1
|
Nelder MP, Schats R, Poinar HN, Cooke A, Brickley MB. Pathogen prospecting of museums: Reconstructing malaria epidemiology. Proc Natl Acad Sci U S A 2024; 121:e2310859121. [PMID: 38527214 PMCID: PMC11009618 DOI: 10.1073/pnas.2310859121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.
Collapse
Affiliation(s)
- Mark P. Nelder
- Enteric, Zoonotic and Vector-Borne Diseases, Health Protection, Public Health Ontario, Toronto, ONM5G 1M1, Canada
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, 2333 CCLeiden, The Netherlands
| | - Hendrik N. Poinar
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
- Department of Biochemistry, McMaster University, Hamilton, ONL8S 4L9, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Amanda Cooke
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Megan B. Brickley
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| |
Collapse
|
2
|
Santos BS, Marques MP, Ceríaco LMP. Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation. AN ACAD BRAS CIENC 2024; 96:e20230622. [PMID: 38451598 DOI: 10.1590/0001-3765202420230622] [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: 05/31/2023] [Accepted: 08/27/2023] [Indexed: 03/08/2024] Open
Abstract
Natural History Collections (NHCs) represent the world's largest repositories of long-term biodiversity datasets. Specimen collection and voucher deposition has been the backbone of NHCs since their inception, but recent decades have seen a drastic decline in rates of growth via active collecting. Amphibians and reptiles are amongst the most threatened zoological groups on the planet and are historically underrepresented in most worldwide NHCs. As part of an ongoing project to review the Portuguese zoological collections in the country's NHCs, herpetological data from its three major museums and smaller collections was gathered and used to examine the coverage and representation of the different taxa extant in Portugal. These collections are not taxonomically, geographically, or temporally complete. Approximately 90% of the Portuguese herpetological taxa are represented in the country's NHCs, and around half of the taxa are represented by less than 50 specimens. Geographically, the collections cover less than 30% of the country's territory and almost all of the occurring taxa have less than 10% of their known distribution represented in the collections. A discussion on the implications for science of such incomplete collections and a review of the current status of Portuguese NHCs is presented.
Collapse
Affiliation(s)
- Bruna S Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- Universidade do Porto, Departamento de Biologia, Faculdade de Ciências, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Mariana P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- Universidade do Porto, Departamento de Biologia, Faculdade de Ciências, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213, U.S.A
| | - Luis M P Ceríaco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213, U.S.A
- Universidade Federal do Rio de Janeiro, Departamento de Vertebrados, Museu Nacional, Quinta da Boavista, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
| |
Collapse
|
3
|
Astudillo-Clavijo V, Mankis T, López-Fernández H. Opening the Museum's Vault: Historical Field Records Preserve Reliable Ecological Data. Am Nat 2024; 203:305-322. [PMID: 38358812 DOI: 10.1086/728422] [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] [Indexed: 02/17/2024]
Abstract
AbstractMuseum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with but beyond physical specimens, a concept known as "extended specimens." Field notes penned by generations of naturalists contain firsthand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research because of their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.
Collapse
|
4
|
Loaiza JR, Gittens RA, Zapata R, Armien B, González-Santamaría J, Laporta GZ, Franco L. The bibliometric landscape of infectious disease research in Panama (1990-2019). DIALOGUES IN HEALTH 2023; 2:100117. [PMID: 38515494 PMCID: PMC10953851 DOI: 10.1016/j.dialog.2023.100117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/11/2023] [Accepted: 02/20/2023] [Indexed: 03/23/2024]
Abstract
Background This work aims to analyze the landscape of scientific publications on subjects related to One Health and infectious diseases in Panama. The research questions are: How does the One Health research landscape look like in Panama? Are historical research efforts aligned with the One Health concept? What infectious diseases have received more attention from the local scientific community since 1990? Methods Boolean searches on the Web of Science, SCOPUS and PubMed were undertaken to evaluate the main trends of publications related to One Health and infectious disease research in the country of Panama, between 1990 and 2019. Results 4546 publications were identified since 1990, including 3564 peer-reviewed articles interconnected with One Health related descriptors, and 211 articles focused particularly on infectious diseases. A pattern of exponential growth in the number of publications with various contributions from Panamanian institutions was observed. The rate of multidisciplinary research was moderate, whereas those of interinstitutional and intersectoral research ranged from low to very low. Research efforts have centered largely on protozoan, neglected and arthropod-borne diseases with a strong emphasis on malaria, Chagas and leishmaniasis. Conclusion Panama has scientific capabilities on One Health to tackle future infectious disease threats, but the official collaboration schemes and strategic investment to develop further competencies need to be conciliated with modern times, aka the pandemics era. The main proposition here, addressed to the government of Panama, is to launch a One Health regional center to promote multidisciplinary, interinstitutional and intersectoral research activities in Panama and beyond.
Collapse
Affiliation(s)
- Jose R. Loaiza
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Panama
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panama City, Panama
| | - Rolando A. Gittens
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama
| | - Robinson Zapata
- Secretaria Nacional de Ciencia, Tecnología e Innovación de Panamá, Panama
| | - Blas Armien
- Grupo de Biología Celular y Molecular de Arbovirus, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama
| | - José González-Santamaría
- Grupo de Biología Celular y Molecular de Arbovirus, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama
| | - Gabriel Z. Laporta
- Graduate Research and Innovation Program, Centro Universitario FMABC, Santo André, SP, Brazil
| | - Leticia Franco
- Health Emergencies Department, Pan American Health Organization, Washington, DC, United States of America
| |
Collapse
|
5
|
Weber N, Nagy M, Markotter W, Schaer J, Puechmaille SJ, Sutton J, Dávalos LM, Dusabe MC, Ejotre I, Fenton MB, Knörnschild M, López-Baucells A, Medellin RA, Metz M, Mubareka S, Nsengimana O, O'Mara MT, Racey PA, Tuttle M, Twizeyimana I, Vicente-Santos A, Tschapka M, Voigt CC, Wikelski M, Dechmann DK, Reeder DM. Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats. Biol Lett 2023; 19:20230358. [PMID: 37964576 PMCID: PMC10646460 DOI: 10.1098/rsbl.2023.0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.
Collapse
Affiliation(s)
- Natalie Weber
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
| | - Martina Nagy
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juliane Schaer
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Sébastien J. Puechmaille
- ISEM, University of Montpellier, Montpellier, France
- Institut Universitaire de France, Paris, France
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | | | - Liliana M. Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, USA
| | | | - Imran Ejotre
- Institute of Biology, Humboldt University, Berlin, Germany
- Muni University, Arua, Uganda
| | - M. Brock Fenton
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Mirjam Knörnschild
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Evolutionary Ethology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Rodrigo A. Medellin
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico
| | | | - Samira Mubareka
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | - M. Teague O'Mara
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Bat Conservation International Austin, TX, USA
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, USA
| | - Paul A. Racey
- Centre for Ecology and Conservation, University of Exeter, Exeter, UK
| | - Merlin Tuttle
- Merlin Tuttle's Bat Conservation, Austin, TX USA
- Department of Integrative Biology, University of Texas, Austin, USA
| | | | - Amanda Vicente-Santos
- Graduate Program in Population Biology, Ecology and Emory University, Atlanta, GA, USA
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Marco Tschapka
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dina K.N. Dechmann
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | |
Collapse
|
6
|
Enabulele EE, Le Clec'h W, Roberts EK, Thompson CW, McDonough MM, Ferguson AW, Bradley RD, Anderson TJC, Platt RN. Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment. Emerg Infect Dis 2023; 29:1566-1579. [PMID: 37486179 PMCID: PMC10370864 DOI: 10.3201/eid2908.221818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
More than 60 zoonoses are linked to small mammals, including some of the most devastating pathogens in human history. Millions of museum-archived tissues are available to understand natural history of those pathogens. Our goal was to maximize the value of museum collections for pathogen-based research by using targeted sequence capture. We generated a probe panel that includes 39,916 80-bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Laboratory-generated, mock-control samples showed that we are capable of enriching targeted loci from pathogen DNA 2,882‒6,746-fold. We identified bacterial species in museum-archived samples, including Bartonella, a known human zoonosis. These results showed that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.
Collapse
|
7
|
Lund MC, Larsen BB, Rowsey DM, Otto HW, Gryseels S, Kraberger S, Custer JM, Steger L, Yule KM, Harris RE, Worobey M, Van Doorslaer K, Upham NS, Varsani A. Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families cricetidae and heteromyidae. Virology 2023; 585:42-60. [PMID: 37276766 DOI: 10.1016/j.virol.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Abstract
Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species of rodents, we identify 346 distinct circular DNA viral genomes. Of these, a large portion are circular, single-stranded DNA viruses in the families Anelloviridae (n = 3), Circoviridae (n = 5), Genomoviridae (n = 7), Microviridae (n = 297), Naryaviridae (n = 4), Vilyaviridae (n = 15) and in the phylum Cressdnaviricota (n = 13) that cannot be assigned established families. We also identified two large bacteriophages of 36 and 50 kb that are part of the class Caudoviricetes. Some of these viruses are clearly those that infect rodents, however, most of these likely infect various organisms associated with rodents, their environment or their diet.
Collapse
Affiliation(s)
- Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98102, USA
| | - Dakota M Rowsey
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium; Department of Biology, University of Antwerp, 2000, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Museum of Natural Sciences, 1000, Brussels, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Laura Steger
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Kelsey M Yule
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robin E Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
| |
Collapse
|
8
|
Colella JP, Cobos ME, Salinas I, Cook JA. Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens. PLoS Pathog 2023; 19:e1011410. [PMID: 37319170 DOI: 10.1371/journal.ppat.1011410] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Affiliation(s)
- Jocelyn P Colella
- University of Kansas Biodiversity Institute and Department of Ecology & Evolutionary Biology, Lawrence, Kansas, United States of America
| | - Marlon E Cobos
- University of Kansas Biodiversity Institute and Department of Ecology & Evolutionary Biology, Lawrence, Kansas, United States of America
| | - Irene Salinas
- University of New Mexico, Department of Biology, Albuquerque, New Mexico, United States of America
- Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph A Cook
- University of New Mexico, Department of Biology, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| |
Collapse
|
9
|
Angeles NAC, Catap ES. Challenges on the Development of Biodiversity Biobanks: The Living Archives of Biodiversity. Biopreserv Biobank 2023; 21:5-13. [PMID: 35133889 DOI: 10.1089/bio.2021.0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biodiversity biobanks or ex situ biodiversity biorepositories tend to receive less attention compared with their biomedical counterparts. In this review, we highlight the necessity for these biorepositories by presenting their significant role in health, biodiversity, linking of big data, other translational research, and biodiversity conservation efforts. Moreover, the significant challenges in developing and maintaining biodiversity biobanks based on successful biobanks in some megadiverse developing countries are examined to provide insights into what needs to be done and what can be improved by up-and-coming biodiversity biobanks. These challenges include lack of financial support and political will; availability of experts; development of standard policies; and information management system. In addition, issues regarding access and benefit sharing and Digital Sequence Information must be addressed by biodiversity biobanks.
Collapse
Affiliation(s)
- Nestly Anne C Angeles
- Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines.,Department of Science and Technology-Science Education Institute, Taguig, Philippines
| | - Elena S Catap
- Functional Bioactivity Screening Lab, Institute of Biology, College of Science National Science Complex, University of the Philippines-Diliman, Quezon City, Philippines
| |
Collapse
|
10
|
Wood CL, Vanhove MPM. Is the world wormier than it used to be? We'll never know without natural history collections. J Anim Ecol 2023; 92:250-262. [PMID: 35959636 DOI: 10.1111/1365-2656.13794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Many disease ecologists and conservation biologists believe that the world is wormier than it used to be-that is, that parasites are increasing in abundance through time. This argument is intuitively appealing. Ecologists typically see parasitic infections, through their association with disease, as a negative endpoint, and are accustomed to attributing negative outcomes to human interference in the environment, so it slots neatly into our worldview that habitat destruction, biodiversity loss and climate change should have the collateral consequence of causing outbreaks of parasites. But surprisingly, the hypothesis that parasites are increasing in abundance through time remains entirely untested for the vast majority of wildlife parasite species. Historical data on parasites are nearly impossible to find, which leaves no baseline against which to compare contemporary parasite burdens. If we want to know whether the world is wormier than it used to be, there is only one major research avenue that will lead to an answer: parasitological examination of specimens preserved in natural history collections. Recent advances demonstrate that, for many specimen types, it is possible to extract reliable data on parasite presence and abundance. There are millions of suitable specimens that exist in collections around the world. When paired with contemporaneous environmental data, these parasitological data could even point to potential drivers of change in parasite abundance, including climate, pollution or host density change. We explain how to use preserved specimens to address pressing questions in parasite ecology, give a few key examples of how collections-based parasite ecology can resolve these questions, identify some pitfalls and workarounds, and suggest promising areas for research. Natural history specimens are 'parasite time capsules' that give ecologists the opportunity to test whether infectious disease is on the rise and to identify what forces might be driving these changes over time. This approach will facilitate major advances in a new sub-discipline: the historical ecology of parasitism.
Collapse
Affiliation(s)
- Chelsea L Wood
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Maarten P M Vanhove
- Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Diepenbeek, Belgium
| |
Collapse
|
11
|
Astorga F, Groom Q, Shimabukuro PHF, Manguin S, Noesgaard D, Orrell T, Sinka M, Hirsch T, Schigel D. Biodiversity data supports research on human infectious diseases: Global trends, challenges, and opportunities. One Health 2023; 16:100484. [PMID: 36714536 PMCID: PMC9880238 DOI: 10.1016/j.onehlt.2023.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/06/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
The unprecedented generation of large volumes of biodiversity data is consistently contributing to a wide range of disciplines, including disease ecology. Emerging infectious diseases are usually zoonoses caused by multi-host pathogens. Therefore, their understanding may require the access to biodiversity data related to the ecology and the occurrence of the species involved. Nevertheless, despite several data-mobilization initiatives, the usage of biodiversity data for research into disease dynamics has not yet been fully leveraged. To explore current contribution, trends, and to identify limitations, we characterized biodiversity data usage in scientific publications related to human health, contrasting patterns of studies citing the Global Biodiversity Information Facility (GBIF) with those obtaining data from other sources. We found that the studies mainly obtained data from scientific literature and other not aggregated or standardized sources. Most of the studies explored pathogen species and, particularly those with GBIF-mediated data, tended to explore and reuse data of multiple species (>2). Data sources varied according to the taxa and epidemiological roles of the species involved. Biodiversity data repositories were mainly used for species related to hosts, reservoirs, and vectors, and barely used as a source of pathogens data, which was usually obtained from human and animal-health related institutions. While both GBIF- and not GBIF-mediated data studies explored similar diseases and topics, they presented discipline biases and different analytical approaches. Research on emerging infectious diseases may require the access to geographical and ecological data of multiple species. The One Health challenge requires interdisciplinary collaboration and data sharing, which is facilitated by aggregated repositories and platforms. The contribution of biodiversity data to understand infectious disease dynamics should be acknowledged, strengthened, and promoted.
Collapse
Affiliation(s)
- Francisca Astorga
- Facultad de Ciencias, Universidad Mayor, Chile,Corresponding author.
| | - Quentin Groom
- Biodiversity Informatics, Meise Botanic Garden, Belgium Nieuwelaan 38, 1860, Meise, Belgium
| | | | - Sylvie Manguin
- HSM, University Montpellier, CNRS, IRD, 911 Av. Agropolis, 34394 Montpellier, France
| | - Daniel Noesgaard
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Thomas Orrell
- Smithsonian Institution, National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | | | - Tim Hirsch
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Dmitry Schigel
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| |
Collapse
|
12
|
How to use natural history collections to resurrect information on historical parasite abundances. J Helminthol 2023; 97:e6. [PMID: 36633512 DOI: 10.1017/s0022149x2200075x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many of the most contentious questions that concern the ecology of helminths could be resolved with data on helminth abundance over the past few decades or centuries, but unfortunately these data are rare. A new sub-discipline - the historical ecology of parasitism - is resurrecting long-term data on the abundance of parasites, an advancement facilitated by the use of biological natural history collections. Because the world's museums hold billions of suitable specimens collected over more than a century, these potential parasitological datasets are broad in scope and finely resolved in taxonomic, temporal and spatial dimensions. Here, we set out best practices for the extraction of parasitological information from natural history collections, including how to conceive of a project, how to select specimens, how to engage curators and receive permission for proposed projects, standard operating protocols for dissections and how to manage data. Our hope is that other helminthologists will use this paper as a reference to expand their own research programmes along the dimension of time.
Collapse
|
13
|
Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
| |
Collapse
|
14
|
Cardenas Alegria O, Pires Quaresma M, Dias Dantas CW, Silva Guedes Lobato EM, de Oliveira Aragão A, Patroca da Silva S, Costa Barros da Silva A, Ribeiro Cruz AC, Ramos RTJ, Carneiro AR. Impacts of soybean agriculture on the resistome of the Amazonian soil. Front Microbiol 2022; 13:948188. [PMID: 36160259 PMCID: PMC9500545 DOI: 10.3389/fmicb.2022.948188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/16/2022] [Indexed: 11/15/2022] Open
Abstract
The soils of the Amazon are complex environments with different organisms cohabiting in continuous adaptation processes; this changes significantly when these environments are modified for the development of agricultural activities that alter the chemical, macro, and microbiological compositions. The metagenomic variations and the levels of the environmental impact of four different soil samples from the Amazon region were evaluated, emphasizing the resistome. Soil samples from the organic phase from the different forest, pasture, and transgenic soybean monocultures of 2–14 years old were collected in triplicate at each site. The samples were divided into two groups, and one group was pre-treated to obtain genetic material to perform sequencing for metagenomic analysis; another group carried out the chemical characterization of the soil, determining the pH, the content of cations, and heavy metals; these were carried out in addition to identifying with different databases the components of the microbiological communities, functional genes, antibiotic and biocide resistance genes. A greater diversity of antibiotic resistance genes was observed in the forest soil. In contrast, in monoculture soils, a large number of biocide resistance genes were evidenced, highlighting the diversity and abundance of crop soils, which showed better resistance to heavy metals than other compounds, with a possible dominance of resistance to iron due to the presence of the acn gene. For up to 600 different genes for resistance to antibiotics and 256 genes for biocides were identified, most of which were for heavy metals. The most prevalent was resistance to tetracycline, cephalosporin, penam, fluoroquinolone, chloramphenicol, carbapenem, macrolide, and aminoglycoside, providing evidence for the co-selection of these resistance genes in different soils. Furthermore, the influence of vegetation cover on the forest floor was notable as a protective factor against the impact of human contamination. Regarding chemical characterization, the presence of heavy metals, different stress response mechanisms in monoculture soils, and the abundance of mobile genetic elements in crop and pasture soils stand out. The elimination of the forest increases the diversity of genes for resistance to biocides, favoring the selection of genes for resistance to antibiotics in soils.
Collapse
Affiliation(s)
- Oscar Cardenas Alegria
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- *Correspondence: Oscar Cardenas Alegria
| | - Marielle Pires Quaresma
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | | | - Andressa de Oliveira Aragão
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Sandro Patroca da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute-IEC/SVS/MS, Ananindeua, Brazil
| | - Amanda Costa Barros da Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Ana Cecília Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute-IEC/SVS/MS, Ananindeua, Brazil
| | - Rommel Thiago Jucá Ramos
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Adriana Ribeiro Carneiro
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| |
Collapse
|
15
|
Islam S, Weiland C, Addink W. From data pipelines to FAIR data infrastructures: A vision for the new horizons of bio- and geodiversity data for scientific research. RESEARCH IDEAS AND OUTCOMES 2022. [DOI: 10.3897/rio.8.e93816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural science collections are vast repositories of bio- and geodiversity specimens. These collections, originating from natural history cabinets or expeditions, are increasingly becoming unparalleled sources of data facilitating multidisciplinary research (Meineke et al. 2018, Heberling et al. 2019, Cook et al. 2020, Thompson et al. 2021). Due to various global data mobilization and digitisation efforts (Blagoderov et al. 2012,Nelson and Ellis 2018), this digitised information about specimens includes database records along with two/three-dimensional images, sonograms, sound or video recordings, computerised tomography scans, machine-readable texts from labels on the specimens as well as media items and notes related to the discovery sites and acquisition (Hedrick et al. 2020,Phillipson 2022).
The scope and practice of specimen gathering are also evolving. The term extended specimen was coined to refer to the specimen and associated data extending beyond the singular physical object to other physical or digital entities such as chemical composition, genetic sequence data or species data. Thus the specimen becomes an interconnected network of data resources that have incredible potential to enhance integrative and data-driven research (Webster 2017,Lendemer et al. 2019,Hardisty et al. 2022). These practices also reflect the role of data and the curatorial data life-cycle starting from the initial material sampling process to the downstream analysis. We are also seeing growing acknowledgement that disparate and domain specific data elements prevent interdisciplinarity which is crucial for a holistic understanding of biodiversity and climate crisis (Hicks et al. 2010, Craven et al. 2019, Folk and Siniscalchi 2021).
Thus the data elements are not just records or rows in a database or data pipelines going from one repository to another. They have the potential to become self-describing digital artefacts that can revolutionise how machines interpret and work with specimen data. Within this context, the Distributed System of Scientific Collections (DiSSCo), a new European Research Infrastructure for natural science collections, envisions an infrastructure based on FAIR Digital Objects (FDO) that can unify more than 170 European natural science collections under common and FAIR-compliant (Findable, Accessible, Interoperable, Reusable) (Wilkinson et al. 2016) access and curation policies and practices. DiSSCo’s key element in achieving FAIR is the implementation of Digital Specimen (a domain specific FDO) that closely aligns with the extended specimen practices. The idea behind Digital Specimen – an FDO that acts as a digital surrogate for a specific physical specimen in a natural science collection – was influenced by global conversations around the implementation of the Digital Object Architecture for biodiversity data (De Smedt et al. 2020, Islam et al. 2020,Hardisty et al. 2020).
The main purpose of this talk is to explain the vision of how FAIR and FDO can create a data infrastructure that can not only take advantage of existing databases and repositories but at the same time provide support for innovative services such as AI and digital twinning. With scientific use cases in mind, the talk will highlight a few key FAIR and FDO components (persistent identifiers, metadata, ontologies) within the collaborative modelling activity of Digital Specimen specification. These components provide the template for specifying how a Digital Specimen should look so DiSSCo can build a FAIR service ecosystem based on FDOs (Addink et al. 2021). We will also give examples of envisioned services that can help with image feature extraction, and model training (Grieb et al. 2021,Hardisty et al. 2022) and digital twinning (Schultes et al. 2022). We believe this is an exciting new paradigm powered by FAIR and FDO that can help both humans and machines to accelerate the use of specimen data. From physical objects curated over hundred years, we have developed data pipelines, aggregators and repositories (Barberousse 2021). Now is the time to look for solutions where these data records can become FAIR Digital Objects to enable wider access and multidisciplinary research.
Collapse
|
16
|
Hardisty AR, Ellwood ER, Nelson G, Zimkus B, Buschbom J, Addink W, Rabeler RK, Bates J, Bentley A, Fortes JAB, Hansen S, Macklin JA, Mast AR, Miller JT, Monfils AK, Paul DL, Wallis E, Webster M. Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet. Bioscience 2022; 72:978-987. [PMID: 36196222 PMCID: PMC9525127 DOI: 10.1093/biosci/biac060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.
Collapse
Affiliation(s)
| | | | - Gil Nelson
- Florida Museum of Natural History , Gainesville, Florida, United States
| | - Breda Zimkus
- Museum of Comparative Zoology , Cambridge, Massachusetts, United States
| | | | | | - Richard K Rabeler
- University of Michigan Herbarium , Ann Arbor, Michigan, United States
| | - John Bates
- Field Museum of Natural History , Chicago, Illinois, United States
| | - Andrew Bentley
- Biodiversity Institute, University of Kansas , Lawrence, Kansas, United States
| | | | - Sara Hansen
- Central Michigan University Herbarium, Central Michigan University , Mt. Pleasant, Michigan, United States
| | | | - Austin R Mast
- Department of Biological Science, Florida State University , Tallahassee, Florida, United States
| | - Joseph T Miller
- Global Biodiversity Information Facility Secretariat , Copenhagen, Denmark
| | - Anna K Monfils
- Central Michigan University Herbarium, Central Michigan University , Mt. Pleasant, Michigan, United States
| | - Deborah L Paul
- University of Illinois Urbana Champaign , Champaign, Illinois, United States
| | - Elycia Wallis
- Atlas of Living Australia, CSIRO , Melbourne, Australia
| | - Michael Webster
- Macaulay Library, Cornell Lab of Ornithology , Ithaca, New York, United States
| |
Collapse
|
17
|
Becker DJ, Albery GF, Sjodin AR, Poisot T, Bergner LM, Chen B, Cohen LE, Dallas TA, Eskew EA, Fagre AC, Farrell MJ, Guth S, Han BA, Simmons NB, Stock M, Teeling EC, Carlson CJ. Optimising predictive models to prioritise viral discovery in zoonotic reservoirs. THE LANCET. MICROBE 2022; 3:e625-e637. [PMID: 35036970 PMCID: PMC8747432 DOI: 10.1016/s2666-5247(21)00245-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use the bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of probable reservoir hosts. In early 2020, we generated an ensemble of eight statistical models that predicted host-virus associations and developed priority sampling recommendations for potential bat reservoirs of betacoronaviruses and bridge hosts for SARS-CoV-2. During a time frame of more than a year, we tracked the discovery of 47 new bat hosts of betacoronaviruses, validated the initial predictions, and dynamically updated our analytical pipeline. We found that ecological trait-based models performed well at predicting these novel hosts, whereas network methods consistently performed approximately as well or worse than expected at random. These findings illustrate the importance of ensemble modelling as a buffer against mixed-model quality and highlight the value of including host ecology in predictive models. Our revised models showed an improved performance compared with the initial ensemble, and predicted more than 400 bat species globally that could be undetected betacoronavirus hosts. We show, through systematic validation, that machine learning models can help to optimise wildlife sampling for undiscovered viruses and illustrates how such approaches are best implemented through a dynamic process of prediction, data collection, validation, and updating.
Collapse
Affiliation(s)
- Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Anna R Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Timothée Poisot
- Université de Montréal, Département de Sciences Biologiques, Montréal, QC, Canada
| | - Laura M Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Medical Research Centre, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Binqi Chen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad A Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Evan A Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
- Bat Health Foundation, Fort Collins, CO, USA
| | - Maxwell J Farrell
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sarah Guth
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Barbara A Han
- Cary Institute of Ecosystem Studies, Millbrook, NY, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Michiel Stock
- Research Unit Knowledge-based Systems, Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium
| | - Emma C Teeling
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
| | - Colin J Carlson
- Department of Biology, Georgetown University, Washington, DC, USA
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| |
Collapse
|
18
|
Novaes RLM, Wilson DE, Moratelli R. Catalogue of primary types of Neotropical Myotis (Chiroptera, Vespertilionidae). Zookeys 2022; 1105:127-164. [PMID: 36760324 PMCID: PMC9848626 DOI: 10.3897/zookeys.1105.85055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022] Open
Abstract
Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Neotropical Myotis have an accentuated phenotypic conservatism, which makes species delimitation and identification difficult, hindering our understanding of the diversity, distribution, and phylogenetic relationships of taxa. To encourage new systematic reviews of the genus, a catalogue of the primary types and names is presented, current and in synonymy, for Neotropical Myotis. Currently 33 valid species (and three subspecies) are recognized, and their primary types are deposited in 12 scientific collections in the USA (30 types), Brazil (two types), England (two types), and France (one type). The names of 29 Neotropical Myotis species currently in synonymy were found. However, it is possible that some synonyms represent independent evolutionary lineages, considering recent results provided by taxonomic revisions.
Collapse
Affiliation(s)
- Roberto Leonan M. Novaes
- Fundação Oswaldo Cruz, Fiocruz Mata Atlântica, R. Sampaio Correa s/n, Taquara, 22713-560, Rio de Janeiro, BrazilFundação Oswaldo Cruz, Fiocruz Mata AtlânticaRio de JaneiroBrazil
| | - Don E. Wilson
- Smithsonian Institution, National Museum of Natural History, Division of Mammals. 10th St. & Constitution Ave. NW, 20013-7012, Washington, DC, USANational Museum of Natural HistoryWashington, DCUnited States of America
| | - Ricardo Moratelli
- Fundação Oswaldo Cruz, Fiocruz Mata Atlântica, R. Sampaio Correa s/n, Taquara, 22713-560, Rio de Janeiro, BrazilFundação Oswaldo Cruz, Fiocruz Mata AtlânticaRio de JaneiroBrazil
| |
Collapse
|
19
|
Galán AP, Hamer SA, Folmar HA, Campbell TA, Light JE. Baseline Biodiversity Assessment of South Texas Small Mammals and Host-Associated Hard Ticks with No Detection of Selected Tick-Borne Pathogens. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Aleyda P. Galán
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843
| | - Sarah A. Hamer
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843
| | - Hunter A. Folmar
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843
| | | | - Jessica E. Light
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843
| |
Collapse
|
20
|
Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. Gigascience 2022; 11:6529104. [PMID: 35169842 PMCID: PMC8847733 DOI: 10.1093/gigascience/giac003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. Results As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. Conclusions Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.
Collapse
Affiliation(s)
| | - Ruth E Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Catarina Inês Mendes
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Andrew J Page
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK
| | - Nabil-Fareed Alikhan
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK
| | - Dan Fornika
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 1W5, Canada
| | - Josefina Campos
- INEI-ANLIS “Dr Carlos G. Malbrán,” Buenos Aires C1282AFF, Argentina
| | - Daniel Park
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Idowu B Olawoye
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria
| | - Paul E Oluniyi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria
| | - Dominique Anderson
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Rhiannon Cameron
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Lee S Katz
- Center for Food Safety, University of Georgia, Atlanta, GA 30333, USA
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA
| | - Allison Black
- Department of Epidemiology, University of Washington, WA 98109, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tanya Barrett
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anjanette Johnston
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | | | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin 12277, Germany
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Brian Alcock
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- The Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Emma Hodcroft
- Biozentrum, University of Basel, Basel 3012, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - William W L Hsiao
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7 V6T 1Z7, Canada
| | - Ana Tereza R Vasconcelos
- Bioinformatics Laboratory National Laboratory of Scientific Computation LNCC/MCTI, Petrópolis 25651-075, Brazil
| | - Duncan R MacCannell
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA
| |
Collapse
|
21
|
Poo S, Whitfield SM, Shepack A, Watkins-Colwell GJ, Nelson G, Goodwin J, Bogisich A, Brennan PLR, D'Agostino J, Koo MS, Mendelson JR, Snyder R, Wilson S, Aronsen GP, Bentley AC, Blackburn DC, Borths MR, Campbell ML, Conde DA, Cook JA, Daza JD, Dembiec DP, Dunnum JL, Early CM, Ferguson AW, Greene A, Guralnick R, Janney C, Johnson D, Knightly F, Poulin S, Rocha L, Soltis PS, Thiers B, Chakrabarty P. OUP accepted manuscript. Bioscience 2022; 72:449-460. [PMID: 35592056 PMCID: PMC9113241 DOI: 10.1093/biosci/biac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Zoos and natural history museums are both collections-based institutions with important missions in biodiversity research and education. Animals in zoos are a repository and living record of the world's biodiversity, whereas natural history museums are a permanent historical record of snapshots of biodiversity in time. Surprisingly, despite significant overlap in institutional missions, formal partnerships between these institution types are infrequent. Life history information, pedigrees, and medical records maintained at zoos should be seen as complementary to historical records of morphology, genetics, and distribution kept at museums. Through examining both institution types, we synthesize the benefits and challenges of cross-institutional exchanges and propose actions to increase the dialog between zoos and museums. With a growing recognition of the importance of collections to the advancement of scientific research and discovery, a transformational impact could be made with long-term investments in connecting the institutions that are caretakers of living and preserved animals.
Collapse
Affiliation(s)
| | | | | | | | - Gil Nelson
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | - Jillian Goodwin
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | | | | | | | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States
| | | | - Rebecca Snyder
- Oklahoma City Zoo, Oklahoma City, Oklahoma, United States
| | | | | | | | - David C Blackburn
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | | | - Mariel L Campbell
- Museum of Southwestern Biology, Albuquerque, New Mexico, United States
| | | | - Joseph A Cook
- Museum of Southwestern Biology, Albuquerque, New Mexico, United States
| | - Juan D Daza
- Sam Houston State University, Huntsville, Texas, United States
| | | | - Jonathan L Dunnum
- Museum of Southwestern Biology, Albuquerque, New Mexico, United States
| | | | | | - Amanda Greene
- Duke Lemur Center, Durham, North Carolina, United States
| | - Robert Guralnick
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | - Courtney Janney
- Memphis Zoological Society, Memphis, Tennessee, United States
| | | | | | - Stephane Poulin
- Arizona-Sonora Desert Museum, Tucson, Arizona, United States
| | - Luiz Rocha
- California Academy of Sciences, San Francisco, United States
| | - Pamela S Soltis
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | | | | |
Collapse
|
22
|
Borges M, Petti MA, Fukuda MV, Cassano V, Fujii MT, Amaral ACZ. Marine planktonic and benthic organisms: an ocean of diversity in the collections of the State of São Paulo. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Brazil is characterized as a megadiverse country, and one of the factors that guarantees the knowledge and preservation of this biodiversity is an improvement in the biological collections. They represent a country's biological, scientific, cultural, and genetic heritage and their preservation depends on a joint effort of researchers, institutions, and public authorities. Marine biological collections of invertebrates and algae of the state of São Paulo represent a high percentage of the national collections, with five biological collections deposited in state institutions. Currently, these collections safeguard the vast majority of the state's marine collection and make up one of the largest in the country. Therefore, the objective of this research is to present information on marine biological collections in the state of São Paulo, their current status, funding, and future perspectives, creating communication opportunities and considering the factors that impact their development. Support from the São Paulo Research Foundation (FAPESP) surpasses state limits, since many studies address broader areas and/or establish diverse partnerships with other institutions from outside São Paulo. This is reflected in the taxonomic and geographic scope of the biological collections in the state, since these host specimens/species from different regions of the country, or even from other countries. However, it is worth mentioning that it is not enough to invest in expeditions to enrich the collections without valuing the training of qualified personnel, both for the collections maintenance and for their taxonomic refinement.
Collapse
Affiliation(s)
| | | | | | | | | | - A. Cecília Z. Amaral
- Universidade Estadual de Campinas, Brasil; Universidade Estadual de Campinas, Brasil
| |
Collapse
|
23
|
Sayers EW, Cavanaugh M, Clark K, Pruitt KD, Schoch CL, Sherry S, Karsch-Mizrachi I. GenBank. Nucleic Acids Res 2021; 50:D161-D164. [PMID: 34850943 PMCID: PMC8690257 DOI: 10.1093/nar/gkab1135] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/20/2021] [Accepted: 11/08/2021] [Indexed: 11/14/2022] Open
Abstract
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 15.3 trillion base pairs from over 2.5 billion nucleotide sequences for 504 000 formally described species. Recent updates include resources for data from the SARS-CoV-2 virus, including a SARS-CoV-2 landing page, NCBI Datasets, NCBI Virus and the Submission Portal. We also discuss upcoming changes to GI identifiers, a new data management interface for BioProject, and advice for providing contextual metadata in submissions.
Collapse
Affiliation(s)
- Eric W Sayers
- To whom correspondence should be addressed. Tel: +1 301 496 2475; Fax: +1 301 480 9241;
| | - Mark Cavanaugh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Stephen T Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600RockvillePike, Bethesda, MD 20894, USA
| |
Collapse
|
24
|
Fischhoff IR, Castellanos AA, Rodrigues JPGLM, Varsani A, Han BA. Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2. Proc Biol Sci 2021; 288:20211651. [PMID: 34784766 PMCID: PMC8596006 DOI: 10.1098/rspb.2021.1651] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Back and forth transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between humans and animals will establish wild reservoirs of virus that endanger long-term efforts to control COVID-19 in people and to protect vulnerable animal populations. Better targeting surveillance and laboratory experiments to validate zoonotic potential requires predicting high-risk host species. A major bottleneck to this effort is the few species with available sequences for angiotensin-converting enzyme 2 receptor, a key receptor required for viral cell entry. We overcome this bottleneck by combining species' ecological and biological traits with three-dimensional modelling of host-virus protein-protein interactions using machine learning. This approach enables predictions about the zoonotic capacity of SARS-CoV-2 for greater than 5000 mammals-an order of magnitude more species than previously possible. Our predictions are strongly corroborated by in vivo studies. The predicted zoonotic capacity and proximity to humans suggest enhanced transmission risk from several common mammals, and priority areas of geographic overlap between these species and global COVID-19 hotspots. With molecular data available for only a small fraction of potential animal hosts, linking data across biological scales offers a conceptual advance that may expand our predictive modelling capacity for zoonotic viruses with similarly unknown host ranges.
Collapse
Affiliation(s)
- Ilya R. Fischhoff
- Cary Institute of Ecosystem Studies, Box AB Millbrook, NY 12545, USA
| | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7700 Cape Town, Rondebosch, South Africa
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies, Box AB Millbrook, NY 12545, USA
| |
Collapse
|
25
|
Goodfellow SM, Nofchissey RA, Schwalm KC, Cook JA, Dunnum JL, Guo Y, Ye C, Mertz GJ, Chandran K, Harkins M, Domman DB, Dinwiddie DL, Bradfute SB. Tracing Transmission of Sin Nombre Virus and Discovery of Infection in Multiple Rodent Species. J Virol 2021; 95:e0153421. [PMID: 34549977 PMCID: PMC8577387 DOI: 10.1128/jvi.01534-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Sin Nombre orthohantavirus (SNV), a negative-sense, single-stranded RNA virus that is carried and transmitted by the North American deer mouse Peromyscus maniculatus, can cause infection in humans through inhalation of aerosolized excreta from infected rodents. This infection can lead to hantavirus cardiopulmonary syndrome (HCPS), which has an ∼36% case-fatality rate. We used reverse transcriptase quantitative PCR (RT-qPCR) to confirm SNV infection in a patient and identified SNV in lung tissues in wild-caught rodents from potential sites of exposure. Using viral whole-genome sequencing (WGS), we identified the likely site of transmission and discovered SNV in multiple rodent species not previously known to carry the virus. Here, we report, for the first time, the use of SNV WGS to pinpoint a likely site of human infection and identify SNV simultaneously in multiple rodent species in an area of known host-to-human transmission. These results will impact epidemiology and infection control for hantaviruses by tracing zoonotic transmission and investigating possible novel host reservoirs. IMPORTANCE Orthohantaviruses cause severe disease in humans and can be lethal in up to 40% of cases. Sin Nombre orthohantavirus (SNV) is the main cause of hantavirus disease in North America. In this study, we sequenced SNV from an infected patient and wild-caught rodents to trace the location of infection. We also discovered SNV in rodent species not previously known to carry SNV. These studies demonstrate for the first time the use of virus sequencing to trace the transmission of SNV and describe infection in novel rodent species.
Collapse
Affiliation(s)
- Samuel M. Goodfellow
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Robert A. Nofchissey
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Kurt C. Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Joseph A. Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L. Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Yan Guo
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Chunyan Ye
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Gregory J. Mertz
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Kartik Chandran
- Albert Einstein College of Medicine, Department of Microbiology and Immunology, Bronx, New York, USA
| | - Michelle Harkins
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Daryl B. Domman
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Darrell L. Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Steven B. Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| |
Collapse
|
26
|
Monfils AK, Krimmel ER, Linton DL, Marsico TD, Morris AB, Ruhfel BR. Collections Education: The Extended Specimen and Data Acumen. Bioscience 2021; 72:177-188. [PMID: 35145351 PMCID: PMC8824687 DOI: 10.1093/biosci/biab109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Biodiversity scientists must be fluent across disciplines; they must possess the quantitative, computational, and data skills necessary for working with large, complex data sets, and they must have foundational skills and content knowledge from ecology, evolution, taxonomy, and systematics. To effectively train the emerging workforce, we must teach science as we conduct science and embrace emerging concepts of data acumen alongside the knowledge, tools, and techniques foundational to organismal biology. We present an open education resource that updates the traditional plant collection exercise to incorporate best practices in twenty-first century collecting and to contextualize the activities that build data acumen. Students exposed to this resource gained skills and content knowledge in plant taxonomy and systematics, as well as a nuanced understanding of collections-based data resources. We discuss the importance of the extended specimen in fostering scientific discovery and reinforcing foundational concepts in biodiversity science, taxonomy, and systematics.
Collapse
Affiliation(s)
- Anna K Monfils
- Central Michigan University, Mount Pleasant, Michigan, United States
| | - Erica R Krimmel
- Florida State University, Tallahassee, Florida, United States
| | - Debra L Linton
- Central Michigan University, Mount Pleasant, Michigan, United States
| | | | - Ashley B Morris
- Furman University, Greenville, South Carolina, United States
| | - Brad R Ruhfel
- University of Michigan, Ann Arbor, Michigan, United States
| |
Collapse
|
27
|
Ceríaco LM, Parrinha D, Marques MP. Saving collections: taxonomic revision of the herpetological collection of the Instituto de Investigação Científica Tropical, Lisbon (Portugal) with a protocol to rescue abandoned collections. Zookeys 2021; 1052:85-156. [PMID: 34393554 PMCID: PMC8346433 DOI: 10.3897/zookeys.1052.64607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
The herpetological collections of the Instituto de Investigação Científica Tropical, Lisbon, are amongst the most important collections from the former Portuguese territories in Africa and Asia. The collection comprises more than 5000 preserved specimens, including type specimens of nine taxa, Trachylepis adamastor, Trachypelis thomensis, Panaspis thomensis, Naja peroescobari, Dalophia angolensis, Hemidactylus nzingae, Boaedon fradei, Platysaurus maculatus maculatus, and Platysaurus maculatus lineicauda. The collection was abandoned in the early years of 2000s and was at risk of being lost. In this paper the entire collection is reviewed, a catalogue provided of the extant specimens, and a brief account of the history of herpetological research at IICT given. Details are also provided on the recovery of the collection and a protocol to rescue abandoned collections.
Collapse
Affiliation(s)
- Luis M.P. Ceríaco
- Museu de História Natural e da Ciência da Universidade do Porto, Praça Gomes Teixeira 4099-002 Porto, PortugalUniversidade de LisboaLisboaPortugal
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Diogo Parrinha
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Mariana P. Marques
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO, Universidade do Porto, Rua Padre Armando Quintas 7, Vairão, 4485-661 Porto, PortugalUniversidade do PortoPortoPortugal
| |
Collapse
|
28
|
Fischhoff IR, Castellanos AA, Rodrigues JP, Varsani A, Han BA. Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.18.431844. [PMID: 33619481 PMCID: PMC7899445 DOI: 10.1101/2021.02.18.431844] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Back and forth transmission of SARS-CoV-2 between humans and animals may lead to wild reservoirs of virus that can endanger efforts toward long-term control of COVID-19 in people, and protecting vulnerable animal populations that are particularly susceptible to lethal disease. Predicting high risk host species is key to targeting field surveillance and lab experiments that validate host zoonotic potential. A major bottleneck to predicting animal hosts is the small number of species with available molecular information about the structure of ACE2, a key cellular receptor required for viral cell entry. We overcome this bottleneck by combining species' ecological and biological traits with 3D modeling of virus and host cell protein interactions using machine learning methods. This approach enables predictions about the zoonotic capacity of SARS-CoV-2 for over 5,000 mammals - an order of magnitude more species than previously possible. The high accuracy predictions achieved by this approach are strongly corroborated by in vivo empirical studies. We identify numerous common mammal species whose predicted zoonotic capacity and close proximity to humans may further enhance the risk of spillover and spillback transmission of SARS-CoV-2. Our results reveal high priority areas of geographic overlap between global COVID-19 hotspots and potential new mammal hosts of SARS-CoV-2. With molecular sequence data available for only a small fraction of potential host species, predictive modeling integrating data across multiple biological scales offers a conceptual advance that may expand our predictive capacity for zoonotic viruses with similarly unknown and potentially broad host ranges.
Collapse
Affiliation(s)
- Ilya R. Fischhoff
- Cary Institute of Ecosystem Studies. Box AB Millbrook, NY 12545, USA
| | | | - João P.G.L.M. Rodrigues
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700, Cape Town, South Africa
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies. Box AB Millbrook, NY 12545, USA
| |
Collapse
|
29
|
Dunnum JL, Cook JA. Editor’s Choice. J Mammal 2021. [DOI: 10.1093/jmammal/gyab046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jonathan L Dunnum
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Joseph A Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| |
Collapse
|
30
|
Soniat TJ, Sihaloho HF, Stevens RD, Little TD, Phillips CD, Bradley RD. Temporal-dependent effects of DNA degradation on frozen tissues archived at −80°C. J Mammal 2021. [DOI: 10.1093/jmammal/gyab009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Abstract
Frozen tissues, associated with natural history and biological collections, historically have been archived at temperatures between −20°C and −80°C. More recently, the availability of liquid nitrogen systems has enabled the storage of tissue samples (biobanking) at temperatures as low as −196°C. Currently, it is not known how the degree of coldness (e.g., −80°C or −196°C) or longevity (time in storage) impacts preservation of tissue samples. To examine the effects of long-term storage (−80°C and −196°C) on DNA degradation, tissue samples (muscle and liver) archived for 30, 20, 10, or 1 years were obtained from the Natural Science Research Laboratory at Texas Tech University. The integrity of DNA (measured as molecular weight and fragment length) extracted from samples was determined using automated DNA isolation methods followed by microfluidic distribution measurement. DNA distributions were compared using measures of central tendency, a regression-based molecular mass profile, and as a latent variable in a structural equation model. Muscle samples consistently outperformed liver samples in terms of quality of DNA yield. Also, muscle samples exhibited a significant linear relationship with time in which older samples were more degraded than were recent samples. The signal for a temporal effect on DNA was strongest when considering a latent variable of DNA quality based on mode and kurtosis; 37% of the variation in the latent variable was explained by variation in units of time. More recent time points tended to be more similar, but the temporal effect on the latent variable remained strong even when the oldest samples were removed from the analysis. In contrast, integrity of DNA from liver samples did not have a significant linear relationship with time; however, in some years they exhibited non-normally distributed DNA quality metrics that may have reflected sensitivity of liver tissue to degradation during specimen preparation, DNA extraction, or archive parameters. Results indicated that tissue type and temporal effects influenced rates of DNA degradation, with the latter emphasizing the long-term value of biobanking at the coldest temperatures possible (liquid nitrogen storage) to mitigate degradation of biological samples of ever-increasing scientific value.
Collapse
Affiliation(s)
- Taylor J Soniat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Hendra F Sihaloho
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Richard D Stevens
- Natural Science Research Laboratory, Museum, Texas Tech University, Lubbock, TX 79409-3191, USA
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX 79409-4212, USA
| | - Todd D Little
- Department of Educational Psychology, Texas Tech University, Lubbock, TX 79409-4212, USA
| | - Caleb D Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
- Natural Science Research Laboratory, Museum, Texas Tech University, Lubbock, TX 79409-3191, USA
| | - Robert D Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
- Natural Science Research Laboratory, Museum, Texas Tech University, Lubbock, TX 79409-3191, USA
| |
Collapse
|
31
|
Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network. PLoS Pathog 2021; 17:e1009583. [PMID: 34081744 PMCID: PMC8174688 DOI: 10.1371/journal.ppat.1009583] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO’s virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.
Collapse
|
32
|
Thiers B, Bates J, Bentley AC, Ford LS, Jennings D, Monfils AK, Zaspel JM, Collins JP, Hazbón MH, Pandey JL. Implementing a Community Vision for the Future of Biodiversity Collections. Bioscience 2021. [DOI: 10.1093/biosci/biab036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Barbara Thiers
- New York Botanical Garden, Bronx, New York, United States
| | - John Bates
- Integrative Research Center, Field Museum, Chicago, Illinois, United States
| | - Andrew C Bentley
- University of Kansas Biodiversity Institute, Lawrence, Kansas, United States
| | - Linda S Ford
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States
| | - David Jennings
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States
| | - Anna K Monfils
- Central Michigan University, Mount Pleasant, Michigan, United States
| | - Jennifer M Zaspel
- Department of Zoology, Milwaukee Public Museum, Milwaukee, Wisconsin, United States
| | - James P Collins
- Arizona State University School of Life Sciences, Tempe, Arizona, United States
| | | | - Jyotsna L Pandey
- American Institute of Biological Sciences, Herndon, Virginia, United States
| |
Collapse
|
33
|
Blom MPK. Opportunities and challenges for high-quality biodiversity tissue archives in the age of long-read sequencing. Mol Ecol 2021; 30:5935-5948. [PMID: 33786900 DOI: 10.1111/mec.15909] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022]
Abstract
The technological ability to characterize genetic variation at a genome-wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short- to long-read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long-read sequencing has tremendous potential but sequencing success strongly depends on the long-range integrity of DNA molecules and therefore on the availability of high-quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high-quality samples may soon be a major concern for many projects. The need for high-quality biodiversity tissue archives is therefore urgent but sampling and preserving high-quality samples is not a trivial exercise. In this review, I will briefly outline how long-read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high-quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high-quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long-term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.
Collapse
Affiliation(s)
- Mozes P K Blom
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| |
Collapse
|
34
|
Comizzoli P, Pagenkopp Lohan KM, Muletz-Wolz C, Hassell J, Coyle B. The Interconnected Health Initiative: A Smithsonian Framework to Extend One Health Research and Education. Front Vet Sci 2021; 8:629410. [PMID: 33834047 PMCID: PMC8021902 DOI: 10.3389/fvets.2021.629410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/26/2021] [Indexed: 01/09/2023] Open
Abstract
To better tackle diseases and sustain healthy ecosystems, One Health programs must efficiently bridge health in humans, domestic/livestock species, wild animals and plants, agriculture/aquaculture, and the environment. The Smithsonian Institution proposes to address this by considering ‘health' in a broad sense – the absence of undue pathogens and unnecessary stress for any organisms as well as access to good living conditions in functional environments. Considering the interconnectedness of all life forms, the Smithsonian plans to create a framework that will integrate cultural, social, and educational components into health research on humans, animals, plants, or ecosystems. The objectives of this perspective article are to (1) propose an innovative framework to support an interconnected/integrated approach to health and (2) provide examples fostering impactful collaborations on One Health research and education. Based on the core strengths of the Smithsonian (multidisciplinary research, outreach and education programs, libraries/archives, and collections) and central institutional support, this framework has the potential to extend existing health-related projects, address new needs and situations (e.g., response to pandemics), provide invaluable resources to inform policy and decision makers, and educate all audiences globally.
Collapse
Affiliation(s)
- Pierre Comizzoli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States.,Office of the Under-Secretary for Science and Research, Smithsonian Institution, Washington, DC, United States
| | | | - Carly Muletz-Wolz
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States
| | - James Hassell
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States
| | - Brian Coyle
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States.,Office of the Under-Secretary for Science and Research, Smithsonian Institution, Washington, DC, United States
| |
Collapse
|
35
|
Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang M, Khan FAA, Paul DL, Reeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 2021; 12:e02698-20. [PMID: 33436435 PMCID: PMC7844540 DOI: 10.1128/mbio.02698-20] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
Collapse
Affiliation(s)
- Cody W Thompson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marc W Allard
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Adam W Ferguson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Magnus Gelang
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Deborah L Paul
- Florida State University, Tallahassee, Florida, USA
- Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Maarten P M Vanhove
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | |
Collapse
|
36
|
Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
Collapse
Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| |
Collapse
|
37
|
Caraballo DA, Montani ME, Martínez LM, Antoniazzi LR, Sambrana TC, Fernández C, Cisterna DM, Beltrán FJ, Colombo VC. Heterogeneous taxonomic resolution of cytochrome b gene identification of bats from Argentina: Implications for field studies. PLoS One 2021; 15:e0244750. [PMID: 33382800 PMCID: PMC7775095 DOI: 10.1371/journal.pone.0244750] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022] Open
Abstract
Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus, for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera (Eumops, Dasypterus, Molossops) and has infrageneric resolution in more complex lineages (Eptesicus, Myotis, Molossus). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.
Collapse
Affiliation(s)
- Diego A. Caraballo
- Instituto de Zoonosis Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, Rosario, Santa Fe, Argentina
- Programa de Investigaciones de Biodiversidad Argentina (PIDBA), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
- Programa de Conservación de los Murciélagos de Argentina (PCMA), San Miguel de Tucumán, Tucumán, Argentina
| | - Leila M. Martínez
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leandro R. Antoniazzi
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Tomás C. Sambrana
- Departamento de Zoonosis, Laboratorio Central de Referencia, Dirección de Promoción y Prevención, Ministerio de Salud de la provincia de Santa Fe, Ciudad de Santa Fe, Santa Fe, Argentina
| | - Camilo Fernández
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Daniel M. Cisterna
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando J. Beltrán
- Instituto de Zoonosis Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria C. Colombo
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| |
Collapse
|
38
|
Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller E, Schulman L, Tilley L, Robertson T. White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). RESEARCH IDEAS AND OUTCOMES 2020. [DOI: 10.3897/rio.6.e62361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure (RI) is presently in its preparatory phase. DiSSCo is developing a new distributed RI to operate as a one-stop-shop for the envisaged European Natural Science Collection (NSC) and all its derived information. Through mass digitisation, DiSSCo will transform the fragmented landscape of NSCs, including an estimated 1.5 billion specimens, into an integrated knowledge base that will provide interconnected evidence of the natural world. Data derived from European NSCs underpin countless discoveries and innovations, including tens of thousands of scholarly publications and official reports annually (supporting legislative and regulatory processes on sustainability, environmental change, land use, societal infrastructure, health, food, security, etc.); base-line biodiversity data; inventions and products essential to bio-economy; databases, maps and descriptions of scientific observations; educational material for students; and instructive and informative resources for the public. To expand the user community, DiSSCo will strengthen capacity building across Europe for maximum engagement of stakeholders in the biodiversity-related field and beyond, including industry and the private sector, but also policy-driving entities. Hence, it is opportune to reach out to relevant stakeholders in the European environmental policy domain represented by the European Environment Agency (EEA). The EEA aims to support sustainable development by helping to achieve significant and measurable improvement in Europe's environment, through the provision of timely, targeted, relevant and reliable information to policy-making agents and the public. The EEA provides information through the European Environment Information and Observation System (Eionet). The aim of this white paper is to open the discussion between DiSSCo and the EEA and identify the common service interests that are relevant for the European environmental policy domain. The first section describes the significance of (digital) Natural Science Collections (NHCs). Section two describes the DiSSCo programme with all DiSSCo aligned projects. Section three provides background information on the EEA and the biodiversity infrastructures that are developed and maintained by the EEA. The fourth section illustrates a number of use cases where the DiSSCo consortium sees opportunities for interaction between the DiSSCo RI and the Eionet portal of the EEA. Opening the discussion with the EEA in this phase of maturity of DiSSCo will ensure that the infrastructural design of DiSSCo and the development of e-Services accommodate the present and future needs of the EEA and assure data interoperability between the two infrastructures.
The aim of this white paper is to present benefits from identifying the common service interests of DiSSCo and the EEA. A brief introduction to natural science collections as well as the two actors is given to facilitate the understanding of the needs and possibilities in the alignment of DiSSCo with the EEA.
Collapse
|
39
|
Incorporating RDA Outputs in the Design of a European Research Infrastructure for Natural Science Collections. DATA SCIENCE JOURNAL 2020. [DOI: 10.5334/dsj-2020-050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
40
|
Colella JP, Agwanda BR, Anwarali Khan FA, Bates J, Carrión Bonilla CA, de la Sancha NU, Dunnum JL, Ferguson AW, Greiman SE, Kiswele PK, Lessa EP, Soltis P, Thompson CW, Vanhove MPM, Webala PW, Weksler M, Cook JA. Build international biorepository capacity. Science 2020; 370:773-774. [PMID: 33184198 DOI: 10.1126/science.abe4813] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Jocelyn P Colella
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045 USA
| | | | | | - John Bates
- Field Museum, Chicago, IL 60605, USA.,Natural Science Collections Alliance, Washington, DC 20005, USA
| | - Carlos A Carrión Bonilla
- Museo de Zoologiá, Escuela de Biología, Pontificia Universidad Catolica del Ecuador, Quito, Ecuador.,Museum of Southwestern Biology and Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
| | - Noé U de la Sancha
- Field Museum, Chicago, IL 60605, USA.,Department of Biological Sciences, Chicago State University, Chicago, IL 60628, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology and Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
| | | | - Stephen E Greiman
- Department of Biology, Georgia Southern University, Statesboro, GA 30458, USA
| | | | - Enrique P Lessa
- Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pamela Soltis
- Florida Museum of Natural History and the University of Florida Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Cody W Thompson
- Department of Ecology and Evolutionary Biology and the Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Maarten P M Vanhove
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joseph A Cook
- Museum of Southwestern Biology and Biology Department, University of New Mexico, Albuquerque, NM 87131, USA.
| |
Collapse
|
41
|
Common ground: The foundation of interdisciplinary research on bat disease emergence. PLoS Biol 2020; 18:e3000947. [PMID: 33166274 PMCID: PMC7676706 DOI: 10.1371/journal.pbio.3000947] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/19/2020] [Indexed: 11/25/2022] Open
Abstract
Human perturbation of natural systems is accelerating the emergence of infectious diseases, mandating integration of disease and ecological research. Bats have been associated with recent zoonoses, but our bibliometric analysis of coauthor relationships identified a separation of bat ecologists and infectious disease researchers with few cross-disciplinary relationships. Of 5,645 papers, true interdisciplinary collaborations occurred primarily in research focused on White Nose Syndrome (WNS). This finding is important because it illustrates how research with outcomes favoring both bat conservation and disease mitigation promotes domain integration and network connectivity. We advocate for increased engagement between ecology and infectious researchers to address such common causes and suggest that efforts focus on leveraging existing activities, building interdisciplinary projects, and networking individuals and networks to integrate domains and coordinate resources. We provide specific opportunities for pursuing these strategies through the Bat One Health Research Network (BOHRN). Limited collaboration between bat ecologists and disease researchers has precluded integrative research on disease emergence. These historical silos are now challenged by the emergence of SARS-CoV-2, which threatens both human and bat health. This Perspective article maintains that interdisciplinary research can be accelerated when disparate domains address common, foundational causes.
Collapse
|
42
|
Ferguson AW. On the role of (and threat to) natural history museums in mammal conservation: an African small mammal perspective. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|