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Urbano F, Viterbi R, Pedrotti L, Vettorazzo E, Movalli C, Corlatti L. Enhancing biodiversity conservation and monitoring in protected areas through efficient data management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 196:12. [PMID: 38051448 PMCID: PMC10697885 DOI: 10.1007/s10661-023-11851-0] [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: 11/05/2022] [Accepted: 09/06/2023] [Indexed: 12/07/2023]
Abstract
A scientifically informed approach to decision-making is key to ensuring the sustainable management of ecosystems, especially in the light of increasing human pressure on habitats and species. Protected areas, with their long-term institutional mandate for biodiversity conservation, play an important role as data providers, for example, through the long-term monitoring of natural resources. However, poor data management often limits the use and reuse of this wealth of information. In this paper, we share lessons learned in managing long-term data from the Italian Alpine national parks. Our analysis and examples focus on specific issues faced by managers of protected areas, which partially differ from those faced by academic researchers, predominantly owing to different mission, governance, and temporal perspectives. Rigorous data quality control, the use of appropriate data management tools, and acquisition of the necessary skills remain the main obstacles. Common protocols for data collection offer great opportunities for the future, and complete recovery and documentation of time series is an urgent priority. Notably, before data can be shared, protected areas should improve their data management systems, a task that can be achieved only with adequate resources and a long-term vision. We suggest strategies that protected areas, funding agencies, and the scientific community can embrace to address these problems. The added value of our work lies in promoting engagement with managers of protected areas and in reporting and analysing their concrete requirements and problems, thereby contributing to the ongoing discussion on data management and sharing through a bottom-up approach.
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Affiliation(s)
| | - Ramona Viterbi
- Gran Paradiso National Park, Via Pio VII 9, 10135, Torino, Italy
| | - Luca Pedrotti
- Stelvio National Park, Via De Simoni 42, 23032, Bormio, Italy
| | - Enrico Vettorazzo
- Dolomiti Bellunesi National Park, Piazzale Zancanaro 1, 32032, Feltre, Italy
| | - Cristina Movalli
- Val Grande National Park, Piazza Pretorio 6, 28805, Vogogna, Italy
| | - Luca Corlatti
- Stelvio National Park, Via De Simoni 42, 23032, Bormio, Italy
- Chair of Wildlife Ecology and Management, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
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2
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Fonseca EM, Pelletier TA, Decker SK, Parsons DJ, Carstens BC. Pleistocene glaciations caused the latitudinal gradient of within-species genetic diversity. Evol Lett 2023; 7:331-338. [PMID: 37829497 PMCID: PMC10565891 DOI: 10.1093/evlett/qrad030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/26/2023] [Accepted: 07/10/2023] [Indexed: 10/14/2023] Open
Abstract
Intraspecific genetic diversity is a key aspect of biodiversity. Quaternary climatic change and glaciation influenced intraspecific genetic diversity by promoting range shifts and population size change. However, the extent to which glaciation affected genetic diversity on a global scale is not well established. Here we quantify nucleotide diversity, a common metric of intraspecific genetic diversity, in more than 38,000 plant and animal species using georeferenced DNA sequences from millions of samples. Results demonstrate that tropical species contain significantly more intraspecific genetic diversity than nontropical species. To explore potential evolutionary processes that may have contributed to this pattern, we calculated summary statistics that measure population demographic change and detected significant correlations between these statistics and latitude. We find that nontropical species are more likely to deviate from neutral expectations, indicating that they have historically experienced dramatic fluctuations in population size likely associated with Pleistocene glacial cycles. By analyzing the most comprehensive data set to date, our results imply that Quaternary climate perturbations may be more important as a process driving the latitudinal gradient in species richness than previously appreciated.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Tara A Pelletier
- Department of Biology, Radford University, Radford, VA, United States
| | - Sydney K Decker
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Danielle J Parsons
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
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Rey PL, Vittoz P, Petitpierre B, Adde A, Guisan A. Linking plant and vertebrate species to Nature's Contributions to People in the Swiss Alps. Sci Rep 2023; 13:7312. [PMID: 37147401 PMCID: PMC10163046 DOI: 10.1038/s41598-023-34236-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/26/2023] [Indexed: 05/07/2023] Open
Abstract
Since the late 1990s, Nature's Contributions to People (NCPs; i.e. ecosystem services) were used as a putative leverage for fostering nature preservation. NCPs have largely been defined and mapped at the landscape level using land use and cover classifications. However, NCP mapping attempts based directly on individual species are still uncommon. Given that species shape ecosystems and ultimately deliver NCPs, mapping NCPs based on species distribution data should deliver highly meaningful results. This requires first establishing a census of the species-to-NCP relationships. However, datasets quantifying these relationships across several species and NCPs are rare. Here, we fill this gap by compiling literature and expert knowledge to establish the relationships of 1816 tracheophyte and 250 vertebrate species with 17 NCPs in the Swiss Alps. We illustrated the 31,098 identified species-NCP relationships for the two lineages and discuss why such a table is a key initial step in building spatial predictions of NCPs directly from species data, e.g. to ultimately complement spatial conservation planning.
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Affiliation(s)
- Pierre-Louis Rey
- Institute of Earth Surface Dynamics, Faculty of Geosciences and Environment, University of Lausanne, Lausanne, Switzerland.
| | - Pascal Vittoz
- Institute of Earth Surface Dynamics, Faculty of Geosciences and Environment, University of Lausanne, Lausanne, Switzerland
| | - Blaise Petitpierre
- Info Flora, c/o Conservatoire et Jardin botaniques de Genève, Chambésy-Genève, Switzerland
| | - Antoine Adde
- Institute of Earth Surface Dynamics, Faculty of Geosciences and Environment, University of Lausanne, Lausanne, Switzerland
| | - Antoine Guisan
- Institute of Earth Surface Dynamics, Faculty of Geosciences and Environment, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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4
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Spear D, van Wilgen NJ, Rebelo AG, Botha JM. Collating biodiversity occurrence data for conservation. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1037282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Plant and animal checklists, with conservation status information, are fundamental for conservation management. Historical field data, more recent data of digital origin and data-sharing platforms provide useful sources for collating species locality data. However, different biodiversity datasets have different formats and inconsistent naming systems. Additionally, most digital data sources do not provide an easy option for download by protected area. Further, data-entry-ready software is not readily available for conservation organization staff with limited technical skills to collate these heterogeneous data and create distribution maps and checklists for protected areas. The insights presented here are the outcome of conceptualizing a biodiversity information system for South African National Parks. We recognize that a fundamental requirement for achieving better standardization, sharing and use of biodiversity data for conservation is capacity building, internet connectivity, national institutional data management support and collaboration. We focus on some of the issues that need to be considered for capacity building, data standardization and data support. We outline the need for using taxonomic backbones and standardizing biodiversity data and the utility of data from the Global Biodiversity Information Facility and other available sources in this process. Additionally, we make recommendations for the fields needed in relational databases for collating species data that can be used to inform conservation decisions and outline steps that can be taken to enable easier collation of biodiversity data, using South Africa as a case study.
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Anderson RP. Integrating habitat-masked range maps with quantifications of prevalence to estimate area of occupancy in IUCN assessments. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14019. [PMID: 36285611 PMCID: PMC10099578 DOI: 10.1111/cobi.14019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Estimates of species geographic ranges constitute critical input for biodiversity assessments, including those for the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species. Area of occupancy (AOO) is one metric that IUCN uses to quantify a species' range, but data limitations typically lead to either under- or overestimates (and unnecessarily wide bounds of uncertainty). Fortunately, existing methods in which range maps and land-cover data are used to estimate the area currently holding habitat for a species can be extended to yield an unbiased range of plausible estimates for AOO. Doing so requires estimating the proportion of sites (currently containing habitat) that a species occupies within its range (i.e., prevalence). Multiplying a quantification of habitat area by prevalence yields an estimate of what the species inhabits (i.e., AOO). For species with intense sampling at many sites, presence-absence data sets or occupancy modeling allow calculation of prevalence. For other species, primary biodiversity data (records of a species' presence at a point in space and time) from citizen-science initiatives and research collections of natural history museums and herbaria could be used. In such cases, estimates of sample prevalence should be corrected by dividing by the species' detectability. To estimate detectability from these data sources, extensions of inventory-completeness analyses merit development. With investments to increase the quality and availability of online biodiversity data, consideration of prevalence should lead to tighter and more realistic bounds of AOO for many taxonomic groups and geographic regions. By leading to more realistic and representative characterizations of biodiversity, integrating maps of current habitat with estimates of prevalence should empower conservation practitioners and decision makers and thus guide actions and policy worldwide.
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Affiliation(s)
- Robert P. Anderson
- Department of Biology, City College of New YorkCity University of New YorkNew YorkNew YorkUSA
- Ph.D. Program in BiologyGraduate Center, City University of New YorkNew YorkNew YorkUSA
- Division of Vertebrate Zoology (Mammalogy)American Museum of Natural HistoryNew YorkNew YorkUSA
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Pelletier TA, Parsons DJ, Decker SK, Crouch S, Franz E, Ohrstrom J, Carstens BC. phylogatR: Phylogeographic data aggregation and repurposing. Mol Ecol Resour 2022; 22:2830-2842. [PMID: 35748425 PMCID: PMC9796472 DOI: 10.1111/1755-0998.13673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/10/2022] [Accepted: 06/07/2022] [Indexed: 01/01/2023]
Abstract
Patterns of genetic diversity within species contain information the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyse sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalysed and increase accessibility to big data for research laboratories and classroom instructors with limited computational expertise and resources.
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Affiliation(s)
| | - Danielle J. Parsons
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
| | - Sydney K. Decker
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
| | | | - Eric Franz
- Ohio Supercomputer CenterColumbusOhioUSA
| | | | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA,Museum of Biological DiversityThe Ohio State UniversityColumbusOhioUSA
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Rodrigues AV, Nakamura G, Staggemeier VG, Duarte L. Species misidentification affects biodiversity metrics: Dealing with this issue using the new R package naturaList. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Mandeville CP, Koch W, Nilsen EB, Finstad AG. Open Data Practices among Users of Primary Biodiversity Data. Bioscience 2021; 71:1128-1147. [PMID: 34733117 PMCID: PMC8560312 DOI: 10.1093/biosci/biab072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Presence-only biodiversity data are increasingly relied on in biodiversity, ecology, and conservation research, driven by growing digital infrastructures that support open data sharing and reuse. Recent reviews of open biodiversity data have clearly documented the value of data sharing, but the extent to which the biodiversity research community has adopted open data practices remains unclear. We address this question by reviewing applications of presence-only primary biodiversity data, drawn from a variety of sources beyond open databases, in the indexed literature. We characterize how frequently researchers access open data relative to data from other sources, how often they share newly generated or collated data, and trends in metadata documentation and data citation. Our results indicate that biodiversity research commonly relies on presence-only data that are not openly available and neglects to make such data available. Improved data sharing and documentation will increase the value, reusability, and reproducibility of biodiversity research.
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Affiliation(s)
- Caitlin P Mandeville
- Department of Natural History, Norwegian University of Science and Technology, Trondheim, Norway
| | - Wouter Koch
- Department of Natural History, Norwegian University of Science and Technology, Trondheim, Norway
| | - Erlend B Nilsen
- Faculty of Biosciences and Aquaculture, Nord University, Steinkjer, Norway
| | - Anders G Finstad
- Department of Natural History, Norwegian University of Science and Technology, Trondheim, Norway
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Pereira CL, Gilbert MTP, Araújo MB, Matias MG. Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Cátia Lúcio Pereira
- Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
- Centre for Macroecology, Evolution and Climate Globe Institute University of Copenhagen Copenhagen Denmark
- Rui Nabeiro Biodiversity Chair MED – Mediterranean Institute for Agriculture Environment and Development University of Évora Évora Portugal
| | - M. Thomas P. Gilbert
- Centre for Evolutionary Hologenomics Globe Institute University of Copenhagen Copenhagen Denmark
- University MuseumNTNU Trondheim Norway
| | - Miguel Bastos Araújo
- Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
- Rui Nabeiro Biodiversity Chair MED – Mediterranean Institute for Agriculture Environment and Development University of Évora Évora Portugal
| | - Miguel Graça Matias
- Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
- Rui Nabeiro Biodiversity Chair MED – Mediterranean Institute for Agriculture Environment and Development University of Évora Évora Portugal
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10
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Chevalier M, Broennimann O, Cornuault J, Guisan A. Data integration methods to account for spatial niche truncation effects in regional projections of species distribution. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02427. [PMID: 34318974 DOI: 10.1002/eap.2427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/12/2021] [Accepted: 03/22/2021] [Indexed: 06/13/2023]
Abstract
Many species distribution models (SDMs) are built with precise but geographically restricted presence-absence data sets (e.g., a country) where only a subset of the environmental conditions experienced by a species across its range is considered (i.e., spatial niche truncation). This type of truncation is worrisome because it can lead to incorrect predictions e.g., when projecting to future climatic conditions belonging to the species niche but unavailable in the calibration area. Data from citizen-science programs, species range maps or atlases covering the full species range can be used to capture those parts of the species' niche that are missing regionally. However, these data usually are too coarse or too biased to support regional management. Here, we aim to (1) demonstrate how varying degrees of spatial niche truncation affect SDMs projections when calibrated with climatically truncated regional data sets and (2) test the performance of different methods to harness information from larger-scale data sets presenting different spatial resolutions to solve the spatial niche truncation problem. We used simulations to compare the performance of the different methods, and applied them to a real data set to predict the future distribution of a plant species (Potentilla aurea) in Switzerland. SDMs calibrated with geographically restricted data sets expectedly provided biased predictions when projected outside the calibration area or time period. Approaches integrating information from larger-scale data sets using hierarchical data integration methods usually reduced this bias. However, their performance varied depending on the level of spatial niche truncation and how data were combined. Interestingly, while some methods (e.g., data pooling, downscaling) performed well on both simulated and real data, others (e.g., those based on a Poisson point process) performed better on real data, indicating a dependency of model performance on the simulation process (e.g., shape of simulated response curves). Based on our results, we recommend to use different data integration methods and, whenever possible, to make a choice depending on model performance. In any case, an ensemble modeling approach can be used to account for uncertainty in how niche truncation is accounted for and identify areas where similarities/dissimilarities exist across methods.
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Affiliation(s)
- Mathieu Chevalier
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, CH-1015, Switzerland
| | - Olivier Broennimann
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, CH-1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Géopolis, Lausanne, CH-1015, Switzerland
| | | | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, CH-1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Géopolis, Lausanne, CH-1015, Switzerland
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Scherrer D, Esperon‐Rodriguez M, Beaumont LJ, Barradas VL, Guisan A. National assessments of species vulnerability to climate change strongly depend on selected data sources. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Daniel Scherrer
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Department of Ecology and Evolution University of Lausanne, Biophore Lausanne Switzerland
| | | | - Linda J. Beaumont
- Department of Biological Sciences Macquarie University North Ryde NSW Australia
| | - Víctor L. Barradas
- Laboratorio de Interacción Planta‐Atmósfera Instituto de Ecología Universidad Nacional Autónoma de MéxicoCiudad Universitaria Mexico City Mexico
| | - Antoine Guisan
- Department of Ecology and Evolution University of Lausanne, Biophore Lausanne Switzerland
- Institute of Earth Surface Dynamics University of Lausanne, Géopolis Lausanne Switzerland
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12
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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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