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

  • 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: http://terms.tdwg.org/wiki/GGBN_Data_Standard.

    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.

    Dear Wycliffe, We have now evaluated the early progress reports and updates you submitted via email as part of the reporting process for BID-AF2015-0035-NAC. We are pleased to note your efforts to improve engagement with your project’s national partners. We believe that a strong engagement of all project partners is essential to a successful project and would like to encourage you to continue fostering communication among Kenya Wildlife Service, Nature Kenya and National Museums of Kenya. Please do not hesitate to raise any concerns with us if you feel that you encounter unexpected difficulties in this area. Following the assessment of your reports, we are happy to inform you that your narrative and financial reports have now been pre-approved by GBIF Secretariat. We have made some edits to the formatting of the narrative report as the template seemed to have caused problems in the version we received – and it was missing the automatic table of contents (see reformatted version attached). Once you have checked this through, you can now send the original signed copies of these reports to GBIF Secretariat by courier to: GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK Please note that, as described in the contract under “Schedule of payments”, it is a requirement to have spent minimum 80% of previous BID payments received, before qualifying for further installments. In your submitted Early Progress Financial Reports we have noted that only 50% have been spent, thus no further installments will be made at this time. However, it is still mandatory to send us original signed copies of the pre-approved narrative and financial reports by courier already now to finalize the early progress reporting process. We ask you to submit an updated Financial report (Financial report by Activity & Expense Types and the Expense Summary Page), at such a time when minimum 80% of already received BID payments have been spent. The format of the Financial Reports should be the same as the Early Progress Financial Reports and can be accepted in electronic format. When you reach this stage, we would invite you to send a short update on progress made in the implementation of your project’s activities, particularly after your further meetings with the project partners. We would also like to remind you of the possibility to request support from the BID mentors by writing to the BID community mailing list at http://bid.gbif.org/en/community/mailing-lists/. You are also very welcome to contact us at BID@gbif.org to request assistance to identify possible mentors based on identified capacity needs. We would recommend contacting the mailing list early to plan any assistance that could be required for your next workshop. With Best Regards

    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


  • Sanín M, Kissling W, Bacon C, Borchsenius F, Galeano G, Svenning J et al. (2016)

    The Neogene rise of the tropical Andes facilitated diversification of wax palms ( Ceroxylon : Arecaceae) through geographical colonization and climatic niche separation

    Botanical Journal of the Linnean Society.

    he tropical Andes are a biodiversity hotspot, partly due to their rich and complex floristic composition. A fundamental question regarding this outstanding biodiversity is what role the Andean orogeny has played in species diversification. Ceroxylon is a genus of endemic Andean palms that stands out in the palm family (Arecaceae) due to its adaptation to cold, mountainous environments. Here, we reconstruct the biogeography and climatic preference of this lineage to test the hypothesis that Andean uplift allowed diversification by providing suitable habitats along climatic and elevational gradients. Ancestral areas were reconstructed under a model allowing for founder-event speciation and climatic niches were inferred from climatic variables at present-day occurrences of all species. Niche evolution in a phylogenetic framework was evaluated by testing differences between the climatic niches of clades. Our analyses identified four main clades, with a general pattern of diversification through geographical colonization from south to north after the Pliocene uplift of the northern Andes. Adaptation to low temperatures was conserved at the generic level, with climatic niche differentiation among clades along elevational temperature gradients. We conclude that the Neogene Andean uplift has facilitated the diversification of this iconic plant group via opportunities for geographical migration and separation within its climatic niche

    Keywords: Miocene, Neotropics, cold adaptation, niche shift, phylogenetic niche conservatism, range expansion


  • Wauchope H, Shaw J, Varpe , Lappo E, Boertmann D, Lanctot R et al. (2016)

    Rapid climate-driven loss of breeding habitat for Arctic migratory birds

    Global Change Biology.

    Millions of birds migrate to and from the Arctic each year, but rapid climate change in the High North could strongly affect where species are able to breed, disrupting migratory connections globally. We modelled the climatically suitable breeding conditions of 24 Arctic specialist shorebirds and projected them to 2070 and to the mid-Holocene climatic optimum, the world's last major warming event ~6000 years ago. We show that climatically suitable breeding conditions could shift, contract and decline over the next 70 years, with 66–83% of species losing the majority of currently suitable area. This exceeds, in rate and magnitude, the impact of the mid-Holocene climatic optimum. Suitable climatic conditions are predicted to decline acutely in the most species rich region, Beringia (western Alaska and eastern Russia), and become concentrated in the Eurasian and Canadian Arctic islands. These predicted spatial shifts of breeding grounds could affect the species composition of the world's major flyways. Encouragingly, protected area coverage of current and future climatically suitable breeding conditions generally meets target levels; however, there is a lack of protected areas within the Canadian Arctic where resource exploitation is a growing threat. Given that already there are rapid declines of many populations of Arctic migratory birds, our results emphasize the urgency of mitigating climate change and protecting Arctic biodiversity.

    Keywords: Beringia, flyway, maxent, mid-Holocene, protected areas, shorebirds, species distribution modelling, waders


  • Zhang J, Nielsen S, Chen Y, Georges D, Qin Y, Wang S et al. (2016)

    Extinction risk of North American seed plants elevated by climate and land-use change

    Journal of Applied Ecology.

    Climate and land-use change are expected to substantially alter future plant species distributions leading to higher extinction rates. However, little is known about how plant species ranges, richness and phylogenetic diversity of continents will be affected by these dynamics. We address this gap here by examining the patterns of species' distributions and phylogenetic relationships for 7465 seed plant taxa in North America. An ensemble of species distribution models was used to estimate the potential suitable habitat of species under different sets of climate, land-use and dispersal constraint scenarios. We then evaluated the vulnerability and extinction risk of individual species to changes in climate and land use, and examined whether rare, endangered and evolutionarily distinct species were disproportionally threatened by climate and land-use change. We show that ~2000 species may lose >80% of their suitable habitats under the A1b emission scenario for the 2080s, while ~100 species may experience >80% range expansions (a 20 : 1 ratio of loss to gain). When considering >50% range retraction and expansion, the ratio of loss to gain was 13 : 1. A greater loss of species diversity is expected at low latitudes, while larger gains are expected at high latitudes. Evolutionarily distinct species are predicted to have significantly higher extinction risks than extant species. This suggests a disproportionate future loss of phylogenetic diversity for the North American flora. Synthesis and applications. Our study provides continental-scale evidence of plant species extinction risk caused by future climate and land-use change, and highlights the importance of integrating phylogenetic measures into conservation risk assessments. This work provides insight into the status, trends and threats for a large share of North America's plant species by identifying risks and prioritizing conservation in a rapidly changing world.

    Keywords: Beringia, flyway, maxent, mid-Holocene, protected areas, shorebirds, species distribution modelling, waders