1
|
Manthey C, Cepon-Robins T, Warrener A. Hyperandrogenism associated with polycystic ovary syndrome may have a protective effect against fracture risk in female athletes: A pilot study. Am J Hum Biol 2024; 36:e24070. [PMID: 38488301 DOI: 10.1002/ajhb.24070] [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: 09/08/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 08/03/2024] Open
Abstract
OBJECTIVES Polycystic ovary syndrome (PCOS), characterized by polycystic ovaries, anovulation, and hyperandrogenism, is believed to be an evolutionary mismatch disease. Past research has examined PCOS as a uniform disease, despite variation in phenotypes across diagnostic categories, but establishing an evolutionary mismatch requires a focus on individual traits. We suggest PCOS hyperandrogenism may have been beneficial in ancestral environments because it reduced fracture risk and associated morbidity and mortality due to increased bone mineral density (BMD). We test this hypothesis by assessing fracture frequency, a proxy for BMD, in highly active females with and without PCOS hyperandrogenism. METHODS Sixty-seven reproductive-aged women were surveyed and grouped as: high intensity interval training (HIIT; a proxy for metabolic and physical stress) athletes with hyperandrogenic PCOS (31.24%), HIIT athletes without PCOS (29.85%), and nonathletes with hyperandrogenic PCOS (38.81%). Fracture occurrence was compared between the groups using independent samples Kruskal-Wallis tests for non-normally distributed data, and multiple regression analysis was used to examine anthropometrics, lifestyle and reproductive factors, PCOS status, and exercise frequency on fracture occurrence. RESULTS Fracture occurrence was higher in non-PCOS athletes (3.8 ± 4.3) than PCOS-athletes (1.2 ± 1.4, p = .11) and PCOS-non-athletes (1.0 ± 1.4, p < .01). PCOS-athletes and nonathletes did not differ significantly in fracture occurrence (p = .33). These results were independent of factors associated with bone health. CONCLUSIONS These preliminary findings suggest females with PCOS-related hyperandrogenism may be less likely to experience bone fractures and provide an initial step to explaining why PCOS has persisted despite marked negative reproductive consequences in modern populations.
Collapse
Affiliation(s)
- Courtney Manthey
- The University of Colorado Colorado Springs, Colorado Springs, Colorado, USA
| | - Tara Cepon-Robins
- The University of Colorado Colorado Springs, Colorado Springs, Colorado, USA
| | - Anna Warrener
- The University of Colorado Denver, Denver, Colorado, USA
| |
Collapse
|
2
|
Baranzini SE, Graves JS. What doesn't kill you makes you stronger . . . or does it? Mult Scler 2024; 30:292-294. [PMID: 38366936 DOI: 10.1177/13524585241231664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Affiliation(s)
- Sergio E Baranzini
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer S Graves
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
3
|
Rayfield KM, Mychajliw AM, Singleton RR, Sholts SB, Hofman CA. Uncovering the Holocene roots of contemporary disease-scapes: bringing archaeology into One Health. Proc Biol Sci 2023; 290:20230525. [PMID: 38052246 DOI: 10.1098/rspb.2023.0525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
The accelerating pace of emerging zoonotic diseases in the twenty-first century has motivated cross-disciplinary collaboration on One Health approaches, combining microbiology, veterinary and environmental sciences, and epidemiology for outbreak prevention and mitigation. Such outbreaks are often caused by spillovers attributed to human activities that encroach on wildlife habitats and ecosystems, such as land use change, industrialized food production, urbanization and animal trade. While the origin of anthropogenic effects on animal ecology and biogeography can be traced to the Late Pleistocene, the archaeological record-a long-term archive of human-animal-environmental interactions-has largely been untapped in these One Health approaches, thus limiting our understanding of these dynamics over time. In this review, we examine how humans, as niche constructors, have facilitated new host species and 'disease-scapes' from the Late Pleistocene to the Anthropocene, by viewing zooarchaeological, bioarchaeological and palaeoecological data with a One Health perspective. We also highlight how new biomolecular tools and advances in the '-omics' can be holistically coupled with archaeological and palaeoecological reconstructions in the service of studying zoonotic disease emergence and re-emergence.
Collapse
Affiliation(s)
- Kristen M Rayfield
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alexis M Mychajliw
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biology & Program in Environmental Studies, Middlebury College, Middlebury, VT 05753-6203, USA
| | - Robin R Singleton
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
| | - Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Veilleux CC, Garrett EC, Pajic P, Saitou M, Ochieng J, Dagsaan LD, Dominy NJ, Perry GH, Gokcumen O, Melin AD. Human subsistence and signatures of selection on chemosensory genes. Commun Biol 2023; 6:683. [PMID: 37400713 DOI: 10.1038/s42003-023-05047-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/15/2023] [Indexed: 07/05/2023] Open
Abstract
Chemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. The transition from hunting and gathering to agriculture dramatically altered how humans acquire food. Recent genetic and linguistic studies suggest agriculture may have precipitated olfactory degeneration. Here, we explore the effects of subsistence behaviors on olfactory (OR) and taste (TASR) receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia. We analyze 378 functional OR and 26 functional TASR genes in 133 individuals across populations in Uganda (Twa, Sua, BaKiga) and the Philippines (Agta, Mamanwa, Manobo) with differing subsistence histories. We find no evidence of relaxed selection on chemosensory genes in agricultural populations. However, we identify subsistence-related signatures of local adaptation on chemosensory genes within each geographic region. Our results highlight the importance of culture, subsistence economy, and drift in human chemosensory perception.
Collapse
Affiliation(s)
- Carrie C Veilleux
- Department of Anatomy, Midwestern University, 19555 N 59th Ave, Glendale, AZ, 85308, USA.
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
| | - Eva C Garrett
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA, 02215, USA
| | - Petar Pajic
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Marie Saitou
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Joseph Ochieng
- Department of Anatomy, Makerere University College of Health Sciences, Kampala, Uganda
| | - Lilia D Dagsaan
- National Commission for Indigenous Peoples, Botolan, Philippines
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, 6047 Silsby Hall, Hanover, NH, 03755, USA
| | - George H Perry
- Departments of Anthropology and Biology, The Pennsylvania State University, 410 Carpenter Building, University Park, PA, 16802, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada.
| |
Collapse
|
6
|
Kerner G, Neehus AL, Philippot Q, Bohlen J, Rinchai D, Kerrouche N, Puel A, Zhang SY, Boisson-Dupuis S, Abel L, Casanova JL, Patin E, Laval G, Quintana-Murci L. Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe. CELL GENOMICS 2023; 3:100248. [PMID: 36819665 PMCID: PMC9932995 DOI: 10.1016/j.xgen.2022.100248] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/24/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.
Collapse
Affiliation(s)
- Gaspard Kerner
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Nacim Kerrouche
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, New York, NY 10065, USA
- Department of Pediatrics, Necker Hospital for Sick Children, 75015 Paris, France
| | - Etienne Patin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Guillaume Laval
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Lluis Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
- Collège de France, Chair of Human Genomics and Evolution, 75005 Paris, France
| |
Collapse
|
7
|
Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
Collapse
Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
| |
Collapse
|
8
|
Kessler SE, Aunger R. The evolution of the human healthcare system and implications for understanding our responses to COVID-19. Evol Med Public Health 2022; 10:87-107. [PMID: 35284079 PMCID: PMC8908543 DOI: 10.1093/emph/eoac004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/14/2022] [Indexed: 12/15/2022] Open
Abstract
The COVID-19 pandemic has revealed an urgent need for a comprehensive, multidisciplinary understanding of how healthcare systems respond successfully to infectious pathogens-and how they fail. This study contributes a novel perspective that focuses on the selective pressures that shape healthcare systems over evolutionary time. We use a comparative approach to trace the evolution of care-giving and disease control behaviours across species and then map their integration into the contemporary human healthcare system. Self-care and pro-health environmental modification are ubiquitous across animals, while derived behaviours like care for kin, for strangers, and group-level organizational responses have evolved via different selection pressures. We then apply this framework to our behavioural responses to COVID-19 and demonstrate that three types of conflicts are occurring: (1) conflicting selection pressures on individuals, (2) evolutionary mismatches between the context in which our healthcare behaviours evolved and our globalized world of today and (3) evolutionary displacements in which older forms of care are currently dispensed through more derived forms. We discuss the significance of understanding how healthcare systems evolve and change for thinking about the role of healthcare systems in society during and after the time of COVID-19-and for us as a species as we continue to face selection from infectious diseases.
Collapse
Affiliation(s)
- Sharon E Kessler
- Department of Psychology, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Robert Aunger
- Environmental Health Group, London School of Hygiene and Tropical Medicine, London, UK
| |
Collapse
|
9
|
Nova N. Cross-Species Transmission of Coronaviruses in Humans and Domestic Mammals, What Are the Ecological Mechanisms Driving Transmission, Spillover, and Disease Emergence? Front Public Health 2021; 9:717941. [PMID: 34660513 PMCID: PMC8514784 DOI: 10.3389/fpubh.2021.717941] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022] Open
Abstract
Coronaviruses cause respiratory and digestive diseases in vertebrates. The recent pandemic, caused by the novel severe acute respiratory syndrome (SARS) coronavirus 2, is taking a heavy toll on society and planetary health, and illustrates the threat emerging coronaviruses can pose to the well-being of humans and other animals. Coronaviruses are constantly evolving, crossing host species barriers, and expanding their host range. In the last few decades, several novel coronaviruses have emerged in humans and domestic animals. Novel coronaviruses have also been discovered in captive wildlife or wild populations, raising conservation concerns. The evolution and emergence of novel viruses is enabled by frequent cross-species transmission. It is thus crucial to determine emerging coronaviruses' potential for infecting different host species, and to identify the circumstances under which cross-species transmission occurs in order to mitigate the rate of disease emergence. Here, I review (broadly across several mammalian host species) up-to-date knowledge of host range and circumstances concerning reported cross-species transmission events of emerging coronaviruses in humans and common domestic mammals. All of these coronaviruses had similar host ranges, were closely related (indicative of rapid diversification and spread), and their emergence was likely associated with high-host-density environments facilitating multi-species interactions (e.g., shelters, farms, and markets) and the health or well-being of animals as end- and/or intermediate spillover hosts. Further research is needed to identify mechanisms of the cross-species transmission events that have ultimately led to a surge of emerging coronaviruses in multiple species in a relatively short period of time in a world undergoing rapid environmental change.
Collapse
Affiliation(s)
- Nicole Nova
- Department of Biology, Stanford University, Stanford, CA, United States
| |
Collapse
|
10
|
Brinkworth JF, Valizadegan N. Sepsis and the evolution of human increased sensitivity to lipopolysaccharide. Evol Anthropol 2021; 30:141-157. [PMID: 33689211 DOI: 10.1002/evan.21887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/29/2020] [Accepted: 01/30/2021] [Indexed: 01/03/2023]
Abstract
Among mammals, humans are exquisitely sensitive to lipopolysaccharide (LPS), an environmentally pervasive bacterial cell membrane component. Very small doses of LPS trigger powerful immune responses in humans and can even initiate symptoms of sepsis. Close evolutionary relatives such as African and Asian monkeys require doses that are an order of magnitude higher to do the same. Why humans have evolved such an energetically expensive antimicrobial strategy is a question that biological anthropologists are positioned to help address. Here we compare LPS sensitivity in primate/mammalian models and propose that human high sensitivity to LPS is adaptive, linked to multiple immune tactics against pathogens, and part of multi-faceted anti-microbial strategy that strongly overlaps with that of other mammals. We support a notion that LPS sensitivity in humans has been driven by microorganisms that constitutively live on us, and has been informed by human behavioral changes over our species' evolution (e.g., meat eating, agricultural practices, and smoking).
Collapse
Affiliation(s)
- Jessica F Brinkworth
- Evolutionary Immunology and Genomics Laboratory, Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA.,Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Animal Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Negin Valizadegan
- Evolutionary Immunology and Genomics Laboratory, Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA.,Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
11
|
Fatumo S, Ebenezer TE, Ekenna C, Isewon I, Ahmad U, Adetunji C, Oladipo EK, Adebiyi M, Adebiyi E, Nashiru O. The Nigerian Bioinformatics and Genomics Network (NBGN): a collaborative platform to advance bioinformatics and genomics in Nigeria. Glob Health Epidemiol Genom 2020; 5:e3. [PMID: 32742665 PMCID: PMC7372179 DOI: 10.1017/gheg.2020.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/24/2020] [Accepted: 04/20/2020] [Indexed: 12/29/2022] Open
Abstract
Africa plays a central importance role in the human origins, and disease susceptibility, agriculture and biodiversity conservation. Nigeria as the most populous and most diverse country in Africa, owing to its 250 ethnic groups and over 500 different native languages is imperative to any global genomic initiative. The newly inaugurated Nigerian Bioinformatics and Genomics Network (NBGN) becomes necessary to facilitate research collaborative activities and foster opportunities for skills' development amongst Nigerian bioinformatics and genomics investigators. NBGN aims to advance and sustain the fields of genomics and bioinformatics in Nigeria by serving as a vehicle to foster collaboration, provision of new opportunities for interactions between various interdisciplinary subfields of genomics, computational biology and bioinformatics as this will provide opportunities for early career researchers. To provide the foundation for sustainable collaborations, the network organises conferences, workshops, trainings and create opportunities for collaborative research studies and internships, recognise excellence, openly share information and create opportunities for more Nigerians to develop the necessary skills to exceed in genomics and bioinformatics. NBGN currently has attracted more than 650 members around the world. Research collaborations between Nigeria, Africa and the West will grow and all stakeholders, including funding partners, African scientists, researchers across the globe, physicians and patients will be the eventual winners. The exponential membership growth and diversity of research interests of NBGN just within weeks of its establishment and the unanticipated attendance of its activities suggest the significant importance of the network to bioinformatics and genomics research in Nigeria.
Collapse
Affiliation(s)
- Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, UK
- Uganda Medical Informatics Centre, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- H3 Africa Bioinformatics Network (H3 ABioNet) Node, CGRI/NABDA, Abuja, Nigeria
| | - ThankGod E. Ebenezer
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park Innovation Centre, NorwichNR4 7UZ, UK
| | | | - Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Umar Ahmad
- Medical Genetics Laboratory, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra, Selangor, Malaysia
- Department of Anatomy, Faculty of Medicine, Bauchi State University, Gadau, Nigeria
| | | | - Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Marion Adebiyi
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Department of Computer Science, Landmark University, Omu-Aran, Nigeria
| | - Ezekiel Adebiyi
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Oyekanmi Nashiru
- H3 Africa Bioinformatics Network (H3 ABioNet) Node, CGRI/NABDA, Abuja, Nigeria
| | | |
Collapse
|
12
|
Arning N, Wilson DJ. The past, present and future of ancient bacterial DNA. Microb Genom 2020; 6:mgen000384. [PMID: 32598277 PMCID: PMC7478633 DOI: 10.1099/mgen.0.000384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.
Collapse
Affiliation(s)
- Nicolas Arning
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| |
Collapse
|
13
|
Aoki K. A three-population wave-of-advance model for the European early Neolithic. PLoS One 2020; 15:e0233184. [PMID: 32428013 PMCID: PMC7237037 DOI: 10.1371/journal.pone.0233184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/29/2020] [Indexed: 11/19/2022] Open
Abstract
Ancient DNA studies have shown that early farming spread through most of Europe by the range expansion of farmers of Anatolian origin rather than by the conversion to farming of the local hunter-gatherers, and have confirmed that these hunter-gatherers continued to coexist with the incoming farmers. In this short report, I extend a previous three-population wave-of-advance model to accommodate these new findings, and derive the conditions supportive of such a scenario in terms of the relative magnitudes of the parameters. The revised model predicts that the conversion rate must, not surprisingly, be low, but also that the hunter-gatherers must compete more strongly with the converted farmers than with the alien farmers. Moreover, competition with the hunter-gatherers diminishes the speed of the wave-of advance of the farmers. In addition, I briefly consider how the wave-of-advance approach may contribute to interpreting the results of archaeological studies using the summed probability distribution of radiocarbon dates.
Collapse
Affiliation(s)
- Kenichi Aoki
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Nakano-ku, Tokyo, Japan
- * E-mail:
| |
Collapse
|
14
|
Zheng Z, Wang X, Li M, Li Y, Yang Z, Wang X, Pan X, Gong M, Zhang Y, Guo Y, Wang Y, Liu J, Cai Y, Chen Q, Okpeku M, Colli L, Cai D, Wang K, Huang S, Sonstegard TS, Esmailizadeh A, Zhang W, Zhang T, Xu Y, Xu N, Yang Y, Han J, Chen L, Lesur J, Daly KG, Bradley DG, Heller R, Zhang G, Wang W, Chen Y, Jiang Y. The origin of domestication genes in goats. SCIENCE ADVANCES 2020; 6:eaaz5216. [PMID: 32671210 PMCID: PMC7314551 DOI: 10.1126/sciadv.aaz5216] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/06/2020] [Indexed: 05/22/2023]
Abstract
Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene, which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7200 and 8100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanisms of animal domestication.
Collapse
Affiliation(s)
- Zhuqing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yunjia Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhirui Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiangyu Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Mian Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Moses Okpeku
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Discipline of Genetics, School of Life Science, University of Kwazulu-Natal, Durban 4000, South Africa
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, via Emilia Parmense n. 84, 29122, Piacenza (PC), Italy
- BioDNA–Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, via Emilia Parmense n. 84, 29122, Piacenza (PC), Italy
| | - Dawei Cai
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Shisheng Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Tingting Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yangbin Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Naiyi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yi Yang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100193, China
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | | | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
15
|
Donat R, Mokrane FZ, Rousseau H, Dedouit F, Telmon N, Crubézy É. The antiquity of the spondyloarthritides: Presentation of one of the oldest Neolithic cases in Western Europe. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 24:229-235. [PMID: 30597411 DOI: 10.1016/j.ijpp.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
In humans, little is yet known about the origins of the inflammatory rheumatisms of the spondyloarthritides group, especially regarding the period of their emergence. However, a better knowledge of their history would help to clarify their aetiology. We report a paleopathological case of European origin, dated from the late Neolithic (3621-3023 cal BC), consisting of an isolated vertebral block combining erosion, ossification and severe anterior and posterior ankylosis. The lesional presentation is very suggestive of a severe form of axial spondyloarthritis. This specimen and some other rare cases from the same period found in Western Europe suggest that these diseases appeared, in this geographical region, in evolving groups of humans as part of the demographic and epidemiological transition that constituted the Neolithic period. The emergence of infectious agents and the profound dietary changes that occurred during this period of human history may have favoured the appearance of the spondyloarthritides.
Collapse
Affiliation(s)
- Richard Donat
- Laboratory of Molecular Anthropology and Image Synthesis (AMIS), University of Toulouse, French National Centre for Scientific Research (CNRS), UMR 5288, Faculty of Medicine Purpan, 37, Allées Jules Guesde, 31000, Toulouse, France.
| | - Fatima-Zohra Mokrane
- Laboratory of Molecular Anthropology and Image Synthesis (AMIS), University of Toulouse, French National Centre for Scientific Research (CNRS), UMR 5288, Faculty of Medicine Purpan, 37, Allées Jules Guesde, 31000, Toulouse, France; Department of Radiology, CHU Toulouse-Rangueil, 1, avenue du Pr Jean Poulhès TSA 50032, 31059, Toulouse Cedex 9, France; Department of Radiology, New York-Presbyterian, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY, 10032, USA
| | - Hervé Rousseau
- Department of Radiology, CHU Toulouse-Rangueil, 1, avenue du Pr Jean Poulhès TSA 50032, 31059, Toulouse Cedex 9, France
| | - Fabrice Dedouit
- Laboratory of Molecular Anthropology and Image Synthesis (AMIS), University of Toulouse, French National Centre for Scientific Research (CNRS), UMR 5288, Faculty of Medicine Purpan, 37, Allées Jules Guesde, 31000, Toulouse, France; University Center of Legal Medicine, Lausanne-Geneva, Forensic Imaging and Anthropology Unit, Chemin de la Vulliette 4, CH-1000, Lausanne 25, Switzerland
| | - Norbert Telmon
- Laboratory of Molecular Anthropology and Image Synthesis (AMIS), University of Toulouse, French National Centre for Scientific Research (CNRS), UMR 5288, Faculty of Medicine Purpan, 37, Allées Jules Guesde, 31000, Toulouse, France; Department of Forensic Medicine, CHU Toulouse-Rangueil, 1, avenue du Pr Jean Poulhès TSA 50032, 31059, Toulouse Cedex 9, France
| | - Éric Crubézy
- Laboratory of Molecular Anthropology and Image Synthesis (AMIS), University of Toulouse, French National Centre for Scientific Research (CNRS), UMR 5288, Faculty of Medicine Purpan, 37, Allées Jules Guesde, 31000, Toulouse, France
| |
Collapse
|
16
|
Shoko R, Manasa J, Maphosa M, Mbanga J, Mudziwapasi R, Nembaware V, Sanyika WT, Tinago T, Chikwambi Z, Mawere C, Matimba A, Mugumbate G, Mufandaedza J, Mulder N, Patterton H. Strategies and opportunities for promoting bioinformatics in Zimbabwe. PLoS Comput Biol 2018; 14:e1006480. [PMID: 30496170 PMCID: PMC6264469 DOI: 10.1371/journal.pcbi.1006480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Ryman Shoko
- Department of Biology, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- * E-mail:
| | - Justen Manasa
- African Institute of Biomedical Science & Technology, Harare, Zimbabwe
| | - Mcebisi Maphosa
- Department of Crop and Soil Science, School of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Joshua Mbanga
- Department of Applied Biology and Biochemistry, Faculty of Applied Sciences, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Reagan Mudziwapasi
- Department of Crop and Soil Science, School of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Victoria Nembaware
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Walter T. Sanyika
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Tawanda Tinago
- Department of Biology, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Zedias Chikwambi
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Cephas Mawere
- Department of Biotechnology, School of Industrial Science and Technology, Harare Institute of Technology, Harare, Zimbabwe
| | - Alice Matimba
- Department of Clinical Pharmacology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Grace Mugumbate
- Department of Chemistry, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | | | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hugh Patterton
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
17
|
Hedrick SM. The Imperative to Vaccinate. J Pediatr 2018; 201:259-263. [PMID: 30054163 PMCID: PMC7131101 DOI: 10.1016/j.jpeds.2018.06.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/01/2018] [Accepted: 06/13/2018] [Indexed: 11/16/2022]
Affiliation(s)
- Stephen M. Hedrick
- Reprint requests: Stephen M. Hedrick, PhD, UC San Diego, Molecular Biology, 9500 Gilman Dr, La Jolla, CA 92093-0377
| |
Collapse
|
18
|
Social Structure Facilitated the Evolution of Care-giving as a Strategy for Disease Control in the Human Lineage. Sci Rep 2018; 8:13997. [PMID: 30262928 PMCID: PMC6160448 DOI: 10.1038/s41598-018-31568-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/21/2018] [Indexed: 01/18/2023] Open
Abstract
Humans are the only species to have evolved cooperative care-giving as a strategy for disease control. A synthesis of evidence from the fossil record, paleogenomics, human ecology, and disease transmission models, suggests that care-giving for the diseased evolved as part of the unique suite of cognitive and socio-cultural specializations that are attributed to the genus Homo. Here we demonstrate that the evolution of hominin social structure enabled the evolution of care-giving for the diseased. Using agent-based modeling, we simulate the evolution of care-giving in hominin networks derived from a basal primate social system and the three leading hypotheses of ancestral human social organization, each of which would have had to deal with the elevated disease spread associated with care-giving. We show that (1) care-giving is an evolutionarily stable strategy in kin-based cooperatively breeding groups, (2) care-giving can become established in small, low density groups, similar to communities that existed before the increases in community size and density that are associated with the advent of agriculture in the Neolithic, and (3) once established, care-giving became a successful method of disease control across social systems, even as community sizes and densities increased. We conclude that care-giving enabled hominins to suppress disease spread as social complexity, and thus socially-transmitted disease risk, increased.
Collapse
|
19
|
Skelly E, Kapellas K, Cooper A, Weyrich LS. Consequences of colonialism: A microbial perspective to contemporary Indigenous health. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:423-437. [DOI: 10.1002/ajpa.23637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Emily Skelly
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Kostas Kapellas
- Australian Research Centre for Population Oral Health, Adelaide Dental School University of Adelaide Adelaide South Australia Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| |
Collapse
|
20
|
Orr MR, Kocurek KM, Young DL. Gut Microbiota and Human Health: Insights From Ecological Restoration. THE QUARTERLY REVIEW OF BIOLOGY 2018. [DOI: 10.1086/698021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
21
|
Abstract
The emergence of novel zoonotic pathogens is one of the greatest challenges to global health security. The advent of increasingly sophisticated diagnostics tools has revolutionized our capacity to detect and respond to these health threats more rapidly than ever before. Yet, no matter how sophisticated these tools become, the initial identification of emerging infectious diseases begins at the local community level. It is here that the initial human or animal case resides, and it is here that early pathogen detection would have maximum benefit. Unfortunately, many areas at highest risk of zoonotic disease emergence lack sufficient infrastructure capacity to support robust laboratory diagnostic systems. Multiple factors are essential for pathogen detection networks, including an understanding of the complex sociological and ecological factors influencing disease transmission risk, community engagement, surveillance along high-risk human-animal interfaces, and a skilled laboratory workforce. Here we discuss factors relevant to the emerging disease paradigm, recent technical advances in diagnostic methods, and strategies for comprehensive and sustainable approaches to rapid zoonotic disease detection.
Collapse
Affiliation(s)
- Brian H Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| | - Jonna A K Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| |
Collapse
|
22
|
Kessler SE, Bonnell TR, Byrne RW, Chapman CA. Selection to outsmart the germs: The evolution of disease recognition and social cognition. J Hum Evol 2017. [PMID: 28622934 DOI: 10.1016/j.jhevol.2017.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The emergence of providing care to diseased conspecifics must have been a turning point during the evolution of hominin sociality. On a population level, care may have minimized the costs of socially transmitted diseases at a time of increasing social complexity, although individual care-givers probably incurred increased transmission risks. We propose that care-giving likely originated within kin networks, where the costs may have been balanced by fitness increases obtained through caring for ill kin. We test a novel hypothesis of hominin cognitive evolution in which disease may have selected for the cognitive ability to recognize when a conspecific is infected. Because diseases may produce symptoms that are likely detectable via the perceptual-cognitive pathways integral to social cognition, we suggest that disease recognition and social cognition may have evolved together. Using agent-based modeling, we test 1) under what conditions disease can select for increasing disease recognition and care-giving among kin, 2) whether providing care produces greater selection for cognition than an avoidance strategy, and 3) whether care-giving alters the progression of the disease through the population. The greatest selection was produced by diseases with lower risks to the care-giver and prevalences low enough not to disrupt the kin networks. When care-giving and avoidance strategies were compared, only care-giving reduced the severity of the disease outbreaks and subsequent population crashes. The greatest selection for increased cognitive abilities occurred early in the model runs when the outbreaks and population crashes were most severe. Therefore, over the course of human evolution, repeated introductions of novel diseases into naïve populations could have produced sustained selection for increased disease recognition and care-giving behavior, leading to the evolution of increased cognition, social complexity, and, eventually, medical care in humans. Finally, we lay out predictions derived from our disease recognition hypothesis that we encourage paleoanthropologists, bioarchaeologists, primatologists, and paleogeneticists to test.
Collapse
Affiliation(s)
- Sharon E Kessler
- Department of Anthropology, McGill University, Canada; Durham University, Department of Anthropology, UK.
| | | | - Richard W Byrne
- School of Psychology and Neuroscience, University of St. Andrews, UK
| | - Colin A Chapman
- Department of Anthropology, McGill University, Canada; Wildlife Conservation Society, New York, USA
| |
Collapse
|
23
|
Shehata HR, Griffiths MW, Raizada MN. Seeds of the Wild Progenitor of Maize Possess Bacteria That Antagonize Foodborne Pathogens. Foodborne Pathog Dis 2017; 14:202-209. [DOI: 10.1089/fpd.2016.2225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hanan R. Shehata
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
- Department of Microbiology, School of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mansel W. Griffiths
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
24
|
Braud M, Magee DA, Park SDE, Sonstegard TS, Waters SM, MacHugh DE, Spillane C. Genome-Wide microRNA Binding Site Variation between Extinct Wild Aurochs and Modern Cattle Identifies Candidate microRNA-Regulated Domestication Genes. Front Genet 2017; 8:3. [PMID: 28197171 PMCID: PMC5281612 DOI: 10.3389/fgene.2017.00003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 01/09/2017] [Indexed: 12/21/2022] Open
Abstract
The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs. To investigate this, we analyzed the open reading frame DNA sequence of 19,994 orthologous protein-coding gene pairs from extant Bos taurus genomes and a single extinct B. primigenius genome. We identified miRNA binding site polymorphisms in the 3′ UTRs of 1,620 of these orthologous genes. These 1,620 genes with altered miRNA binding sites between the B. taurus and B. primigenius lineages represent candidate domestication genes. Using a novel Score Site ratio metric we have ranked these miRNA-regulated genes according to the extent of divergence between miRNA binding site presence, frequency and copy number between the orthologous genes from B. taurus and B. primigenius. This provides an unbiased approach to identify cattle genes that have undergone the most changes in miRNA binding (i.e., regulation) between the wild aurochs and modern-day cattle breeds. In addition, we demonstrate that these 1,620 candidate domestication genes are enriched for roles in pigmentation, fertility, neurobiology, metabolism, immunity and production traits (including milk quality and feed efficiency). Our findings suggest that directional selection of miRNA regulatory variants was important in the domestication and subsequent artificial selection that gave rise to modern taurine cattle.
Collapse
Affiliation(s)
- Martin Braud
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, University Road Galway, Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin Dublin, Ireland
| | - Stephen D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre Dublin, Ireland
| | | | - Sinead M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Dunsany, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College DublinDublin, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College DublinDublin, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, University Road Galway, Ireland
| |
Collapse
|
25
|
Darling MI, Donoghue HD. Insights from paleomicrobiology into the indigenous peoples of pre-colonial America - a review. Mem Inst Oswaldo Cruz 2016; 109:131-9. [PMID: 24714964 PMCID: PMC4015261 DOI: 10.1590/0074-0276140589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 02/06/2023] Open
Abstract
This review investigates ancient infectious diseases in the Americas dated to the
pre-colonial period and considers what these findings can tell us about the history
of the indigenous peoples of the Americas. It gives an overview, but focuses on four
microbial pathogens from this period: Helicobacter pylori,
Mycobacterium tuberculosis, Trypanosoma cruzi
and Coccidioides immitis, which cause stomach ulceration and gastric
cancer, tuberculosis, Chagas disease and valley fever, respectively. These pathogens
were selected as H. pylori can give insight into ancient human
migrations into the Americas, M. tuberculosis is associated with
population density and urban development, T. cruzi can elucidate
human living conditions and C. immitis can indicate agricultural
development. A range of methods are used to diagnose infectious disease in ancient
human remains, with DNA analysis by polymerase chain reaction one of the most
reliable, provided strict precautions are taken against cross contamination. The
review concludes with a brief summary of the changes that took place after European
exploration and colonisation.
Collapse
Affiliation(s)
- Millie I Darling
- Division of Biosciences, Centre for Clinical Microbiology, University College London, London, UK
| | - Helen D Donoghue
- Division of Biosciences, Centre for Clinical Microbiology, University College London, London, UK
| |
Collapse
|
26
|
Heath KM, Axton JH, McCullough JM, Harris N. The evolutionary adaptation of the C282Y mutation to culture and climate during the European Neolithic. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:86-101. [PMID: 26799452 PMCID: PMC5066702 DOI: 10.1002/ajpa.22937] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 12/20/2015] [Accepted: 12/20/2015] [Indexed: 01/10/2023]
Abstract
OBJECTIVES The C282Y allele is the major cause of hemochromatosis as a result of excessive iron absorption. The mutation arose in continental Europe no earlier than 6,000 years ago, coinciding with the arrival of the Neolithic agricultural revolution. Here we hypothesize that this new Neolithic diet, which originated in the sunny warm and dry climates of the Middle East, was carried by migrating farmers into the chilly and damp environments of Europe where iron is a critical micronutrient for effective thermoregulation. We argue that the C282Y allele was an adaptation to this novel environment. MATERIALS AND METHODS To address our hypothesis, we compiled C282Y allele frequencies, known Neolithic sites in Europe and climatic data on temperature and rainfall for statistical analysis. RESULTS Our findings indicate that the geographic cline for C282Y frequency in Europe increases as average temperatures decrease below 16°C, a critical threshold for thermoregulation, with rainy days intensifying the trend. DISCUSSION The results indicate that the deleterious C282Y allele, responsible for most cases of hemochromatosis, may have evolved as a selective advantage to culture and climate during the European Neolithic.
Collapse
Affiliation(s)
- Kathleen M. Heath
- Department of Earth and Environmental SystemsIndiana State UniversityTerre HauteIN47809
| | - Jacob H. Axton
- Department of BiologyIndiana State UniversityTerre HauteIN47809
| | | | - Nathan Harris
- Department of AnthropologyUniversity of UtahSalt Lake CityUT84112
| |
Collapse
|
27
|
Abstract
Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.
Collapse
Affiliation(s)
- Thomas K. Karikari
- Department of Science Laboratory Technology, School of Applied Science and Technology, Wa Polytechnic, Wa, Ghana
- * E-mail:
| |
Collapse
|
28
|
Ancient pathogen genomics: insights into timing and adaptation. J Hum Evol 2014; 79:137-49. [PMID: 25532802 DOI: 10.1016/j.jhevol.2014.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 09/08/2014] [Accepted: 11/05/2014] [Indexed: 12/15/2022]
Abstract
Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.
Collapse
|
29
|
Weyrich LS, Dobney K, Cooper A. Ancient DNA analysis of dental calculus. J Hum Evol 2014; 79:119-24. [PMID: 25476244 DOI: 10.1016/j.jhevol.2014.06.018] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 05/19/2014] [Accepted: 06/19/2014] [Indexed: 12/22/2022]
Abstract
Dental calculus (calcified tartar or plaque) is today widespread on modern human teeth around the world. A combination of soft starchy foods, changing acidity of the oral environment, genetic pre-disposition, and the absence of dental hygiene all lead to the build-up of microorganisms and food debris on the tooth crown, which eventually calcifies through a complex process of mineralisation. Millions of oral microbes are trapped and preserved within this mineralised matrix, including pathogens associated with the oral cavity and airways, masticated food debris, and other types of extraneous particles that enter the mouth. As a result, archaeologists and anthropologists are increasingly using ancient human dental calculus to explore broad aspects of past human diet and health. Most recently, high-throughput DNA sequencing of ancient dental calculus has provided valuable insights into the evolution of the oral microbiome and shed new light on the impacts of some of the major biocultural transitions on human health throughout history and prehistory. Here, we provide a brief historical overview of archaeological dental calculus research, and discuss the current approaches to ancient DNA sampling and sequencing. Novel applications of ancient DNA from dental calculus are discussed, highlighting the considerable scope of this new research field for evolutionary biology and modern medicine.
Collapse
Affiliation(s)
- Laura S Weyrich
- The Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, Australia
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK
| | - Alan Cooper
- The Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, Australia.
| |
Collapse
|
30
|
Brinkworth JF, Barreiro LB. The contribution of natural selection to present-day susceptibility to chronic inflammatory and autoimmune disease. Curr Opin Immunol 2014; 31:66-78. [PMID: 25458997 DOI: 10.1016/j.coi.2014.09.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022]
Abstract
Chronic inflammatory and autoimmune diseases have been the focus of many genome-wide association studies (GWAS) because they represent a significant cause of illness and morbidity, and many are heritable. Almost a decade of GWAS studies suggests that the pathological inflammation associated with these diseases is controlled by a limited number of networked immune system genes. Chronic inflammatory and autoimmune diseases are enigmatic from an evolutionary perspective because they exert a negative affect on reproductive fitness. The persistence of these conditions may be partially explained by the important roles the implicated immune genes play in pathogen defense and other functions thought to be under strong natural selection in humans. The evolutionary reasons for chronic inflammatory and autoimmune disease persistence and uneven distribution across populations are the focus of this review.
Collapse
Affiliation(s)
- Jessica F Brinkworth
- Sainte-Justine Hospital Research Centre, Montréal, Quebec H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec H3T 1J4, Canada
| | - Luis B Barreiro
- Sainte-Justine Hospital Research Centre, Montréal, Quebec H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec H3T 1J4, Canada.
| |
Collapse
|