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Watanabe Y, Ohashi J. Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations. iScience 2023; 26:106130. [PMID: 36879818 PMCID: PMC9984562 DOI: 10.1016/j.isci.2023.106130] [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: 09/26/2022] [Revised: 12/02/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,Genome Medical Science Project Toyama Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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Komarnytsky S, Retchin S, Vong CI, Lila MA. Gains and Losses of Agricultural Food Production: Implications for the Twenty-First Century. Annu Rev Food Sci Technol 2021; 13:239-261. [PMID: 34813357 DOI: 10.1146/annurev-food-082421-114831] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The world food supply depends on a diminishing list of plant crops and animal livestock to not only feed the ever-growing human population but also improve its nutritional state and lower the disease burden. Over the past century or so, technological advances in agricultural and food processing have helped reduce hunger and poverty but have not adequately addressed sustainability targets. This has led to an erosion of agricultural biodiversity and balanced diets and contributed to climate change and rising rates of chronic metabolic diseases. Modern food supply chains have progressively lost dietary fiber, complex carbohydrates, micronutrients, and several classes of phytochemicals with high bioactivity and nutritional relevance. This review introduces the concept of agricultural food systems losses and focuses on improved sources of agricultural diversity, proteins with enhanced resilience, and novel monitoring, processing, and distribution technologies that are poised to improve food security, reduce food loss and waste, and improve health profiles in the near future. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Slavko Komarnytsky
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
| | - Sophia Retchin
- Kenan-Flagler Business School, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Chi In Vong
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
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Pritchard DI, Falcone FH, Mitchell PD. The evolution of IgE-mediated type I hypersensitivity and its immunological value. Allergy 2021; 76:1024-1040. [PMID: 32852797 DOI: 10.1111/all.14570] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/12/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022]
Abstract
The allergic phenotype manifests itself in a spectrum of troublesome to life-threatening diseases, from seasonal hay fever, through the food allergies, atopic eczema, asthma, to anaphylaxis. Allergy, that is an overreaction to allergen in hypersensitive individuals, results from the production of IgE, mast cell and basophil sensitisation and degranulation, requiring a range of medications to manage the conditions. Yet it is highly likely that allergy evolved for a purpose and that allergic diseases are accidental consequences of an insufficiently regulated immune response. This article presents a viewpoint from which to restore the immunological reputation of the allergic phenotype. We consider the evolutionary origins of potential allergens, toxins and parasites, and how they might have influenced early-mammal species in existence when IgE first developed. We conclude that the allergic phenotype has likely saved the lives of many more mammals than have ever died from allergy, so justifying the positive role of IgE in our evolution.
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Affiliation(s)
| | - Franco H. Falcone
- Institute for Parasitology Justus‐Liebig‐University Gießen Gießen Germany
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Ortiz-Prado E, Simbaña-Rivera K, Gómez-Barreno L, Tamariz L, Lister A, Baca JC, Norris A, Adana-Diaz L. Potential research ethics violations against an indigenous tribe in Ecuador: a mixed methods approach. BMC Med Ethics 2020; 21:100. [PMID: 33069227 PMCID: PMC7568418 DOI: 10.1186/s12910-020-00542-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 10/06/2020] [Indexed: 01/22/2023] Open
Abstract
Background Biomedical and ethnographic studies among indigenous people are common practice in health and geographical research. Prior health research misconduct has been documented, particularly when obtaining genetic material. The objective of this study was to crossmatch previously published data with the perceptions of the Waorani peoples about the trading of their genetic material and other biological samples. Methods We conducted a mixed methods study design using a tailored 15-item questionnaire in 72 participants and in-depth interviews in 55 participants belonging to 20 Waorani communities about their experiences and perceptions of participating in biomedical research projects. Additionally, we conducted a systematic review of the literature in order to crossmatch the published results of studies stating the approval of an ethics committee and individual consent within their work. Results A total of 40 men (60%) and 32 women (40%), with a mean age of 57 ± 15 years agreed to be interviewed for inclusion. Five main categories around the violation of good clinical practices were identified, concerning the obtention of blood samples from a recently contacted Waorani native community within the Amazonian region of Ecuador. These themes are related to the lack of adequate communication between community members and researchers as well as the voluntariness to participate in health research. Additionally, over 40 years, a total of 38 manuscripts related to the use of biological samples in Waorani indigenous people were published. The majority of the studies (68%) did not state within their article obtaining research ethics board approval, and 71% did not report obtaining the informed consent of the participants prior to the execution of the project. Conclusion Clinical Research on the Waorani community in the Ecuadorian Amazon basin has been performed on several occasions. Unfortunately, the majority of these projects did not follow the appropriate ethical and professional standards in either reporting the results or fulfilling them. The results of our investigation suggest that biological material, including genetic material, has been used by researchers globally, with some omitting the minimum information required to guarantee transparency and good clinical practices. We highlight the importance of stating ethics within research to avoid breaches in research transparency.
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Affiliation(s)
- Esteban Ortiz-Prado
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas, Ecuador Calle de los Colimes y Avenida De los Granados, Quito, 170137, Ecuador.
| | - Katherine Simbaña-Rivera
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas, Ecuador Calle de los Colimes y Avenida De los Granados, Quito, 170137, Ecuador
| | - Lenin Gómez-Barreno
- One Health Research Group, Faculty of Medicine, Universidad de Las Americas, Ecuador Calle de los Colimes y Avenida De los Granados, Quito, 170137, Ecuador
| | - Leonardo Tamariz
- Division of Population Health and Computational Medicine, University of Miami, Florida, USA
| | - Alex Lister
- Public Health Program, Faculty of Medicine, University of Southampton, Southampton, England
| | - Juan Carlos Baca
- Grassland Group, Technical University of Munich, Munich, Germany
| | | | - Lila Adana-Diaz
- Faculty of Psychology, Universidad de Las Americas, Quito, Ecuador
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Trumble BC, Finch CE. THE EXPOSOME IN HUMAN EVOLUTION: FROM DUST TO DIESEL. THE QUARTERLY REVIEW OF BIOLOGY 2019; 94:333-394. [PMID: 32269391 PMCID: PMC7141577 DOI: 10.1086/706768] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Global exposures to air pollution and cigarette smoke are novel in human evolutionary history and are associated with about 16 million premature deaths per year. We investigate the history of the human exposome for relationships between novel environmental toxins and genetic changes during human evolution in six phases. Phase I: With increased walking on savannas, early human ancestors inhaled crustal dust, fecal aerosols, and spores; carrion scavenging introduced new infectious pathogens. Phase II: Domestic fire exposed early Homo to novel toxins from smoke and cooking. Phases III and IV: Neolithic to preindustrial Homo sapiens incurred infectious pathogens from domestic animals and dense communities with limited sanitation. Phase V: Industrialization introduced novel toxins from fossil fuels, industrial chemicals, and tobacco at the same time infectious pathogens were diminishing. Thereby, pathogen-driven causes of mortality were replaced by chronic diseases driven by sterile inflammogens, exogenous and endogenous. Phase VI: Considers future health during global warming with increased air pollution and infections. We hypothesize that adaptation to some ancient toxins persists in genetic variations associated with inflammation and longevity.
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Affiliation(s)
- Benjamin C Trumble
- School of Human Evolution & Social Change and Center for Evolution and Medicine, Arizona State University Tempe, Arizona 85287 USA
| | - Caleb E Finch
- Leonard Davis School of Gerontology and Dornsife College, University of Southern California Los Angeles, California 90089-0191 USA
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Williams AC, Hill LJ. Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions? Int J Tryptophan Res 2019; 12:1178646919855944. [PMID: 31258332 PMCID: PMC6585247 DOI: 10.1177/1178646919855944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/28/2022] Open
Abstract
Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.
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Affiliation(s)
- Adrian C Williams
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lisa J Hill
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
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Tallavaara M, Eronen JT, Luoto M. Productivity, biodiversity, and pathogens influence the global hunter-gatherer population density. Proc Natl Acad Sci U S A 2018; 115:1232-1237. [PMID: 29282314 PMCID: PMC5819417 DOI: 10.1073/pnas.1715638115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The environmental drivers of species distributions and abundances are at the core of ecological research. However, the effects of these drivers on human abundance are not well-known. Here, we report how net primary productivity, biodiversity, and pathogen stress affect human population density using global ethnographic hunter-gatherer data. Our results show that productivity has significant effects on population density globally. The most important direct drivers, however, depend on environmental conditions: biodiversity influences population density exclusively in low-productivity regions, whereas pathogen stress does so in high-productivity regions. Our results also indicate that subtropical and temperate forest biomes provide the highest carrying capacity for hunter-gatherer populations. These findings document that environmental factors play a key role in shaping global population density patterns of preagricultural humans.
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Affiliation(s)
- Miikka Tallavaara
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland;
| | - Jussi T Eronen
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland
- BIOS Research Unit, FI-00170 Helsinki, Finland
| | - Miska Luoto
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland
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Page AE, Viguier S, Dyble M, Smith D, Chaudhary N, Salali GD, Thompson J, Vinicius L, Mace R, Migliano AB. Reproductive trade-offs in extant hunter-gatherers suggest adaptive mechanism for the Neolithic expansion. Proc Natl Acad Sci U S A 2016; 113:4694-9. [PMID: 27071109 PMCID: PMC4855554 DOI: 10.1073/pnas.1524031113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Neolithic demographic transition remains a paradox, because it is associated with both higher rates of population growth and increased morbidity and mortality rates. Here we reconcile the conflicting evidence by proposing that the spread of agriculture involved a life history quality-quantity trade-off whereby mothers traded offspring survival for increased fertility, achieving greater reproductive success despite deteriorating health. We test this hypothesis by investigating fertility, mortality, health, and overall reproductive success in Agta hunter-gatherers whose camps exhibit variable levels of sedentarization, mobility, and involvement in agricultural activities. We conducted blood composition tests in 345 Agta and found that viral and helminthic infections as well as child mortality rates were significantly increased with sedentarization. Nonetheless, both age-controlled fertility and overall reproductive success were positively affected by sedentarization and participation in cultivation. Thus, we provide the first empirical evidence, to our knowledge, of an adaptive mechanism in foragers that reconciles the decline in health and child survival with the observed demographic expansion during the Neolithic.
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Affiliation(s)
- Abigail E Page
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Sylvain Viguier
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Mark Dyble
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Daniel Smith
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Nikhil Chaudhary
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Gul Deniz Salali
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - James Thompson
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Lucio Vinicius
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Ruth Mace
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
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Houldcroft CJ, Underdown SJ. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:379-88. [PMID: 27063929 DOI: 10.1002/ajpa.22985] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 02/10/2016] [Accepted: 03/03/2016] [Indexed: 12/13/2022]
Abstract
High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Charlotte J Houldcroft
- Division of Biological Anthropology, Department of Archaeology & Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Infection, Inflammation and Rheumatology Section, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Simon J Underdown
- Human Origins and Palaeoenvironmental Research Group (HOPE), Department of Anthropology & Geography, Oxford Brookes University, Oxford, OX3 0BP, UK
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Abstract
Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases.
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