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Rujano MA, Boiten JW, Ohmann C, Canham S, Contrino S, David R, Ewbank J, Filippone C, Connellan C, Custers I, van Nuland R, Mayrhofer MT, Holub P, Álvarez EG, Bacry E, Hughes N, Freeberg MA, Schaffhauser B, Wagener H, Sánchez-Pla A, Bertolini G, Panagiotopoulou M. Sharing sensitive data in life sciences: an overview of centralized and federated approaches. Brief Bioinform 2024; 25:bbae262. [PMID: 38836701 DOI: 10.1093/bib/bbae262] [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: 02/06/2024] [Revised: 04/19/2024] [Indexed: 06/06/2024] Open
Abstract
Biomedical data are generated and collected from various sources, including medical imaging, laboratory tests and genome sequencing. Sharing these data for research can help address unmet health needs, contribute to scientific breakthroughs, accelerate the development of more effective treatments and inform public health policy. Due to the potential sensitivity of such data, however, privacy concerns have led to policies that restrict data sharing. In addition, sharing sensitive data requires a secure and robust infrastructure with appropriate storage solutions. Here, we examine and compare the centralized and federated data sharing models through the prism of five large-scale and real-world use cases of strategic significance within the European data sharing landscape: the French Health Data Hub, the BBMRI-ERIC Colorectal Cancer Cohort, the federated European Genome-phenome Archive, the Observational Medical Outcomes Partnership/OHDSI network and the EBRAINS Medical Informatics Platform. Our analysis indicates that centralized models facilitate data linkage, harmonization and interoperability, while federated models facilitate scaling up and legal compliance, as the data typically reside on the data generator's premises, allowing for better control of how data are shared. This comparative study thus offers guidance on the selection of the most appropriate sharing strategy for sensitive datasets and provides key insights for informed decision-making in data sharing efforts.
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Affiliation(s)
- Maria A Rujano
- European Clinical Research Infrastructure Network (ECRIN), Boulevard Saint Jacques 30, 75014, Paris, France
| | - Jan-Willem Boiten
- Foundation Lygature, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Christian Ohmann
- European Clinical Research Infrastructure Network (ECRIN), Boulevard Saint Jacques 30, 75014, Paris, France
| | - Steve Canham
- European Clinical Research Infrastructure Network (ECRIN), Boulevard Saint Jacques 30, 75014, Paris, France
| | - Sergio Contrino
- European Clinical Research Infrastructure Network (ECRIN), Boulevard Saint Jacques 30, 75014, Paris, France
| | - Romain David
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA AISBL), rue du Trône 98/Boîte 4B, 1050, Brussels, Belgium
| | - Jonathan Ewbank
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA AISBL), rue du Trône 98/Boîte 4B, 1050, Brussels, Belgium
| | - Claudia Filippone
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA AISBL), rue du Trône 98/Boîte 4B, 1050, Brussels, Belgium
| | - Claire Connellan
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA AISBL), rue du Trône 98/Boîte 4B, 1050, Brussels, Belgium
| | - Ilse Custers
- Foundation Lygature, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Rick van Nuland
- Foundation Lygature, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Michaela Th Mayrhofer
- Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-ERIC), Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
| | - Petr Holub
- Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-ERIC), Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
| | - Eva García Álvarez
- Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-ERIC), Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
| | - Emmanuel Bacry
- Health Data Hub (HDH), rue Georges Pitard 9, 75015, Paris, France
| | - Nigel Hughes
- Janssen Research and Development, Antwerpseweg 15, 2340, Beerse, Belgium
| | - Mallory A Freeberg
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, CB10 1SD, Hinxton, Cambridgeshire, United Kingdom
| | - Birgit Schaffhauser
- Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland
| | - Harald Wagener
- Center for Digital Health, BIH@Charité University Medicine, Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Alex Sánchez-Pla
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Guido Bertolini
- Laboratory of Clinical Epidemiology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via GB Camozzi 3, 24020, Ranica (Bergamo), Italy
| | - Maria Panagiotopoulou
- European Clinical Research Infrastructure Network (ECRIN), Boulevard Saint Jacques 30, 75014, Paris, France
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Ratnasingham S, Wei C, Chan D, Agda J, Agda J, Ballesteros-Mejia L, Boutou HA, El Bastami ZM, Ma E, Manjunath R, Rea D, Ho C, Telfer A, McKeowan J, Rahulan M, Steinke C, Dorsheimer J, Milton M, Hebert PDN. BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data. Methods Mol Biol 2024; 2744:403-441. [PMID: 38683334 DOI: 10.1007/978-1-0716-3581-0_26] [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: 05/01/2024]
Abstract
BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, makes it a central resource for biodiversity science. It enables rapid, accurate identification of specimens and also reveals patterns of genetic diversity and evolutionary relationships among taxa.Launched in 2005, BOLD has become an increasingly powerful tool for advancing the understanding of planetary biodiversity. It currently hosts 17 million specimen records and 14 million barcodes that provide coverage for more than a million species from every continent and ocean. The platform has the long-term goal of providing a consistent, accurate system for identifying all species of eukaryotes.BOLD's integrated analytical tools, full data lifecycle support, and secure collaboration framework distinguish it from other biodiversity platforms. BOLD v4 brought enhanced data management and analysis capabilities as well as novel functionality for data dissemination and publication. Its next version will include features to strengthen its utility to the research community, governments, industry, and society-at-large.
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Affiliation(s)
| | - Catherine Wei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dean Chan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jireh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Josh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Hamza Ait Boutou
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Eddie Ma
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dana Rea
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Angela Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jaclyn McKeowan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Miduna Rahulan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Justin Dorsheimer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Megan Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- College of Biological Science, University of Guelph, Guelph, ON, Canada
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3
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Kim EH, Hitchmough JD, Cameron RW, Schrodt F, Martin KWE, Cubey R. Applying the concept of niche breadth to understand urban tree mortality in the UK. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166304. [PMID: 37619719 DOI: 10.1016/j.scitotenv.2023.166304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Accelerated climate change has raised concerns about heightened vulnerability of urban trees, spurring the need to reevaluate their suitability. The urgency has also driven the widespread application of climatic niche-based models. In particular, the concept of niche breadth (NB), the range of environmental conditions that species can tolerate, is commonly estimated based on species occurrence data over the selected geographic range to predict species response to changing conditions. However, in urban environments where many species are cultivated out of the NB of their natural distributions, additional empirical evidence beyond presence and absence is needed not only to test the true tolerance limits but also to evaluate species' adaptive capacity to future climate. In this research, mortality trends of Acer and Quercus species spanning a 21-year period (2000-2021) from tree inventories of three major UK botanic gardens - the Royal Botanic Gardens, Kew (KEW), Westonbirt, the National Arboretum (WESB), and the Royal Botanic Garden Edinburgh (RBGE) - were analyzed in relation to their NB under long-term drought stress. As a result, Acer species were more responsive to drought and heat stress. For Acer, positioning below the lower limits of the precipitation of warmest quarter led to an increase in the probability of annual mortality by 1.2 and 1.3 % at KEW and RBGE respectively. In addition, the mean cumulative mortality rate increased corresponding to an increase in the number of niche positions below the lower limits of the selected bioclimatic variables. On the other hand, Quercus species in general exhibited comparable resilience regardless of their niche positions. Moreover, Mediterranean oaks were most tolerant, with cumulative mortality rates that were lower than those of native oaks in the UK. These findings further highlight the importance of incorporating ecological performance and recognizing species-specific adaptive strategies in climatic niche modeling.
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Affiliation(s)
- Eun Hye Kim
- Department of Landscape Architecture, University of Sheffield, Arts Tower, Sheffield S10 2TN, UK.
| | - James D Hitchmough
- Department of Landscape Architecture, University of Sheffield, Arts Tower, Sheffield S10 2TN, UK
| | - Ross W Cameron
- Department of Landscape Architecture, University of Sheffield, Arts Tower, Sheffield S10 2TN, UK
| | - Franziska Schrodt
- Department of Geography, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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4
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Sandall EL, Maureaud AA, Guralnick R, McGeoch MA, Sica YV, Rogan MS, Booher DB, Edwards R, Franz N, Ingenloff K, Lucas M, Marsh CJ, McGowan J, Pinkert S, Ranipeta A, Uetz P, Wieczorek J, Jetz W. A globally integrated structure of taxonomy to support biodiversity science and conservation. Trends Ecol Evol 2023; 38:1143-1153. [PMID: 37684131 DOI: 10.1016/j.tree.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/30/2023] [Accepted: 08/04/2023] [Indexed: 09/10/2023]
Abstract
All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.
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Affiliation(s)
- Emily L Sandall
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA.
| | - Aurore A Maureaud
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, USA.
| | - Robert Guralnick
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Melodie A McGeoch
- Securing Antarctica's Environmental Future, Department of Environment and Genetics, LaTrobe University, Melbourne, Australia
| | - Yanina V Sica
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Matthew S Rogan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Douglas B Booher
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Robert Edwards
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; Cleveland Museum of Natural History, Cleveland, OH, USA
| | - Nico Franz
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Kate Ingenloff
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Maisha Lucas
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Charles J Marsh
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Jennifer McGowan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; The Nature Conservancy, Arlington, VA, USA
| | - Stefan Pinkert
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; Department of Conservation Ecology, University of Marburg, Marburg, Germany
| | - Ajay Ranipeta
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Peter Uetz
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - John Wieczorek
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; E.O. Wilson Biodiversity Foundation, Durham, NC, USA
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5
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Molina-Paniagua ME, Alves de Melo PH, Ramírez-Barahona S, Monro AK, Burelo-Ramos CM, Gómez-Domínguez H, Ortiz-Rodriguez AE. How diverse are the mountain karst forests of Mexico? PLoS One 2023; 18:e0292352. [PMID: 37792775 PMCID: PMC10550121 DOI: 10.1371/journal.pone.0292352] [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: 12/05/2022] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
Tropical forests on karstic relief (tropical karst forest) are among the most species-rich biomes. These forests play pivotal roles as global climate regulators and for human wellbeing. Their long-term conservation could be central to global climate mitigation and biodiversity conservation. In Mexico, karst landscapes occupy 20% of the total land surface and are distributed mainly in the southeast of the country, along the eastern slope, and in the Yucatan Peninsula. Within each of these areas, the following types of karst occur: coastal karst, plain karst, hill karst, and mountain karst (low, medium, high). Mountain karst cover 2.07% of Mexico's land surface and are covered by tropical rainforests, montane cloud forests, and tropical deciduous forests. These are probably one of the most diverse biomes in Mexico. However, the mountain karst forests of Mexico have received little attention, and very little is known about their diversity. Here, we evaluated the vascular plant species richness within the mountain karst forests of Mexico. We assembled the first, largest, and most comprehensive datasets of Mexican mountain karst forest species, from different public databases (CONABIO, GBIF, IBdata-UNAM), which included a critical review of all data. We compiled a list of the families, genera, and species present within the mountain karst forests of Mexico. Taxa that best characterize these forests were identified based on their spatial correlation with this biome. We explored biodiversity patterns, identifying areas with the highest species richness, endemism centers, and areas of relatively low sampling intensity. We found that within the mountain karst forests of Mexico there are representatives of 11,771 vascular plant species (253 families and 2,254 genera), ca. 50% of the Mexican flora. We identified 372 species endemic to these forests. According to preliminary IUCN red list criteria, 2,477 species are under some category of conservation risk, of which 456 (3.8%) are endangered. Most of the Mexican mountain karst forests have been extensively explored and six allopatric, species-rich areas were identified. Compared to other regions in the world, the mountain karst forests of Mexico are one of the most diverse biomes. They contain more species than some entire montane systems in Mexico such as Sierra Madre Oriental, and Sierra Madre del Sur. Also, the mountain karst forests of Mexico are most diverse than similar forests of South America and Asia, even if considering the effect of different sampling areas. The fact that mountain karst forests are embedded in areas of high biotic diversity, probably contributes to their great floristic diversity. Thus, the mountain karst forests of Mexico are an important source of diversity and shelters a large percentage of the Mexican flora.
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Affiliation(s)
- María Eugenia Molina-Paniagua
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
- Departamento de Botánica, Instituto de Biología, UNAM, Ciudad Universitaria, Ciudad de México, México
| | | | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, UNAM, Ciudad Universitaria, Ciudad de México, México
| | | | - Carlos Manuel Burelo-Ramos
- Herbario UJAT, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
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Bernard C, Santos GS, Deere JA, Rodriguez-Caro R, Capdevila P, Kusch E, Gascoigne SJL, Jackson J, Salguero-Gómez R. MOSAIC - A Unified Trait Database to Complement Structured Population Models. Sci Data 2023; 10:335. [PMID: 37264011 PMCID: PMC10235418 DOI: 10.1038/s41597-023-02070-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 03/14/2023] [Indexed: 06/03/2023] Open
Abstract
Despite exponential growth in ecological data availability, broader interoperability amongst datasets is needed to unlock the potential of open access. Our understanding of the interface of demography and functional traits is well-positioned to benefit from such interoperability. Here, we introduce MOSAIC, an open-access trait database that unlocks the demographic potential stored in the COMADRE, COMPADRE, and PADRINO open-access databases. MOSAIC data were digitised and curated through a combination of existing datasets and new trait records sourced from primary literature. In its first release, MOSAIC (v. 1.0.0) includes 14 trait fields for 300 animal and plant species: biomass, height, growth determination, regeneration, sexual dimorphism, mating system, hermaphrodism, sequential hermaphrodism, dispersal capacity, type of dispersal, mode of dispersal, dispersal classes, volancy, and aquatic habitat dependency. MOSAIC includes species-level phylogenies for 1,359 species and population-specific climate data. We identify how database integration can improve our understanding of traits well-quantified in existing repositories and those that are poorly quantified (e.g., growth determination, modularity). MOSAIC highlights emerging challenges associated with standardising databases and demographic measures.
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Affiliation(s)
- Connor Bernard
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom.
| | - Gabriel Silva Santos
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- Department of Ecology, Rio de Janeiro State University, 20550-900, Rio de Janeiro, Brazil
- National Institute of the Atlantic Forest (INMA), 29650-000, Santa Teresa, Espírito Santo, Brazil
| | - Jacques A Deere
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX, Amsterdam, Netherlands
| | - Roberto Rodriguez-Caro
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- Departamento de Biología Aplicada, Universidad Miguel Hernández. Av. Universidad, s/n, 03202, Elche (Alicante), Spain
| | - Pol Capdevila
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- School of Biological Sciences, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ, United Kingdom
| | - Erik Kusch
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Arhus University, Aarhus, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Arhus University, Aarhus, Denmark
| | - Samuel J L Gascoigne
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
| | - John Jackson
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
| | - Roberto Salguero-Gómez
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- Centre for Biodiversity and Conservation Science, University of Queensland, St. Lucia, QLD, Australia
- Evolutionary Demography Laboratory, Max Plank Institute for Demographic Research, Rostock, Germany
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7
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Peng M, Bervoets S, Chin-A-Woeng T, Granchi Z, Hildén K, Mäkelä MR, de Vries RP. The transcriptomic response of two basidiomycete fungi to plant biomass is modulated by temperature to a different extent. Microbiol Res 2023; 270:127333. [PMID: 36804127 DOI: 10.1016/j.micres.2023.127333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Many fungi show a strong preference for specific habitats and growth conditions. Investigating the molecular mechanisms of fungal adaptation to varying environmental conditions is of great interest to biodiversity research and is important for many industrial applications. In this study, we compared the transcriptome profiles of two previously genome-sequenced white-rot wood-decay fungi, Trametes pubescens and Phlebia centrifuga, during their growth on two common plant biomass substrates (wheat straw and spruce) at two temperatures (15 °C and 25 °C). The results showed that both fungi partially tailored their molecular responses to different types of carbon sources, differentially expressing genes encoding polysaccharide degrading enzymes, transporters, proteases and monooxygenases. Notably, more lignin modification related AA2 genes and cellulose degradation related AA9 genes were differentially expressed in the tested conditions of T. pubescens than P. centrifuga. In addition, we detected more remarkable transcriptome changes to different growth temperature in P. centrifuga than in T. pubescens, which reflected their different ability to adapt to the temperature fluctuations. In P. centrifuga, differentially expressed genes (DEGs) related to temperature response mainly encode protein kinases, trehalose metabolism, carbon metabolic enzymes and glycoside hydrolases, while the main temperature-related DEGs identified in T. pubescens are only the carbon metabolic enzymes and glycoside hydrolases. Our study revealed both conserved and species-specific transcriptome changes during fungal adaptation to a changing environment, improving our understanding of the molecular mechanisms underlying fungal plant biomass conversion at varying temperatures.
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Affiliation(s)
- Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Sander Bervoets
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, the Netherlands
| | | | - Zoraide Granchi
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, the Netherlands
| | - Kristiina Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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8
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Quille RVE, de Almeida FV, Ohara MY, Corrêa PLP, de Freitas LG, Alves-Souza SN, de Almeida JR, Davis M, Prakash G. Architecture of a Data Portal for Publishing and Delivering Open Data for Atmospheric Measurement. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:5374. [PMID: 37047988 PMCID: PMC10094644 DOI: 10.3390/ijerph20075374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Atmospheric data are collected by researchers every day. Campaigns such as GOAmazon 2014/2015 and the Amazon Tall Tower Observatory collect essential data on aerosols, gases, cloud properties, and meteorological parameters in the Brazilian Amazon basin. These data products provide insights and essential information for analyzing and predicting natural processes. However, in Brazil, it is estimated that more than 80% of the scientific data collected are not published due to the lack of web portals that collect and store these data. This makes it difficult, or even impossible, to access and integrate the data, which can result in the loss of significant amounts of information and significantly affect the understanding of the overall data. To address this problem, we propose a data portal architecture and open data deployment that enable Big Data processing, human interaction, and download-oriented approaches with tools that help users catalog, publish and visualize atmospheric data. Thus, we describe the architecture developed, based on the experience of the Atmospheric Radiation Measurement Data Center, which incorporates the principles of FAIR, the infrastructure and content management system for managing scientific data. The portal partial results were tested with environmental data from contaminated areas at the University of São Paulo. Overall, this data portal creates more shared knowledge about atmospheric processes by providing users with access to open environmental data.
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Affiliation(s)
- Rosa Virginia Encinas Quille
- School of Arts, Sciences and Humanities, University of São Paulo, Rua Arlindo Béttio, 1000-Ermelino Matarazzo, São Paulo 03828-000, Brazil
- Residues and Contaminated Areas Laboratory (LARC), Institute for Technological Research (IPT), Av. Prof. Almeida Prado, 532-Butantã, São Paulo 05508-901, Brazil
| | - Felipe Valencia de Almeida
- Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto, 380-Butantã, São Paulo 05508-010, Brazil; (F.V.d.A.)
| | - Mauro Yuji Ohara
- Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto, 380-Butantã, São Paulo 05508-010, Brazil; (F.V.d.A.)
| | - Pedro Luiz Pizzigatti Corrêa
- School of Arts, Sciences and Humanities, University of São Paulo, Rua Arlindo Béttio, 1000-Ermelino Matarazzo, São Paulo 03828-000, Brazil
- Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto, 380-Butantã, São Paulo 05508-010, Brazil; (F.V.d.A.)
| | - Leandro Gomes de Freitas
- Residues and Contaminated Areas Laboratory (LARC), Institute for Technological Research (IPT), Av. Prof. Almeida Prado, 532-Butantã, São Paulo 05508-901, Brazil
| | - Solange Nice Alves-Souza
- School of Arts, Sciences and Humanities, University of São Paulo, Rua Arlindo Béttio, 1000-Ermelino Matarazzo, São Paulo 03828-000, Brazil
- Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto, 380-Butantã, São Paulo 05508-010, Brazil; (F.V.d.A.)
| | - Jorge Rady de Almeida
- Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto, 380-Butantã, São Paulo 05508-010, Brazil; (F.V.d.A.)
| | - Maggie Davis
- Environmental Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Giri Prakash
- Environmental Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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9
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Malatesta L, Alves T, Attorre F, Brito D, Cianciullo S, Datizua C, De Abreu D, De Felici S, De Sousa C, Langa C, Mate B, Matimele H, Nicosia E, Odorico D, Raiva R, Sandramo D, Santana Afonso P, Sardinha C, Souane J, Timane R, Tomo G, Ntumi C. BioNoMo: the Biodiversity Network of Mozambique. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2023. [DOI: 10.1007/s12210-023-01144-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
AbstractMozambique biodiversity richness plays a pivotal role to achieve the sustainable development of the country. However, Mozambique’s flora and fauna diversity still remains broadly unknown and poorly documented. To properly address this issue, one of the strategic needs expressed by the Mozambican institutions was the development of a national biodiversity data repository to aggregate, manage and make data available online. Thus, a sustainable infrastructure for the standardisation, aggregation, organisation and sharing of primary biodiversity data was developed. Named the “Biodiversity Network of Mozambique” (BioNoMo), such a tool serves as a national repository of biodiversity data and aggregates occurrence records of plants and animals in the country obtained from floristic and faunistic observations and from specimens of biological collections. In this paper, the authors present the structure and data of BioNoMO, including software details, the process of data gathering and aggregation, the taxonomic coverage and the WebGIS development. Currently, aggregating a total of 273,172 records, including 85,092 occurrence records of plants and 188,080 occurrence records of animals (41.2% terrestrial, 58,8% aquatic), BioNoMo represents the largest aggregator of primary biodiversity data in Mozambique and it is planned to grow further by aggregating new datasets.
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10
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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11
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D'Antraccoli M, Bedini G, Peruzzi L. Maps of relative floristic ignorance and virtual floristic lists: An R package to incorporate uncertainty in mapping and analysing biodiversity data. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2021.101512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Potapov AM, Beaulieu F, Birkhofer K, Bluhm SL, Degtyarev MI, Devetter M, Goncharov AA, Gongalsky KB, Klarner B, Korobushkin DI, Liebke DF, Maraun M, Mc Donnell RJ, Pollierer MM, Schaefer I, Shrubovych J, Semenyuk II, Sendra A, Tuma J, Tůmová M, Vassilieva AB, Chen T, Geisen S, Schmidt O, Tiunov AV, Scheu S. Feeding habits and multifunctional classification of soil‐associated consumers from protists to vertebrates. Biol Rev Camb Philos Soc 2022; 97:1057-1117. [DOI: 10.1111/brv.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Anton M. Potapov
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Frédéric Beaulieu
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri‐Food Canada Ottawa ON K1A 0C6 Canada
| | - Klaus Birkhofer
- Department of Ecology Brandenburg University of Technology Karl‐Wachsmann‐Allee 6 03046 Cottbus Germany
| | - Sarah L. Bluhm
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Maxim I. Degtyarev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Miloslav Devetter
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anton A. Goncharov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Konstantin B. Gongalsky
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Bernhard Klarner
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Daniil I. Korobushkin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Dana F. Liebke
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Mark Maraun
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Rory J. Mc Donnell
- Department of Crop and Soil Science Oregon State University Corvallis OR 97331 U.S.A
| | - Melanie M. Pollierer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Ina Schaefer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Julia Shrubovych
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Institute of Systematics and Evolution of Animals PAS Slawkowska 17 Pl 31‐016 Krakow Poland
- State Museum Natural History of NAS of Ukraine Teatralna 18 79008 Lviv Ukraine
| | - Irina I. Semenyuk
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
- Joint Russian‐Vietnamese Tropical Center №3 Street 3 Thang 2, Q10 Ho Chi Minh City Vietnam
| | - Alberto Sendra
- Colecciones Entomológicas Torres‐Sala, Servei de Patrimoni Històric, Ajuntament de València València Spain
- Departament de Didàctica de les Cièncias Experimentals i Socials, Facultat de Magisteri Universitat de València València Spain
| | - Jiri Tuma
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Biology Centre CAS, Institute of Entomology Branisovska 1160/31 370 05 Ceske Budejovice Czech Republic
| | - Michala Tůmová
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anna B. Vassilieva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Ting‐Wen Chen
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Stefan Geisen
- Department of Nematology Wageningen University & Research 6700ES Wageningen The Netherlands
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science University College Dublin Belfield Dublin 4 Ireland
| | - Alexei V. Tiunov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- Centre of Biodiversity and Sustainable Land Use Büsgenweg 1 37077 Göttingen Germany
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Grenié M, Berti E, Carvajal‐Quintero J, Dädlow GML, Sagouis A, Winter M. Harmonizing taxon names in biodiversity data: a review of tools, databases, and best practices. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13802] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matthias Grenié
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Leipzig University Ritterstraße 26 04109 Leipzig Germany
| | - Emilio Berti
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Friedrich‐Schiller University Jena Jena Germany
| | - Juan Carvajal‐Quintero
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Leipzig University Ritterstraße 26 04109 Leipzig Germany
| | - Gala Mona Louise Dädlow
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Leipzig University Ritterstraße 26 04109 Leipzig Germany
| | - Alban Sagouis
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Department of Computer Science Martin Luther University Halle‐Wittenberg, Halle Germany
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Leipzig University Ritterstraße 26 04109 Leipzig Germany
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14
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Chapman AD. BIOTA-FAPESP – supporting biodiversity, building partnerships, and filling the knowledge gaps. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1405] [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 ECO92, a United Nations Conference on Environment and Development, hosted by Brazil in 1992 was a catalyst for much activity on biodiversity in the State of São Paulo and eventually led to the establishment of BIOTA-FAPESP. BIOTA-FAPESP quickly evolved into a world-leading research program that has broadened to cover all aspects of biodiversity in the State from genes through species and to ecosystems and the interactions between them. Through the funding of multi-disciplinary projects, the development of collaborative links within the State, nationally and internationally, and the astute use of databases to link the program’s project outputs it has set a platform for filling the biodiversity knowledge gaps. Having achieved much in the last two decades, it still has some way to go, but the stage is set.
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15
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Canhos DAL, Almeida EAB, Assad AL, Cunha Bustamante MMD, Canhos VP, Chapman AD, Giovanni RD, Imperatriz-Fonseca VL, Lohmann LG, Maia LC, Miller JT, Nelson G, Peterson AT, Pirani JR, Souza SD, Stehmann JR, Thiers B. speciesLink: rich data and novel tools for digital assessments of biodiversity. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1394] [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 speciesLink is a large-scale biodiversity information portal that exists thanks to a broad collaborative network of people and institutions. CRIA’s involvement with the scientific community of Brazil and other countries is responsible for the significant results achieved, currently reaching more than 15 million primary biodiversity data records, 95% of which are associated with preserved specimens and about 25% with high-quality digital images. The network provides data on over 200,000 species, of which over 110,000 occur in Brazil. This article describes thematic networks within speciesLink, as well as some of the most useful tools developed. The importance and contributions of speciesLink are outlined, as are concerns about securing stable budgetary support for such biodiversity data e-infrastructures. Here we review the value of speciesLink as a major source of biodiversity information for research, education, informed decision-making, policy development, and bioeconomy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Gil Nelson
- Integrated Digitized Biocollections, USA
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16
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Reddy MM, Jennings L, Thomas OP. Marine Biodiscovery in a Changing World. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2021; 116:1-36. [PMID: 34698944 DOI: 10.1007/978-3-030-80560-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The term "marine biodiscovery" has been recently been adopted to describe the area of marine natural products dedicated to the search of new drugs. Several maritime countries such as Australia, New Zealand, South Korea, and Japan as well as some European countries have invested significantly in this area of research over the last 50 years. In the late 2000s, research in this field has received significant interest and support in Ireland for exploring new marine bioresources from the nutrient-rich waters of the Northeastern Atlantic Ocean. Despite undeniable success exemplified by the marketing of new drugs, especially in oncology, the integration of new technical but also environmental aspects should be considered. Indeed, global change, particularly in our oceans, such as climate change, biodiversity loss, and the emergence of microbial pathogens, not only affects the environment but ultimately contributes to social inequalities. In this contribution, new avenues and best practices are proposed, such as the development of biorepositories and shared data for the future of marine biodiscovery research. The extension of this type of scientific work will allow humanity to finally make the optimum use of marine bioresources.
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Affiliation(s)
- Maggie M Reddy
- Marine Biodiscovery, School of Chemistry and Ryan Institute, NUI Galway, University Road, Galway, H91TK33, Ireland
| | - Laurence Jennings
- Marine Biodiscovery, School of Chemistry and Ryan Institute, NUI Galway, University Road, Galway, H91TK33, Ireland
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, NUI Galway, University Road, Galway, H91TK33, Ireland.
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17
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Global and national trends, gaps, and opportunities in documenting and monitoring species distributions. PLoS Biol 2021; 19:e3001336. [PMID: 34383738 PMCID: PMC8360587 DOI: 10.1371/journal.pbio.3001336] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Conserving and managing biodiversity in the face of ongoing global change requires sufficient evidence to assess status and trends of species distributions. Here, we propose novel indicators of biodiversity data coverage and sampling effectiveness and analyze national trajectories in closing spatiotemporal knowledge gaps for terrestrial vertebrates (1950 to 2019). Despite a rapid rise in data coverage, particularly in the last 2 decades, strong geographic and taxonomic biases persist. For some taxa and regions, a tremendous growth in records failed to directly translate into newfound knowledge due to a sharp decline in sampling effectiveness. However, we found that a nation’s coverage was stronger for species for which it holds greater stewardship. As countries under the post-2020 Global Biodiversity Framework renew their commitments to an improved, rigorous biodiversity knowledge base, our findings highlight opportunities for international collaboration to close critical information gaps. Conserving and managing biodiversity in the face of ongoing global change requires sufficient evidence to assess status and trends of species distributions. This study analyzes national trajectories in closing spatiotemporal knowledge gaps for terrestrial vertebrates (1950-2019) based on novel indicators of data coverage and sampling effectiveness.
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18
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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.
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19
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Etherington TR. Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method. PeerJ 2021; 9:e11436. [PMID: 34026369 PMCID: PMC8121071 DOI: 10.7717/peerj.11436] [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: 01/15/2021] [Accepted: 04/20/2021] [Indexed: 11/24/2022] Open
Abstract
The Mahalanobis distance is a statistical technique that has been used in statistics and data science for data classification and outlier detection, and in ecology to quantify species-environment relationships in habitat and ecological niche models. Mahalanobis distances are based on the location and scatter of a multivariate normal distribution, and can measure how distant any point in space is from the centre of this kind of distribution. Three different methods for calculating the multivariate location and scatter are commonly used: the sample mean and variance-covariance, the minimum covariance determinant, and the minimum volume ellipsoid. The minimum covariance determinant and minimum volume ellipsoid were developed to be robust to outliers by minimising the multivariate location and scatter for a subset of the full sample, with the proportion of the full sample forming the subset being controlled by a user-defined parameter. This outlier robustness means the minimum covariance determinant and the minimum volume ellipsoid are highly relevant for ecological niche analyses, which are usually based on natural history observations that are likely to contain errors. However, natural history observations will also contain extreme bias, to which the minimum covariance determinant and the minimum volume ellipsoid will also be sensitive. To provide guidance for selecting and parameterising a multivariate location and scatter method, a series of virtual ecological niche modelling experiments were conducted to demonstrate the performance of each multivariate location and scatter method under different levels of sample size, errors, and bias. The results show that there is no optimal modelling approach, and that choices need to be made based on the individual data and question. The sample mean and variance-covariance method will perform best on very small sample sizes if the data are free of error and bias. At larger sample sizes the minimum covariance determinant and minimum volume ellipsoid methods perform as well or better, but only if they are appropriately parameterised. Modellers who are more concerned about the prevalence of errors should retain a smaller proportion of the full data set, while modellers more concerned about the prevalence of bias should retain a larger proportion of the full data set. I conclude that Mahalanobis distances are a useful niche modelling technique, but only for questions relating to the fundamental niche of a species where the assumption of multivariate normality is reasonable. Users of the minimum covariance determinant and minimum volume ellipsoid methods must also clearly report their parameterisations so that the results can be interpreted correctly.
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20
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Gallinat AS, Pearse WD. Phylogenetic generalized linear mixed modeling presents novel opportunities for eco‐evolutionary synthesis. OIKOS 2021. [DOI: 10.1111/oik.08048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Amanda S. Gallinat
- Dept of Biology and Ecology Center, Utah State Univ. Logan UT USA
- Dept of Geography, Univ. of Wisconsin‐Milwaukee Milwaukee WI USA
| | - William D. Pearse
- Dept of Biology and Ecology Center, Utah State Univ. Logan UT USA
- Dept of Life Sciences, Imperial College London Silwood Park Campus Ascot Berkshire UK
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21
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Heberling JM, Miller JT, Noesgaard D, Weingart SB, Schigel D. Data integration enables global biodiversity synthesis. Proc Natl Acad Sci U S A 2021; 118:e2018093118. [PMID: 33526679 PMCID: PMC8017944 DOI: 10.1073/pnas.2018093118] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world's largest biodiversity data network, the Global Biodiversity Information Facility (GBIF). Data available through GBIF increased 12-fold since 2007, a trend matched by global data use with roughly two publications using GBIF-mediated data per day in 2019. Data-use patterns were diverse by authorship, geographic extent, taxonomic group, and dataset type. Despite facilitating global authorship, legacies of colonial science remain. Studies involving species distribution modeling were most prevalent (31% of literature surveyed) but recently shifted in focus from theory to application. Topic prevalence was stable across the 17-y period for some research areas (e.g., macroecology), yet other topics proportionately declined (e.g., taxonomy) or increased (e.g., species interactions, disease). Although centered on biological subfields, GBIF-enabled research extends surprisingly across all major scientific disciplines. Biodiversity data mobilization through global data aggregation has enabled basic and applied research use at temporal, spatial, and taxonomic scales otherwise not possible, launching biodiversity sciences into a new era.
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Affiliation(s)
- J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA 15213;
| | - Joseph T Miller
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
| | - Daniel Noesgaard
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
| | - Scott B Weingart
- Digital Humanities Program, University Libraries, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Dmitry Schigel
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
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22
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Syrota Y, du Preez LH. ParaSiteDB - A user-friendly database for managing a parasitological collection. Parasitol Int 2020; 81:102266. [PMID: 33278605 DOI: 10.1016/j.parint.2020.102266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/16/2020] [Accepted: 11/30/2020] [Indexed: 11/19/2022]
Abstract
ParaSiteDB is an application for arranging and managing a parasitological collection. It has been designed to provide a user-friendly, easily manageable and searchable site and is suitable for small to bigger collections. The source code of the application is available on GitHub: https://github.com/goobar4/aacrg. The demonstration version of the application is available on https://syrota.info/wormbasehttp://syrota.info/wormbase.
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Affiliation(s)
- Yaroslav Syrota
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa; Schmalhausen Institute of Zoology, NAS of Ukraine, vul. B. Khmelnytskogo, 15, Kyiv 01030, Ukraine.
| | - Louis H du Preez
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa; South African Institute for Aquatic Biodiversity, Private Bag 1015, Makhanda, South Africa
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Osawa T, Yoshimatsu S, Nakatani Y. Specimen‐based records and geographic locations of carabid beetles (Coleoptera) collected mainly by Dr. Kazuo Tanaka. Ecol Res 2020. [DOI: 10.1111/1440-1703.12167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Takeshi Osawa
- Graduate School of Urban Environmental Sciences Tokyo Metropolitan University Tokyo Japan
- Japan node of the Global Biodiversity Information Facility
| | - Shin‐ichi Yoshimatsu
- Institute for Agro‐Environmental Sciences, NARO Tsukuba Japan
- Tokyo University of Agriculture Atsugi Kanagawa Japan
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24
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Shin N, Shibata H, Osawa T, Yamakita T, Nakamura M, Kenta T. Toward more data publication of long‐term ecological observations. Ecol Res 2020. [DOI: 10.1111/1440-1703.12115] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nagai Shin
- Earth Surface System Research Center Research Institute for Global Change (RIGC), Japan Agency for Marine‐Earth Science and Technology (JAMSTEC) Yokohama Japan
- Institute of Arctic Climate and Environment Research, RIGC, JAMSTEC Yokohama Japan
| | - Hideaki Shibata
- Field Science Center for Northern Biosphere Hokkaido University Sapporo Japan
| | - Takeshi Osawa
- Graduate School of Urban Environmental Sciences Tokyo Metropolitan University Tokyo Japan
| | - Takehisa Yamakita
- Analyses of Changes in East Japan Marine Ecosystems Research and Development Group (JAM‐TEAMS) Marine Biodiversity and Environmental Assessment Research Center (BioEnv), RIGC, JAMSTEC Yokosuka Japan
| | - Masahiro Nakamura
- Wakayama Experimental Forest Field Science Center for Northern Biosphere, Hokkaido University Wakayama Japan
| | - Tanaka Kenta
- Sugadaira Research Station, Mountain Science Center University of Tsukuba Ueda Japan
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Daru BH, Karunarathne P, Schliep K. phyloregion: R package for biogeographical regionalization and macroecology. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13478] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Barnabas H. Daru
- Department of Life Sciences Texas A&M University‐Corpus Christi, Corpus Christi TX USA
| | - Piyal Karunarathne
- Department of Life Sciences Texas A&M University‐Corpus Christi, Corpus Christi TX USA
| | - Klaus Schliep
- Institute of Computational Biotechnology Graz University of Technology Graz Styria Austria
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Freitas TMS, Montag LFA, De Marco P, Hortal J. How reliable are species identifications in biodiversity big data? Evaluating the records of a neotropical fish family in online repositories. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Tiago M. S. Freitas
- Campus Universitário do Marajó-Breves, Universidade Federal do Pará, Breves, Brazil
| | | | - Paulo De Marco
- Departamento de Ecologia, ICB, Universidade Federal de Goiás, Goiania, Brazil
| | - JoaquÍn Hortal
- Departamento de Ecologia, ICB, Universidade Federal de Goiás, Goiania, Brazil
- Departament of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), C/José Gutiérrez Abascal 2, Madrid 28006, Spain
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28
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Moudrý V, Devillers R. Quality and usability challenges of global marine biodiversity databases: An example for marine mammal data. ECOL INFORM 2020. [DOI: 10.1016/j.ecoinf.2020.101051] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Affiliation(s)
- Takeshi Osawa
- Graduate School of Urban Environmental Sciences Tokyo Metropolitan University Tokyo Japan
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30
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Jiménez L, Soberón J, Christen JA, Soto D. On the problem of modeling a fundamental niche from occurrence data. Ecol Modell 2019. [DOI: 10.1016/j.ecolmodel.2019.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Miller DAW, Pacifici K, Sanderlin JS, Reich BJ. The recent past and promising future for data integration methods to estimate species’ distributions. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13110] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David A. W. Miller
- Department of Ecosystem Science and ManagementPenn State University University Park Pennsylvania
| | - Krishna Pacifici
- Department of Forestry and Environmental ResourcesProgram in Fisheries, Wildlife, and Conservation BiologyNorth Carolina State University Raleigh North Carolina
| | | | - Brian J. Reich
- Department of StatisticsNorth Carolina State University Raleigh North Carolina
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32
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Muñoz G, Kissling WD, van Loon EE. Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodivers Data J 2019:e28737. [PMID: 30692868 PMCID: PMC6344444 DOI: 10.3897/bdj.7.e28737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/19/2018] [Indexed: 11/28/2022] Open
Abstract
Background A considerable portion of primary biodiversity data is digitally locked inside published literature which is often stored as pdf files. Large-scale approaches to biodiversity science could benefit from retrieving this information and making it digitally accessible and machine-readable. Nonetheless, the amount and diversity of digitally published literature pose many challenges for knowledge discovery and retrieval. Text mining has been extensively used for data discovery tasks in large quantities of documents. However, text mining approaches for knowledge discovery and retrieval have been limited in biodiversity science compared to other disciplines. New information Here, we present a novel, open source text mining tool, the Biodiversity Observations Miner (BOM). This web application, written in R, allows the semi-automated discovery of punctual biodiversity observations (e.g. biotic interactions, functional or behavioural traits and natural history descriptions) associated with the scientific names present inside a corpus of scientific literature. Furthermore, BOM enable users the rapid screening of large quantities of literature based on word co-occurrences that match custom biodiversity dictionaries. This tool aims to increase the digital mobilisation of primary biodiversity data and is freely accessible via GitHub or through a web server.
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Affiliation(s)
- Gabriel Muñoz
- NASUA, Biodiversity research and conservation section, Quito, Ecuador NASUA, Biodiversity research and conservation section Quito Ecuador.,Faculty of Arts and Science, Department of Biology, Concordia University, Montreal, Canada Faculty of Arts and Science, Department of Biology, Concordia University Montreal Canada
| | - W Daniel Kissling
- Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam Netherlands
| | - E Emiel van Loon
- Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam Netherlands
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Abstract
The last 50 years have witnessed rapid changes in the ways that natural history specimens are collected, preserved, analyzed, and documented. Those changes have produced unprecedented access to specimens, images, and data as well as impressive research results in organismal biology. The stage is now set for a new generation of collecting, preserving, analyzing, and integrating biological samples—a generation devoted to interdisciplinary research into complex biological interactions and processes. Next-generation collections may be essential for breakthrough research on the spread of infectious diseases, feeding Earth's growing population, adapting to climate change, and other grand research challenges. A decade-long investment in research collection infrastructure will be needed.
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Affiliation(s)
- David E. Schindel
- Smithsonian Institution, Washington, D. C., United States of America
- * E-mail:
| | - Joseph A. Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
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Pacifici M, Attorre F, Martellos S, Bego F, De Sanctis M, Hoda P, Meço M, Rondinini C, Saçdanaku E, Salihaj E, Scepi E, Shuka L, Ghiurghi A. BioNNA: the Biodiversity National Network of Albania. NATURE CONSERVATION 2018. [DOI: 10.3897/natureconservation.25.22387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recently, the Albanian Government started the process to join the European Union. This process also involves matching the EU parameters in protecting its biodiversity. In order to support the Albanian authorities, the Italian Ministry of Foreign Affairs, General Directorate for Development Cooperation (DGCS) and the International Union for Conservation of Nature (IUCN) joined efforts in the project “Institutional Support to the Albanian Ministry of Environment, Forest and Water Administration for Sustainable Biodiversity Conservation and Use in Protected Areas”. This project aims at identifying priority needs in safeguarding ecosystem services and biodiversity conservation. Another project funded by the EU – “Strengthening capacity in National Nature Protection – preparation for Natura 2000 network” – started in 2015 with the aim to raise awareness for assisting local and national Albanian institutions to better exploit the potential of protected areas. One of the main issues encountered during these projects was the need for a national biodiversity data repository. The Biodiversity National Network of Albania (BioNNA) has been created to aggregate occurrence records of plants and animals and aims at becoming the most relevant source of information for biodiversity data as far as Albania is concerned. In this paper, the authors detail structure and data of BioNNA, including the process of data gathering and aggregation, taxonomic coverage, software details and WebGIS development. BioNNA is a milestone on the path towards Albania’s inclusion in the EU and has also a relevant potential social relevance for improving people’s awareness on the importance of biodiversity in the country.
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Pocock MJ, Chandler M, Bonney R, Thornhill I, Albin A, August T, Bachman S, Brown PM, Cunha DGF, Grez A, Jackson C, Peters M, Rabarijaon NR, Roy HE, Zaviezo T, Danielsen F. A Vision for Global Biodiversity Monitoring With Citizen Science. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.06.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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36
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Daru BH, Park DS, Primack RB, Willis CG, Barrington DS, Whitfeld TJS, Seidler TG, Sweeney PW, Foster DR, Ellison AM, Davis CC. Widespread sampling biases in herbaria revealed from large-scale digitization. THE NEW PHYTOLOGIST 2018; 217:939-955. [PMID: 29083043 DOI: 10.1111/nph.14855] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/18/2017] [Indexed: 05/19/2023]
Abstract
Nonrandom collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras online offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in c. 5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE). We identified numerous shared and unique biases among these regions. Shared biases included specimens collected close to roads and herbaria; specimens collected more frequently during biological spring and summer; specimens of threatened species collected less frequently; and specimens of close relatives collected in similar numbers. Regional differences included overrepresentation of graminoids in SA and AU and of annuals in AU; and peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by very few individuals. We hypothesize that these mega-collectors, with their associated preferences and idiosyncrasies, shaped patterns of collection bias via 'founder effects'. Studies using herbarium collections should account for sampling biases, and future collecting efforts should avoid compounding these biases to the extent possible.
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Affiliation(s)
- Barnabas H Daru
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | - Daniel S Park
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | | | - Charles G Willis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | - David S Barrington
- Pringle Herbarium, Plant Biology Department, University of Vermont, Torrey Hall, 27 Colchester Ave, Burlington, VT, 05405, USA
| | - Timothy J S Whitfeld
- Brown University Herbarium, Department of Ecology and Evolutionary Biology, Brown University, 34 Olive Street, Box G-B225, Providence, RI, 02912, USA
| | - Tristram G Seidler
- Biology Department, University of Massachusetts, 611 North Pleasant Street, Amherst, MA, 01003, USA
| | - Patrick W Sweeney
- Division of Botany, Peabody Museum of Natural History, Yale University, New Haven, CT, 06511, USA
| | - David R Foster
- Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA, 01366, USA
| | - Aaron M Ellison
- Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA, 01366, USA
- Tropical Forests & People Research Centre, University of the Sunshine Coast, Maroochydore, Qld, 4558, Australia
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
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37
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Understanding the Processes Underpinning Patterns of Phylogenetic Regionalization. Trends Ecol Evol 2017; 32:845-860. [PMID: 28919204 DOI: 10.1016/j.tree.2017.08.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 07/04/2017] [Accepted: 08/22/2017] [Indexed: 12/16/2022]
Abstract
A key step in understanding the distribution of biodiversity is the grouping of regions based on their shared elements. Historically, regionalization schemes have been largely species centric. Recently, there has been interest in incorporating phylogenetic information into regionalization schemes. Phylogenetic regionalization can provide novel insights into the mechanisms that generate, distribute, and maintain biodiversity. We argue that four processes (dispersal limitation, extinction, speciation, and niche conservatism) underlie the formation of species assemblages into phylogenetically distinct biogeographic units. We outline how it can be possible to distinguish among these processes, and identify centers of evolutionary radiation, museums of diversity, and extinction hotspots. We suggest that phylogenetic regionalization provides a rigorous and objective classification of regional diversity and enhances our knowledge of biodiversity patterns.
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38
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Veiga AK, Saraiva AM, Chapman AD, Morris PJ, Gendreau C, Schigel D, Robertson TJ. A conceptual framework for quality assessment and management of biodiversity data. PLoS One 2017; 12:e0178731. [PMID: 28658288 PMCID: PMC5489162 DOI: 10.1371/journal.pone.0178731] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 05/18/2017] [Indexed: 11/18/2022] Open
Abstract
The increasing availability of digitized biodiversity data worldwide, provided by an increasing number of institutions and researchers, and the growing use of those data for a variety of purposes have raised concerns related to the "fitness for use" of such data and the impact of data quality (DQ) on the outcomes of analyses, reports, and decisions. A consistent approach to assess and manage data quality is currently critical for biodiversity data users. However, achieving this goal has been particularly challenging because of idiosyncrasies inherent in the concept of quality. DQ assessment and management cannot be performed if we have not clearly established the quality needs from a data user's standpoint. This paper defines a formal conceptual framework to support the biodiversity informatics community allowing for the description of the meaning of "fitness for use" from a data user's perspective in a common and standardized manner. This proposed framework defines nine concepts organized into three classes: DQ Needs, DQ Solutions and DQ Report. The framework is intended to formalize human thinking into well-defined components to make it possible to share and reuse concepts of DQ needs, solutions and reports in a common way among user communities. With this framework, we establish a common ground for the collaborative development of solutions for DQ assessment and management based on data fitness for use principles. To validate the framework, we present a proof of concept based on a case study at the Museum of Comparative Zoology of Harvard University. In future work, we will use the framework to engage the biodiversity informatics community to formalize and share DQ profiles related to DQ needs across the community.
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Affiliation(s)
- Allan Koch Veiga
- University of São Paulo, Research Center on Biodiversity and Computing, São Paulo, São Paulo, Brazil
| | - Antonio Mauro Saraiva
- University of São Paulo, Research Center on Biodiversity and Computing, São Paulo, São Paulo, Brazil
| | | | - Paul John Morris
- Harvard University, Museum of Comparative Zoology, Cambridge, Massachusetts, United States of America
| | - Christian Gendreau
- Université de Montréal, Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
| | - Dmitry Schigel
- Global Biodiversity Information Facility, Secretariat, Copenhagen, Denmark
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39
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Data and Metadata Brokering – Theory and Practice from the BCube Project. DATA SCIENCE JOURNAL 2017. [DOI: 10.5334/dsj-2017-001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Devictor V, Bensaude-Vincent B. From ecological records to big data: the invention of global biodiversity. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2016; 38:13. [PMID: 27645228 DOI: 10.1007/s40656-016-0113-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/08/2016] [Indexed: 06/06/2023]
Abstract
This paper is a critical assessment of the epistemological impact of the systematic quantification of nature with the accumulation of big datasets on the practice and orientation of ecological science. We examine the contents of big databases and argue that it is not just accumulated information; records are translated into digital data in a process that changes their meanings. In order to better understand what is at stake in the 'datafication' process, we explore the context for the emergence and quantification of biodiversity in the 1980s, along with the concept of the global environment. In tracing the origin and development of the global biodiversity information facility (GBIF) we describe big data biodiversity projects as a techno-political construction dedicated to monitoring a new object: the global diversity. We argue that, biodiversity big data became a powerful driver behind the invention of the concept of the global environment, and a way to embed ecological science in the political agenda.
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Affiliation(s)
- Vincent Devictor
- CETCOPRA (Centre d'Etudes des Techniques, des Connaissances et des Pratiques), Université Paris 1 Panthèon Sorbonne, Paris, France.
- Institut des Sciences de l'Evolution, Université Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Bernadette Bensaude-Vincent
- CETCOPRA (Centre d'Etudes des Techniques, des Connaissances et des Pratiques), Université Paris 1 Panthèon Sorbonne, Paris, France
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41
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Fourcade Y. Comparing species distributions modelled from occurrence data and from expert-based range maps. Implication for predicting range shifts with climate change. ECOL INFORM 2016. [DOI: 10.1016/j.ecoinf.2016.09.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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42
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Troia MJ, McManamay RA. Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States. Ecol Evol 2016; 6:4654-69. [PMID: 27547303 PMCID: PMC4979697 DOI: 10.1002/ece3.2225] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/30/2016] [Accepted: 05/11/2016] [Indexed: 11/15/2022] Open
Abstract
Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records from the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). We aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov-Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. This comprehensive assessment of biodiversity data across the contiguous United States provides a prioritization scheme to fill in the gaps by contributing existing occurrence records to the public domain and planning future surveys.
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Affiliation(s)
- Matthew J. Troia
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee 7831
| | - Ryan A. McManamay
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee 7831
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43
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Meyer C, Weigelt P, Kreft H. Multidimensional biases, gaps and uncertainties in global plant occurrence information. Ecol Lett 2016; 19:992-1006. [DOI: 10.1111/ele.12624] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/17/2016] [Accepted: 04/14/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Carsten Meyer
- Biodiversity, Macroecology and Conservation Biogeography Group; Faculty of Forest Sciences; University of Göttingen; Büsgenweg 1 37077 Göttingen Germany
- Synthesis Centre (sDiv); German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e 04103 Leipzig Germany
| | - Patrick Weigelt
- Biodiversity, Macroecology and Conservation Biogeography Group; Faculty of Forest Sciences; University of Göttingen; Büsgenweg 1 37077 Göttingen Germany
| | - Holger Kreft
- Biodiversity, Macroecology and Conservation Biogeography Group; Faculty of Forest Sciences; University of Göttingen; Büsgenweg 1 37077 Göttingen Germany
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Leidenberger S, Käck M, Karlsson B, Kindvall O. The Analysis Portal and the Swedish LifeWatch e-infrastructure for biodiversity research. Biodivers Data J 2016:e7644. [PMID: 27099553 PMCID: PMC4822057 DOI: 10.3897/bdj.4.e7644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/22/2016] [Indexed: 11/20/2022] Open
Abstract
Background During the last years, more and more online portals were generated and are now available for ecologists to run advanced models with extensive data sets. Some examples are the Biodiversity Virtual e-Laboratory (BioVel) Portal (https://portal.biovel.eu) for ecological niche modelling and the Mobyle SNAP Workbench (https://snap.hpc.ncsu.edu) for evolutionary and population genetics analysis. Such portals have the main goal to facilitate the run of advanced models, through access to large-capacity computers or servers. In this study, we present the Analysis Portal (www.analysisportal.se), which is a part of the Swedish LifeWatch e-infrastructure for biodiversity research that combines a variety of Swedish web services to perform different kinds of dataprocessing. New information For the first time, the Swedish Analysis Portal for integrated analysis of species occurrence data is described in detail. It was launched in 2013 and today, over 60 Million Swedish species observation records can be assessed, visualized and analyzed via the portal. Datasets can be assembled using sophisticated filtering tools, and combined with environmental and climatic data from a wide range of providers. Different validation tools, for example the official Swedish taxon concept database Dyntaxa, ensure high data quality. Results can be downloaded in different formats as maps, tables, diagrams and reports.
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Affiliation(s)
| | - Martin Käck
- ArtDatabanken, Swedish Species Information Centre, SLU, Uppsala, Sweden
| | - Björn Karlsson
- ArtDatabanken, Swedish Species Information Centre, SLU, Uppsala, Sweden
| | - Oskar Kindvall
- ArtDatabanken, Swedish Species Information Centre, SLU, Uppsala, Sweden
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46
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47
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How Aphia—The Platform behind Several Online and Taxonomically Oriented Databases—Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3041448] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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48
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Meirelles PM, Gadelha LMR, Francini-Filho RB, de Moura RL, Amado-Filho GM, Bastos AC, Paranhos RPDR, Rezende CE, Swings J, Siegle E, Asp Neto NE, Leitão SN, Coutinho R, Mattoso M, Salomon PS, Valle RAB, Pereira RC, Kruger RH, Thompson C, Thompson FL. BaMBa: towards the integrated management of Brazilian marine environmental data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav088. [PMID: 26454874 PMCID: PMC4600340 DOI: 10.1093/database/bav088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/24/2015] [Indexed: 11/12/2022]
Abstract
A new open access database, Brazilian Marine Biodiversity (BaMBa) (https://marinebiodiversity.lncc.br), was developed in order to maintain large datasets from the Brazilian marine environment. Essentially, any environmental information can be added to BaMBa. Certified datasets obtained from integrated holistic studies, comprising physical-chemical parameters, -omics, microbiology, benthic and fish surveys can be deposited in the new database, enabling scientific, industrial and governmental policies and actions to be undertaken on marine resources. There is a significant number of databases, however BaMBa is the only integrated database resource both supported by a government initiative and exclusive for marine data. BaMBa is linked to the Information System on Brazilian Biodiversity (SiBBr, http://www.sibbr.gov.br/) and will offer opportunities for improved governance of marine resources and scientists' integration. Database URL: http://marinebiodiversity.lncc.br.
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Affiliation(s)
- Pedro Milet Meirelles
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373 Sala A1-050, Bloco A do CCS Cidade Universitária, 21941-902 - Rio de Janeiro, RJ, Brazil, Federal University of Rio de Janeiro (UFRJ) / COPPE, SAGE, Rua Moniz Aragão 360, Bloco 2, Ilha do Fundão, 21945-972 - Rio de Janeiro, RJ, Brazil
| | - Luiz M R Gadelha
- National Laboratory for Scientific Computing (LNCC), Av. Getúlio Vargas 333, Quitandinha, 25651-075 - Petropolis, RJ, Brazil
| | - Ronaldo Bastos Francini-Filho
- Department of Environment and Engineering, Federal University of Paraíba, Rio Tinto, Brazil (UFPB), Rua da Mangueira, s/n - Campus IV (Litoral Norte), Centro, 58297-000 - Rio Tinto, PB, Brazil
| | - Rodrigo Leão de Moura
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373 Sala A1-050, Bloco A do CCS Cidade Universitária, 21941-902 - Rio de Janeiro, RJ, Brazil, Federal University of Rio de Janeiro (UFRJ) / COPPE, SAGE, Rua Moniz Aragão 360, Bloco 2, Ilha do Fundão, 21945-972 - Rio de Janeiro, RJ, Brazil
| | - Gilberto Menezes Amado-Filho
- Rio de Janeiro Botanical Garden Research Institute (IP-JBRJ), Rua Pacheco Leão 915, Horto, 22460-030 - Rio de Janeiro, RJ, Brazil
| | - Alex Cardoso Bastos
- Department of Oceanography and Ecology, Federal University of Espírito Santo (UFES), Av. Fernando Ferrari, 514, Goiabeiras, 29090-600 - Vitória, ES Brazil
| | - Rodolfo Pinheiro da Rocha Paranhos
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373 Sala A1-050, Bloco A do CCS Cidade Universitária, 21941-902 - Rio de Janeiro, RJ, Brazil
| | - Carlos Eduardo Rezende
- Environmental Sciences Laboratory (LCA), Northern Rio de Janeiro State University Darcy Ribeiro (UENF), Avenida Alberto Lamego 2000, Parque Califórnia, 28013-602 - Campos dos Goytacazes, RJ, Brazil
| | - Jean Swings
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373 Sala A1-050, Bloco A do CCS Cidade Universitária, 21941-902 - Rio de Janeiro, RJ, Brazil, Federal University of Rio de Janeiro (UFRJ) / COPPE, SAGE, Rua Moniz Aragão 360, Bloco 2, Ilha do Fundão, 21945-972 - Rio de Janeiro, RJ, Brazil
| | - Eduardo Siegle
- Oceanographic Institute, University of São Paulo (IO-USP), Praça do Oceanográfico, 191, Cidade Universitária, 05508-120 - Sao Paulo, SP, Brazil
| | - Nils Edvin Asp Neto
- Institute of Coastal Studies, Federal University of Para (UFPA), Alameda Leandro Ribeiro, s/n. - Bairro Aldeia, UFPA/Campus Universitário de Bragança Aldeia, 68600-000 - Braganca, PA, Brasil
| | - Sigrid Neumann Leitão
- Department of Oceanography, Federal University of Pernambuco (UFPE), Av Arquitetura, S/N, Cidade Universitaria, 50670-901 - Recife, PE, Brazil
| | - Ricardo Coutinho
- Division of Marine Biotechnology, Marine Studies Institute Admiral Paulo Moreira, Rua Kioto 253, Praia dos Anjos, 28930-000 - Arraial do Cabo, RJ, Brazil
| | - Marta Mattoso
- PESC/COPPE - Federal University of Rio de Janeiro, Centro de Tecnologia, Bloco H, sala 319, Ilha do Fundão, 21941972 - Rio de Janeiro, RJ, Brazil
| | - Paulo S Salomon
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373 Sala A1-050, Bloco A do CCS Cidade Universitária, 21941-902 - Rio de Janeiro, RJ, Brazil, Federal University of Rio de Janeiro (UFRJ) / COPPE, SAGE, Rua Moniz Aragão 360, Bloco 2, Ilha do Fundão, 21945-972 - Rio de Janeiro, RJ, Brazil
| | - Rogério A B Valle
- Federal University of Rio de Janeiro (UFRJ) / COPPE, SAGE, Rua Moniz Aragão 360, Bloco 2, Ilha do Fundão, 21945-972 - Rio de Janeiro, RJ, Brazil
| | - Renato Crespo Pereira
- Departament of Marine Biology, Federal Fluminense University (UFF), Morro do Valonguinho s/n, Centro, 24001-970 - Niteroi, RJ, Brazil, and
| | - Ricardo Henrique Kruger
- Laboratory of Enzymology, Department of cellular Biology, Institute of Biology, University of Brasília (UnB), Asa Norte 70910-900 - Brasília, DF - Brazil
| | - Cristiane Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373 Sala A1-050, Bloco A do CCS Cidade Universitária, 21941-902 - Rio de Janeiro, RJ, Brazil, National Laboratory for Scientific Computing (LNCC), Av. Getúlio Vargas 333, Quitandinha, 25651-075 - Petropolis, RJ, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373 Sala A1-050, Bloco A do CCS Cidade Universitária, 21941-902 - Rio de Janeiro, RJ, Brazil, National Laboratory for Scientific Computing (LNCC), Av. Getúlio Vargas 333, Quitandinha, 25651-075 - Petropolis, RJ, Brazil,
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Meyer C, Kreft H, Guralnick R, Jetz W. Global priorities for an effective information basis of biodiversity distributions. Nat Commun 2015; 6:8221. [PMID: 26348291 PMCID: PMC4569846 DOI: 10.1038/ncomms9221] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/29/2015] [Indexed: 11/11/2022] Open
Abstract
Gaps in digital accessible information (DAI) on species distributions hamper prospects of safeguarding biodiversity and ecosystem services, and addressing central ecological and evolutionary questions. Achieving international targets on biodiversity knowledge requires that information gaps be identified and actions prioritized. Integrating 157 million point records and distribution maps for 21,170 terrestrial vertebrate species, we find that outside a few well-sampled regions, DAI on point occurrences provides very limited and spatially biased inventories of species. Surprisingly, many large, emerging economies are even more under-represented in global DAI than species-rich, developing countries in the tropics. Multi-model inference reveals that completeness is mainly limited by distance to researchers, locally available research funding and participation in data-sharing networks, rather than transportation infrastructure, or size and funding of Western data contributors as often assumed. Our results highlight the urgent need for integrating non-Western data sources and intensifying cooperation to more effectively address societal biodiversity information needs.
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Affiliation(s)
- Carsten Meyer
- Biodiversity, Macroecology and Conservation Biogeography Group, Faculty of Forest Sciences, University of Göttingen, Büsgenweg 1, 37077 Göttingen, Germany
| | - Holger Kreft
- Biodiversity, Macroecology and Conservation Biogeography Group, Faculty of Forest Sciences, University of Göttingen, Büsgenweg 1, 37077 Göttingen, Germany
| | - Robert Guralnick
- University of Florida Museum of Natural History, University of Florida at Gainesville, 358 Dickinson Hall, Gainesville, Florida 32611-2710, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, Connecticut 06520, USA
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berks SL5 7PY, UK
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Vanden Berghe E, Coro G, Bailly N, Fiorellato F, Aldemita C, Ellenbroek A, Pagano P. Retrieving taxa names from large biodiversity data collections using a flexible matching workflow. ECOL INFORM 2015. [DOI: 10.1016/j.ecoinf.2015.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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