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

  • Auber A, Travers-Trolet M, Villanueva M, Ernande B (2015)

    Regime Shift in an Exploited Fish Community Related to Natural Climate Oscillations.

    PloS one 10(7) e0129883.

    Identifying the various drivers of marine ecosystem regime shifts and disentangling their respective influence are critical tasks for understanding biodiversity dynamics and properly managing exploited living resources such as marine fish communities. Unfortunately, the mechanisms and forcing factors underlying regime shifts in marine fish communities are still largely unknown although climate forcing and anthropogenic pressures such as fishing have been suggested as key determinants. Based on a 24-year-long time-series of scientific surveys monitoring 55 fish and cephalopods species, we report here a rapid and persistent structural change in the exploited fish community of the eastern English Channel from strong to moderate dominance of small-bodied forage fish species with low temperature preferendum that occurred in the mid-1990s. This shift was related to a concomitant warming of the North Atlantic Ocean as attested by a switch of the Atlantic Multidecadal Oscillation from a cold to a warm phase. Interestingly, observed changes in the fish community structure were opposite to those classically induced by exploitation as larger fish species of higher trophic level increased in abundance. Despite not playing a direct role in the regime shift, fishing still appeared as a forcing factor affecting community structure. Moreover, although related to climate, the regime shift may have been facilitated by strong historic exploitation that certainly primed the system by favoring the large dominance of small-bodied fish species that are particularly sensitive to climatic variations. These results emphasize that particular attention should be paid to multidecadal natural climate variability and its interactions with both fishing and climate warming when aiming at sustainable exploitation and ecosystem conservation.

  • Comte L, Hugueny B, Grenouillet G (2015)

    Climate interacts with anthropogenic drivers to determine extirpation dynamics


    Theoretical studies suggest that the dynamics of a species’ range during a period of climate change depends upon the existence and interplay of various ecological and evolutionary processes. Here we tested how anthropogenic pressures contribute to climate-mediated extirpation patterns of 32 freshwater fish species over the last 20 years. We contrasted two extreme cases to determine whether extirpations were governed by patterns of climate exposure, assuming full adaptation of species to local climate, or instead by the interplay between climate exposure and the distance from the centroid of species’ climatic niches, assuming a fixed niche, and asked whether anthropogenic disturbances interact with these climatic drivers. We found strong support for the fixed niche hypothesis, but showed that species-specific local adaptation to climate may also be important in determining extirpation dynamics. We also demonstrated that anthropogenic disturbance acted in concert with climate, ultimately determining population changes. Our results add novel evidence that unravelling the direct links between range dynamics and climate requires a multifaceted treatment, and that accounting for the cumulative effects of anthropogenic pressures deserves special attention in the context of climate change.

    Keywords: climate exposure, climatic niche, life-history traits, local adaptation, species’ range

  • 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

  • Estrada-Peña A, de la Fuente J, Ostfeld R, Cabezas-Cruz A (2015)

    Interactions between tick and transmitted pathogens evolved to minimise competition through nested and coherent networks.

    Scientific reports 5 10361.

    Natural foci of ticks, pathogens, and vertebrate reservoirs display complex relationships that are key to the circulation of pathogens and infection dynamics through the landscape. However, knowledge of the interaction networks involved in transmission of tick-borne pathogens are limited because empirical studies are commonly incomplete or performed at small spatial scales. Here, we applied the methodology of ecological networks to quantify >14,000 interactions among ticks, vertebrates, and pathogens in the western Palearctic. These natural networks are highly structured, modular, coherent, and nested to some degree. We found that the large number of vertebrates in the network contributes to its robustness and persistence. Its structure reduces interspecific competition and allows ample but modular circulation of transmitted pathogens among vertebrates. Accounting for domesticated hosts collapses the network's modular structure, linking groups of hosts that were previously unconnected and increasing the circulation of pathogens. This framework indicates that ticks and vertebrates interact along the shared environmental gradient, while pathogens are linked to groups of phylogenetically close reservoirs.

    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

  • Glynn F, Houghton JDR, Bastian T, Doyle TK, Fuentes V L (2015)

    High-resolution genetic analysis reveals extensive gene flow within the jellyfish Pelagia noctiluca (Scyphozoa) in the North Atlantic and Mediterranean Sea

    Biological Journal of the Linnean Society.

    Despite the importance of gela tinous zooplankton as component s of marine ecosystems, both ecologically and socio-economically, relatively little is known about population persistence or connectivity in jellyfish. In the present study, we employed a combination of nuclear microsatellite markers and sequence data from the mitochondrial cytoch rome oxidase I (COI) gene to determine levels and patterns of population genetic st ructuring in the holoplanktonic jellyfish Pelagia noctiluca across the northeast Atlantic Ocea n and Mediterranean Sea. Our results indicate a high de gree of connectivity in P. noctiluca , with little evidence of geographical structuring of gene tic variation. A small but si gnificant differentiation of Atlantic Ocean and Mediterranean stocks was de tected based on the micr osatellite data, but no evidence of differentiation was observed with the mtDNA, probably due to the higher power of the microsatellites to detect low levels of genetic structuring. Two clearly distinct groups of genotypes were observed within the mtDNA COI, which probably diverged in the early Pleistocene, but with no evidence of geographical structuri ng. Palaeodistribution modelling of P. noctiluca at the Last Glacial Maximum (LGM; ca . 21 KYA) indicated large areas of suitable habitat south of the species’ current-day distribution, with little reduction in area. The congruent evidence for minimal genetic differentiation from the nuclear microsatellites and the mtDNA, coupled with th e results of the palaeodistribution modelling, supports the idea of long-term population stab ility and connectivity, thus providing key insights into the population dynamics and de mography of this important species.

    Keywords: Gelatinous zooplankton, jellyfish, microsatellites

  • Godefroid M, Cruaud A, Rossi J, Rasplus J (2015)

    Assessing the Risk of Invasion by Tephritid Fruit Flies: Intraspecific Divergence Matters.

    PloS one 10(8) e0135209.

    Widely distributed species often show strong phylogeographic structure, with lineages potentially adapted to different biotic and abiotic conditions. The success of an invasion process may thus depend on the intraspecific identity of the introduced propagules. However, pest risk analyses are usually performed without accounting for intraspecific diversity. In this study, we developed bioclimatic models using MaxEnt and boosted regression trees approaches, to predict the potential distribution in Europe of six economically important Tephritid pests (Ceratitis fasciventris (Bezzi), Bactrocera oleae (Rossi), Anastrepha obliqua (Macquart), Anastrepha fraterculus (Wiedemann), Rhagoletis pomonella (Walsh) and Bactrocera cucurbitae (Coquillet)). We considered intraspecific diversity in our risk analyses by independently modeling the distributions of conspecific lineages. The six species displayed different potential distributions in Europe. A strong signal of intraspecific climate envelope divergence was observed in most species. In some cases, conspecific lineages differed strongly in potential distributions suggesting that taxonomic resolution should be accounted for in pest risk analyses. No models (lineage- and species-based approaches) predicted high climatic suitability in the entire invaded range of B. oleae-the only species whose intraspecific identity of invading populations has been elucidated-in California. Host availability appears to play the most important role in shaping the geographic range of this specialist pest. However, climatic suitability values predicted by species-based models are correlated with population densities of B. oleae globally reported in California. Our study highlights how classical taxonomic boundaries may lead to under- or overestimation of the potential pest distributions and encourages accounting for intraspecific diversity when assessing the risk of biological invasion.

    Keywords: Gelatinous zooplankton, jellyfish, microsatellites

  • Kriticos D, Brunel S, Ota N, Fried G, Oude Lansink A, Panetta F et al. (2015)

    Downscaling Pest Risk Analyses: Identifying Current and Future Potentially Suitable Habitats for Parthenium hysterophorus with Particular Reference to Europe and North Africa

    PLOS ONE 10(9) e0132807.

    Pest Risk Assessments (PRAs) routinely employ climatic niche models to identify endangered areas. Typically, these models consider only climatic factors, ignoring the ‘Swiss Cheese’ nature of species ranges due to the interplay of climatic and habitat factors. As part of a PRA conducted for the European and Mediterranean Plant Protection Organization, we developed a climatic niche model for Parthenium hysterophorus, explicitly including the effects of irrigation where it was known to be practiced. We then downscaled the climatic risk model using two different methods to identify the suitable habitat types: expert opinion (following the EPPO PRA guidelines) and inferred from the global spatial distribution. The PRA revealed a substantial risk to the EPPO region and Central and Western Africa, highlighting the desirability of avoiding an invasion by P. hysterophorus. We also consider the effects of climate change on the modelled risks. The climate change scenario indicated the risk of substantial further spread of P. hysterophorus in temperate northern hemisphere regions (North America, Europe and the northern Middle East), and also high elevation equatorial regions (Western Brazil, Central Africa, and South East Asia) if minimum temperatures increase substantially. Downscaling the climate model using habitat factors resulted in substantial (approximately 22–53%) reductions in the areas estimated to be endangered. Applying expert assessments as to suitable habitat classes resulted in the greatest reduction in the estimated endangered area, whereas inferring suitable habitats factors from distribution data identified more land use classes and a larger endangered area. Despite some scaling issues with using a globally conformal Land Use Systems dataset, the inferential downscaling method shows promise as a routine addition to the PRA toolkit, as either a direct model component, or simply as a means of better informing an expert assessment of the suitable habitat types.

    Keywords: Gelatinous zooplankton, jellyfish, microsatellites

  • Lin Y, Deng D, Lin W, Lemmens R, Crossman N, Henle K et al. (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

  • Ouvrard D, Burckhardt D, Cocquempot C (2015)

    An annotated checklist of the jumping plant-lice (Insecta: Hemiptera: Psylloidea) from the Mercantour National Park, with seven new records for France and one new Synonymy

    Zoosystema 37(1) 251-271.

    ABSTRACT A total of 68 psyllid species are listed from the Mercantour National Park in Southeast France, where a targeted collecting campaign was conducted between 2009 and 2012, as part of the project “ATBI+M” Mercantour. The insects were collected using Malaise traps, flight intercept traps and sweep nets to sample in the vegetation. Additional information on distribution, biology and host-plants is provided for each species. Seven species are recorded for the first time from France: Craspedolepta artemisiae (Foerster, 1848), Craspedolepta nebulosa (Zetterstedt, 1828), Cacopsylla propinqua (Schaefer, 1949), Cyamophila prohaskai (Priesner, 1927), Eryngiofaga cf. refuga (Loginova, 1966), Bactericera parastriola Conci, Ossiannilsson & Tamanini, 1988 and Trioza flixiana Burckhardt & Lauterer, 2002. Trioza (Trioza) rapisardai Conci & Tamanini, 1984 is a new subjective synonym of Trioza brachyceraea Hodkinson & White, 1979, which was previously known only from the male holotype. The abundance, distribution an...

    Keywords: Alpes, Alps, France, Psylles, Psyllids, Sternorrhyncha, faunistics, faunistique, host plants, new records, plantes-hŝtes, signalisations nouvelles