Uses of GBIF in scientific research

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

List of publications

  • De Pooter D, Appeltans W, Bailly N, Bristol S, Deneudt K, Eliezer M et al. (2017)

    Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

    Biodiversity Data Journal 5 e10989.

    The Ocean Biogeographic Information System (OBIS) is the world’s most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.

    Keywords: Darwin Core Archive, data standardisation, ecosystem data, environmental data, oceanographic data, sample event, species occurrence, telemetry data


  • Senczuk G, Colangelo P, De Simone E, Aloise G, Castiglia R (2017)

    A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus

    BMC Evolutionary Biology 17(1) 6.

    The current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n = 277 from 115 localities) and nuclear mc1r and β-fibint7genes (n = 262 and n = 91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM). We identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula. Our population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.

    Keywords: Evolutionary history, Glacial expansion, Italian wall lizard, Niche modelling, Phylogeography, Podarcis siculus


  • 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


  • Branquart E, Brundu G, Buholzer S, Chapman D, Ehret P, Fried G et al. (2016)

    A prioritization process for invasive alien plant species incorporating the requirements of EU Regulation no. 1143/2014

    EPPO Bulletin 46(3) 603-617.

    When faced with a large species pool of invasive or potentially invasive alien plants, prioritization is an essential prerequisite for focusing limited resources on species which inflict high impacts, have a high rate of spread and can be cost-effectively managed. The prioritization process as detailed within this paper is the first tool to assess species for priority for risk assessment (RA) in the European Union (EU) specifically designed to incorporate the requirements of EU Regulation no. 1143/2014. The prioritization process can be used for any plant species alien to the EU, whether currently present within the territory or absent. The purpose of the prioritization is to act as a preliminarily evaluation to determine which species have the highest priority for RA at the EU level and may eventually be proposed for inclusion in the list of invasive alien species of EU concern. The preliminary risk assessment stage (Stage 1), prioritizes species into one of four lists (EU List of Invasive Alien Plants, EU Observation List of Invasive Alien Plants, EU List of Minor Concern and the Residual List) based on their potential for spread coupled with impacts. The impacts on native species and ecosystem functions and related ecosystem services are emphasized in line with Article 4.3(c) of the Regulation. Only those species included in the EU List of Invasive Alien Plants proceed to Stage 2 where potential for further spread and establishment coupled with evaluating preventative and management actions is evaluated. The output of Stage 2 is to prioritize those species which have the highest priority for a RA at the EU level or should be considered under national measures which may involve a trade ban, cessation of cultivation, monitoring, control, containment or eradication. When considering alien plant species for the whole of the EPPO region, or for species under the Plant Health Regulation, the original EPPO prioritization process for invasive alien plants remains the optimum tool. Un processus de priorisation pour les plantes exotiques envahissantes, intégrant les exigences du Règlement UE No 1143/2014 Face à un grand nombre d'espèces de plantes exotiques envahissantes, ou potentiellement envahissantes, prioriser est un pré-requis afin de concentrer des ressources limitées sur les espèces à forts impacts, ayant un potentiel important de dissémination, et pouvant être gérées de façon efficace. Le processus de priorisation, tel que décrit dans le présent article, est le premier outil permettant d’évaluer le besoin de réaliser, en priorité, pour une espèce, une évaluation du risque pour l'Union Européenne (UE), et ce en cohérence avec les exigences du Règlement UE No 1143/2014. Ce processus de priorisation peut être appliqué à toute plante exotique au territoire de l’UE, qu'elle soit présente ou non sur ce territoire. L'objectif est de déterminer, lors d'une étape préliminaire, les espèces prioritaires pour lesquelles une évaluation du risque doit être conduite au niveau de l’UE, et qui pourraient éventuellement être proposées à l'inscription au sein de la liste des espèces exotiques envahissantes préoccupantes pour l’UE. L’évaluation du risque préliminaire (étape 1), classe les espèces au sein de l'une des quatre listes (liste des plantes exotiques envahissantes pour l’UE, liste d'observation des plantes exotiques envahissantes pour l’UE, liste d'importance réduite pour l’UE et liste résiduelle) sur la base de leur capacité de dissémination et de leurs impacts. Pour les impacts, l'accent est mis sur les espèces autochtones, sur les fonctions écosystémiques, ainsi que les services écosystémiques, en cohérence avec l'article 4.3(c) du Règlement UE. Seulement les espèces classées dans la liste des plantes exotiques envahissantes pour l’UE passent à la seconde étape. Au cours de cette étape sont analysés les risques de dissémination et d’établissement, ainsi que les mesures prophylactiques ou mesures de gestion possibles. L’étape 2 classe les espèces les plus prioritaires pour la réalisation d'une évaluation du risque au niveau de l’UE, ou qui devraient faire l'objet de mesures nationales telles que l'interdiction du commerce, l'arrêt de la culture, la surveillance, le contrôle, l'enrayement ou l’éradication. Le processus de priorisation OEPP d'origine reste néanmoins l'outil optimal lorsque le processus est à réaliser sur l'ensemble de la région OEPP, ou pour des espèces réglementées dans le cadre phytosanitaire.

    Keyword: Kelp forests Expert consultation Status and tempor


  • Bubadué J, Cáceres N, Carvalho R, Sponchiado J, Passaro F, Saggese F et al. (2016)

    Character displacement under influence of Bergmann’s rule in Cerdocyon thous (Mammalia: Canidae)

    Hystrix, the Italian Journal of Mammalogy 27(2).

    In South America, the crab-eating fox Cerdocyon thous occurs in sympatry to the ecologically similar, and phylogenetically close Lycalopex vetulus to the North, and Lycalopex gymnocercus to the South of its range. We studied character displacement in Cerdocyon under the effect of Bergmann's rule and the presence (or absence either) of Lycalopex within the crab-eating fox range. We performed skull shape analysis on 191 C. thous specimens and divided them in three distinct groups, depending on whether Cerdocyon occurs in sympatry or in allopatry to Lycalopex species. We tested for differences in size and shape between Cerdocyon groups and regressed both skull size and sexual size dimorphism against latitude and temperature, while controlling for spatial autocorrelation in the phenotypes. Southern Cerdocyon specimens present enlarged temporalis muscle and slender carnassial, both suggestive of a shift towards increased carnivory. Such a niche shift is interpreted as a mean to reduce competition to the larger Lycalopex species, which is still smaller than Cerdocyon . Consistently with the above, the degree of sexual shape and size dimorphism in Cerdocyon increases southward. We found a complex but coherent pattern of size and shape differentiation in Cerdocyon groups, which is consistent with the effects of both competition and Bergmann's rule. Cerdocyon reduces competition to Lycalopex by growing larger in the North. To the South, Cerdocyon is still larger, in keeping with Bergmann's rule, but strongly differs in skull shape from both its Lycalopex competitor and from any other Cerdocyon . Since the Southern Lycalopex species is much more similar in size to Cerdocyon than its Northern congeneric, this suggests that shape differences serve the goal of reducing competition between Cerdocyon and Lycalopex to the South, as size differences do to the North. The absence of the hypercarnivorous canid Speothos venaticus from the southern range of Cerdocyon may have allowed such a pattern to take place.

    Keywords: Bergmann’s rule, Canidae, South America, character displacement, crab-eating fox, geometric morphometrics, sexual size dimorphism, shape disparity


  • Calderón L, Campagna L, Wilke T, Lormee H, Eraud C, Dunn J et al. (2016)

    Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove

    BMC Evolutionary Biology 16(1) 237.

    Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove, Streptopelia turtur, is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations. Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size (Ne) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the Ne that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the Ne are coincident with recent changes in the availability of suitable habitat. We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.

    Keywords: Climate change, Conservation, Demography, Genomics, Migratory birds, Paleoclimatic, Population genetic structure, niche modelling


  • Coro G, Magliozzi C, Vanden Berghe E, Bailly N, Ellenbroek A, Pagano P (2016)

    Estimating absence locations of marine species from data of scientific surveys in OBIS

    Ecological Modelling 323 61-76.

    Estimating absence locations of a species is important in conservation biology and conservation planning. For instance, using reliable absence as much as presence information, species distribution models can enhance their performance and produce more accurate predictions of the distribution of a species. Unfortunately, estimating reliable absence locations is difficult and often requires a deep knowledge of the species’ distribution and of its abiotic and biotic environmental preferences and tolerance. In this paper, we propose a methodology to reconstruct reliable absence information from presence-only information, and the conditions that those presence-only data have to meet to make this possible. Large species occurrence data collections (otherwise called occurrence datasets) contain high quality and expert-reviewed species observation records from scientific surveys. These surveys can be used to retrieve species presence locations, but they also record places where the species in their target list were not observed. Although these absences could be simply due to sampling variation, it is possible to intersect many of these reports to estimate true absence locations, i.e. those due to habitat unsuitability or geographical hindrances. In this paper, we present a method to generate reliable absence locations of this type for marine species, using scientific surveys reports contained in the Ocean Biogeographic Information System (OBIS), an authoritative species occurrence dataset. Our method spatially aggregates information from surveys focussing on the same target species. It detects absence locations for a given species as those locations in which repeated surveys (that included the species of interest in their target list) reported information only on other species. We qualitatively demonstrate the reliability of our method using distribution records of the Atlantic cod as a case study. Additionally, we quantitatively estimate its performance using another authoritative large species occurrence dataset, the Global Biodiversity Information Facility (GBIF). We also demonstrate that our approach has higher accuracy and presents complementary behaviour with respect to another method using environmental envelopes. Our process can support species distribution models (as well as other types of models, e.g. climate change models) by providing reliable data to presence/absence approaches. It can manage regional as well as global scale scenarios and runs within a collaborative e-Infrastructure (D4Science) that publishes it as-a-Service, allowing biologists to reproduce, repeat and share experimental results.

    Keywords: Absence locations, Ecological niche modelling, Marine biodiversity, Occurrence data, Scientific surveys, Species distribution maps


  • Droege G, Barker K, Seberg O, Coddington J, Benson E, Berendsohn W et al. (2016)

    The Global Genome Biodiversity Network (GGBN) Data Standard specification.

    Database : the journal of biological databases and curation 2016 baw125.

    Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard.

    Keywords: Absence locations, Ecological niche modelling, Marine biodiversity, Occurrence data, Scientific surveys, Species distribution maps


  • Febbraro M, Martinoli A, Russo D, Preatoni D, Bertolino S (2016)

    Modelling the effects of climate change on the risk of invasion by alien squirrels

    Hystrix, the Italian Journal of Mammalogy 27(1).

    Assessing invasion risk by alien organisms implies evaluating the likelihood of successful establishment and spread once they are accidentally or deliberately introduced. The importance of implementing accurate risk–assessment procedures is further stressed by the evidence that ongoing climate change can promote invasion processes, from initial introduction through establishment and spread. Although squirrels are considered powerful invaders with well–documented negative impacts on biodiversity and human activities, there is a noticeable gap of comprehensive investigations specifically focused on this group, especially as far as the effect of climate change on worldwide invasion risk is concerned. In this study we predicted current and 2070 potential distributions of eight squirrel species with a SDM–based framework, also detecting current potential hotspots of invasion and evaluating how these could be modified by climate change in 2070. SDM predicted the eight species to potentially occur in large areas worldwide (12.12% to 39.23% of the mainland), with 70 to 129 countries vulnerable to a potential invasion. Model projections over the 2070 climate change scenarios predicted five to seven squirrel species undergoing an increase in their future potential distribution in non–native ranges. Current hotspots of potential invasion were predicted to occur in southeastern Asia, northeastern Australia, tropical Africa and South America, as well as Central and North America. Projections to 2070 showed most of the hotspots of invasion to remain substantially stable in terms of number of potential invasive species, regardless of the scenario. The most relevant increase/reduction in extent of species distribution and in the number of potential invasive species in invasiveness hotspots were predicted for 2070 under the most severe scenarios. We emphasize a strong species–specific response to climate change, which could also affect invasive species by making them less competitive, therefore potentially leading to a retreat from the invaded ranges.

    Keywords: Sciuridae, biological invasions, conservation, management, risk-assessment, species introductions