; Laboratorio di Biologia Sotterranea "Enrico Pezzoli", Parco Regionale del Monte Barro, Galbiate, Italy
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy; Laboratoire d'Écologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
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33
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Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily. iScience 2022; 25:104244. [PMID: 35494246 PMCID: PMC9051636 DOI: 10.1016/j.isci.2022.104244] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 11/23/2022] Open
Abstract
Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700–4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell’Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition. Genetic transition between Early Mesolithic and Late Mesolithic hunter-gatherers A near-complete genetic turnover during the Mesolithic-Neolithic transition Exchange of subsistence practices between hunter-gatherers and early farmers
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Suchan T, Chauvey L, Poullet M, Tonasso‐Calvière L, Schiavinato S, Clavel P, Clavel B, Lepetz S, Seguin‐Orlando A, Orlando L. Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA. Mol Ecol Resour 2022; 22:2262-2274. [DOI: 10.1111/1755-0998.13619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Tomasz Suchan
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
- W. Szafer Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Marine Poullet
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Laure Tonasso‐Calvière
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Benoit Clavel
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE) Muséum National d’Histoire Naturelle CNRS CP 55 rue Buffon Paris France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE) Muséum National d’Histoire Naturelle CNRS CP 55 rue Buffon Paris France
| | - Andaine Seguin‐Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
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Zavala EI, Aximu-Petri A, Richter J, Nickel B, Vernot B, Meyer M. Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA. Mol Ecol Resour 2022; 22:2196-2207. [PMID: 35263821 DOI: 10.1111/1755-0998.13607] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/29/2022]
Abstract
The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains (Mathieson et al., 2015; Narasimhan et al., 2019) or sediments (Vernot et al., 2021; Wang et al., 2021; Zavala et al., 2021) in single studies. Nevertheless, demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents, consumables and time. Here we explore the possibility of improving the economics of sample preparation via multiplex capture, i.e. the hybridization capture of pools of double-indexed ancient DNA libraries. We demonstrate that this strategy is feasible, at least for small genomic targets such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post-capture amplification to avoid index swapping by jumping PCR, which manifests as cross-contamination in resulting sequence data. We also show that the re-amplification of double-indexed libraries to PCR plateau before or after hybridization capture can sporadically lead to small, but detectable cross-contamination even if libraries are amplified in separate reactions. We provide protocols for both manual capture and automated capture in 384-well format that are compatible with single- and multiplex capture and effectively suppress cross-contamination and artefact formation. Last, we provide a simple computational method for quantifying cross-contamination due to index swapping in double-indexed libraries, which we recommend using for routine quality checks in studies that are sensitive to cross-contamination.
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Affiliation(s)
- Elena I Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ayinuer Aximu-Petri
- 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
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Fagernäs Z, Salazar-García DC, Haber Uriarte M, Avilés Fernández A, Henry AG, Lomba Maurandi J, Ozga AT, Velsko IM, Warinner C. Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation. FEMS MICROBES 2022; 3:xtac006. [PMID: 37332506 PMCID: PMC10117714 DOI: 10.1093/femsmc/xtac006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 10/22/2023] Open
Abstract
The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.
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Affiliation(s)
- Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, 46010, Spain
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, 01006, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, 7701, South Africa
| | - María Haber Uriarte
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Azucena Avilés Fernández
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Amanda G Henry
- Faculty of Archaeology, Leiden University, Leiden, 2332 CC, The Netherlands
| | - Joaquín Lomba Maurandi
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Andrew T Ozga
- Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA
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Silvestrini S, Romandini M, Marciani G, Arrighi S, Carrera L, Fiorini A, López‐García JM, Lugli F, Ranaldo F, Slon V, Tassoni L, Higgins OA, Bortolini E, Curci A, Meyer M, Meyer MC, Oxilia G, Zerboni A, Benazzi S, Spinapolice EE. Integrated multidisciplinary ecological analysis from the Uluzzian settlement at the Uluzzo C Rock Shelter, south-eastern Italy. JOURNAL OF QUATERNARY SCIENCE 2022; 37:235-256. [PMID: 35874301 PMCID: PMC9290050 DOI: 10.1002/jqs.3341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/15/2023]
Abstract
The Middle to Upper Palaeolithic transition, between 50 000 and 40 000 years ago, is a period of important ecological and cultural changes. In this framework, the Rock Shelter of Uluzzo C (Apulia, southern Italy) represents an important site due to Late Mousterian and Uluzzian evidence preserved in its stratigraphic sequence. Here, we present the results of a multidisciplinary analysis performed on the materials collected between 2016 and 2018 from the Uluzzian stratigraphic units (SUs) 3, 15 and 17. The analysis involved lithic technology, use-wear, zooarchaeology, ancient DNA of sediments and palaeoproteomics, completed by quartz single-grain optically stimulated luminescence dating of the cave sediments. The lithic assemblage is characterized by a volumetric production and a debitage with no or little management of the convexities (by using the bipolar technique), with the objective to produce bladelets and flakelets. The zooarchaeological study found evidence of butchery activity and of the possible exploitation of marine resources, while drawing a picture of a patchy landscape, composed of open forests and dry open environments surrounding the shelter. Ancient mitochondrial DNA from two mammalian taxa were recovered from the sediments. Preliminary zooarchaeology by mass spectrometry results are consistent with ancient DNA and zooarchaeological taxonomic information, while further palaeoproteomics investigations are ongoing. Our new data from the re-discovery of the Uluzzo C Rock Shelter represent an important contribution to better understand the meaning of the Uluzzian in the context of the Middle/Upper Palaeolithic transition in south-eastern Italy.
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Affiliation(s)
- Sara Silvestrini
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Matteo Romandini
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Giulia Marciani
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
- U.R. Università di SienaDipartimento di Scienze Fisiche, della Terra e dell'AmbienteSienaItaly
| | - Simona Arrighi
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
- U.R. Università di SienaDipartimento di Scienze Fisiche, della Terra e dell'AmbienteSienaItaly
| | - Lisa Carrera
- Università degli Studi di Bologna, Dipartimento di Scienze BiologicheGeologiche e AmbientaliBolognaItaly
| | - Andrea Fiorini
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Juan Manuel López‐García
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES‐CERCA)TarragonaSpain
- Universitat Rovira i VirgiliDepartament d'Història i Història de l'ArtTarragonaSpain
| | - Federico Lugli
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Filomena Ranaldo
- U.R. Università di SienaDipartimento di Scienze Fisiche, della Terra e dell'AmbienteSienaItaly
- Museo della Preistoria Nardò
| | - Viviane Slon
- Department of Evolutionary GeneticsMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and BiochemistrySackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- The Dan David Center for Human Evolution and Biohistory ResearchTel Aviv UniversityTel AvivIsrael
| | - Laura Tassoni
- Università degli Studi di Ferrara, Dipartimento di Studi UmanisticiSezione di Scienze Preistoriche e AntropologicheFerraraItaly
| | | | | | - Antonio Curci
- Università di BolognaDipartimento di Storia Culture CiviltàBolognaItaly
| | - Matthias Meyer
- Department of Evolutionary GeneticsMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | | | - Gregorio Oxilia
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Andrea Zerboni
- Università degli Studi di MilanoDipartimento di Scienze delle Terra “A. Desio”MilanoItaly
| | - Stefano Benazzi
- Università di BolognaDipartimento di Beni Culturali di RavennaItaly
| | - Enza Elena Spinapolice
- Università degli Studi di Roma “La Sapienza”Dipartimento di Scienze dell'AntichitàRoma00185Italy
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38
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Capo E, Monchamp ME, Coolen MJL, Domaizon I, Armbrecht L, Bertilsson S. Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential. Environ Microbiol 2022; 24:2201-2209. [PMID: 35049133 PMCID: PMC9304175 DOI: 10.1111/1462-2920.15913] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 11/30/2022]
Abstract
In‐depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo‐genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human‐induced global changes.
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Affiliation(s)
- Eric Capo
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Marie-Eve Monchamp
- Department of Biology, McGill University, Montréal, QC, H3A 1B1, Canada.,Groupe de recherche interuniversitaire en limnologie (GRIL)
| | - Marco J L Coolen
- Western Australia Organic and Isotope Geochemistry Centre (WA-OIGC), Curtin University, Bentley, 6102, Australia
| | - Isabelle Domaizon
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200 Thonon les Bains, France.,UMR CARRTEL, Pôle R&D ECLA, 74200 Thonon les Bains, France
| | - Linda Armbrecht
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia.,Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
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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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40
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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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41
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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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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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43
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Pedersen MW, Antunes C, De Cahsan B, Moreno-Mayar JV, Sikora M, Vinner L, Mann D, Klimov PB, Black S, Michieli CT, Braig HR, Perotti MA. Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits. Mol Biol Evol 2021; 39:6481551. [PMID: 34963129 PMCID: PMC8829908 DOI: 10.1093/molbev/msab351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.
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Affiliation(s)
- Mikkel W Pedersen
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Catia Antunes
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Binia De Cahsan
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Martin Sikora
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Lasse Vinner
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Darren Mann
- Oxford University Museum of Natural History, Oxford, United Kingdom
| | - Pavel B Klimov
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Department of Ecology and Evolutionary Biology, University of Michigan, Museum of Zoology, Ann Arbor, USA
| | - Stuart Black
- Department of Geography and Environmental Science, Wager Building, University of Reading, Reading, United Kingdom
| | - Catalina Teresa Michieli
- Instituto de Investigaciones Arqueológicas y Museo "Prof. Mariano Gambier", Universidad Nacional de San Juan, San Juan, Argentina
| | - Henk R Braig
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Institute and Museum of Natural Sciences, Faculty of Exact, Physical and Natural Sciences, National University of San Juan, San Juan, Argentina
| | - M Alejandra Perotti
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
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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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45
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Ancient DNA diffuses from human bones to cave stones. iScience 2021; 24:103397. [PMID: 34988387 PMCID: PMC8710462 DOI: 10.1016/j.isci.2021.103397] [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: 08/19/2021] [Revised: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
Recent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.
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46
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An infant burial from Arma Veirana in northwestern Italy provides insights into funerary practices and female personhood in early Mesolithic Europe. Sci Rep 2021; 11:23735. [PMID: 34907203 PMCID: PMC8671481 DOI: 10.1038/s41598-021-02804-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/23/2021] [Indexed: 12/16/2022] Open
Abstract
The evolution and development of human mortuary behaviors is of enormous cultural significance. Here we report a richly-decorated young infant burial (AVH-1) from Arma Veirana (Liguria, northwestern Italy) that is directly dated to 10,211-9910 cal BP (95.4% probability), placing it within the early Holocene and therefore attributable to the early Mesolithic, a cultural period from which well-documented burials are exceedingly rare. Virtual dental histology, proteomics, and aDNA indicate that the infant was a 40-50 days old female. Associated artifacts indicate significant material and emotional investment in the child's interment. The detailed biological profile of AVH-1 establishes the child as the earliest European near-neonate documented to be female. The Arma Veirana burial thus provides insight into sex/gender-based social status, funerary treatment, and the attribution of personhood to the youngest individuals among prehistoric hunter-gatherer groups and adds substantially to the scant data on mortuary practices from an important period in prehistory shortly following the end of the last Ice Age.
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47
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Murchie TJ, Monteath AJ, Mahony ME, Long GS, Cocker S, Sadoway T, Karpinski E, Zazula G, MacPhee RDE, Froese D, Poinar HN. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nat Commun 2021; 12:7120. [PMID: 34880234 PMCID: PMC8654998 DOI: 10.1038/s41467-021-27439-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada.
| | - Alistair J Monteath
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.,School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Matthew E Mahony
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - George S Long
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Scott Cocker
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Tara Sadoway
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,The Hospital for Sick Children, Toronto, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Whitehorse, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, United States
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada. .,Department of Biochemistry, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. .,CIFAR Humans and the Microbiome Program, Toronto, Canada.
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48
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Wang Y, Pedersen MW, Alsos IG, De Sanctis B, Racimo F, Prohaska A, Coissac E, Owens HL, Merkel MKF, Fernandez-Guerra A, Rouillard A, Lammers Y, Alberti A, Denoeud F, Money D, Ruter AH, McColl H, Larsen NK, Cherezova AA, Edwards ME, Fedorov GB, Haile J, Orlando L, Vinner L, Korneliussen TS, Beilman DW, Bjørk AA, Cao J, Dockter C, Esdale J, Gusarova G, Kjeldsen KK, Mangerud J, Rasic JT, Skadhauge B, Svendsen JI, Tikhonov A, Wincker P, Xing Y, Zhang Y, Froese DG, Rahbek C, Bravo DN, Holden PB, Edwards NR, Durbin R, Meltzer DJ, Kjær KH, Möller P, Willerslev E. Late Quaternary dynamics of Arctic biota from ancient environmental genomics. Nature 2021; 600:86-92. [PMID: 34671161 PMCID: PMC8636272 DOI: 10.1038/s41586-021-04016-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022]
Abstract
During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.
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Affiliation(s)
- Yucheng Wang
- Department of Zoology, University of Cambridge, Cambridge, UK
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Hannah Lois Owens
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Youri Lammers
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Daniel Money
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nicolaj Krog Larsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anna A Cherezova
- Institute of Earth Sciences, St Petersburg State University, St Petersburg, Russia
- Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Mary E Edwards
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
- Alaska Quaternary Center, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Grigory B Fedorov
- Institute of Earth Sciences, St Petersburg State University, St Petersburg, Russia
- Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - James Haile
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Sand Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- National Research University, Higher School of Economics, Moscow, Russia
| | - David W Beilman
- Department of Geography and Environment, University of Hawaii, Honolulu, HI, USA
| | - Anders A Bjørk
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Jialu Cao
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Julie Esdale
- Center for Environmental Management of Military Lands, Colorado State University, Fort Collins, CO, USA
| | - Galina Gusarova
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
- Faculty of Biology, St Petersburg State University, St Petersburg, Russia
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Jan Mangerud
- Department of Earth Science, University of Bergen, Bergen, Norway
- Bjerknes Centre for Climate Research, Bergen, Norway
| | - Jeffrey T Rasic
- US National Park Service, Gates of the Arctic National Park and Preserve, Fairbanks, AK, USA
| | | | - John Inge Svendsen
- Department of Earth Science, University of Bergen, Bergen, Norway
- Bjerknes Centre for Climate Research, Bergen, Norway
| | - Alexei Tikhonov
- Zoological Institute, , Russian Academy of Sciences, St Petersburg, Russia
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Yingchun Xing
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing, China
| | - Yubin Zhang
- College of Plant Science, Jilin University, Changchun, China
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Nogues Bravo
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Philip B Holden
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Neil R Edwards
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | - Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Per Möller
- Department of Geology, Quaternary Sciences, Lund University, Lund, Sweden
| | - Eske Willerslev
- Department of Zoology, University of Cambridge, Cambridge, UK.
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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49
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The Potential of Micromammals for the Stratigraphy and the Timing of Human Occupations at La Roche-à-Pierrot (Saint-Césaire, France). QUATERNARY 2021. [DOI: 10.3390/quat4040033] [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
As micromammals are highly sensitive to changes in their habitat, variations in species representation are often used to reconstruct local environmental conditions. However, taphonomic aspects of micromammals are often overlooked, despite the fact that they can provide important information for our understanding of archaeological sites. La Roche-à-Pierrot, Saint-Césaire, is a major archaeological site for our understanding of the Middle-to-Upper Palaeolithic transition in Western Europe. Clearly documenting site formation processes, the post-depositional reworking of deposits and the sequence of human occupations is fundamental for providing a secure archaeostratigraphic context of the site. The exceptionally large accumulation of micromammals from recently excavated stratigraphic units at the site makes it possible to track variations in the density of micromammals across the stratigraphic sequence. The taphonomic analysis of micromammals demonstrates these variations are not related to a change in the main accumulation agent or post-depositional phenomena. A negative correlation between small mammal remains and archaeological material suggests that peaks in micromammal densities can potentially be correlated with periods when the site was abandoned or when human occupation was less intense, and therefore provide new data for interpreting the Saint-Césaire stratigraphic sequence.
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50
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Suchan T, Kusliy MA, Khan N, Chauvey L, Tonasso-Calvière L, Schiavinato S, Southon J, Keller M, Kitagawa K, Krause J, Bessudnov AN, Bessudnov AA, Graphodatsky AS, Valenzuela-Lamas S, Wilczyński J, Pospuła S, Tunia K, Nowak M, Moskal-delHoyo M, Tishkin AA, Pryor AJE, Outram AK, Orlando L. Performance and automation of ancient DNA capture with RNA hyRAD probes. Mol Ecol Resour 2021; 22:891-907. [PMID: 34582623 PMCID: PMC9291508 DOI: 10.1111/1755-0998.13518] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 01/23/2023]
Abstract
DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.
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Affiliation(s)
- Tomasz Suchan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Mariya A Kusliy
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.,Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - John Southon
- Earth System Science Department, University of California, Irvine, Irvine, California, USA
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Keiko Kitagawa
- SFB 1070 ResourceCultures, University of Tübingen, Tübingen, Germany.,Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Alexander A Bessudnov
- Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Silvia Valenzuela-Lamas
- Institución Milà i Fontanals de Humanidades, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Sylwia Pospuła
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Marek Nowak
- Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | | | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | | | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
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