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Costanzo S, Pappalardo M, Starnini E, Rossoni-Notter E, Notter O, Moussous A, Soares-Remiseiro M, Fermo P, Cremaschi M, Zerboni A. Integrating musealized archaeological sediment collections into current geoarchaeological analytical frameworks for sustainable research practices. MethodsX 2024; 13:102897. [PMID: 39233753 PMCID: PMC11372796 DOI: 10.1016/j.mex.2024.102897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/06/2024] [Indexed: 09/06/2024] Open
Abstract
We present a review of the latest framework achievements in geoarchaeological sciences applied to microstratigraphic and biomolecular studies of prehistoric archaeological contexts, highlighting the importance of musealized archaeological stratigraphies. We assess how today's scientific and technological accomplishments can be tailored for archaeological human ecology studies with analytical ensembles that provide unprecedented results. Sampling and processing workflows originating from resin consolidation and thin section micromorphology of undisturbed blocks of archaeological soils and sediments, guarantee subsampling accuracy at the micrometre scale granting access to individual components otherwise impossible to target: the achievable information yield makes even the smallest soil samples potential sources of pioneering discoveries. Yet, archaeological excavations are still the primary mode of retrieving new soil samples. We argue that, when dealing with archaeological sites that were excavated and partially musealised in the past, the exploration of related museum collections should be prioritized as perspective source of new study samples. Analysing old and potentially very informative samples, with an approach that we define as "Green Archaeology", may represent a source of well-structured primary data as well as a means for planning new excavations, delivering novel discoveries while safeguarding site integrity and promoting Third Mission valorisation of sites and heritage dormant collections.
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Affiliation(s)
- Stefano Costanzo
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milan, Italy
| | - Marta Pappalardo
- Dipartimento di Scienze della Terra, Università di Pisa, Pisa, Italy
| | | | | | | | | | - Miguel Soares-Remiseiro
- The interdisciplinary Center for Archaeology and Evolution of Human Behaviour, Universidade do Algarve, Faro, Portugal
| | - Paola Fermo
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
| | - Mauro Cremaschi
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milan, Italy
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milan, Italy
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2
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Oberreiter V, Gelabert P, Brück F, Franz S, Zelger E, Szedlacsek S, Cheronet O, Cano FT, Exler F, Zagorc B, Karavanić I, Banda M, Gasparyan B, Straus LG, Gonzalez Morales MR, Kappelman J, Stahlschmidt M, Rattei T, Kraemer SM, Sawyer S, Pinhasi R. Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach. Sci Rep 2024; 14:19388. [PMID: 39169089 PMCID: PMC11339378 DOI: 10.1038/s41598-024-69741-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.
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Affiliation(s)
- Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - Florian Brück
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stefan Franz
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Evelyn Zelger
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Sophie Szedlacsek
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | | | - Florian Exler
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Ivor Karavanić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Marko Banda
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, USA
- EvoAdapta Group Universidad de Cantabria, Santander, Spain
| | - Manuel R Gonzalez Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Gobierno de Cantabria, Banco Santander, Spain
| | - John Kappelman
- Department of Anthropology and Department of Earth and Planetary Sciences, The University of Texas, Austin, TX, USA
| | - Mareike Stahlschmidt
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephan M Kraemer
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institut für Analytische Chemie, University of Vienna, Vienna, Austria
- Forschungsverbund Umwelt und Klima, University of Vienna, Vienna, Austria
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
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3
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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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4
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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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5
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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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6
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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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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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Dalén L, Heintzman PD, Kapp JD, Shapiro B. Deep-time paleogenomics and the limits of DNA survival. Science 2023; 382:48-53. [PMID: 37797036 PMCID: PMC10586222 DOI: 10.1126/science.adh7943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.
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Affiliation(s)
- Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE- 10405 Stockholm, Sweden
| | - Peter D. Heintzman
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden
- Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Joshua D. Kapp
- Department of Biomolecular Engineering, University of California Santa Cruz; Santa Cruz, California, 95064, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz; Santa Cruz, California, 95064, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz; Santa Cruz, California, 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz; Santa Cruz, California, 95064, USA
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9
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Wegner CE, Stahl R, Velsko I, Hübner A, Fagernäs Z, Warinner C, Lehmann R, Ritschel T, Totsche KU, Küsel K. A glimpse of the paleome in endolithic microbial communities. MICROBIOME 2023; 11:210. [PMID: 37749660 PMCID: PMC10518947 DOI: 10.1186/s40168-023-01647-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/09/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards. RESULTS By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past. CONCLUSIONS Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.
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Affiliation(s)
- Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Irina Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Alex Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Thomas Ritschel
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
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10
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Cazenave M, Kivell TL. Challenges and perspectives on functional interpretations of australopith postcrania and the reconstruction of hominin locomotion. J Hum Evol 2023; 175:103304. [PMID: 36563461 DOI: 10.1016/j.jhevol.2022.103304] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 12/24/2022]
Abstract
In 1994, Hunt published the 'postural feeding hypothesis'-a seminal paper on the origins of hominin bipedalism-founded on the detailed study of chimpanzee positional behavior and the functional inferences derived from the upper and lower limb morphology of the Australopithecus afarensis A.L. 288-1 partial skeleton. Hunt proposed a model for understanding the potential selective pressures on hominins, made robust, testable predictions based on Au. afarensis functional morphology, and presented a hypothesis that aimed to explain the dual functional signals of the Au. afarensis and, more generally, early hominin postcranium. Here we synthesize what we have learned about Au. afarensis functional morphology and the dual functional signals of two new australopith discoveries with relatively complete skeletons (Australopithecus sediba and StW 573 'Australopithecus prometheus'). We follow this with a discussion of three research approaches that have been developed for the purpose of drawing behavioral inferences in early hominins: (1) developments in the study of extant apes as models for understanding hominin origins; (2) novel and continued developments to quantify bipedal gait and locomotor economy in extant primates to infer the locomotor costs from the anatomy of fossil taxa; and (3) novel developments in the study of internal bone structure to extract functional signals from fossil remains. In conclusion of this review, we discuss some of the inherent challenges of the approaches and methodologies adopted to reconstruct the locomotor modes and behavioral repertoires in extinct primate taxa, and notably the assessment of habitual terrestrial bipedalism in early hominins.
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Affiliation(s)
- Marine Cazenave
- Division of Anthropology, American Museum of Natural History, New York, USA; Skeletal Biology Research Centre, School of Anthropology and Conservation, University of Kent, Canterbury, UK; Department of Anatomy, Faculty of Health Sciences, University of Pretoria, South Africa.
| | - Tracy L Kivell
- Skeletal Biology Research Centre, School of Anthropology and Conservation, University of Kent, Canterbury, UK; Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg, South Africa
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Li H, Zhang H, Chang F, Liu Q, Zhang Y, Liu F, Zhang X. Sedimentary DNA for tracking the long-term changes in biodiversity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17039-17050. [PMID: 36622608 DOI: 10.1007/s11356-023-25130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Yang Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Fengwen Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
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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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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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Phosphate Record in Pleistocene-Holocene Sediments from Denisova Cave: Formation Mechanisms and Archaeological Implications. MINERALS 2022. [DOI: 10.3390/min12050553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The distribution of authigenic phosphates in the sedimentary sequence of prehistoric Denisova Cave (Altai, South Siberia) has important archeological implications. The sampled Late Pleistocene–Early Holocene sedimentary sequence in the East Chamber of the cave consists of argilo-sandy-phosphatic sediments intercalated with guano layers of insectivorous bats. The sediments bear partially degraded N-rich organic matter (OM); chitin fragments enriched in S, P, Zn, and Cu; and a set of phosphates. The guano layers record at least three prolonged episodes of cave occupation by colonies of insectivorous bats between 10 kyr and 5 kyr BP, after people had left the cave or visited it rarely in small groups. The formation of phosphates follows the OM biodegradation pathways, with acidic leaching and gradual neutralization of P-rich solutions. The depth profile of authigenic phosphates shows a suite of mineral assemblages that mark a trend from acidic to slightly alkaline pH conditions of guano degradation (from top to bottom): ardealite, taranakite, and leucophosphite corresponding to acidic environments; whitlockite, brushite, and hydroxylapatite, which are stable under slightly acidic and neutral conditions; and hydroxylapatite in coexistence with calcite and stable at the bottom of the leaching profile under alkaline conditions. Authigenic phosphates can be used as reliable indicators of human non-occupation (abandonment) periods of Denisova Cave. Acidic leaching is responsible for disturbance and/or elimination of archaeological and paleontological materials in Late Pleistocene–Early Holocene sediments that were exposed to at least three “acidic waves”.
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