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Yamamoto K, Namba S, Sonehara K, Suzuki K, Sakaue S, Cooke NP, Higashiue S, Kobayashi S, Afuso H, Matsuura K, Mitsumoto Y, Fujita Y, Tokuda T, Matsuda K, Gakuhari T, Yamauchi T, Kadowaki T, Nakagome S, Okada Y. Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations. Nat Commun 2024; 15:9780. [PMID: 39532881 PMCID: PMC11558008 DOI: 10.1038/s41467-024-54052-0] [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: 12/06/2023] [Accepted: 10/30/2024] [Indexed: 11/16/2024] Open
Abstract
The tripartite ancestral structure is a recently proposed model for the genetic origin of modern Japanese, comprising indigenous Jomon hunter-gatherers and two additional continental ancestors from Northeast Asia and East Asia. To investigate the impact of the tripartite structure on genetic and phenotypic variation today, we conducted biobank-scale analyses by merging Biobank Japan (BBJ; n = 171,287) with ancient Japanese and Eurasian genomes (n = 22). We demonstrate the applicability of the tripartite model to Japanese populations throughout the archipelago, with an extremely strong correlation between Jomon ancestry and genomic variation among individuals. We also find that the genetic legacy of Jomon ancestry underlies an elevated body mass index (BMI). Genome-wide association analysis with rigorous adjustments for geographical and ancestral substructures identifies 132 variants that are informative for predicting individual Jomon ancestry. This prediction model is validated using independent Japanese cohorts (Nagahama cohort, n = 2993; the second cohort of BBJ, n = 72,695). We further confirm the phenotypic association between Jomon ancestry and BMI using East Asian individuals from UK Biobank (n = 2286). Our extensive analysis of ancient and modern genomes, involving over 250,000 participants, provides valuable insights into the genetic legacy of ancient hunter-gatherers in contemporary populations.
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Affiliation(s)
- Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Children's health and Genetics, Division of Health Sciences, Osaka University Graduate School of Medicine, Suite, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ken Suzuki
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Niall P Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Shuzo Kobayashi
- Tokushukai Group, Tokyo, Japan
- Department of Kidney Disease & Transplant Center, Shonan Kamakura General Hospital, Kamakura, Japan
| | | | | | | | | | | | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Tokyo, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
- Sapiens Life Sciences, Evolution and Medicine Research Center, Kanazawa University, Kanazawa, Japan
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland.
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan.
- Sapiens Life Sciences, Evolution and Medicine Research Center, Kanazawa University, Kanazawa, Japan.
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Premium Research Institute for Human Metaverse (WPI-PRIMe), Osaka University, Suita, Japan.
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Ventura L, Romeo G, Grimaldi B, Causarano A, Caruso C, Voi G, Pensiero V. The "Queen of the Moors". Paleopathological investigation of a natural mummy from Scicli, South-Eastern Sicily. Pathologica 2022; 114:152-158. [PMID: 35481566 PMCID: PMC9248255 DOI: 10.32074/1591-951x-256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/11/2022] [Indexed: 11/30/2022] Open
Abstract
A natural, well-preserved mummy belonging to a 45-55 year old female was found in the Church of Santa Maria della Consolazione in Scicli, south-eastern Sicily. The body was submitted to external examination, digital radiology, and computed tomography scanning. Paleopathological investigation allowed us to detect pulmonary pathology related to tuberculosis, atherosclerosis, and phleboliths. The presence of the latter, along with good dental condition with focal caries and obesity indicates a subject belonging to a high social class in good nutritional status. Along with other examples, this case allows to infer that tuberculosis was a common disease in that area, if not in the whole island, prior to the antibiotic era. Mummies need to be properly surveyed and protected, but also adequately studied by multidisciplinary teams of experts. The presence in such a team of at least one skilled anatomic/surgical pathologist, as long as well trained in the study of ancient human remains, represents an undeniable condition.
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Affiliation(s)
- Luca Ventura
- Division of Pathology, San Salvatore Hospital, L'Aquila, Italy.,Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy
| | - Guido Romeo
- Division of Radiology, Busacca Hospital, Scicli, Italy.,Department of Diagnostic Imaging and Radiology, Maggiore Hospital, Modica, Italy
| | - Bettina Grimaldi
- Division of Radiology, Busacca Hospital, Scicli, Italy.,Department of Diagnostic Imaging and Radiology, Maggiore Hospital, Modica, Italy
| | | | | | - Giuseppe Voi
- Health Care Residence, Busacca Hospital, Scicli, Italy
| | - Valentina Pensiero
- NEPTIS Training Project, Researchers and experts in high technology and technological innovation applied to cultural heritage, University of Palermo, Italy
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Littlejohn GO. Historical bioarcheological aspects of diffuse idiopathic skeletal hyperostosis in humans. Semin Arthritis Rheum 2021; 52:151942. [PMID: 34998578 DOI: 10.1016/j.semarthrit.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/04/2021] [Accepted: 12/20/2021] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To identify diffuse idiopathic skeletal hyperostosis (DISH) in the human bioarcheological record to seek out temporal, geographic and dietary information to enhance better understanding of this common condition. MATERIALS AND METHODS A review of available literature was conducted. RESULTS DISH has been identified in hominin populations over millions of years, including several different human species. The distribution of DISH in ancient populations is diverse, both temporally and geographically. Where available, dietary intake of subjects with DISH, in contrast to those without DISH, suggests that metabolic factors associate with DISH. CONCLUSION DISH is a ubiquitous human disorder over the ages. Metabolic factors appear important in ancient populations of those with DISH.
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Affiliation(s)
- Geoffrey O Littlejohn
- Emeritus Director Monash Health Rheumatology, Adjunct Clinical Professor, Monash University, Melbourne, Victoria, Australia.
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