Uses of GBIF in scientific research

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

List of publications

  • Chomicki, G., Renner, S., 2015.

    Phylogenetics and molecular clocks reveal the repeated evolution of ant-plants after the late Miocene in Africa and the early Miocene in Australasia and the Neotropics.

    The New phytologist.

    Ant-plant symbioses involve over 110 ant species in five subfamilies that are facultative or obligate occupants of stem, leaf or root domatia formed by hundreds of ant-plant species. The phylogenetic distribution and geological ages of these associations, and the frequency of gains or losses of domatium, are largely unknown. We compiled an up-to-date list of ant domatium-bearing plants, estimated their probable true number from model-based statistical inference, generated dated phylogenies that include c. 50% of ant-plant lineages, and traced the occurrence of domatia and extrafloral nectaries on a 1181-species tree, using likelihood and Bayesian methods. We found 681 vascular plants with domatia (159 genera in 50 families) resulting from minimally 158 inferred domatium origins and 43 secondary losses over the last 19 Myr. The oldest African ant-plant symbioses are younger than those in Australasia and the Neotropics. The best statistical model suggests that the true number of myrmecophytes may approach 1140 species. The phylogenetic distribution of ant-plants shows that domatia evolved from a range of pre-adapted morphological structures and have been lost frequently, suggesting that domatia have no generalizable effect on diversification. The Miocene origin of ant-plant symbioses is consistent with inferred changes in diet and behaviour during ant evolution.

    Keywords: ant-plant symbioses, domatia, extrafloral nectaries (EFNs), mutualism, myrmecophytes, radiations, symbioses


  • Feuda, R., Bannikova, A., Zemlemerova, E., Di Febbraro, M., Loy, A., Hutterer, R., Aloise, G., Zykov, A., Annesi, F., Colangelo, P., 2015.

    Tracing the evolutionary history of the mole, Talpa europaea , through mitochondrial DNA phylogeography and species distribution modelling

    Biological Journal of the Linnean Society 114(3) 495-512.

    Our understanding of the effect of Pleistocene climatic changes on the biodiversity of European mammals mostly comes from phylogeographical studies of non-subterranean mammals, whereas the influence of glaciation cycles on subterranean mammals has received little attention. The lack of data raises the question of how and to what extent the current amount and distribution of genetic variation in subterranean mammals is the result of Pleistocene range contractions/expansions. The common mole (Talpa europaea) is a strictly subterranean mammal, widespread across Europe, and represents one of the best candidates for studying the influence of Quaternary climatic oscillation on subterranean mammals. Cytochrome b sequences, as obtained from a sampling covering the majority of the distribution area, were used to evaluate whether Pleistocene climate change influenced the evolution of T. europaea and left a trace in the genetic diversity comparable to that observed in non-subterranean small mammals. Subsequently, we investigated the occurrence of glacial refugia by comparing the results of phylogeographical analysis with species distribution modelling. We found three differentiated mitochondrial DNA lineages: two restricted to Spain and Italy and a third that was widespread across Europe. Phylogenetic inferences and the molecular clock suggest that the Spanish moles represent a highly divergent and ancient lineage, highlighting for the first time the paraphyly of T. europaea. Furthermore, our analyses suggest that the genetic break between the Italian and the European lineages predates the last glacial phase. Historical demography and spatial principal component analysis further suggest that the Last Glacial Maximum left a signature both in the Italian and in the European lineages. Genetic data combined with species distribution models support the presence of at least three putative glacial refugia in southern Europe (France, Balkan Peninsula and Black Sea) during thelast glacial maximum that likely contributed to post-glacial recolonization of Europe. By contrast, the Italian lineage remained trapped in the Italian peninsula and, according to the pattern observed in other subterranean mammals, did not contribute to the recolonization of northern latitudes

    Keywords: Europe, Last Glacial Maximum, SDM, cytochrome b, glacial refugia, historical demography, paraphyly, phylogenetics, sPCA


  • Gnoumou, A., Ouedraogo, O., Schmidt, M., Thiombiano, A., 2015.

    Floristic diversity of classified forest and partial faunal reserve of Comoé-Léraba, southwest Burkina Faso

    Check List: he Journal of Biodiversity Data 11(1) 1557.

    : The classified forest and partial faunal reserve of Comoé-Léraba belongs to the South Sudanian phytogeographical sector of Burkina Faso and is located in the most humid area of the country. This study aims to present a detailed list of the Comoé-L é raba reserve’s flora for a better knowledge and conservation. Floristic inventories have permitted to record 540 plant species belonging to 342 genera and 91 families, thus representing 26.12% of Burkina Faso’s phytodiversity (2067 species). Fabaceae and Poaceae with 89 and 51 species respectively, were the dominant families. The vegetation is characterized by the dominance of both phanerophytes (45.51%) and therophytes (32.73%). The importance of Guineo–­Con­golian species proves that the Comoé-Léraba flora belongs to the Sudano–Guinean transition sector. Comoé-Léraba also accounts the highest number of exclusive species followed by the reserve of Sahel in the country. Exclusive species bring out its value in flora conservation.

    Keywords: life form, phytodiversity, phytogeography, protected area, savanna


  • Householder, J., Wittmann, F., Tobler, M., Janovec, J., 2015.

    Montane bias in lowland Amazonian Peatlands: Plant assembly on heterogeneous landscapes and potential significance to palynological inference

    Palaeogeography, Palaeoclimatology, Palaeoecology 423 138-148.

    Past temperature changes in tropical mountain regions are commonly inferred from vertical elevational shifts of montane indicator taxa in the palynological record. However temperature is one of several abiotic factors driving the low-elevational limits of species and many montane taxa can occur in warmer lowlands by tracking appropriate habitat types, especially highly flooded wetlands. In this paper we explore ways in which lowland habitat heterogeneity might introduce error into paleo-temperature reconstructions, based on field data of seven modern peatland vegetation communities in the southern Peruvian Amazon (~200masl). Peat-rich substrates are common edaphic transitions in pollen cores and provide detailed records of past vegetation change. The data show that indicators of modern peatlands include genera with montane as well as lowland distributions, while indicators of surrounding forests on mineral substrates have predominantly lowland distributions. Based on family-level analyses we find that modern peatland vegetation communities have taxonomic compositions appearing to be 389m to 1557m (mean=1050±391m) above their actual elevations due to a high abundance and number of families with high elevation optima. We interpret the relatively higher prevalence of montane elements in modern peatlands as habitat tracking of a conserved montane niche on heterogeneous lowland landscapes. We suggest that both high moisture availability and stressful edaphic conditions of peatland habitat may explain the montane bias observed. To the extent that fossilization provides a better record of past vegetation that occurred proximate to the site of deposition, we suggest that habitat tracking of montane elements may introduce a cool bias in lowland paleo-temperature reconstructions based on pollen proxies.

    Keywords: Amazon, Andes, Climate history, Gentry, Montane, Peatland, Wetland


  • Lin, Y., Deng, D., Lin, W., Lemmens, R., Crossman, N., Henle, K., Schmeller, D., 2015.

    Uncertainty analysis of crowd-sourced and professionally collected field data used in species distribution models of Taiwanese moths

    Biological Conservation 181 102-110.

    The purposes of this study are to extract the names of species and places for a citizen-science monitoring program, to obtain crowd-sourced data of acceptable quality, and to assess the quality and the uncertainty of predictions based on crowd-sourced data and professional data. We used Natural Language Processing to extract names of species and places from text messages in a citizen science project. Bootstrap and Maximum Entropy methods were used to assess the uncertainty in the model predictions based on crowd-sourced data from the EnjoyMoths project in Taiwan. We compared uncertainty in the predictions obtained from the project and from the Global Biodiversity Information Facility (GBIF) field data for seven focal species of moth. The proximity to locations of easy access and the Ripley K method were used to test the level of spatial bias and randomness of the crowd-sourced data against GBIF data. Our results show that extracting information to identify the names of species and their locations from crowd-sourced data performed well. The results of the spatial bias and randomness tests revealed that the crowd-sourced data and GBIF data did not differ significantly in respect to both spatial bias and clustering. The prediction models developed using the crowd-sourced dataset were the most effective, followed by those that were developed using the combined dataset. Those that performed least well were based on the small sample size GBIF dataset. Our method demonstrates the potential for using data collected by citizen scientists and the extraction of information from vast social networks. Our analysis also shows the value of citizen science data to improve biodiversity information in combination with data collected by professionals.

    Keywords: Citizen science, Large-scale monitoring program, Natural language, Prediction of species distribution, Social media, Uncertainty, Volunteer survey


  • Padonou, E., Teka, O., Bachmann, Y., Schmidt, M., Lykke, A., Sinsin, B., 2015.

    Using species distribution models to select species resistant to climate change for ecological restoration of bowé in West Africa

    African Journal of Ecology n/a-n/a.

    Bowalization is a particular form of land degradation and leads to lateral expansion of ferricrete horizons. The process occurs only in tropical regions. In this study, the most adapted and resistant species towards climate change were identified on bowé. The 15 most common bowé species of the subhumid and semi-arid climate zones of Benin were submitted together with significant environmental variables (elevation, current bioclimatic variables, soil types) to three ecological niche modelling programmes (Maxent, Domain and GARP). For future prediction (2050), IPCC4/CIAT and IPCC5/CMIP5 climate data were applied. Asparagus africanus, Andropogon pseudapricus and Combretum nigricans were identified as the most resistant species for ecological restoration of bowé in the semi-arid climate zone and Asparagus africanus, Detarium microcarpum and Lannea microcarpa in the subhumid climate zone. The ‘Pull’ strategies were identified as appropriate for ecological restoration of bowé in Benin.

    Keywords: Benin, Bowé, climate change, ecological restoration, resistant species, subhumid and semi-arid climate zones


  • Antunes Carvalho, F., Filer, D., Renner, S., 2014.

    Taxonomy in the electronic age and an e-monograph of the papaya family (Caricaceae) as an example

    Cladistics Forthcoming.

    The need for taxonomists to take full advantage of biodiversity informatics has been clear for at least 10 years. Significant progress has been made in providing access to taxonomic resources online, including images of specimens (especially types), ori- ginal species descriptions, and georeferenced collection data. However, in spite of persuasive calls for e-monography, there are few, if any, completed project, even though monographic research is the only mechanism for reducing synonymous names, which are estimated to comprise 50% of all published names. Caricaceae is an economically important family of flowering plants from Africa and the Neotropics, best known for the fruit crop papaya. There is a large amount of information on the family, espe- cially on chemistry, crop improvement, genomics, and the sex chromosomes of papaya, but up-to-date information on the 230 names and which species they might belong to was not available. A dynamically updated e-monograph of the Caricaceae now brings together all information on this family, including keys, species descriptions, and specimen data relating the 230 names to 34 species and one hybrid. This may be the first taxonomic monograph of a plant family completely published online. The curated information will be continuously updated to improve the monograph’s comprehensiveness and utility.

    Keywords: Benin, Bowé, climate change, ecological restoration, resistant species, subhumid and semi-arid climate zones


  • Beck, J., Böller, M., Erhardt, A., Schwanghart, W., 2014.

    Spatial bias in the GBIF database and its effect on modeling species' geographic distributions

    Ecological Informatics 19 10-15.

    Species distribution modelling, in combination with databases of specimen distribution records, is advocated as a solution to the problem of distributional data limitation in biogeography and ecology. The global biodiversity information facility (GBIF), a portal that collates digitized collection and survey data, is the largest online provider of distribution records. However, all distributional databases are spatially biased due to uneven effort of sampling, data storage and mobilization. Such bias is particularly pronounced in GBIF, where nation-wide differences in funding and data sharing lead to huge differences in contribution to GBIF. We use a common Eurasian butterfly (Aglais urticae) as an exemplar taxon to provide evidence that range model quality is decreasing due to the spatial clustering of distributional records in GBIF. Furthermore, we show that such loss of model quality would go unnoticed with standard methods of model quality evaluation. Using evaluations of model predictions of the Swiss distribution of the species, we compare distribution models of full data with data where a subsampling procedure removes spatial bias at the cost of record numbers, but not of spatial extent of records. We show that data with less spatial bias produce better predictive models even though they are based on less input data. Our subsampling routine may therefore be a suitable method to reduce the impact of spatial bias to species distribution models. Our results warn of automatized applications of species distribution models to distributional databases (as has been advocated and implemented), as internal model evaluation did not show the decline of model quality with increased spatial bias (but rather the opposite) while expert evaluation clearly did.

    Keywords: AUC, CSCF, Ecological niche modelling, Lepidoptera, Maxent, Small tortoiseshell


  • Bellot, S., Renner, S., 2014.

    The systematics of the worldwide endoparasite family Apodanthaceae (Cucurbitales), with a key, a map, and color photos of most species

    PhytoKeys 36 41-57.

    Using morphological, nuclear, and mitochondrial data, we here revise the taxonomy of Apodanthaceae and allocate the 36 names published in the family to ten biological species in two genera, Apodanthes and Pilostyles. All species are endo-parasites that live permanently inside trees or shrubs of the families Salicaceae or Fabaceae and that only emerge to flower. Because of this life history, Apodanthaceae are among the least known families of flowering plants. Nevertheless, the World’s herbaria as of 2013 hold at least 785 collections that, in combination with DNA phylogenies, permit well-founded species circum- scriptions and geographic range maps. We also provide a key to all species, discuss the newly accepted or synonymized names, and make available color photos of six of the ten species.

    Keywords: apodanthaceae, genus circumscriptions, mitochondrial dna sequences, nuclear dna sequences, parasitic, plants, species circumscriptions


  • Boeckmann, M., Joyner, T., 2014.

    Old health risks in new places? An ecological niche model for I. ricinus tick distribution in Europe under a changing climate.

    Health & place 30 70-7.

    Climate change will likely have impacts on disease vector distribution. Posing a significant health threat in the 21st century, risk of tick-borne diseases may increase with higher annual mean temperatures and changes in precipitation. We modeled the current and future potential distribution of the Ixodes ricinus tick species in Europe. The Genetic Algorithm for Rule-set Prediction (GARP) was utilized to predict potential distributions of I. ricinus based on current (1990-2010 averages) and future (2040-2060 averages) environmental variables. A ten model best subset was created out of a possible 200 models based on omission and commission criteria. Our results show that under the A2 climate change scenario the potential habitat range for the I. ricinus tick in Europe will expand into higher elevations and latitudes (e.g., Scandinavia, the Baltics, and Belarus), while contracting in other areas (e.g., Alps, Pyrenees, interior Italy, and northwestern Poland). Overall, a potential habitat expansion of 3.8% in all of Europe is possible. Our results may be used to inform climate change adaptation efforts in Europe.

    Keywords: Climate change, Climate change adaptation, Ecological niche model, Tick-borne diseases, Vector-borne diseases