Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from Denmark.
For all researches, please visit our "Peer-reviewed publications" page.

List of publications

  • Rasmussen K, Thyrring J, Muscarella R, Borchsenius F (2017)

    Climate-change-induced range shifts of three allergenic ragweeds ( Ambrosia L.) in Europe and their potential impact on human health

    PeerJ 5 e3104.

    Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species ( Ambrosia spp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in ‘high allergy risk’ (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27–100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe.

    Keywords: A. artemisiifolia, Aeroallergen, Allergy, Climate change, Habitat suitability, Invasive species, MAXENT, Public health, Species distribution models, Urban heat islands

  • Taudiere D, Bellanger M, Moreau M, Carcaillet D, Christophe M, Læssøe M et al. (2017)

    Xylobolus subpileatus, a specialized basidiomycete functionally linked to old canopy gaps

    Canadian Journal of Forest Research.

    Documenting succession in forest canopy gaps provides insights into the ecological processes governing the temporal dynamics of species within communities. We analyzed the fruiting patterns of a rare but widely distributed saproxylic macromycete, Xylobolus subpileatus, during the ageing of natural canopy gaps in oak forests. In one of the last remaining Quercus ilex old-growth forests (on the island of Corsica, western Mediterranean basin), we systematically recorded and conducted molecular analyses of X. subpileatus basidiomes in 80 dated natural canopy gaps representing a 45 year-long sequence of residence time of tree logs on the forest floor. X. subpileatus fruited exclusively on Q. ilex logs. The probability of fruiting of X. subpileatus significantly increases during the process of wood decomposition to reach its maximum in the oldest gaps, ca. 40 years after treefall. In contrast, the abundance and the richness of saprobic and ectomycorrhizal fruitbodies de...

    Keywords: Mediterranean forest, coarse woody debris, conservation, natural canopy gaps, old-growth stand

  • Zohner C, Benito B, Fridley J, Svenning J, Renner S (2017)

    Spring predictability explains different leaf-out strategies in the woody floras of North America, Europe and East Asia

    Ecology Letters.

    Intuitively, interannual spring temperature variability (STV) should influence the leaf-out strategies of temperate zone woody species, with high winter chilling requirements in species from regions where spring warming varies greatly among years. We tested this hypothesis using experiments in 215 species and leaf-out monitoring in 1585 species from East Asia (EA), Europe (EU) and North America (NA). The results reveal that species from regions with high STV indeed have higher winter chilling requirements, and, when grown under the same conditions, leaf out later than related species from regions with lower STV. Since 1900, STV has been consistently higher in NA than in EU and EA, and under experimentally short winter conditions NA species required 84% more spring warming for bud break, EU ones 49% and EA ones only 1%. These previously unknown continental-scale differences in phenological strategies underscore the need for considering regional climate histories in global change models.

    Keywords: Mediterranean forest, coarse woody debris, conservation, natural canopy gaps, old-growth stand

  • Beukhof E, Coolen J, van der Weide B, Cuperus J, de Blauwe H, Lust J (2016)

    Records of five bryozoan species from offshore gas platforms rare for the Dutch North Sea

    Marine Biodiversity Records 9(1) 91.

    This study reports on bryozoan species collected at three offshore gas platforms in the Dutch part of the North Sea. Four out of thirteen observed species are considered as rare in the Netherlands, whereas Cribrilina punctata is a new species for Dutch waters.

    Keywords: Arachnidium fibrosum, Bryozoa, Cribrilina punctata, Electra monostachys, Gas platform, Netherlands, North Sea, Offshore, Scruparia ambigua, Scruparia chelata

  • Chandler M, See L, Copas K, Bonde A, López B, Danielsen F et al. (2016)

    Contribution of citizen science towards international biodiversity monitoring

    Biological Conservation.

    To meet collective obligations towards biodiversity conservation and monitoring, it is essential that the world's governments and non-governmental organisations as well as the research community tap all possible sources of data and information, including new, fast-growing sources such as citizen science (CS), in which volunteers participate in some or all aspects of environmental assessments. Through compilation of a database on CS and community-based monitoring (CBM, a subset of CS) programs, we assess where contributions from CS and CBM are significant and where opportunities for growth exist. We use the Essential Biodiversity Variable framework to describe the range of biodiversity data needed to track progress towards global biodiversity targets, and we assess strengths and gaps in geographical and taxonomic coverage. Our results show that existing CS and CBM data particularly provide large-scale data on species distribution and population abundance, species traits such as phenology, and ecosystem function variables such as primary and secondary productivity. Only birds, Lepidoptera and plants are monitored at scale. Most CS schemes are found in Europe, North America, South Africa, India, and Australia. We then explore what can be learned from successful CS/CBM programs that would facilitate the scaling up of current efforts, how existing strengths in data coverage can be better exploited, and the strategies that could maximise the synergies between CS/CBM and other approaches for monitoring biodiversity, in particular from remote sensing. More and better targeted funding will be needed, if CS/CBM programs are to contribute further to international biodiversity monitoring.

    Keywords: Citizen science, Community-based monitoring, Databases, Essential biodiversity variables (EBV), Global Biodiversity Information Facility (GBIF), Group on Earth Observations Biodiversity Observati

  • Deblauwe V, Droissart V, Bose R, Sonké B, Blach-Overgaard A, Svenning J et al. (2016)

    Remotely sensed temperature and precipitation data improve species distribution modelling in the tropics

    Global Ecology and Biogeography.

    Aim Species distribution modelling typically relies completely or partially on climatic variables as predictors, overlooking the fact that these are themselves predictions with associated uncertainties. This is particularly critical when such predictors are interpolated between sparse station data, such as in the tropics. The goal of this study is to provide a new set of satellite-based climatic predictor data and to evaluate its potential to improve modelled species–climate associations and transferability to novel geographical regions. Location Rain forests areas of Central Africa, the Western Ghats of India and South America. Methods We compared models calibrated on the widely used WorldClim station-interpolated climatic data with models where either temperature or precipitation data from WorldClim were replaced by data from CRU, MODIS, TRMM and CHIRPS. Each predictor set was used to model 451 plant species distributions. To test for chance associations, we devised a null model with which to compare the accuracy metric obtained for every species. Results Fewer than half of the studied rain forest species distributions matched the climatic pattern better than did random distributions. The inclusion of MODIS temperature and CHIRPS precipitation estimates derived from remote sensing each allowed for a better than random fit for respectively 40% and 22% more species than models calibrated on WorldClim. Furthermore, their inclusion was positively related to a better transferability of models to novel regions. Main conclusions We provide a newly assembled dataset of ecologically meaningful variables derived from MODIS and CHIRPS for download, and provide a basis for choosing among the plethora of available climate datasets. We emphasize the need to consider the method used in the production of climate data when working on a region with sparse meteorological station data. In this context, remote sensing data should be the preferred choice, particularly when model transferability to novel climates or inferences on causality are invoked.

    Keywords: Association test, CHIRPS, GLM, MODIS, MaxEnt, TRMM, WorldClim, ecological niche model, habitat suitability, null model

  • Droege G, Barker K, Seberg O, Coddington J, Benson E, Berendsohn W et al. (2016)

    The Global Genome Biodiversity Network (GGBN) Data Standard specification.

    Database : the journal of biological databases and curation 2016 baw125.

    Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL:

    Keywords: Association test, CHIRPS, GLM, MODIS, MaxEnt, TRMM, WorldClim, ecological niche model, habitat suitability, null model

  • Gilles D, Zaiss R, Blach-Overgaard A, Catarino L, Damen T, Deblauwe V et al. (2016)

    RAINBIO: a mega-database of tropical African vascular plants distributions

    PhytoKeys 74 1-18.

    The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

    Keywords: Herbarium specimens, biodiversity assessmen, cultivated species, digitization, georeferencing, habit, native species, taxonomic backbone, tropical forests

  • Greve M, Lykke A, Fagg C, Gereau R, Lewis G, Marchant R et al. (2016)

    Realising the potential of herbarium records for conservation biology

    South African Journal of Botany 105 317-323.

    One of the major challenges in ecosystem conservation is obtaining baseline data, particularly for regions that have been poorly inventoried, such as regions of the African continent. Here we use a database of African herbarium records and examples from the literature to show that, although herbarium records have traditionally been collected to build botanical reference “libraries” for taxonomic and inventory purposes, they provide valuable and useful information regarding species, their distribution in time and space, their traits, phenological characteristics, associated species and their physical environment. These data have the potential to provide invaluable information to feed into evidence-based conservation decisions.

    Keywords: Biological collections, Database, Historical records, Label information, Long-term data collections, Trait

  • Kissling W, Blach-Overgaard A, Zwaan R, Wagner P, Pennisi E, Hawkins B et al. (2016)

    Historical colonization and dispersal limitation supplement climate and topography in shaping species richness of African lizards (Reptilia: Agaminae)

    Scientific Reports 6 34014.

    To what extent deep-time dispersal limitation shapes present-day biodiversity at broad spatial scales remains elusive. Here, we compiled a continental dataset on the distributions of African lizard species in the reptile subfamily Agaminae (a relatively young, Neogene radiation of agamid lizards which ancestors colonized Africa from the Arabian peninsula) and tested to what extent historical colonization and dispersal limitation (i.e. accessibility from areas of geographic origin) can explain present-day species richness relative to current climate, topography, and climate change since the late Miocene (~10 mya), the Pliocene (~3 mya), and the Last Glacial Maximum (LGM, 0.021 mya). Spatial and non-spatial multi-predictor regression models revealed that time-limited dispersal via arid corridors is a key predictor to explain macro-scale patterns of species richness. In addition, current precipitation seasonality, current temperature of the warmest month, paleo-temperature changes since the LGM and late Miocene, and topographic relief emerged as important drivers. These results suggest that deep-time dispersal constraints — in addition to climate and mountain building — strongly shape current species richness of Africa’s arid-adapted taxa. Such historical dispersal limitation might indicate that natural movement rates of species are too slow to respond to rates of ongoing and projected future climate and land use change.

    Keywords: Biological collections, Database, Historical records, Label information, Long-term data collections, Trait