Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from Belgium.
Extracted from the Mendeley GBIF Public Library.

List of publications

  • Adriaens, T., Sutton-Croft, M., Owen, K., Brosens, D., van Valkenburg, J., Kilbey, D., Groom, Q., Ehmig, C., Thürkow, F. V, , P., Schneider K (2015)

    Trying to engage the crowd in recording invasive alien species in Europe: experiences from two smartphone applications in northwest Europe

    Management of Biological Invasions 6(2) 215-225.

    New technologies such as smartphone appli cation software (apps) are increasingly used to reach a wider audience on the subject of invasive alien species (IAS) and to involve the public in recording them. In this paper we pr esent two of the more recent smartphone app lications for IAS recording in northwest Europe, the RINSE That’s Invasive! app and the KORINA app. We present an overview of available smartphone apps for IAS recording in Europe and addr ess issues of data integra tion, data openness, data quality, data harmonisation and da tabase interoperability. Finally, we make some recommendations for future app design

    Keywords: biological recording, citizen science, early war

  • Antonelli A, Zizka A, Silvestro D, Scharn R, Cascales-Miñana B, Bacon C (2015)

    An engine for global plant diversity: highest evolutionary turnover and emigration in the American tropics.

    Frontiers in genetics 6 130.

    Understanding the processes that have generated the latitudinal biodiversity gradient and the continental differences in tropical biodiversity remains a major goal of evolutionary biology. Here we estimate the timing and direction of range shifts of extant flowering plants (angiosperms) between tropical and non-tropical zones, and into and out of the major tropical regions of the world. We then calculate rates of speciation and extinction taking into account incomplete taxonomic sampling. We use a recently published fossil calibrated phylogeny and apply novel bioinformatic tools to code species into user-defined polygons. We reconstruct biogeographic history using stochastic character mapping to compute relative numbers of range shifts in proportion to the number of available lineages through time. Our results, based on the analysis of c. 22,600 species and c. 20 million geo-referenced occurrence records, show no significant differences between the speciation and extinction of tropical and non-tropical angiosperms. This suggests that at least in plants, the latitudinal biodiversity gradient primarily derives from other factors than differential rates of diversification. In contrast, the outstanding species richness found today in the American tropics (the Neotropics), as compared to tropical Africa and tropical Asia, is associated with significantly higher speciation and extinction rates. This suggests an exceedingly rapid evolutionary turnover, i.e., Neotropical species being formed and replaced by one another at unparalleled rates. In addition, tropical America stands out from other continents by having "pumped out" more species than it received through most of the last 66 million years. These results imply that the Neotropics have acted as an engine for global plant diversity.

    Keywords: Angiosperms, Latitudinal diversity gradient, biogeography, diversification rates, evolution, phylogenetics, tropical biodiversity

  • Dellicour S, Michez D, Rasplus J, Mardulyn P (2015)

    Impact of past climatic changes and resource availability on the population demography of three food-specialist bees.

    Molecular ecology.

    Past climate change is known to have strongly impacted current patterns of genetic variation of animals and plants in Europe. However, ecological factors also have the potential to influence demographic history, and thus patterns of genetic variation. In this study, we investigated the impact of past climate, and also the potential impact of host plant species abundance, on intraspecific genetic variation in three co-distributed and related specialized solitary bees of the genus Melitta with very similar life history traits and dispersal capacities. We sequenced five independent loci in samples collected from the three species. Our analyses revealed that the species associated with the most abundant host plant species (Melitta leporina) displays unusually high genetic variation, to an extent that is seldom reported in phylogeographic studies of animals and plants. This suggests a potential role of food resource abundance in determining current patterns of genetic variation in specialized herbivorous insects. Patterns of genetic variation in the two other species indicated lower overall levels of diversity, and that M. nigricans could have experienced a recent range expansion. Ecological niche modelling of the three Melitta species and their main host plant species suggested a strong reduction in range size during the last glacial maximum. Comparing observed sequence data with data simulated using spatially explicit models of coalescence suggests that M. leporina recovered a range and population size close to their current levels at the end of the last glaciation, and confirms recent range expansion as the most likely scenario for M. nigricans. Overall, this study illustrates that both demographic history and ecological factors may have contributed to shape current phylogeographic patterns. This article is protected by copyright. All rights reserved.

    Keywords: coalescent simulations, demographic history, food specialization, intraspecific diversity, phylogeography, phytophagous insects, population fragmentation

  • Ertz D, Diederich P (2015)

    Dismantling Melaspileaceae: a first phylogenetic study of Buelliella, Hemigrapha, Karschia, Labrocarpon and Melaspilea

    Fungal Diversity.

    Melaspileaceae is a heterogeneous group of Ascomycota including lichenized, lichenicolous and saprobic fungi. A first phylogenetic study of Melaspileaceae is presented and is based on mtSSU and nuLSU sequence data. We obtained 49 new sequences for 28 specimens representing 15 species. The genera Buelliella, Hemigrapha, Karschia, Labrocarpon and Melaspilea s. str. are included in a molecular phylogeny for the first time. Melaspileaceae is recovered as polyphyletic, with members placed in two main lineages of Dothideomycetes. Melaspilea s. str. is included in Eremithallales. Eremithallaceae is placed in synonymy with Melaspileaceae. The genus Encephalographa is placed in Melaspileaceae. The genera Buelliella, Karschia, Labrocarpon and several members of Melaspilea are demonstrated to belong to Asterinales, while Hemigrapha is confirmed in this order. The genera Melaspileella, Melaspileopsis, Stictographa are reinstated for former Melaspilea species now placed in Asterinales. Karschia cezannei is described as new, and the new combinations Melaspilea costaricensis, M. enteroleuca, M. urceolata, Melaspileella proximella and Melaspileopsis diplasiospora are made. Melaspileaceae as newly defined includes lichenized and saprobic species. The lichenicolous and saprobic life styles form different intermixed lineages in Asterinales that do not include lichenized taxa. The phylogenetic data provide a first framework for dismantling further the genus Melaspilea for which most of the species are expected to belong to Asterinales.

    Keywords: Asterinales, Eremithallales, Lichenicolous fungi, Phylogeny, Taxonomy

  • Groom Q (2015)

    Piecing together the biogeographic history of Chenopodium vulvaria L. using botanical literature and collections.

    PeerJ 3 e723.

    This study demonstrates the value of legacy literature and historic collections as a source of data on environmental history. Chenopodium vulvaria L. has declined in northern Europe and is of conservation concern in several countries, whereas in other countries outside Europe it has naturalised and is considered an alien weed. In its European range it is considered native in the south, but the northern boundary of its native range is unknown. It is hypothesised that much of its former distribution in northern Europe was the result of repeated introductions from southern Europe and that its decline in northern Europe is the result of habitat change and a reduction in the number of propagules imported to the north. A historical analysis of its ecology and distribution was conducted by mining legacy literature and historical botanical collections. Text analysis of habitat descriptions written on specimens and published in botanical literature covering a period of more than 200 years indicate that the habitat and introduction pathways of C. vulvaria have changed with time. Using the non-European naturalised range in a climate niche model, it is possible to project the range in Europe. By comparing this predicted model with a similar model created from all observations, it is clear that there is a large discrepancy between the realized and predicted distributions. This is discussed together with the social, technological and economic changes that have occurred in northern Europe, with respect to their influence on C. vulvaria.

    Keywords: Bioclimatic modelling, Distribution, Habitat change, Herbarium specimens, Introduction pathways, Naturalisation, Text analysis

  • Groom Q (2015)

    Using legacy botanical literature as a source of phytogeographical data

    Plant Ecology and Evolution 148(2) 256-266.

    Aim – Paper-based publications were the main repository for phytogeographical information until the end of the 20th century. These texts are still an important reference source for phytogeography and potentially a valuable source of data for research on environmental change. The recent digitization of biodiversity publications, text-mining and mark-up protocols means that these data are now more accessible than ever before. Here I examine the value of legacy literature specifically for studies on phytogeography. Methods – Three contrasting data mobilisation projects are used as case studies for the extraction of phytogeographic data. Two were digitisations and XML mark-up of floras, the Flore d'Afrique Centrale from the 20th century and the Flora of Northumberland and Durham from the 19th century. A third case study used Chenopodium vulvaria L. as a test case, where I attempted to recover as much phytogeographic data as possible for one species, both from literature and from herbarium specimens. Results – A large amount of useful information was extractable from legacy literature. The main limitations are that most localities need georeferencing and that observations are only rarely associated with a precise date. In the case of C. vulvaria literature contributed about 20% of all available observations of the species. Literature becomes a progressively more important source of data the further back in time one looks. However, useful observations become much rarer earlier than about 1850. Main conclusions – Sourcing phytogeographic data from legacy literature is valuable. It contains observations and links to other data that are unavailable from any other source. Nevertheless, its extraction takes a substantial investment in time. Before commencing on such a project it is important to prioritise work and understand the limitations of such data, particularly with regard to georeferencing

    Keywords: Bioclimatic modelling, Distribution, Habitat change, Herbarium specimens, Introduction pathways, Naturalisation, Text analysis

  • Groom, Q. J., Desmet, P., Vanderhoeven, S., Adriaens T (2015)

    The importance of open data for invasive alien species research, policy and management

    Management of Biological Invasions 6.

    Rapidly changing environmental conditions a nd the increasing establishment of invasive alien species present many challenges fo r policy makers, managers and researchers. The traditional policies for data management, or lack thereof, are obstructing an adequate re sponse to invasive alien species, which requires accurate and up-to-date info rmation. This information can only be provided if data regar ding invasive alien species are available and useable by a ll, irrespective of country, status or pur pose. The best way forward is for researc hers to publish their data openly, by making use of repositories in which the da ta are licenced in a permissive manner, while making sure they are credited by the adequate provision of citation. Re ducing the barriers to data sharing will im prove our ability to respond to the growing issue of biological invasions.

    Keywords: Lithob, biological observations, data publication

  • Kerr J, Pindar A, Galpern P, Packer L, Potts S, Roberts S et al. (2015)

    Climate change impacts on bumblebees converge across continents

    Science 349(6244) 177-180.

    For many species, geographical ranges are expanding toward the poles in response to climate change, while remaining stable along range edges nearest the equator. Using long-term observations across Europe and North America over 110 years, we tested for climate change-related range shifts in bumblebee species across the full extents of their latitudinal and thermal limits and movements along elevation gradients. We found cross-continentally consistent trends in failures to track warming through time at species' northern range limits, range losses from southern range limits, and shifts to higher elevations among southern species. These effects are independent of changing land uses or pesticide applications and underscore the need to test for climate impacts at both leading and trailing latitudinal and thermal limits for species.

    Keywords: Animals, Bees, Bees: drug effects, Bees: physiology, Biological, Climate Change, Europe, Extinction, North America, Pesticides, Pesticides: adverse effects, Population Dynamics

  • Kraemer M, Sinka M, Duda K, Mylne A, Shearer F, Barker C et al. (2015)

    The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus

    eLife 4 e08347.

    Dengue and chikungunya are increasing global public health concerns due to their rapid geographical spread and increasing disease burden. Knowledge of the contemporary distribution of their shared vectors, Aedes aegypti and Ae. albopictus remains incomplete and is complicated by an ongoing range expansion fuelled by increased global trade and travel. Mapping the global distribution of these vectors and the geographical determinants of their ranges is essential for public health planning. Here we compile the largest contemporary database for both species and pair it with relevant environmental variables predicting their global distribution. We show Aedes distributions to be the widest ever recorded; now extensive in al l continents, including North America and Europe. These maps will help define the spatial limits of current autochthonous transmission of dengue and chikungunya viruses. It is only with this kind of rigorous entomological baseline that we can hope to project future health impacts of these viruses.

    Keywords: Aedes aegypti, Aedes albopictus, arboviruses, chikungunya, dengue, ecological niche, yellow fever

  • Strubbe D, Jackson H, Groombridge J, Matthysen E (2015)

    Invasion success of a global avian invader is explained by within-taxon niche structure and association with humans in the native range

    Diversity and Distributions 21(6) 675-685.

    Aim To mitigate the threat invasive species pose to ecosystem functioning, reliable risk assessment is paramount. Spatially explicit predictions of invasion risk obtained through bioclimatic envelope models calibrated with native species distribution data can play a critical role in invasive species management. Forecasts of invasion risk to novel environments, however, remain controversial. Here, we assess how species’ association with human-modified habitats in the native range and within-taxon niche structure shape the distribution of invasive populations at biogeographical scales and influence the reliability of predictions of invasion risk. Location Africa, Asia and Europe. Methods We use ~1200 native and invasive ring-necked parakeet (Psittacula krameri) occurrences and associated data on establishment success in combination with mtDNA-based phylogeographic structure to assess niche dynamics during biological invasion and to generate predictions of invasion risk. Niche dynamics were quantified in a gridded environmental space while bioclimatic models were created using the biomod2 ensemble modelling framework. Results Ring-necked parakeets show considerable niche expansion into climates colder than their native range. Only when incorporating a measure of human modification of habitats within the native range do bioclimatic envelope models yield credible predictions of invasion risk for parakeets across Europe. Invasion risk derived from models that account for differing niche requirements of phylogeographic lineages and those that do not achieve similar statistical accuracy, but there are pronounced differences in areas predicted to be susceptible for invasion. Main conclusions Information on within-taxon niche structure and especially association with humans in the native range can substantially improve predictive models of invasion risk. To provide policymakers with robust predictions of invasion risk, including these factors into bioclimatic envelope models is recommended.

    Keywords: Bioclimatic envelope models, Psittacula krameri, human influence, invasive species, niche shift, risk assessment