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Gancz AS, Wright SL, Weyrich LS. Ancient human dental calculus metadata collection and sampling strategies: Recommendations for best practices. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24871. [PMID: 37994571 DOI: 10.1002/ajpa.24871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
OBJECTIVES Ancient human dental calculus is a unique, nonrenewable biological resource encapsulating key information about the diets, lifestyles, and health conditions of past individuals and populations. With compounding calls its destructive analysis, it is imperative to refine the ways in which the scientific community documents, samples, and analyzes dental calculus so as to maximize its utility to the public and scientific community. MATERIALS AND METHODS Our research team conducted an IRB-approved survey of dental calculus researchers with diverse academic backgrounds, research foci, and analytical specializations. RESULTS This survey reveals variation in how metadata is collected and utilized across different subdisciplines and highlights how these differences have profound implications for dental calculus research. Moreover, the survey suggests the need for more communication between those who excavate, curate, and analyze biomolecular data from dental calculus. DISCUSSION Challenges in cross-disciplinary communication limit researchers' ability to effectively utilize samples in rigorous and reproducible ways. Specifically, the lack of standardized skeletal and dental metadata recording and contamination avoidance procedures hinder downstream anthropological applications, as well as the pursuit of broader paleodemographic and paleoepidemiological inquiries that rely on more complete information about the individuals sampled. To provide a path forward toward more ethical and standardized dental calculus sampling and documentation approaches, we review the current methods by which skeletal and dental metadata are recorded. We also describe trends in sampling and contamination-control approaches. Finally, we use that information to suggest new guidelines for ancient dental calculus documentation and sampling strategies that will improve research practices in the future.
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Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sterling L Wright
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Laura S Weyrich
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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2
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Morton-Hayward AL, Anderson RP, Saupe EE, Larson G, Cosmidis JG. Human brains preserve in diverse environments for at least 12 000 years. Proc Biol Sci 2024; 291:20232606. [PMID: 38503334 PMCID: PMC10950470 DOI: 10.1098/rspb.2023.2606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
The brain is thought to be among the first human organs to decompose after death. The discovery of brains preserved in the archaeological record is therefore regarded as unusual. Although mechanisms such as dehydration, freezing, saponification, and tanning are known to allow for the preservation of the brain on short time scales in association with other soft tissues (≲4000 years), discoveries of older brains, especially in the absence of other soft tissues, are rare. Here, we collated an archive of more than 4400 human brains preserved in the archaeological record across approximately 12 000 years, more than 1300 of which constitute the only soft tissue preserved amongst otherwise skeletonized remains. We found that brains of this type persist on time scales exceeding those preserved by other means, which suggests an unknown mechanism may be responsible for preservation particular to the central nervous system. The untapped archive of preserved ancient brains represents an opportunity for bioarchaeological studies of human evolution, health and disease.
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Affiliation(s)
- Alexandra L. Morton-Hayward
- Department of Earth Sciences, University of Oxford, Oxford, UK
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Ross P. Anderson
- Department of Earth Sciences, University of Oxford, Oxford, UK
- All Souls College, University of Oxford, Oxford, UK
| | - Erin E. Saupe
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
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3
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Forshaw R. Windows into the past: recent scientific techniques in dental analysis. Br Dent J 2024; 236:205-211. [PMID: 38332093 PMCID: PMC10853062 DOI: 10.1038/s41415-024-7053-0] [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: 03/31/2023] [Revised: 06/07/2023] [Accepted: 06/21/2023] [Indexed: 02/10/2024]
Abstract
Teeth are the hardest and most chemically stable tissues in the body, are well-preserved in archaeological remains and, being resistant to decomposition in the soil, survive long after their supporting structures have deteriorated. It has long been recognised that visual and radiographic examination of teeth can provide considerable information relating to the lifestyle of an individual. This paper examines the latest scientific approaches that have become available to investigate recent and ancient teeth. These techniques include DNA analysis, which can be used to determine the sex of an individual, indicate familial relationships, study population movements, provide phylogenetic information and identify the presence of disease pathogens. A stable isotopic approach can shed light on aspects of diet and mobility and even research climate change. Proteomic analysis of ancient dental calculus can reveal specific information about individual diets. Synchrotron microcomputed tomography is a non-invasive technique which can be used to visualise physiological impactful events, such as parturition, menopause and diseases in cementum microstructure - these being displayed as aberrant growth lines.
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Affiliation(s)
- Roger Forshaw
- KNH Centre for Biomedical Egyptology, Faculty of Biology, Medicine and Health, Stopford Building, Oxford Road, University of Manchester, Manchester, M13 9PL, UK.
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4
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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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5
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Chocholova E, Roudnicky P, Potesil D, Fialova D, Krystofova K, Drozdova E, Zdrahal Z. Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus. J Proteome Res 2023; 22:3311-3319. [PMID: 37699853 PMCID: PMC10563166 DOI: 10.1021/acs.jproteome.3c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.
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Affiliation(s)
- Eva Chocholova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Pavel Roudnicky
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - David Potesil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Dana Fialova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Karolina Krystofova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Eva Drozdova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Zbynek Zdrahal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
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Wilkin S, Hommel P, Ventresca Miller A, Boivin N, Pedergnana A, Shishlina N, Trifonov V. Curated cauldrons: Preserved proteins from early copper-alloy vessels illuminate feasting practices in the Caucasian steppe. iScience 2023; 26:107482. [PMID: 37744407 PMCID: PMC10517358 DOI: 10.1016/j.isci.2023.107482] [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: 03/11/2023] [Revised: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 09/26/2023] Open
Abstract
Large metal and metal-alloy cauldrons first appear on the far western steppe and Caucasus region during the Maykop period (3700-2900 BCE); however, the types of foods or beverages cooked in and served from these vessels have remained mysterious. Here, we present proteomic analysis of nine residues from copper-alloy cauldrons from Maykop burial contexts where we identify muscle, blood, and milk proteins specific to domesticated, and possibly wild, ruminants. This study clearly demonstrates that the earliest, large-volume feasting vessels contained both primary and secondary animal products, likely prepared in the form of a stew.
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Affiliation(s)
- Shevan Wilkin
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Max Planck Institute of Geoanthropology, Jena, Germany
- Australian Research Centre for Human Evolution (ARCHE), Griffith University, Brisbane, QLD, Australia
| | - Peter Hommel
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Alicia Ventresca Miller
- Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI, USA
| | - Nicole Boivin
- Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- School of Social Science, University of Queensland, Brisbane, QLD, Australia
- Griffith Sciences, Griffith University, Brisbane, QLD, Australia
| | | | - Natalia Shishlina
- State Historical Museum, Moscow, Russia
- Peter the Great Museum of Anthropology and Ethnography (the Kunstkamera), St Petersburg, Russia
| | - Viktor Trifonov
- Institute for the History of Material Culture, St Petersburg, Russia
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7
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Radini A, Nikita E. Beyond dirty teeth: Integrating dental calculus studies with osteoarchaeological parameters. QUATERNARY INTERNATIONAL : THE JOURNAL OF THE INTERNATIONAL UNION FOR QUATERNARY RESEARCH 2023; 653-654:3-18. [PMID: 37089908 PMCID: PMC10109118 DOI: 10.1016/j.quaint.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 02/23/2022] [Accepted: 03/04/2022] [Indexed: 05/03/2023]
Abstract
The study of ancient human dental calculus (mineralized dental plaque, also known as tartar) is becoming increasingly important in osteoarchaeology, human palaeoecology and environmental archaeology. Microremains of different origin (e.g. starch granules, pollen, phytoliths, feather barbules) as well as biomolecules and chemical compounds retrieved from its mineral matrix may represent an important link between past humans and their physical, biological and social environment, but they are rarely fully linked to the evidence from skeletal remains. This paper critically reviews the lines of evidence retrieved from dental calculus in relation to osteoarchaeological parameters, employing macroscopic, microscopic and biomolecular approaches, assessing synergy potential and limitations. The scope of this paper is also to contribute to the building of a much needed theoretical framework in this emerging subfield.
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Affiliation(s)
- Anita Radini
- BioArCh, Department of Archaeology, The University of York, Wentworth Way, York, UK
- York JEOL Nanocentre, The University of York, Science Park, York, UK
- Corresponding author. BioArCh, Department of Archaeology, The University of York, Wentworth Way, York, UK.
| | - Efthymia Nikita
- Science and Technology in Archaeology and Culture Research Center, The Cyprus Institute, 2121, Aglantzia, Nicosia, Cyprus
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8
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Tang L, Wilkin S, Richter KK, Bleasdale M, Fernandes R, He Y, Li S, Petraglia M, Scott A, Teoh FK, Tong Y, Tsering T, Tsho Y, Xi L, Yang F, Yuan H, Chen Z, Roberts P, He W, Spengler R, Lu H, Wangdue S, Boivin N. Paleoproteomic evidence reveals dairying supported prehistoric occupation of the highland Tibetan Plateau. SCIENCE ADVANCES 2023; 9:eadf0345. [PMID: 37043579 PMCID: PMC10096579 DOI: 10.1126/sciadv.adf0345] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The extreme environments of the Tibetan Plateau offer considerable challenges to human survival, demanding novel adaptations. While the role of biological and agricultural adaptations in enabling early human colonization of the plateau has been widely discussed, the contribution of pastoralism is less well understood, especially the dairy pastoralism that has historically been central to Tibetan diets. Here, we analyze ancient proteins from the dental calculus (n = 40) of all human individuals with sufficient calculus preservation from the interior plateau. Our paleoproteomic results demonstrate that dairy pastoralism began on the highland plateau by ~3500 years ago. Patterns of milk protein recovery point to the importance of dairy for individuals who lived in agriculturally poor regions above 3700 m above sea level. Our study suggests that dairy was a critical cultural adaptation that supported expansion of early pastoralists into the region's vast, non-arable highlands, opening the Tibetan Plateau up to widespread, permanent human occupation.
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Affiliation(s)
- Li Tang
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Center for Archaeological Science, Sichuan University, Chengdu, China
- Institute for Prehistoric and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, Australia
- Institute for Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - Kristine Korzow Richter
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, USA
| | - Madeleine Bleasdale
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Archaeology, University of York, York, UK
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Faculty of Arts, Masaryk University, Brno, Czech Republic
- Climate Change and History Research Initiative, Princeton University, Princeton, NJ, USA
| | - Yuanhong He
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
| | - Shuai Li
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
- Center for Tibetan Studies, Sichuan University, Chengdu, China
| | - Michael Petraglia
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, Australia
- School of Social Science, University of Queensland, Brisbane, Australia
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Ashley Scott
- Department of Anthropology, Harvard University, Cambridge, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fallen K.Y. Teoh
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Yan Tong
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Tinlei Tsering
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Yang Tsho
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xian, China
| | - Feng Yang
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
- Center for Tibetan Studies, Sichuan University, Chengdu, China
| | - Haibing Yuan
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
| | - Zujun Chen
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- School of Social Science, University of Queensland, Brisbane, Australia
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Wei He
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Robert Spengler
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Hongliang Lu
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
- Center for Tibetan Studies, Sichuan University, Chengdu, China
| | - Shargan Wangdue
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - 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, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Griffith Sciences, Griffith University, Brisbane, Australia
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Ventresca Miller AR, Wilkin S, Bayarsaikhan J, Ramsøe A, Clark J, Byambadorj B, Vanderwarf S, Vanwezer N, Haruda A, Fernandes R, Miller B, Boivin N. Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13 th century. Commun Biol 2023; 6:351. [PMID: 37002413 PMCID: PMC10066276 DOI: 10.1038/s42003-023-04723-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Domesticated yaks endure as iconic symbols of high-altitude frozen landscapes, where herding communities depend on their high-fat milk, transport, dung, and natural fibers. While there is established proteomic evidence for ancient consumption of ruminant and horse milk in the mountains and steppes of northern Eurasia, yak dairy products have yet to be detected. Yak domestication and the species' dispersal from Tibet into the mountainous zones to the north are also poorly resolved due to a paucity of zooarchaeological data. To examine the potential of paleoproteomics to shed light on domesticated yak in Mongolia, we analyzed human dental calculus from Mongol era elite individuals recovered from permafrost burials in Khovsgol province, where people continue to herd yak to this day. We report the first evidence for yak dairy consumption, linked to local resource control. In addition, we confirm a large diversity of recovered whey, curd, tissue, and blood proteins, likely reflecting the excellent preservation conditions found at permafrost sites.
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Affiliation(s)
- Alicia R Ventresca Miller
- Department of Anthropology, University of Michigan, Ann Arbor, 48109, MI, USA.
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, 48109, MI, USA.
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany.
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany.
- Institute for Evolutionary Medicine, Faculty of Medicine, University of Zürich, 8057, Zürich, Switzerland.
- Australian Research Centre for Human Evolution (ARCHE), Griffith University, Brisbane, 4111, QLD, Australia.
| | - Jamsranjav Bayarsaikhan
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
- National Museum of Mongolia, Juulchin Street-1, Ulaanbaatar, Mongolia
| | - Abigail Ramsøe
- Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Julia Clark
- NOMAD Science, Glen, MT, USA
- Flinders University: Department of Archaeology, Flinders University, Bedford Park, 5042, Adelaide, SA, Australia
- Department of Sociology, Social Work and Anthropology, Utah State University, Logan, UT, USA
| | - Batsuren Byambadorj
- Department of Anthropology and Archaeology, National University of Mongolia, Baga toiruu-44, Ulaanbaatar, 46a, Mongolia
| | | | - Nils Vanwezer
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
| | - Ashleigh Haruda
- School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, UK
- Department of Archaeology, University of Exeter, Laver Building, North Parks Road, Exeter, UK
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
- School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, UK
- Faculty of Arts, Masaryk University, Arne Nováka 1, 602 00, Brno-střed, Czechia
| | - Bryan Miller
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, 48109, MI, USA
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
- History of Art Department University of Michigan, Ann Arbor, 48109, MI, USA
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
- School of Social Science, University of Queensland, Brisbane, QLD, Australia
- Department of Archaeology, University of Calgary, Calgary, AB, Canada
- Smithsonian Institution, New York, NY, USA
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10
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Evans M, Lundy J, Lucquin A, Hagan R, Kowalski Ł, Wilczyńki J, Bickle P, Adamczak K, Craig OE, Robson HK, Hendy J. Detection of dairy products from multiple taxa in Late Neolithic pottery from Poland: an integrated biomolecular approach. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230124. [PMID: 36938542 PMCID: PMC10014250 DOI: 10.1098/rsos.230124] [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: 02/01/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The detection of dairy processing is pivotal to our understanding of ancient subsistence strategies. This culinary process is linked to key arguments surrounding the evolution of lactase persistence in prehistory. Despite extensive evidence indicating the presence of dairy products in ceramics in the European Neolithic, questions remain about the nature and extent of milk (and lactose) processing and consumption. In order to investigate past patterns of dairy processing, here we analyse ancient proteins identified from Late Neolithic Funnel Beaker ceramics, scrutinizing the principle that curd and whey proteins partition during the production of dairy foods from milk. Our results indicate the presence of casein-rich dairy products in these vessels suggesting the creation of curd-enriched products from raw milk. Moreover, this analysis reveals the use of multiple species for their dairy products in the Late Neolithic, adding to a growing body of evidence for the period. Alongside palaeoproteomic analysis, we applied well-established lipid residue analysis. Differential interpretations between these two approaches show that palaeoproteomics is especially useful where the effects from isotope mixing may underestimate the frequency of dairy products in archaeological ceramics, highlighting the potential utility of a multi-stranded approach to understand life histories of vessel use.
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Affiliation(s)
- Miranda Evans
- Department of Archaeology, University of York, Heslington YO10 5DD, UK
- Department of Archaeology, The University of Cambridge, Cambridge CB2 3DZ, UK
| | - Jasmine Lundy
- Department of Archaeology, University of York, Heslington YO10 5DD, UK
| | - Alexandre Lucquin
- Department of Archaeology, University of York, Heslington YO10 5DD, UK
| | - Richard Hagan
- Department of Archaeology, University of York, Heslington YO10 5DD, UK
| | - Łukasz Kowalski
- Institute of Archaeology, Centre for Applied Archaeology, Nicolaus Copernicus University in Toruń, Szosa Bydgoska 44/48, 87-100 Toruń, Poland
| | - Jarosław Wilczyńki
- Department of Vertebrate Zoology, Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, Poland
| | - Penny Bickle
- Department of Archaeology, University of York, Heslington YO10 5DD, UK
| | - Kamil Adamczak
- Institute of Archaeology, Centre for Applied Archaeology, Nicolaus Copernicus University in Toruń, Szosa Bydgoska 44/48, 87-100 Toruń, Poland
| | - Oliver E. Craig
- Department of Archaeology, University of York, Heslington YO10 5DD, UK
| | - Harry K. Robson
- Department of Archaeology, University of York, Heslington YO10 5DD, UK
| | - Jessica Hendy
- Department of Archaeology, University of York, Heslington YO10 5DD, UK
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11
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Gancz AS, Weyrich LS. Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases. F1000Res 2023; 12:109. [PMID: 37065506 PMCID: PMC10090864 DOI: 10.12688/f1000research.129036.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2023] [Indexed: 01/31/2023] Open
Abstract
Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.
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Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
| | - Laura S Weyrich
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
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12
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Gancz AS, Weyrich LS. Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases. F1000Res 2023; 12:109. [PMID: 37065506 PMCID: PMC10090864 DOI: 10.12688/f1000research.129036.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 04/19/2023] Open
Abstract
Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.
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Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
| | - Laura S Weyrich
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
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13
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Li Q, Luo K, Su Z, Huang F, Wu Y, Zhou F, Li Y, Peng X, Li J, Ren B. Dental calculus: A repository of bioinformation indicating diseases and human evolution. Front Cell Infect Microbiol 2022; 12:1035324. [PMID: 36579339 PMCID: PMC9791188 DOI: 10.3389/fcimb.2022.1035324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Dental calculus has long been considered as a vital contributing factor of periodontal diseases. Our review focuses on the role of dental calculus as a repository and discusses the bioinformation recently reported to be concealed in dental calculus from three perspectives: time-varying oral condition, systemic diseases, and anthropology at various times. Molecular information representing an individual's contemporary oral health status could be detected in dental calculus. Additionally, pathogenic factors of systemic diseases were found in dental calculus, including bacteria, viruses and toxic heavy metals. Thus, dental calculus has been proposed to play a role as biological data storage for detection of molecular markers of latent health concerns. Through the study of environmental debris in dental calculus, an overview of an individual's historical dietary habits and information about the environment, individual behaviors and social culture changes can be unveiled. This review summarizes a new role of dental calculus as a repository of bioinformation, with potential use in the prediction of oral diseases, systemic diseases, and even anthropology.
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Affiliation(s)
- Qinyang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Kaihua Luo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhifei Su
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fangting Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yajie Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fangjie Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China,*Correspondence: Jiyao Li, ; Biao Ren,
| | - Biao Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China,*Correspondence: Jiyao Li, ; Biao Ren,
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14
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The Hidden Secrets of the Dental Calculus: Calibration of a Mass Spectrometry Protocol for Dental Calculus Protein Analysis. Int J Mol Sci 2022; 23:ijms232214387. [PMID: 36430863 PMCID: PMC9698480 DOI: 10.3390/ijms232214387] [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: 10/19/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Dental calculus is a solid deposit that forms and accumulates on the tooth surface, entrapping oral microorganisms, biomolecules, and other micro-debris found in the oral cavity. A mass spectrometry analysis of its protein content opens a vista into the subject's diet, oral flora, and even some aspects of health, thus providing new insight and expanding our knowledge of archaic cultures. Multiple experimental protocols have been proposed for the optimal extraction of proteins from dental calculus. Herein, we compared various experimental conditions in order to calibrate and validate a protocol for protein extraction. Our results show that a high concentration of acetic acid followed by mechanical crushing and sonication provided the highest protein yield, while acetone precipitation enabled the identification of more distinct proteins. We validated this protocol using archeological samples, identifying human and microbial proteins in specimens from the eighth and seventeenth centuries (approximately 250-1300 years ago). These findings demonstrate that the developed protocol is useful for studying excavated archaeological samples and that it might be utilized to explore the biohistory, dietary habits, and microbiome of archaic populations.
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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16
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Chidimuro B, Mundorff A, Speller C, Radini A, Boudreault N, Lucas M, Holst M, Lamb A, Collins M, Alexander M. Isotope analysis of human dental calculus δ 13 CO 3 2- : Investigating a potential new proxy for sugar consumption. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9286. [PMID: 35261104 PMCID: PMC9286614 DOI: 10.1002/rcm.9286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE Dental calculus (mineralised dental plaque) is composed primarily of hydroxyapatite. We hypothesise that the carbonate component of dental calculus will reflect the isotopic composition of ingested simple carbohydrates. Therefore, dental calculus carbonates may be an indicator for sugar consumption, and an alternative to bone carbonate in isotopic palaeodiet studies. METHODS We utilised Fourier transform infrared attenuated total reflectance analysis to characterise the composition and crystallisation of bone and dental calculus before isotope analysis of carbonate. Using a Sercon 20-22 mass spectrometer coupled with a Sercon GSL sample preparation system and an IsoPrime 100 dual inlet mass spectrometer plus Multiprep device to measure carbon, we tested the potential of dental calculus carbonate to identify C4 resources in diet through analysis of δ13 C values in paired bone, calculus and teeth mineral samples. RESULTS The modern population shows higher δ13 C values in all three tissue carbonates compared to both archaeological populations. Clear differences in dental calculus δ13 C values are observed between the modern and archaeological individuals suggesting potential for utilising dental calculus in isotope palaeodiet studies. The offset between dental calculus and either bone or enamel carbonate δ13 C values is large and consistent in direction, with no consistent offset between the δ13 C values for the three tissues per individual. CONCLUSIONS Our results support dental calculus carbonate as a new biomaterial to identify C4 sugar through isotope analysis. Greater carbon fractionation in the mouth is likely due to the complex formation of dental calculus as a mineralized biofilm, which results in consistently high δ13 C values compared to bone and enamel.
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Affiliation(s)
- Blessing Chidimuro
- Department of Geography and Environmental ScienceUniversity of ReadingReadingUK
- BioArCh, Department of ArchaeologyUniversity of YorkYorkUK
| | - Amy Mundorff
- Department of AnthropologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Camilla Speller
- BioArCh, Department of ArchaeologyUniversity of YorkYorkUK
- Department of AnthropologyUniversity of British ColumbiaVancouverBCCanada
| | - Anita Radini
- BioArCh, Department of ArchaeologyUniversity of YorkYorkUK
| | | | - Mary Lucas
- BioArCh, Department of ArchaeologyUniversity of YorkYorkUK
- Department of ArchaeologyMax Planck Institute for the Science of Human HistoryJenaGermany
| | - Malin Holst
- BioArCh, Department of ArchaeologyUniversity of YorkYorkUK
- York Osteoarchaeology Ltd, Bishop WiltonYorkUK
| | - Angela Lamb
- National Environmental Isotope Facility, British Geological SurveyKeyworthUK
| | - Matthew Collins
- BioArCh, Department of ArchaeologyUniversity of YorkYorkUK
- Natural History MuseumUniversity of CopenhagenDenmark
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
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17
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The spread of herds and horses into the Altai: How livestock and dairying drove social complexity in Mongolia. PLoS One 2022; 17:e0265775. [PMID: 35544454 PMCID: PMC9094512 DOI: 10.1371/journal.pone.0265775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
The initial movement of herders and livestock into the eastern steppe is of great interest, as this region has long been home to pastoralist groups. Due to a paucity of faunal remains, however, it has been difficult to discern the timing of the adoption of domesticated ruminants and horses into the region, though recent research on ancient dairying has started to shed new light on this history. Here we present proteomic evidence for shifts in dairy consumption in the Altai Mountains, drawing on evidence from sites dating from the Early Bronze to the Late Iron Age. We compare these finds with evidence for the rise of social complexity in western Mongolia, as reflected in material remains signaling population growth, the establishment of structured cemeteries, and the erection of large monuments. Our results suggest that the subsistence basis for the development of complex societies began at the dawn of the Bronze Age, with the adoption of ruminant livestock. Investments in pastoralism intensified over time, enabling a food production system that sustained growing populations. While pronounced social changes and monumental constructions occurred in tandem with the first evidence for horse dairying, ~1350 cal BCE, these shifts were fueled by a long-term economic dependence on ruminant livestock. Therefore, the spread into the Mongolian Altai of herds, and then horses, resulted in immediate dietary changes, with subsequent social and demographic transformations occurring later.
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18
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Siano F, Picariello G, Caruso T, Esposito S, Rescigno C, Addeo F, Vasca E. Proteomics and Integrated Techniques to Characterize Organic Residues in Funerary Findings from Italic Populations of the First Millennium BC. J Proteome Res 2022; 21:1330-1339. [DOI: 10.1021/acs.jproteome.2c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Siano
- Istituto di Scienze dell’Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma 64, 83100 Avellino, Italy
| | - Gianluca Picariello
- Istituto di Scienze dell’Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma 64, 83100 Avellino, Italy
| | - Tonino Caruso
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno), Italy
| | - Sara Esposito
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno), Italy
| | - Carlo Rescigno
- Dipartimento di Lettere e Beni Culturali, Università degli Studi della Campania “Luigi Vanvitelli”, Via Raffaele Perla 21, 81055 Santa Maria Capua Vetere (Caserta), Italy
| | - Francesco Addeo
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Parco Gussone, Via Università 100, 80055 Portici (Napoli), Italy
| | - Ermanno Vasca
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno), Italy
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19
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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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20
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21
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Trends in deamidation across archaeological bones, ceramics and dental calculus. Methods 2021; 200:67-79. [PMID: 34450289 DOI: 10.1016/j.ymeth.2021.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 08/14/2021] [Indexed: 11/23/2022] Open
Abstract
The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.
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22
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Runge AKW, Hendy J, Richter KK, Masson-MacLean E, Britton K, Mackie M, McGrath K, Collins M, Cappellini E, Speller C. Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome. Proc Biol Sci 2021; 288:20210020. [PMID: 34229485 PMCID: PMC8261203 DOI: 10.1098/rspb.2021.0020] [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] [Indexed: 12/20/2022] Open
Abstract
The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.
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Affiliation(s)
- Anne Kathrine W Runge
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK.,Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 København K, Denmark
| | - Jessica Hendy
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07743 Jena, Germany
| | - Kristine K Richter
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07743 Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | | | - Kate Britton
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103
| | - Meaghan Mackie
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 København K, Denmark.,The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200 København N, Denmark
| | - Krista McGrath
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK.,Department of Prehistory and Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Matthew Collins
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 København K, Denmark.,Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Enrico Cappellini
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 København K, Denmark
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK.,Department of Anthropology, University of British Columbia, 6303 NW Marine Drive, Vancouver, Canada V6T 1Z1
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23
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Salazar-García DC, Power RC, Rudaya N, Kolobova K, Markin S, Krivoshapkin A, Henry AG, Richards MP, Viola B. Dietary evidence from Central Asian Neanderthals: A combined isotope and plant microremains approach at Chagyrskaya Cave (Altai, Russia). J Hum Evol 2021; 156:102985. [PMID: 34051612 DOI: 10.1016/j.jhevol.2021.102985] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
Neanderthals are known primarily from their habitation of Western Eurasia, but they also populated large expanses of Northern Asia for thousands of years. Owing to a sparse archaeological record, relatively little is known about these eastern Neanderthal populations. Unlike in their western range, there are limited zooarchaeological and paleobotanical studies that inform us about the nature of their subsistence. Here, we perform a combined analysis of carbon and nitrogen stable isotopes on bone collagen and microbotanical remains in dental calculus to reconstruct the diet of eastern Neanderthals at Chagyrskaya Cave in the Altai Mountains of Southern Siberia, Russia. Stable isotopes identify one individual as possessing a high trophic level due to the hunting of large- and medium-sized ungulates, while the analysis of dental calculus also indicates the presence of plants in the diet of this individual and others from the site. These findings indicate eastern Neanderthals may have had broadly similar subsistence patterns to those elsewhere in their range.
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Affiliation(s)
- Domingo C Salazar-García
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Departament de Prehistòria, Arqueologia I Història Antiga, Universitat de València, València, Spain; Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain; Department of Geological Sciences, University of Cape Town, Cape Town, South Africa.
| | - Robert C Power
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Schellingstraße, 1280799, München, Germany.
| | - Natalia Rudaya
- Institute for Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Pr. Akademika Lavrentieva 17, Novosibirsk, 630090, Russia
| | - Ksenya Kolobova
- Institute for Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Pr. Akademika Lavrentieva 17, Novosibirsk, 630090, Russia
| | - Sergey Markin
- Institute for Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Pr. Akademika Lavrentieva 17, Novosibirsk, 630090, Russia
| | - Andrey Krivoshapkin
- Institute for Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Pr. Akademika Lavrentieva 17, Novosibirsk, 630090, Russia
| | - Amanda G Henry
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | | | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Canada
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Environmental implications and evidence of natural products from dental calculi of a Neolithic-Chalcolithic community (central Italy). Sci Rep 2021; 11:10665. [PMID: 34021220 PMCID: PMC8140145 DOI: 10.1038/s41598-021-89999-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/05/2021] [Indexed: 02/04/2023] Open
Abstract
In this contribution, we investigated the role of plants in the prehistoric community of Casale del Dolce (Anagni, FR, central Italy), through microparticles recovered from dental calculus. The finding of a great amount of pollen types, even in form of compact lumps, could indicate use of natural substances, such as honeybee products and/or conifer resins. This plant-microremain record also suggested environmental implications relative to the Neolithic and Chalcolithic period. Additionally, the stability of the tartar microenvironment had preserved starches and other microparticles, such as one epidermal trichome, a sporangium, and fragments of plant tissue, rarely detected in ancient dental calculus. The detection of secondary metabolites in the ancient matrix confirmed the familiarity of this community with plant resources. All these data supply various interesting food for thought and expand the knowledge about the potential of dental calculus in archaeological and archaeobotanical fields with a special focus on palaeoecology.
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25
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Rogóż J, Podbielska M, Szpyrka E, Wnuk M. Characteristics of Dietary Fatty Acids Isolated from Historic Dental Calculus of the 17th- and 18th-Century Inhabitants of the Subcarpathian Region (Poland). Molecules 2021; 26:molecules26102951. [PMID: 34063539 PMCID: PMC8155891 DOI: 10.3390/molecules26102951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Dental calculus analysis can be a valuable source of archaeological knowledge, since it preserves not only microbial and host biomolecules but also dietary and environmental debris, as well as metabolic products likely originating from dietary and craft activities. Here we described GC-MS analysis of a set of historic dental calculus samples from the front teeth of the mandibles of seven individuals found in 17th- and 18th-century graves in the city of Rzeszow, located in South-eastern Poland. We have found that only saturated fatty acids, which are characteristic for fats of animal origin, were present in the tested samples. Our preliminary results indicate that the diet of modern-period inhabitants of Rzeszow was rich in animal products, such as meat and dairy products.
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Affiliation(s)
- Joanna Rogóż
- Institute of Archaeology, University of Rzeszow, Aleja Rejtana 16c, 35-959 Rzeszow, Poland;
| | - Magdalena Podbielska
- Department of Biotechnology, University of Rzeszow, Aleja Rejtana 16c, 35-959 Rzeszow, Poland; (M.P.); (E.S.)
| | - Ewa Szpyrka
- Department of Biotechnology, University of Rzeszow, Aleja Rejtana 16c, 35-959 Rzeszow, Poland; (M.P.); (E.S.)
| | - Maciej Wnuk
- Department of Biotechnology, University of Rzeszow, Aleja Rejtana 16c, 35-959 Rzeszow, Poland; (M.P.); (E.S.)
- Correspondence:
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26
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Assessing the degradation of ancient milk proteins through site-specific deamidation patterns. Sci Rep 2021; 11:7795. [PMID: 33833277 PMCID: PMC8032661 DOI: 10.1038/s41598-021-87125-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/23/2021] [Indexed: 12/04/2022] Open
Abstract
The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramic residues, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins such as beta-lactoglobulin (BLG) and caseins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation (i.e., deamidation occurring in specific positions in the protein chain) can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then compare this to previously published palaeoproteomic data from six studies reporting ancient milk peptides. We confirm that site-specific deamidation rates, on average, are more advanced in BLG recovered from ancient dental calculus and pottery residues. Nevertheless, deamidation rates displayed a high degree of variability, making it challenging to authenticate samples with relatively few milk peptides. We demonstrate that site-specific deamidation is a useful tool for identifying modern contamination but highlight the need for multiple lines of evidence to authenticate ancient protein data.
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27
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Tanasi D, Cucina A, Cunsolo V, Saletti R, Di Francesco A, Greco E, Foti S. Paleoproteomic profiling of organic residues on prehistoric pottery from Malta. Amino Acids 2021; 53:295-312. [PMID: 33582869 PMCID: PMC7910365 DOI: 10.1007/s00726-021-02946-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/22/2021] [Indexed: 11/02/2022]
Abstract
Mass spectrometry-based approaches have been successfully applied for identifying ancient proteins in bones and other tissues. On the contrary, there are relatively few examples of the successful recovery and identification of archeological protein residues from ceramic artifacts; this is because ceramics contain much lower levels of proteins which are extensively degraded by diagenetic effects. In this paper, we report the results of the characterization of proteins extracted from pottery of the Maltese site of Baħrija, the guide-site for the Baħrija period (half of 9th-second half of eighth century BCE), recently identified as the final part of the Borġ in-Nadur culture. Proteomic data here reported confirm that one of the major issue of these kind of studies is represented by contamination of animal and human agents that may complicate endogenous protein identification and authentication. The samples tested included a small group of ceramic forms, namely three tableware and six coarse ware thought to have been used in food preparation and/or storage. In this context, the limited availability of paleobotanical and archeozoological analyses may be compensated by the outcomes of the first proteomics profiling which, even if obtained on a limited selection of vessels, revealed the centrality of wheat in the diet of the ancient community of Baħrija. The data have been deposited to the ProteomeXchange with identifier < PXD022848 > .
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Affiliation(s)
- Davide Tanasi
- Department of History, University of South Florida, SOC107 4202 E. Fowler Ave, Tampa, FL, 33620, USA
| | - Annamaria Cucina
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Vincenzo Cunsolo
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Rosaria Saletti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Antonella Di Francesco
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Enrico Greco
- Aix-Marseille Université, Institut de Chimie Radicalaire, Service 512, Avenue Escadrille Normandie Niemen, 13013, Marseille, France
| | - Salvatore Foti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
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28
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Davidson R, Fehren-Schmitz L, Llamas B. A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations. Genes (Basel) 2021; 12:215. [PMID: 33540755 PMCID: PMC7913103 DOI: 10.3390/genes12020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.
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Affiliation(s)
- Roberta Davidson
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics (NCIG), Australian National University, Canberra, ACT 0200, Australia
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29
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Bleasdale M, Richter KK, Janzen A, Brown S, Scott A, Zech J, Wilkin S, Wang K, Schiffels S, Desideri J, Besse M, Reinold J, Saad M, Babiker H, Power RC, Ndiema E, Ogola C, Manthi FK, Zahir M, Petraglia M, Trachsel C, Nanni P, Grossmann J, Hendy J, Crowther A, Roberts P, Goldstein ST, Boivin N. Ancient proteins provide evidence of dairy consumption in eastern Africa. Nat Commun 2021; 12:632. [PMID: 33504791 PMCID: PMC7841170 DOI: 10.1038/s41467-020-20682-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 12/10/2020] [Indexed: 11/09/2022] Open
Abstract
Consuming the milk of other species is a unique adaptation of Homo sapiens, with implications for health, birth spacing and evolution. Key questions nonetheless remain regarding the origins of dairying and its relationship to the genetically-determined ability to drink milk into adulthood through lactase persistence (LP). As a major centre of LP diversity, Africa is of significant interest to the evolution of dairying. Here we report proteomic evidence for milk consumption in ancient Africa. Using liquid chromatography tandem mass spectrometry (LC-MS/MS) we identify dairy proteins in human dental calculus from northeastern Africa, directly demonstrating milk consumption at least six millennia ago. Our findings indicate that pastoralist groups were drinking milk as soon as herding spread into eastern Africa, at a time when the genetic adaptation for milk digestion was absent or rare. Our study links LP status in specific ancient individuals with direct evidence for their consumption of dairy products.
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Affiliation(s)
- Madeleine Bleasdale
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
- Department of Archaeology, University of York, King's Manor, Exhibition Square, York, YO1 7EP, UK.
| | - Kristine K Richter
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Anneke Janzen
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Samantha Brown
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ashley Scott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jana Zech
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jocelyne Desideri
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, Université de Genève, Geneva, Switzerland
| | - Marie Besse
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, Université de Genève, Geneva, Switzerland
| | - Jacques Reinold
- Section française de la Direction des antiquités du Soudan, Khartoum, Sudan
| | - Mohamed Saad
- National Corporation for Antiquities and Museums of Sudan, M.Bolheim Bioarchaeology Laboratory, Khartoum, Sudan
| | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Robert C Power
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Pre-and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Emmanuel Ndiema
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Christine Ogola
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Fredrick K Manthi
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Muhammad Zahir
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Archaeology, Hazara University, Mansehra, Pakistan
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DA, USA
| | - Christian Trachsel
- Functional Genomics Center, University of Zurich/ETH, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center, University of Zurich/ETH, Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Center, University of Zurich/ETH, Zurich, Switzerland
| | - Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Alison Crowther
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
| | - Steven T Goldstein
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia.
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DA, USA.
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada.
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30
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Hendy J. Ancient protein analysis in archaeology. SCIENCE ADVANCES 2021; 7:7/3/eabb9314. [PMID: 33523896 PMCID: PMC7810370 DOI: 10.1126/sciadv.abb9314] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/20/2020] [Indexed: 05/10/2023]
Abstract
The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.
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Affiliation(s)
- Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany.
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31
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Exotic foods reveal contact between South Asia and the Near East during the second millennium BCE. Proc Natl Acad Sci U S A 2020; 118:2014956117. [PMID: 33419922 DOI: 10.1073/pnas.2014956117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although the key role of long-distance trade in the transformation of cuisines worldwide has been well-documented since at least the Roman era, the prehistory of the Eurasian food trade is less visible. In order to shed light on the transformation of Eastern Mediterranean cuisines during the Bronze Age and Early Iron Age, we analyzed microremains and proteins preserved in the dental calculus of individuals who lived during the second millennium BCE in the Southern Levant. Our results provide clear evidence for the consumption of expected staple foods, such as cereals (Triticeae), sesame (Sesamum), and dates (Phoenix). We additionally report evidence for the consumption of soybean (Glycine), probable banana (Musa), and turmeric (Curcuma), which pushes back the earliest evidence of these foods in the Mediterranean by centuries (turmeric) or even millennia (soybean). We find that, from the early second millennium onwards, at least some people in the Eastern Mediterranean had access to food from distant locations, including South Asia, and such goods were likely consumed as oils, dried fruits, and spices. These insights force us to rethink the complexity and intensity of Indo-Mediterranean trade during the Bronze Age as well as the degree of globalization in early Eastern Mediterranean cuisine.
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32
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Millard AR, Annis RG, Caffell AC, Dodd LL, Fischer R, Gerrard CM, Graves CP, Hendy J, Mackenzie L, Montgomery J, Nowell GM, Radini A, Beaumont J, Koon HEC, Speller CF. Scottish soldiers from the Battle of Dunbar 1650: A prosopographical approach to a skeletal assemblage. PLoS One 2020; 15:e0243369. [PMID: 33347451 PMCID: PMC7751964 DOI: 10.1371/journal.pone.0243369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 11/20/2020] [Indexed: 11/18/2022] Open
Abstract
After the Battle Dunbar between English and Scottish forces in 1650, captured Scottish soldiers were imprisoned in Durham and many hundreds died there within a few weeks. The partial skeletal remains of 28 of these men were discovered in 2013. Building on previous osteological work, here we report wide-ranging scientific studies of the remains to address the following questions: Did they have comparable diet, health and disease throughout their lives? Did they have common histories of movement (or lack of movement) during their childhoods? Can we create a collective biography of these men? Strontium and oxygen isotope analysis of tooth enamel investigated childhood movement. Carbon and nitrogen isotope analysis of incrementally sampled dentine addressed childhood diet and nutrition. Metaproteomic analysis of dental calculus investigated oral microbiomes and food residues; this was complemented by microscopic analysis of debris in calculus from ingested materials. Selected individuals were examined for dental microwear. The extent of hydroxylation of proline in collagen was examined as a potential biomarker for scurvy. An osteobiography for each man was created using the full range of data generated about him, and these were synthesised using an approach based on the historical method for a collective biography or prosopography. The childhood residences of the men were primarily within the Midland Valley of Scotland, though some spent parts of their childhood outside the British Isles. This is concordant with the known recruitment areas of the Scottish army in 1650. Their diets included oats, brassicas and milk but little seafood, as expected for lowland rather than highland diets of the period. Childhood periods of starvation or illness were almost ubiquitous, but not simultaneous, suggesting regionally variable food shortages in the 1620s and 1630s. It is likely there was widespread low-level scurvy, ameliorating in later years of life, which suggests historically unrecorded shortages of fruit and vegetables in the early 1640s. Almost all men were exposed to burnt plant matter, probably as inhaled soot, and this may relate to the high proportion of them with of sinusitis. Interpersonal violence causing skeletal trauma was rare. Based on commonalities in their osteobiographies, we argue that these men were drawn from the same stratum of society. This study is perhaps the most extensive to date of individuals from 17th century Scotland. Combined with a precise historical context it allows the lives of these men to be investigated and compared to the historical record with unprecedented precision. It illustrates the power of archaeological science methods to confirm, challenge and complement historical evidence.
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Affiliation(s)
- Andrew R. Millard
- Department of Archaeology, Durham University, Durham, United Kingdom
- * E-mail:
| | - Richard G. Annis
- Archaeological Services, Durham University, Durham, United Kingdom
| | - Anwen C. Caffell
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Laura L. Dodd
- Department of Archaeology, Durham University, Durham, United Kingdom
- KDK Archaeology Ltd, Leighton Buzzard, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | | | - C. Pamela Graves
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Jessica Hendy
- Department of Archaeology, University of York, York, United Kingdom
| | - Lisa Mackenzie
- Department of Archaeology, University of York, York, United Kingdom
| | - Janet Montgomery
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Geoff M. Nowell
- Department of Earth Sciences, Durham University, Durham, United Kingdom
| | - Anita Radini
- Department of Archaeology, University of York, York, United Kingdom
| | - Julia Beaumont
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | - Hannah E. C. Koon
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | - Camilla F. Speller
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
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33
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D’Agostino A, Canini A, Di Marco G, Nigro L, Spagnoli F, Gismondi A. Investigating Plant Micro-Remains Embedded in Dental Calculus of the Phoenician Inhabitants of Motya (Sicily, Italy). PLANTS 2020; 9:plants9101395. [PMID: 33092237 PMCID: PMC7590007 DOI: 10.3390/plants9101395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 01/13/2023]
Abstract
Plant records reveal remarkable evidence about past environments and human cultures. Exploiting dental calculus analysis and using a combined approach of microscopy and gas chromatography mass spectrometry, our research outlines dietary ecology and phytomedicinal practices of the ancient community of Motya (Sicily, eight to sixth century BC), one of the most important Phoenician settlements in the Mediterranean basin. Micro-remains suggest use or consumption of Triticeae cereals, and animal-derived sources (e.g., milk and aquatic birds). Markers of grape (or wine), herbs, and rhizomes, endemic of Mediterranean latitudes and the East, provide insight into the subsistence of this colony, in terms of foodstuffs and phytotherapeutic products. The application of resins and wood of Gymnosperms for social and cultural purposes is hypothesized through the identification of Pinaceae secondary metabolites and pollen grains. The information hidden in dental calculus discloses the strong human-plant interaction in Motya’s Phoenician community, in terms of cultural traditions and land use.
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Affiliation(s)
- Alessia D’Agostino
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.D.); (G.D.M.)
| | - Antonella Canini
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.D.); (G.D.M.)
- Correspondence: (A.C.); (A.G.); Tel.: +39-06-7259-4330 (A.C.); +39-06-7259-4344 (A.G.); Fax: +39-06-2023-500 (A.C. & A.G.)
| | - Gabriele Di Marco
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.D.); (G.D.M.)
| | - Lorenzo Nigro
- Department Italian Institute of Oriental Studies—ISO, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy; (L.N.); (F.S.)
| | - Federica Spagnoli
- Department Italian Institute of Oriental Studies—ISO, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy; (L.N.); (F.S.)
| | - Angelo Gismondi
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (A.D.); (G.D.M.)
- Correspondence: (A.C.); (A.G.); Tel.: +39-06-7259-4330 (A.C.); +39-06-7259-4344 (A.G.); Fax: +39-06-2023-500 (A.C. & A.G.)
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Living off the land: Terrestrial-based diet and dairying in the farming communities of the Neolithic Balkans. PLoS One 2020; 15:e0237608. [PMID: 32817620 PMCID: PMC7444498 DOI: 10.1371/journal.pone.0237608] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/29/2020] [Indexed: 01/01/2023] Open
Abstract
The application of biomolecular techniques to archaeological materials from the Balkans is providing valuable new information on the prehistory of the region. This is especially relevant for the study of the neolithisation process in SE Europe, which gradually affected the rest of the continent. Here, to answer questions regarding diet and subsistence practices in early farming societies in the central Balkans, we combine organic residue analyses of archaeological pottery, taxonomic and isotopic study of domestic animal remains and biomolecular analyses of human dental calculus. The results from the analyses of the lipid residues from pottery suggest that milk was processed in ceramic vessels. Dairy products were shown to be part of the subsistence strategies of the earliest Neolithic communities in the region but were of varying importance in different areas of the Balkan. Conversely, milk proteins were not detected within the dental calculus. The molecular and isotopic identification of meat, dairy, plants and beeswax in the pottery lipids also provided insights into the diversity of diet in these early Neolithic communities, mainly based on terrestrial resources. We also present the first compound-specific radiocarbon dates for the region, obtained directly from absorbed organic residues extracted from pottery, identified as dairy lipids.
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Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan. PLoS One 2020; 15:e0226654. [PMID: 32130218 PMCID: PMC7055813 DOI: 10.1371/journal.pone.0226654] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/01/2019] [Indexed: 11/21/2022] Open
Abstract
Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th–19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.
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Wilkin S, Ventresca Miller A, Taylor WTT, Miller BK, Hagan RW, Bleasdale M, Scott A, Gankhuyg S, Ramsøe A, Uliziibayar S, Trachsel C, Nanni P, Grossmann J, Orlando L, Horton M, Stockhammer PW, Myagmar E, Boivin N, Warinner C, Hendy J. Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years. Nat Ecol Evol 2020; 4:346-355. [PMID: 32127685 PMCID: PMC7212056 DOI: 10.1038/s41559-020-1120-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/17/2020] [Indexed: 01/20/2023]
Abstract
Dairy pastoralism is integral to contemporary and past lifeways on the eastern Eurasian steppe, facilitating survival in agriculturally challenging environments. While previous research has indicated that ruminant dairy pastoralism was practiced in the region by circa 1300 BC, the origin, extent and diversity of this custom remain poorly understood. Here, we analyse ancient proteins from human dental calculus recovered from geographically diverse locations across Mongolia and spanning 5,000 years. We present the earliest evidence for dairy consumption on the eastern Eurasian steppe by circa 3000 BC and the later emergence of horse milking at circa 1200 BC, concurrent with the first evidence for horse riding. We argue that ruminant dairying contributed to the demographic success of Bronze Age Mongolian populations and that the origins of traditional horse dairy products in eastern Eurasia are closely tied to the regional emergence of mounted herding societies during the late second millennium BC.
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Affiliation(s)
- Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Alicia Ventresca Miller
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
| | - William T T Taylor
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, Museum of Natural History, University of Colorado, Boulder, CO, USA
| | - Bryan K Miller
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Faculty of History, University of Oxford, Oxford, UK
| | - Richard W Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Madeleine Bleasdale
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ashley Scott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sumiya Gankhuyg
- Anthropology and Archaeology Department, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Abigail Ramsøe
- BioArCh, Department of Archaeology, University of York, York, UK.,Department of Earth Sciences, Natural History Museum, London, UK
| | - S Uliziibayar
- Institute of Archaeology and Ethnology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Christian Trachsel
- Functional Genomics Centre, University of Zürich/ETH, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Centre, University of Zürich/ETH, Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Centre, University of Zürich/ETH, Zurich, Switzerland
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France.,Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark Horton
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Royal Agricultural University, Cirencester, UK
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians University, Munich, Germany
| | - Erdene Myagmar
- Anthropology and Archaeology Department, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,School of Social Science, The University of Queensland, Brisbane, Queensland, Australia.,Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada.,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Evolutionary Medicine, University of Zürich, Zurich, Switzerland.,Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,BioArCh, Department of Archaeology, University of York, York, UK
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37
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Gismondi A, Baldoni M, Gnes M, Scorrano G, D’Agostino A, Di Marco G, Calabria G, Petrucci M, Müldner G, Von Tersch M, Nardi A, Enei F, Canini A, Rickards O, Alexander M, Martínez-Labarga C. A multidisciplinary approach for investigating dietary and medicinal habits of the Medieval population of Santa Severa (7th-15th centuries, Rome, Italy). PLoS One 2020; 15:e0227433. [PMID: 31990948 PMCID: PMC6986732 DOI: 10.1371/journal.pone.0227433] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/18/2019] [Indexed: 12/31/2022] Open
Abstract
A multidisciplinary approach, combining stable isotope analysis from bone proteins and investigations on dental calculus using DNA analysis, light microscopy, and gas chromatography coupled with mass spectrometry, was applied to reconstruct dietary and medicinal habits of the individuals recovered in the cemetery of the Castle of Santa Severa (7th-15th centuries CE; Rome, Italy). Stable isotope analysis was performed on 120 humans, 41 faunal specimens and 8 charred seeds. Dental calculus analyses were carried out on 94 samples. Overall, isotope data indicated an omnivorous diet based on C3-terrestrial protein, although some individuals possessed carbon values indicative of C4 plant consumption. In terms of animal protein, the diet was probably based on cattle, sheep, pig and chicken products, as witnessed by the archaeozoological findings. Evidence from calculus suggested the consumption of C3 cereals, Fabaceae, Fagaceae, milk and dairy products. Secondary metabolites of herbs and wine were also detected. The detection of marine fish ancient DNA, as well as of ω3 fatty acids in calculus, hypothesized the consumption of marine foodstuffs for this coastal population, despite the lack of a clear marine isotopic signal and the presence of polyunsaturated fatty acids in plant tissues. Moreover, the knowledge of ethnopharmacological tradition and the application of medicinal plants (e.g. Punica granatum L., Ephedra sp. L.) were also identified. The detection of artemisinin, known to have antimalarial properties, led to hypothesize the presence of malaria in the area. Altogether, the combined application of microscopy and biomolecular techniques provided an innovative reconstruction of Medieval lifeways in Central Italy.
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Affiliation(s)
- Angelo Gismondi
- Laboratory of Botany, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Marica Baldoni
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Micaela Gnes
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Gabriele Scorrano
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Alessia D’Agostino
- Laboratory of Botany, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Gabriele Di Marco
- Laboratory of Botany, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Giulietta Calabria
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Michela Petrucci
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Gundula Müldner
- Department of Archaeology, University of Reading, Reading, England, United Kingdom
| | - Matthew Von Tersch
- Department of Archaeology, BioArCh, University of York, York, England, United Kingdom
| | - Alessandra Nardi
- Department of Mathematics, University of Rome “Tor Vergata”, Rome, Italy
| | - Flavio Enei
- Museo Civico di Santa Marinella “Museo del Mare e della Navigazione Antica”, Castello di Santa Severa (Roma–Italia)
| | - Antonella Canini
- Laboratory of Botany, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Olga Rickards
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Michelle Alexander
- Department of Archaeology, BioArCh, University of York, York, England, United Kingdom
| | - Cristina Martínez-Labarga
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- * E-mail:
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D’Agostino A, Gismondi A, Di Marco G, Lo Castro M, Olevano R, Cinti T, Leonardi D, Canini A. Lifestyle of a Roman Imperial community: ethnobotanical evidence from dental calculus of the Ager Curensis inhabitants. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2019; 15:62. [PMID: 31801550 PMCID: PMC6894264 DOI: 10.1186/s13002-019-0334-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/15/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND The analysis of ancient calcified dental plaque is a powerful archaeobotanical method to elucidate the key role of the plants in human history. METHODS In this research, by applying both optic microscopy and gas chromatography mass spectrometry on this matrix, a detailed qualitative investigation for reconstructing the lifestyle of a Roman imperial community of the Ager Curensis (Sabina Tiberina, Central Italy) was performed. RESULTS The detection of animal micro-remains and molecules (e.g., hairs, feather barbules, markers of dairy products), starch granules of several cereals and legumes, pollen (e.g., Juglans regia L., Hedera sp. L.) and other plant micro-debris (e.g., trichome of Olea sp., hemp fibers), and phytochemicals (e.g., Brassicaceae, Lamiaceae herbs, Ferula sp., Trigonella foenum-graecum L., wine, and Humulus lupulus L.) in the dental calculus sample demonstrated that plant-derived foods were regularly consumed together with animal resources. CONCLUSIONS This nutritional plan, consistent with the information reported in ancient written texts, suggested that the studied population based its own subsistence on both agriculture and husbandry, probably also including beekeeping and hunting activities. All together, these results represent proofs for the comprehension of food habits, phytotherapeutic practices, and cultural traditions of one of the first Roman settlements in the Sabina Tiberina area.
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Affiliation(s)
- Alessia D’Agostino
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Angelo Gismondi
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Gabriele Di Marco
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Mauro Lo Castro
- Società Cooperativa “Il Bètilo” - Servizi per i Beni Culturali a r. l., Via Remigio De Paolis 15, 00030 San Vito Romano (RM), Italy
| | - Rosaria Olevano
- Società Cooperativa “Il Bètilo” - Servizi per i Beni Culturali a r. l., Via Remigio De Paolis 15, 00030 San Vito Romano (RM), Italy
| | - Tiziano Cinti
- Società Cooperativa “Il Bètilo” - Servizi per i Beni Culturali a r. l., Via Remigio De Paolis 15, 00030 San Vito Romano (RM), Italy
| | - Donatella Leonardi
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Antonella Canini
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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39
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Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine. Proc Natl Acad Sci U S A 2019; 116:19380-19385. [PMID: 31501337 DOI: 10.1073/pnas.1908839116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Food and diet were class markers in 19th-century Ireland, which became evident as nearly 1 million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845 to 1852. Famine took hold after a blight (Phytophthora infestans) destroyed virtually the only means of subsistence-the potato crop-for a significant proportion of the population. This study seeks to elucidate the variability of diet in mid-19th-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the famine. The samples derive from remains of people who died between August 1847 and March 1851 while receiving poor relief as inmates in the union workhouse in the city of Kilkenny (52°39' N, -7°15' W). The results corroborate the historical accounts of food provisions before and during the famine, with evidence of corn (maize), potato, and cereal starch granules from the microparticle analysis and milk protein from the proteomic analysis. Unexpectedly, there is also evidence of egg protein-a food source generally reserved only for export and the better-off social classes-which highlights the variability of the prefamine experience for those who died. Through historical contextualization, this study shows how the notoriously monotonous potato diet of the poor was opportunistically supplemented by other foodstuffs. While the Great Irish Famine was one of the worst subsistence crises in history, it was foremost a social disaster induced by the lack of access to food and not the lack of food availability.
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40
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Palaeoproteomic identification of breast milk protein residues from the archaeological skeletal remains of a neonatal dog. Sci Rep 2019; 9:12841. [PMID: 31492911 PMCID: PMC6731306 DOI: 10.1038/s41598-019-49183-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/19/2019] [Indexed: 01/07/2023] Open
Abstract
Accurate postmortem estimation of breastfeeding status for archaeological or forensic neonatal remains is difficult. Confident identification of milk-specific proteins associated with these remains would provide direct evidence of breast milk consumption. We used liquid chromatography coupled to tandem mass spectrometry (MS) to confidently identify beta-lactoglobulin-1 (LGB1) and whey acidic protein (WAP), major whey proteins associated with a neonatal dog (Canis lupus familiaris) skeleton (430–960 cal AD), from an archaeological site in Hokkaido, Japan. The age at death of the individual was estimated to be approximately two weeks after birth. Protein residues extracted from rib and vertebra fragments were analyzed and identified by matching tandem MS spectra against the dog reference proteome. A total of 200 dog protein groups were detected and at least one peptide from canine LGB1 and two peptides from canine WAP were confidently identified. These milk proteins most probably originated from the mother’s breast milk, ingested by the neonate just before it died. We suggest the milk diffused outside the digestive apparatus during decomposition, and, by being absorbed into the bones, it partially preserved. The result of this study suggests that proteomic analysis can be used for postmortem reconstruction of the breastfeeding status at the time of death of neonatal mammalian, by analyzing their skeletal archaeological remains. This method is also applicable to forensic and wildlife studies.
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41
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Bleasdale M, Ponce P, Radini A, Wilson AS, Doherty S, Daley P, Brown C, Spindler L, Sibun L, Speller C, Alexander MM. Multidisciplinary investigations of the diets of two post-medieval populations from London using stable isotopes and microdebris analysis. ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES 2019; 11:6161-6181. [PMID: 31814854 PMCID: PMC6874522 DOI: 10.1007/s12520-019-00910-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/02/2019] [Indexed: 05/29/2023]
Abstract
This paper presents the first multi-tissue study of diet in post-medieval London using both the stable light isotope analysis of carbon and nitrogen and analysis of microdebris in dental calculus. Dietary intake was explored over short and long timescales. Bulk bone collagen was analysed from humans from the Queen's Chapel of the Savoy (QCS) (n = 66) and the St Barnabas/St Mary Abbots (SB) (n = 25). Incremental dentine analysis was performed on the second molar of individual QCS1123 to explore childhood dietary intake. Bulk hair samples (n = 4) were sampled from adults from QCS, and dental calculus was analysed from four other individuals using microscopy. In addition, bone collagen from a total of 46 animals from QCS (n = 11) and the additional site of Prescot Street (n = 35) was analysed, providing the first animal dietary baseline for post-medieval London. Overall, isotopic results suggest a largely C3-based terrestrial diet for both populations, with the exception of QCS1123 who exhibited values consistent with the consumption of C4 food sources throughout childhood and adulthood. The differences exhibited in δ15Ncoll across both populations likely reflect variations in diet due to social class and occupation, with individuals from SB likely representing wealthier individuals consuming larger quantities of animal and marine fish protein. Microdebris analysis results were limited but indicate the consumption of domestic cereals. This paper demonstrates the utility of a multidisciplinary approach to investigate diet across long and short timescales to further our understanding of variations in social status and mobility.
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Affiliation(s)
- Madeleine Bleasdale
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- BioArch, Department of Archaeology, University of York, York, UK
| | - Paola Ponce
- PalaeoHub, Department of Archaeology, University of York, York, UK
| | - Anita Radini
- BioArch, Department of Archaeology, University of York, York, UK
| | - Andrew S. Wilson
- School of Archaeological & Forensic Sciences, University of Bradford, Bradford, UK
| | - Sean Doherty
- BioArch, Department of Archaeology, University of York, York, UK
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Patrick Daley
- School of Archaeological & Forensic Sciences, University of Bradford, Bradford, UK
| | - Chloe Brown
- BioArch, Department of Archaeology, University of York, York, UK
| | - Luke Spindler
- BioArch, Department of Archaeology, University of York, York, UK
- Oxford Radiocarbon Accelerator Unit, University of Oxford, Oxford, UK
| | - Lucy Sibun
- Archaeology South-East, Institute of Archaeology, University College London, London, UK
| | - Camilla Speller
- BioArch, Department of Archaeology, University of York, York, UK
- Department of Anthropology, University of British Columbia, Vancouver, Canada
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Velsko IM, Fellows Yates JA, Aron F, Hagan RW, Frantz LAF, Loe L, Martinez JBR, Chaves E, Gosden C, Larson G, Warinner C. Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage. MICROBIOME 2019; 7:102. [PMID: 31279340 PMCID: PMC6612086 DOI: 10.1186/s40168-019-0717-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/24/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates. RESULTS Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins. CONCLUSIONS Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.
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Affiliation(s)
- Irina M Velsko
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK.
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Richard W Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, OX2 0ES, UK
| | | | - Eros Chaves
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma City, 73117, OK, USA
- Current address: Pinellas Dental Specialties, Largo, FL, 33776, USA
| | - Chris Gosden
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma City, 73117, OK, USA.
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
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Late Bronze Age cultural origins of dairy pastoralism in Mongolia. Proc Natl Acad Sci U S A 2018; 115:12083-12085. [PMID: 30420514 DOI: 10.1073/pnas.1817559115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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44
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Cleland TP. Human Bone Paleoproteomics Utilizing the Single-Pot, Solid-Phase-Enhanced Sample Preparation Method to Maximize Detected Proteins and Reduce Humics. J Proteome Res 2018; 17:3976-3983. [DOI: 10.1021/acs.jproteome.8b00637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Timothy P. Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
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