Uses of GBIF in scientific research

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

List of publications

  • 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

  • Ferretti, F., Morey Verd, G., Seret, B., Sulić Šprem, J., Micheli, F., 2015.

    Falling through the cracks: the fading history of a large iconic predator

    Fish and Fisheries n/a-n/a.

    Human impact on the oceans predates scientific observation, which for many animal populations has captured only recent changes. Such a limited knowledge can hamper finding optimal management and conservation strategies including setting appropriate recovery targets. Sawfishes are among the most endangered marine vertebrates in the ocean. Historical human impacts have resulted in sawfish extinction in many coastal areas around the world; however, in the Mediterranean Sea, their past presence and possible extinction have been debated for decades. Recently, it was concluded that the region never hosted resident populations because of unsuitable environmental conditions. Through an extensive bibliographic and archival search and an extinction analysis, we reconstructed the history of sawfishes in the Mediterranean Sea. Between 1576 and 1959, there were 48 independent accounts of the occurrence of two sawfish species (Pristis pristis, Pristidae and Pristis pectinata, Pristidae), including 24 documented catches. Sawfishes were mainly recorded in the western Mediterranean, in areas close to large rivers with light human impact. Most of the documented individuals were juveniles, suggesting local parturition. Extinction analyses yielded variable results and were affected by the sparseness of records but suggested that both species went extinct in the Mediterranean Sea in the 1960s–1970s. Our results challenge current assumptions on sawfish ecology and biogeography, offer new options for sawfish conservation in the Atlantic and highlight the importance of historical analyses for reconstructing ecosystem baselines and setting recovery targets.

    Keywords: bibliographic analysis, ecological baselines, extinction analyses, historical ecology, museum records, sawfish

  • 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

  • Wisz, M., Broennimann, O., Grønkjær, P., Møller, P., Olsen, S., Swingedouw, D., Hedeholm, R., Nielsen, E., Guisan, A., Pellissier, L., 2015.

    Arctic warming will promote Atlantic–Pacific fish interchange

    Nature Climate Change.

    Throughout much of the Quaternary Period, inhospitable environmental conditions above the Arctic Circle have been a formidable barrier separating most marine organisms in the North Atlantic from those in the North Pacific1, 2. Rapid warming has begun to lift this barrier3, potentially facilitating the interchange of marine biota between the two seas4. Here, we forecast the potential northward progression of 515 fish species following climate change, and report the rate of potential species interchange between the Atlantic and the Pacific via the Northwest Passage and the Northeast Passage. For this, we projected niche-based models under climate change scenarios and simulated the spread of species through the passages when climatic conditions became suitable. Results reveal a complex range of responses during this century, and accelerated interchange after 2050. By 2100 up to 41 species could enter the Pacific and 44 species could enter the Atlantic, via one or both passages. Consistent with historical and recent biodiversity interchanges5, 6, this exchange of fish species may trigger changes for biodiversity and food webs in the North Atlantic and North Pacific, with ecological and economic consequences to ecosystems that at present contribute 39% to global marine fish landings.

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

  • Aubert, S., Boucher, F., Lavergne, S., Renaud, J., Choler, P., 2014.

    1914–2014: A revised worldwide catalogue of cushion plants 100 years after Hauri and Schröter

    Alpine Botany 124(1) 59-70.

    Cushion plants have long fascinated botanists for their ability to cope with extreme environments in most mountains and arctic regions of the world. One century ago, a first worldwide catalogue of species forming cushions was published by Hauri and Schröter (Bot Jahrb Syst Pflanzengesch Pflanzengeogr 50:618–656, 1914). Here, we defined a simplified typology of cushion plants and updated the worldwide catalogue of cushion species, along with information on their geographic distribution. This compilation was based on available information in floras and catalogues but also in efloras and virtual encyclopedias, which were screened using automated database queries. We established a list of 1,309 cushion-forming species distributed in 272 genera and 63 families of angiosperms. Compact cushions are represented by 678 species, among which 587 species exhibit a hemispherical shape, and 91 species exhibit a flat to mat shape. We found 398 species forming non-compact hemispherical cushions. The list of cushion species has significantly increased since Hauri and Shröter, due to the description of new species, updated regional inventories, and improved access to electronic databases. Uncertainties in the delineation of the cushion life form are discussed, notably for non-compact growth forms. A website has been launched to display the catalogue and enable a collaborative improvement of the database ( The distribution of the species is presented on the basis of the world geographical scheme for recording plant distributions and global biodiversity information facility data. This catalogue will serve as a reference database for further analyses on the biogeography and evolutionary history of cushion plants and arctico-alpine biotas.

    Keywords: Adaptive convergence, Alpine plants, Biodiversity informatics, Biogeography, Cushion plants, Plant life form

  • Brito, J., Godinho, R., Martínez-Freiría, F., Pleguezuelos, J., Rebelo, H., Santos, X., Vale, C., Velo-Antón, G., Boratyński, Z., Carvalho, S., Ferreira, S., Gonçalves, D., Silva, T., Tarroso, P., Campos, J., Leite, J., Nogueira, J., Alvares, F., Sillero, N., Sow, A., Fahd, S., Crochet, P., Carranza, S., 2014.

    Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel

    Biological Reviews of the Cambridge Philosophical Society 89(1) 215-31.

    Deserts and arid regions are generally perceived as bare and rather homogeneous areas of low diversity. The Sahara is the largest warm desert in the world and together with the arid Sahel displays high topographical and climatic heterogeneity, and has experienced recent and strong climatic oscillations that have greatly shifted biodiversity distribution and community composition. The large size, remoteness and long-term political instability of the Sahara-Sahel, have limited knowledge on its biodiversity. However, over the last decade, there have been an increasing number of published scientific studies based on modern geomatic and molecular tools, and broad sampling of taxa of these regions. This review tracks trends in knowledge about biodiversity patterns, processes and threats across the Sahara-Sahel, and anticipates needs for biodiversity research and conservation. Recent studies are changing completely the perception of regional biodiversity patterns. Instead of relatively low species diversity with distribution covering most of the region, studies now suggest a high rate of endemism and larger number of species, with much narrower and fragmented ranges, frequently limited to micro-hotspots of biodiversity. Molecular-based studies are also unravelling cryptic diversity associated with mountains, which together with recent distribution atlases, allows identifying integrative biogeographic patterns in biodiversity distribution. Mapping of multivariate environmental variation (at 1 km × 1 km resolution) of the region illustrates main biogeographical features of the Sahara-Sahel and supports recently hypothesised dispersal corridors and refugia. Micro-scale water-features present mostly in mountains have been associated with local biodiversity hotspots. However, the distribution of available data on vertebrates highlights current knowledge gaps that still apply to a large proportion of the Sahara-Sahel. Current research is providing insights into key evolutionary and ecological processes, including causes and timing of radiation and divergence for multiple taxa, and associating the onset of the Sahara with diversification processes for low-mobility vertebrates. Examples of phylogeographic patterns are showing the importance of allopatric speciation in the Sahara-Sahel, and this review presents a synthetic overview of the most commonly hypothesised diversification mechanisms. Studies are also stressing that biodiversity is threatened by increasing human activities in the region, including overhunting and natural resources prospection, and in the future by predicted global warming. A representation of areas of conflict, landmines, and natural resources extraction illustrates how human activities and regional insecurity are hampering biodiversity research and conservation. Although there are still numerous knowledge gaps for the optimised conservation of biodiversity in the region, a set of research priorities is provided to identify the framework data needed to support regional conservation planning.

    Keywords: Africa, Sahara, Sahel, biodiversity, climate change, conservation, deserts, distribution, diversification, phylogeography

  • Chao, Y., Rouhan, G., Amoroso, V., Chiou, W., 2014.

    Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)

    Annals of Botany 109-124.

    BACKGROUND AND AIMS: Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented. METHODS: A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications. KEY RESULTS: The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions. CONCLUSIONS: This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.

    Keywords: actiniopteris, allopatric speciation, biogeography, brake ferns, long-distance dispersal, mat k, morphological character evolution, onychium, parapatric speciation, phylogeny, platyzoma, pteridaceae, pteris, rbc l

  • Coppens d'Eeckenbrugge, G., Lacape, J., 2014.

    Distribution and Differentiation of Wild, Feral, and Cultivated Populations of Perennial Upland Cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean

    PloS one 9(9) e107458.

    Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race 'yucatanense' from northern Yucatán. 'Marie-Galante', the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats), wild/feral (protected habitats), and truly wild cotton (TWC) populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida), as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating 'Marie-Galante' from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively low genetic divergence between the Mesoamerican and Caribbean domesticated pools supports the hypothesis of domestication of G. hirsutum in northern Yucatán.

    Keywords: actiniopteris, allopatric speciation, biogeography, brake ferns, long-distance dispersal, mat k, morphological character evolution, onychium, parapatric speciation, phylogeny, platyzoma, pteridaceae, pteris, rbc l

  • Creemers, R., Denoël, M., Campos, J., Vences, M., Crochet, P., Gonçalves, J., de Pous, P., Kuzmin, S., Speybroeck, J., Toxopeus, B., Corti, C., Vieites, D., Ficetola, G., Bonardi, A., Crnobrnja Isailović, J., Rodríguez, A., Lymberakis, P., Sindaco, R., Sillero, N., 2014.

    Updated distribution and biogeography of amphibians and reptiles of Europe

    Amphibia-Reptilia 35(1) 1-31.

    A precise knowledge of the spatial distribution of taxa is essential for decision-making processes in land management and biodiversity conservation, both for present and under future global change scenarios. This is a key base for several scientific disciplines (e.g. macro-ecology, biogeography, evolutionary biology, spatial planning, or environmental impact assessment) that rely on species distribution maps. An atlas summarizing the distribution of European amphibians and reptiles with 50 × 50 km resolution maps based on ca. 85 000 grid records was published by the Societas Europaea Herpetologica (SEH) in 1997. Since then, more detailed species distribution maps covering large parts of Europe became available, while taxonomic progress has led to a plethora of taxonomic changes including new species descriptions. To account for these progresses, we compiled information from different data sources: published in books and websites, ongoing national atlases, personal data kindly provided to the SEH, the 1997 European Atlas, and the Global Biodiversity Information Facility (GBIF). Databases were homogenised, deleting all information except species names and coordinates, projected to the same coordinate system (WGS84) and transformed into a 50 × 50 km grid. The newly compiled database comprises more than 384 000 grid and locality records distributed across 40 countries. We calculated species richness maps as well as maps of Corrected Weighted Endemism and defined species distribution types (i.e. groups of species with similar distribution patterns) by hierarchical cluster analysis using Jaccard’s index as association measure. Our analysis serves as a preliminary step towards an interactive, dynamic and online distributed database system (NA2RE system) of the current spatial distribution of European amphibians and reptiles. The NA2RE system will serve as well to monitor potential temporal changes in their distributions. Grid maps of all species are made available along with this paper as a tool for decision-making and conservation-related studies and actions. We also identify taxonomic and geographic gaps of knowledge that need to be filled, and we highlight the need to add temporal and altitudinal data for all records, to allow tracking potential species distribution changes as well as detailed modelling of the impacts of land use and climate change on European amphibians and reptiles.

    Keywords: European herpetofauna, IUCN red list, biogeography, conservation, distribution atlas, distribution types, endemism, species richness

  • Ficetola, G., Rondinini, C., Bonardi, A., Baisero, D., Padoa-Schioppa, E., 2014.

    Habitat availability for amphibians and extinction threat: a global analysis

    Diversity and Distributions n/a-n/a.

    Aim Habitat loss and degradation are the factors threatening the largest number of amphibian species. However, quantitative measures of habitat availability only exist for a small subset of them. We evaluated the relationships between habitat availability, extinction risk and drivers of threat for the world's amphibians. We developed deductive habitat suitability models to estimate the extent of suitable habitat and the proportion of suitable habitat (PSH) inside the geographic range of each species, covering species and areas for which little or no high-resolution distribution data are available. Location Global. Methods We used information on habitat preferences to develop habitat suitability models at 300-m resolution, by integrating range maps with land cover and elevation. Model performance was assessed by comparing model output with point localities where species were recorded. We then used habitat availability as a surrogate of area of occupancy. Using the IUCN criteria, we identified species having narrow area of occupancy, for which extinction risk is likely underestimated. Results We developed models for 5363 amphibians. Validation success of models was high (94%), being better for forest specialists and generalists than for open habitat specialists. Generalists had proportionally more habitat than forest or open habitat specialists. The PSH was lower for species having small geographical ranges, currently listed as threatened, and for which habitat loss is recognized as a threat. Differences in habitat availability among biogeographical realms were strong. We identified 61 forest species for which the extinction risk may be higher that currently assessed in the Red List, due to limited extent of suitable habitat. Main conclusions Habitat models can accurately predict amphibian distribution at fine scale and allow describing biogeographical patterns of habitat availability. The strong relationship between amount of suitable habitat and extinction threat may help the conservation assessment in species for which limited information is currently available.

    Keywords: Amphibian decline, IUCN RedList, deductive habitat suitability model, deforestation, extinction risk, land use, terrestrial habitat