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Uchida-Fukuhara Y, Shimamura S, Sawafuji R, Nishiuchi T, Yoneda M, Ishida H, Matsumura H, Tsutaya T. Palaeoproteomic investigation of an ancient human skeleton with abnormal deposition of dental calculus. Sci Rep 2024; 14:5938. [PMID: 38467689 PMCID: PMC10928219 DOI: 10.1038/s41598-024-55779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Detailed investigation of extremely severe pathological conditions in ancient human skeletons is important as it could shed light on the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate an ancient human skeletal individual with severe oral pathology, focusing our research on bacterial pathogenic factors and host defense response. This female skeleton, from the Okhotsk period (i.e., fifth to thirteenth century) of Northern Japan, poses relevant amounts of abnormal dental calculus deposition and exhibits oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from the calculus of the subject. We identified two pathogenic or bioinvasive proteins originating from two of the three "red complex" bacteria, the core species associated with severe periodontal disease in modern humans, as well as two additional bioinvasive proteins of periodontal-associated bacteria. Moreover, we discovered defense response system-associated human proteins, although their proportion was mostly similar to those reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily more intense in ancient individuals with significant amounts of abnormal dental calculus deposition.
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Affiliation(s)
- Yoko Uchida-Fukuhara
- Department of Oral Morphology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8525, Japan.
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.
| | - Shigeru Shimamura
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Rikai Sawafuji
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Takumi Nishiuchi
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
- Mt. Olive Hospital, Okinawa, 903-0804, Japan
| | - Hirofumi Matsumura
- School of Health Sciences, Sapporo Medical University, Hokkaido, 060-8556, Japan
| | - Takumi Tsutaya
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan.
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Sato T, Adachi N, Kimura R, Hosomichi K, Yoneda M, Oota H, Tajima A, Toyoda A, Kanzawa-Kiriyama H, Matsumae H, Koganebuchi K, Shimizu KK, Shinoda KI, Hanihara T, Weber A, Kato H, Ishida H. Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan. Genome Biol Evol 2021; 13:6355032. [PMID: 34410389 PMCID: PMC8449830 DOI: 10.1093/gbe/evab192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 12/18/2022] Open
Abstract
Recent studies on paleogenomics have reported some Paleolithic and Neolithic genomes that have provided new insights into the human population history in East and Northeast Asia. However, there remain some cases where more recent migration events need to be examined to elucidate the detailed formation process of local populations. Although the area around northern Japan is one of the regions archaeologically suggested to have been affected by migration waves after the Neolithic period, the genetic source of these migrations are still unclear. Thus, genomic data from such past migrant populations would be highly informative to clarify the detailed formation process of local populations in this region. Here, we report the genome sequence of a 900-year-old adult female (NAT002) belonging to the prehistoric Okhotsk people, who have been considered to be the past migrants to northern Japan after the Neolithic period. We found a close relationship between NAT002 and modern Lower Amur populations and past admixture events between the Amur, Jomon, and Kamchatka ancestries. The admixture dating suggested migration of Amur-related ancestry at approximately 1,600 BP, which is compatible with the archaeological evidence regarding the settlement of the Okhotsk people. Our results also imply migration of Kamchatka-related ancestry at approximately 2,000 BP. In addition, human leukocyte antigen (HLA) typing detected the HLA-B*40 allele, which is reported to increase the risk of arthritis, suggesting the genetic vulnerability of NAT002 to hyperostosis, which was observed around her chest clavicle.
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Affiliation(s)
- Takehiro Sato
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan.,Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Hiroki Oota
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | | | - Hiromi Matsumae
- Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan.,Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
| | - Kae Koganebuchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kentaro K Shimizu
- Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan
| | - Andrzej Weber
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada.,Research Centre "Baikal Region", Irkutsk State University, Irkutsk, Russia.,Laboratoire Méditerranéen de Préhistoire Europe Afrique (LAMPEA) - UMR 7269, Aix-Marseille Université, Aix-en-Provence, France
| | - Hirofumi Kato
- Centre for Ainu and Indigenous Studies, Hokkaido University, Sapporo, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
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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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Leipe C, Sergusheva EA, Müller S, Spengler RN, Goslar T, Kato H, Wagner M, Weber AW, Tarasov PE. Barley (Hordeum vulgare) in the Okhotsk culture (5th-10th century AD) of northern Japan and the role of cultivated plants in hunter-gatherer economies. PLoS One 2017; 12:e0174397. [PMID: 28355249 PMCID: PMC5371317 DOI: 10.1371/journal.pone.0174397] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/08/2017] [Indexed: 11/19/2022] Open
Abstract
This paper discusses archaeobotanical remains of naked barley recovered from the Okhotsk cultural layers of the Hamanaka 2 archaeological site on Rebun Island, northern Japan. Calibrated ages (68% confidence interval) of the directly dated barley remains suggest that the crop was used at the site ca. 440–890 cal yr AD. Together with the finds from the Oumu site (north-eastern Hokkaido Island), the recovered seed assemblage marks the oldest well-documented evidence for the use of barley in the Hokkaido Region. The archaeobotanical data together with the results of a detailed pollen analysis of contemporaneous sediment layers from the bottom of nearby Lake Kushu point to low-level food production, including cultivation of barley and possible management of wild plants that complemented a wide range of foods derived from hunting, fishing, and gathering. This qualifies the people of the Okhotsk culture as one element of the long-term and spatially broader Holocene hunter–gatherer cultural complex (including also Jomon, Epi-Jomon, Satsumon, and Ainu cultures) of the Japanese archipelago, which may be placed somewhere between the traditionally accepted boundaries between foraging and agriculture. To our knowledge, the archaeobotanical assemblages from the Hokkaido Okhotsk culture sites highlight the north-eastern limit of prehistoric barley dispersal. Seed morphological characteristics identify two different barley phenotypes in the Hokkaido Region. One compact type (naked barley) associated with the Okhotsk culture and a less compact type (hulled barley) associated with Early–Middle Satsumon culture sites. This supports earlier suggestions that the “Satsumon type” barley was likely propagated by the expansion of the Yayoi culture via south-western Japan, while the “Okhotsk type” spread from the continental Russian Far East region, across the Sea of Japan. After the two phenotypes were independently introduced to Hokkaido, the boundary between both barley domains possibly existed ca. 600–1000 cal yr AD across the island region. Despite a large body of studies and numerous theoretical and conceptual debates, the question of how to differentiate between hunter–gatherer and farming economies persists reflecting the wide range of dynamic subsistence strategies used by humans through the Holocene. Our current study contributes to the ongoing discussion of this important issue.
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Affiliation(s)
- Christian Leipe
- Institute of Geological Sciences, Section Paleontology, Freie Universität Berlin, Malteserstr. 74–100, Building D, Berlin, Germany
- * E-mail:
| | - Elena A. Sergusheva
- Institute of History, Archaeology and Ethnography, Far Eastern Branch of the Russian Academy of Sciences, Pushkinskaya 89, Vladivostok, Russia
| | - Stefanie Müller
- Institute of Geological Sciences, Section Paleontology, Freie Universität Berlin, Malteserstr. 74–100, Building D, Berlin, Germany
- Eurasia Department and Beijing Branch Office, German Archaeological Institute, Im Dol 2–6, Building II, Berlin, Germany
| | - Robert N. Spengler
- Institute for the Study of the Ancient World, New York University, New York, NY, United States of America
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Tomasz Goslar
- Faculty of Physics, Adam Mickiewicz University, Umultowska 85, Poznan, Poland
- Poznan Radiocarbon Laboratory, Foundation of the A. Mickiewicz University, Rubiez 46, Poznan, Poland
| | - Hirofumi Kato
- Center for Ainu and Indigenous Studies, Hokkaido University, Kita 8, Nishi 6, Kita-ku Sapporo, Hokkaido, Japan
| | - Mayke Wagner
- Eurasia Department and Beijing Branch Office, German Archaeological Institute, Im Dol 2–6, Building II, Berlin, Germany
| | - Andrzej W. Weber
- Department of Anthropology, University of Alberta, Tory Bldg. 13–15, Edmonton, Alberta, Canada
- Aix Marseille Univ, CNRS, Minist Culture & Com, LAMPEA, Aix-en-Provence, France
| | - Pavel E. Tarasov
- Institute of Geological Sciences, Section Paleontology, Freie Universität Berlin, Malteserstr. 74–100, Building D, Berlin, Germany
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