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

  • Bellard, C., Thuiller, W., Leroy, B., Genovesi, P., Bakkenes, M., Courchamp, F.

    Will climate change promote future invasions?

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Biological invasion is increasingly recognized as one of the greatest threats to biodiversity. Using ensemble forecasts from species distribution models to project future suitable areas of the 100 of the world's worst invasive species defined by the International Union for the Conservation of Nature, we show that both climate and land use changes will likely cause drastic species range shifts. Looking at potential spatial aggregation of invasive species, we identify three future hotspots of invasion in Europe, northeastern North America, and Oceania. We also emphasize that some regions could lose a significant number of invasive alien species, creating opportunities for ecosystem restoration. From the list of 100, scenarios of potential range distributions show a consistent shrinking for invasive amphibians and birds, while for aquatic and terrestrial invertebrates distributions are projected to substantially increase in most cases. Given the harmful impacts these invasive species currently have on ecosystems, these species will likely dramatically influence the future of biodiversity.

    Keywords: climate change, invasive species, land use change, species distribution models


  • 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.

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

    Biological reviews of the Cambridge Philosophical Society 1.

    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, biodiversity, climate change, conservation, deserts, distribution, diversification, phylogeography, Sahara, Sahel


  • Burguiere, T., Causse, F., Ung, V., Vignes-Lebbe, R.

    IKey + : A New Single-Access Key Generation Web Service

    Systematic Biology 62(1) 157-161.

    Single-access keys are amajor tool for biologistswhoneed toidentify specimens.The construction process of these keys is particularly complex (especially if the input data set is large) so having an automatic single-access key generation tool is essential. As part of the European project ViBRANT, our aim was to develop such a tool as a web service, thus allowing end-users to integrate it directly into theirworkflow. IKey+ generates single-access keys on demand, for single users or research institutions. It receives user input data (using the standard SDD format), accepts several key-generation parameters (affecting the key topology and representation), and supports several output formats. IKey+ is freely available (sources and binary packages) at www.identificationkey.fr. Furthermore, it is deployed on our server and can be queried (for testing purposes) through a simple web client also available at www.identificationkey.fr (last accessed 13 August 2012). Finally, a client plugin will be integrated to the Scratchpads biodiversity networking tool (scratchpads.eu).

    Keywords: biodiversity informatics, single-access key, Systematics, taxonomy, web service


  • Gasc, A., Sueur, J., Pavoine, S., Pellens, R., Grandcolas, P.

    Biodiversity sampling using a global acoustic approach: contrasting sites with microendemics in new caledonia.

    (Journal name unavailable from Mendeley API. To be updated soon...)

    New Caledonia is a Pacific island with a unique biodiversity showing an extreme microendemism. Many species distributions observed on this island are extremely restricted, localized to mountains or rivers making biodiversity evaluation and conservation a difficult task. A rapid biodiversity assessment method based on acoustics was recently proposed. This method could help to document the unique spatial structure observed in New Caledonia. Here, this method was applied in an attempt to reveal differences among three mountain sites (Mandjélia, Koghis and Aoupinié) with similar ecological features and species richness level, but with high beta diversity according to different microendemic assemblages. In each site, several local acoustic communities were sampled with audio recorders. An automatic acoustic sampling was run on these three sites for a period of 82 successive days. Acoustic properties of animal communities were analysed without any species identification. A frequency spectral complexity index (NP) was used as an estimate of the level of acoustic activity and a frequency spectral dissimilarity index (Df ) assessed acoustic differences between pairs of recordings. As expected, the index NP did not reveal significant differences in the acoustic activity level between the three sites. However, the acoustic variability estimated by the index Df , could first be explained by changes in the acoustic communities along the 24-hour cycle and second by acoustic dissimilarities between the three sites. The results support the hypothesis that global acoustic analyses can detect acoustic differences between sites with similar species richness and similar ecological context, but with different species assemblages. This study also demonstrates that global acoustic methods applied at broad spatial and temporal scales could help to assess local biodiversity in the challenging context of microendemism. The method could be deployed over large areas, and could help to compare different sites and determine conservation priorities.

    Keywords: biodiversity informatics, single-access key, Systematics, taxonomy, web service


  • Kouamé, F., Silvestre, V., Bedi, G., Loquet, D., Robins, R., Tea, I.

    Phytochemical investigation of the leaves of Leptoderris fasciculata

    Phytochemistry Letters 6(2) 253-256.

    Keyword: leptoderris fasciculata


  • Luque, G., Bellard, C., Bertelsmeier, C., Bonnaud, E., Genovesi, P., Simberloff, D., Courchamp, F.

    The 100th of the world’s worst invasive alien species

    Biological Invasions.

    Biological invasions are among the greatest threats to global biodiversity, but in contrast to most other global threats, they suffer from specific communication issues. Our paper presents the first new addition to the widely cited IUCN list of ‘‘100 of the world’s worst invasive species’’, a list created a decade ago in response to these communication issues. We briefly present this list, the recent removal of one species from that list, and the rationale to include a novel, 100th species to replace it. The new species of this list, giant salvinia (Salvinia molesta), was chosen by the community of invasion biologists (over 650 experts from over 60 countries). This new addition to the list will draw public attention to the damage caused by invasive alien species and it will help stimulate the necessary discussion of this critical issue in science and policy circles. G.

    Keywords: biological invasions, ISSG, salvinia molesta


  • Manda, S., Saborido, A., Dubois, M.

    Control of Conyza spp. with Glyphosate – A Review of the Situation in Europe

    (Journal name unavailable from Mendeley API. To be updated soon...)

    In Europe, glyphosate resistant populations have developed in some weed species in perennial crops, includ- ing three species of the genus Conyza documented by the International Survey of Herbicide Resistant Weeds. Conyza spp. biology is reviewed in this paper and related to population dynamics and the development of resist- ant populations. Suboptimal growth stage at application, improper agricultural practices such as overreliance on glyphosate and long-term use of sublethal doses are identified as the most important factors of resistance development. Current control methods in perennial crops including mixtures of glyphosate with other active ingredients are discussed and effective weed management strategies are described to manage the development and spread of glyphosate resistant Conyza spp. in Europe.

    Keywords: Conyza bonariensis (L.) Cronquist, Conyza canadensis (L.) Cronquist, Conyza sumatrensis (Retz.) E. H. Walker, resistance, weed management


  • Mouillot, D., Bellwood, D., Baraloto, C., Chave, J., Galzin, R., Harmelin-Vivien, M., Kulbicki, M., Lavergne, S., Lavorel, S., Mouquet, N., Paine, C., Renaud, J., Thuiller, W.

    Rare Species Support Vulnerable Functions in High- Diversity Ecosystems

    PLoS biology 11(5).

    Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across spatial scales. As such, they are likely to insure against future uncertainty arising from climate change and the ever-increasing anthropogenic pressures on ecosystems. Our results call for a more detailed understanding of the role of rarity and functional vulnerability in ecosystem functioning.

    Keywords: Conyza bonariensis (L.) Cronquist, Conyza canadensis (L.) Cronquist, Conyza sumatrensis (Retz.) E. H. Walker, resistance, weed management


  • Poncet, V., Munoz, F., Munzinger, J., Pillon, Y., Gomez, C., Couderc, M., Tranchant-Dubreuil, C., Hamon, S., de Kochko, A.

    Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

    Molecular ecology.

    Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant Angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range-wide genetic diversity based on nuclear microsatellite data, and detected four well-differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modeled the ecological niche of Amborella based on current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of suitable habitat at the last glacial maximum (LGM, ca. 21 000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra- and inter-specific diversity in New Caledonian plants, and revealed the possibility of an as-yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographic history of an emblematic taxon. This article is protected by copyright. All rights reserved.

    Keywords: amborella trichopoda, genetic variation, habitat suitability, last, niche modelling, refugia


  • Porretta, D., Mastrantonio, V., Mona, S., Epis, S., Montagna, M., Sassera, D., Bandi, C., Urbanelli, S.

    The integration of multiple independent data reveals an unusual response to Pleistocene climatic changes in the hard tick Ixodes ricinus.

    Molecular ecology 22(6) 1666-82.

    In the last few years, improved analytical tools and the integration of genetic data with multiple sources of information have shown that temperate species exhibited more complex responses to ice ages than previously thought. In this study, we investigated how Pleistocene climatic changes affected the current distribution and genetic diversity of European populations of the tick Ixodes ricinus, an ectoparasite with high ecological plasticity. We first used mitochondrial and nuclear genetic markers to investigate the phylogeographic structure of the species and its Pleistocene history using coalescent-based methods; then we used species distribution modelling to infer the climatic niche of the species at last glacial maximum; finally, we reviewed the literature on the I. ricinus hosts to identify the locations of their glacial refugia. Our results support the scenario that during the last glacial phase, I. ricinus never experienced a prolonged allopatric divergence in separate glacial refugia, but persisted with interconnected populations across Southern and Central Europe. The generalist behaviour in host choice of I. ricinus would have played a major role in maintaining connections between its populations. Although most of the hosts persisted in separate refugia, from the point of view of I. ricinus, they represented a continuity of 'bridges' among populations. Our study highlights the importance of species-specific ecology in affecting responses to Pleistocene glacial-interglacial cycles. Together with other cases in Europe and elsewhere, it contributes to setting new hypotheses on how species with wide ecological plasticity coped with Pleistocene climatic changes.

    Keywords: ice ages, parasites, phylogeography, species distribution modelling, western