Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from France.
For all researches, please visit our "Peer-reviewed publications" page.

List of publications

  • Moreau C, Saucède T, Jossart Q, Agüera A, Brayard A, Danis B (2017)

    Reproductive strategy as a piece of the biogeographic puzzle: a case study using Antarctic sea stars (Echinodermata, Asteroidea)

    Journal of Biogeography.

    Aim To describe and analyse asteroid biogeographic patterns in the Southern Ocean (SO) and test whether reproductive strategy (brooder versus broadcaster) can explain distribution patterns at the scale of the entire class. We hypothesize that brooding and broadcasting species display different biogeographic patterns. Location Southern Ocean, south of 45 °S. Methods Over 14,000 asteroid occurrences are analysed using bootstrapped spanning network (BSN), non-metrical multidimensional scaling (nMDS) and clustering to uncover the spatial structure of faunal similarities among 25 bioregions. Results Main biogeographic patterns are congruent with previous works based on other taxa and highlight the isolation of New Zealand, the high richness in the Scotia Arc area particularly of brooding species, an East/West Antarctic differentiation, and the faunal affinities between South America and sub-Antarctic Islands. Asteroids show lower endemism levels than previously reported with 29% of species occurring in Antarctica only. In particular, asteroids from Tierra del Fuego showed affinities with those of West Antarctica at the species level, suggesting a recent mixing of assemblages. Biogeographic patterns are highly linked to reproductive strategy. Patterns also differ according to the taxonomic level, revealing the underlying role of historical factors. Main conclusions Patterns of sea star biogeography are consistent with results obtained for other marine groups and are strongly linked to reproductive strategy.


  • Odonne G, Houël E, Bourdy G, Stien D (2017)

    Treating leishmaniasis in Amazonia: A review of ethnomedicinal concepts and pharmaco-chemical analysis of traditional treatments to inspire modern phytotherapies

    Journal of Ethnopharmacology 199 211-230.

    Ethnopharmacological relevance Cutaneous and mucocutaneous leishmaniasis are neglected tropical diseases that occur in all intertropical regions of the world. Amazonian populations have developed an abundant knowledge of the disease and its remedies. Therefore, we undertook to review traditional antileishmanial plants in Amazonia and have developed new tools to analyze this somewhat dispersed information. Material and methods A literature review of traditional remedies for cutaneous/mucocutaneous leishmaniasis in the Amazon was conducted and the data obtained was used to calculate distribution indexes designed to highlight the most relevant uses in Amazonia. The cultural distribution index represents the distribution rate of a given taxon among different cultural groups and was calculated as the ratio of the number of groups using the taxon to the total number of groups cited. The geographical distribution index allowed us to quantify spatial distribution of a taxon’s uses in Amazonia and was calculated geometrically by measuring the average distance between the points where uses have been reported and the barycenter of those points. The general distribution index was defined as an arithmetic combination of the previous two and provides information on both cultural and spatial criteria. Results 475 use reports, concerning 291 botanical species belonging to 83 families have been gathered depicted from 29 sources. Uses concern 34 cultural groups. While the use of some taxa appears to be Pan-Amazonian, some others are clearly restricted to small geographical regions. Particular attention has been paid to the recipes and beliefs surrounding treatments. Topical application of the remedies dominated the other means of administration and this deserves particular attention as the main treatments against Neotropical leishmaniasis are painful systemic injections. The data set was analyzed using the previously defined distribution indexes and the most relevant taxa were further discussed from a phytochemical and pharmacological point of view. Conclusions The Amazonian biodiversity and cultural heritage host a fantastic amount of data whose systematic investigation should allow a better large-scale understanding of the dynamics of traditional therapies and the consequent discovery of therapeutic solutions for neglected diseases. Distribution indices are indeed powerful tools for emphasizing the most relevant treatments against a given disease and should be very useful in the meta-analysis of other regional pharmacopeia. This focus on renowned remedies that have not yet benefitted from extended laboratory studies, could stimulate future research on new treatments of natural origin for leishmaniasis.

    Keywords: Amazonia, Distribution indexes, Ethnomedecine, Interculturality, Leishmaniasis, Medicinal plants, Traditional medicine


  • Odonne G, Houël E, Bourdy G, Stien D (2017)

    Healing leishmaniasis in Amazonia: review of ethnomedicinal concepts and pharmaco-chemical analysis of traditional treatments to inspire modern phytotherapies

    Journal of Ethnopharmacology.

    ETHNOPHARMACOLOGICAL RELEVANCE Cutaneous/mucocutaneous leishmaniasis are neglected tropical diseases occurring in all intertropical regions of the world. Amazonian populations developed an abundant knowledge related to the disease and its remedies. Therefore, we undertook to review traditional antileishmanial plants in Amazonia, and developed new tools to analyze this somewhat dispersed information. MATERIAL AND METHODS A review of the literature concerning traditional remedies against cutaneous/mucocutaneous leishmaniasis in the Amazon was conducted, and the obtained data used for the calculation of distribution indexes designed to highlight the most relevant uses in Amazonia. The cultural distribution index represents the distribution rate of a given taxon among different cultural groups and was calculated as the ratio of the number of groups using the taxon to the total number of groups cited. The geographical distribution index allowed us to quantify spatial distribution of a taxon's uses in Amazonia and was calculated geometrically by measuring the average distance between the points where uses have been reported and the barycenter of those points. The general distribution index was defined as an arithmetic combination of the previous two, and gives information on both cultural and spatial criteria. RESULTS 475 use reports, concerning 291 botanical species belonging to 83 families, have been depicted from 29 sources. The uses concern 34 cultural groups. While the use of some taxa appears to be Pan-Amazonian, some others are clearly restricted to small geographical regions. Particular attention has been paid to the recipes and beliefs surroundings the treatments. Topical application of the remedies dominated the other means of administration, which deserves particular attention as the main treatments against Neotropical leishmaniasis are painful systemic injections. The data set was analyzed using the previously defined distribution indexes, and the most relevant taxa were further discussed from a phytochemical and pharmacological point of view. CONCLUSIONS The Amazonian biodiversity and cultural heritage host a fantastic amount of data whose systematic investigation should allow a better large-scale understanding of traditional therapies’ dynamic and the consequent discovery of therapeutic solutions for neglected diseases. Distribution indexes are indeed powerful tools for emphasizing the most relevant treatments against a given disease and should be very useful in the meta-analysis of other regional pharmacopeia. Eventually, this focus on renowned remedies which do however not yet benefit from extended laboratory studies could stimulate future research for new treatments from natural origin against leishmaniasis.

    Keywords: Ethnomedecine, distribution indices, interculturality, medicinal plants


  • Rocchini D, Garzon-Lopez C, Marcantonio M, Amici V, Bacaro G, Bastin L et al. (2017)

    Anticipating species distributions: Handling sampling effort bias under a Bayesian framework

    Science of The Total Environment.

    Keywords: Anticipation, Bayesian theorem, Species distribution modeling, Uncertainty, sampling effort bias


  • Antonelli A, Hettling H, Condamine F, Vos K, Nilsson R, Sanderson M et al. (2016)

    Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

    Systematic Biology syw066.

    Rapidly growing biological data –including molecular sequences and fossils– hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyse these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive datasets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.

    Keywords: Bayesian phylogenetics, GenBank, data mining, divide-and-conquer methods, multilocus multispecies coalescent, next-generation sequencing, palms, primates, tree calibration


  • Araújo R, Assis J, Aguillar R, Airoldi L, Bárbara I, Bartsch I et al. (2016)

    Status, trends and drivers of kelp forests in Europe: an expert assessment

    Biodiversity and Conservation 25(7) 1319-1348.

    A comprehensive expert consultation was conducted in order to assess the status, trends and the most important drivers of change in the abundance and geographical distribution of kelp forests in European waters. This consultation included an on-line questionnaire, results from a workshop and data provided by a selected group of experts working on kelp forest mapping and eco-evolutionary research. Differences in status and trends according to geographical areas, species identity and small-scale variations within the same habitat where shown by assembling and mapping kelp distribution and trend data. Significant data gaps for some geographical regions, like the Mediterranean and the southern Iberian Peninsula, were also identified. The data used for this study confirmed a general trend with decreasing abundance of some native kelp species at their southern distributional range limits and increasing abundance in other parts of their distribution (Saccharina latissima and Saccorhiza polyschides). The expansion of the introduced species Undaria pinnatifida was also registered. Drivers of observed changes in kelp forests distribution and abundance were assessed using experts’ opinions. Multiple possible drivers were identified, including global warming, sea urchin grazing, harvesting, pollution and fishing pressure, and their impact varied between geographical areas. Overall, the results highlight major threats for these ecosystems but also opportunities for conservation. Major requirements to ensure adequate protection of coastal kelp ecosystems along European coastlines are discussed, based on the local to regional gaps detected in the study.

    Keyword: Kelp forests Expert consultation Status and tempor


  • Bellard C, Genovesi P, Jeschke J (2016)

    Global patterns in threats to vertebrates by biological invasions

    Proceedings of the Royal Society B: Biological Sciences 283(1823) 20152454.

    Biological invasions as drivers of biodiversity loss have recently been challenged. Fundamentally, we must know where species that are threatened by invasive alien species (IAS) live, and the degree to which they are threatened. We report the first study linking 1372 vertebrates threatened by more than 200 IAS from the completely revised Global Invasive Species Database. New maps of the vulnerability of threatened vertebrates to IAS permit assessments of whether IAS have a major influence on biodiversity, and if so, which taxonomic groups are threatened and where they are threatened. We found that centres of IAS-threatened vertebrates are concentrated in the Americas, India, Indonesia, Australia and New Zealand. The areas in which IAS-threatened species are located do not fully match the current hotspots of invasions, or the current hotspots of threatened species. The relative importance of biological invasions as drivers of biodiversity loss clearly varies across regions and taxa, and changes over time, with mammals from India, Indonesia, Australia and Europe are increasingly being threatened by IAS. The chytrid fungus primarily threatens amphibians, whereas invasive mammals primarily threaten other vertebrates. The differences in IAS threats between regions and taxa can help efficiently target IAS, which is essential for achieving the Strategic Plan 2020 of the Convention on Biological Diversity.

    Keyword: Kelp forests Expert consultation Status and tempor


  • Bellard C, Leroy B, Thuiller W, Rysman J, Courchamp F (2016)

    Major drivers of invasion risks throughout the world

    Ecosphere 7(3).

    In this paper, we investigate how climate, land use, habitat characteristics, and socioeconomic activities contribute to predict the current potential distributions of the “100 among the world's worst invasive alien species”. We calculated the predictive power of each of the 41 variables for the 95 species including a large number of plants, vertebrates and invertebrates. We then calibrated the species distribution models with a set of appropriate variables for each invasive alien species to predict the potential distribution of these species and identify the major regions of origin of the invasive alien species. We found that climate variables were primarily predictors of the distribution of the global invaders studied. In addition, the habitat characteristics were also important predictors following by the socioeconomic variables such as the nearest distance to airports, seaports and human population density. We show that the potential areas at the highest risk of invasions from these species are located in Western Europe, Eastern United States, Central America, the eastern coast of Australia, and some Indonesian islands. We argue that these potential hotspots of invasions should be monitored in priority to prevent new invasions from these species. This study provides evidence of the importance of considering both habitat characteristics, socioeconomic and climate change factors for the current and future predictions of biological invasions.

    Keywords: invasive species, socioeconomic, spatial risk


  • Bocksberger G, Schnitzler J, Chatelain C, Daget P, Janssen T, Schmidt M et al. (2016)

    Climate and the distribution of grasses in West Africa

    Journal of Vegetation Science.

    Questions Which environmental variables influence grass diversity in West Africa? What are the effects of climate and grass functional traits on the spatial patterns (richness and abundance) of the grass clades Andropogoneae, Paniceae and Chloridoideae? Location West Africa, demarcated by the Atlantic Ocean in the west and south (20° W and 4° N), the Sahara desert in the north (25° N) and the border between Niger and Chad in the east (20° E). Methods Based on 38 912 georeferenced occurrence records, we modelled the distribution of 302 grass species (51% of West African grass diversity). We integrated species richness, abundance and functional traits (life cycle, photosynthetic type and height) to determine the contribution of the most speciose grass clades (Andropogoneae, Paniceae and Chloridoideae) to overall grass diversity in West Africa. Results Precipitation is the variable most often influencing the species distribution models of grasses in West Africa. Richness and relative abundance of the tribe Andropogoneae show a centre of diversity in Sudanian savanna regions. The height of Andropogoneae species, generally >150 cm, is driving this ecological dominance. Species richness of the tribe Paniceae is more dispersed and shows two main centres of abundance: The southern regions with higher mean annual precipitation and tree density are dominated by C3 Paniceae species. The Sahelian regions in the north are dominated by short Paniceae species with the C4 NAD-ME photosynthetic subtype, as well as Chloridoideae possessing the same functional attributes. Conclusions Our study provides insight into the environmental correlates of grass species richness in West Africa and contributes to the much-needed research on tropical rangelands. Moreover, the integration of evolutionary history significantly improves our understanding of large-scale biodiversity patterns.

    Keywords: Andropogoneae, Chloridoideae, Maxent, Paniceae, Poaceae, Savanna, Species distribution modelling, West Africa, species richness


  • Boucher F, Lavergne S, Basile M, Choler P, Aubert S (2016)

    Evolution and biogeography of the cushion life form in angiosperms

    Perspectives in Plant Ecology, Evolution and Systematics 20 22-31.

    Cushion-forming species occur in all cold and dry environments worldwide, where they play important engineering roles. Understanding the origins of cushion plants may thus provide insights into the evolutionary assembly of biomes under extreme climatic conditions. Here we investigate the evolutionary and biogeographic history of cushions in Angiosperms based on a global checklist of all cushion plants, along with phylogenetic, climatic, and biogeographic information. Our aim is to measure the frequency of this evolutionary convergence and to identify its historic, environmental, and biogeographic drivers. We show that cushions appeared at least 115 times in Angiosperms and that they mainly belong to families that occupy the coldest and driest environments on Earth. We found that cushions have intensively diversified in the Himalayas, the Andes, or New Zealand, while other regions like Patagonia have probably been hubs enabling cushion species to migrate between different alpine regions. We conclude that the cushion life form is a remarkable example of convergent key innovation, which has favored the colonization of cold and dry habitats.

    Keywords: Alpine, Angiosperms, Arctic, Biogeography, Cushion plants, Evolutionary convergence