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


  • 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


  • 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


  • Smeraldo S, Di Febbraro M, Ćirović D, Bosso L, Trbojević I, Russo D (2017)

    Species distribution models as a tool to predict range expansion after reintroduction: A case study on Eurasian beavers (Castor fiber)

    Journal for Nature Conservation.

    Species Distribution Models (SDMs) may provide important information for the follow-up phase of reintroduction operations by identifying the main areas most likely to be colonized by the reintroduced species. We used SDMs to identify the potential distribution of Eurasian beavers (Castor fiber) reintroduced to Serbia and Bosnia and Herzegovina in 2004–2006 after being historically driven to extinction by overhunting. Models were also used to carry out a gap analysis to assess the degree of protection granted by the national reserve networks to the potentially expanding population. Distances from hydrographic network, broadleaved forest, main watercourses and farmland were the main factors influencing model performance. We estimated that suitable habitat covers 14.0% (31,000 km2) of the whole study area. In Serbia, in 2004–2013 beavers expanded their range at a mean colonization speed of 70.9 ± 12.8 km/year (mean ± SD). Only 2.89% of and 9.72% of beaver’s suitable habitat lie within the national network of protected areas of Bosnia and Serbia respectively. We detected new potential areas where beavers will likely settle in the near future, advising on where further monitoring should be focused. We also identified low suitability areas to be targeted with appropriate management to improve their conditions as well as important regions falling outside reserve boundaries where protection should be granted.

    Keywords: Bosnia and Herzegovina, Conservation gap analyses, Habitat suitability, Riparian habitats, Serbia


  • Taylor N, Kell S, Holubec V, Parra-Quijano M, Chobot K, Maxted N (2017)

    A systematic conservation strategy for crop wild relatives in the Czech Republic

    Diversity and Distributions 23(4) 448-462.

    Aim To create a crop wild relative (CWR) conservation strategy for the Czech Republic: the first national CWR conservation strategy for Central and Eastern Europe. Location Czech Republic. Methods We generated a CWR checklist for the Czech Republic and then prioritized taxa, using widely adopted criteria modified with input from local experts, to create a national CWR inventory. For 204 priority CWR species, we collated 206,760 presence records. We carried out spatial analyses to identify patterns in species richness, gaps in existing conservation actions, complementary conservation networks and collecting strategies to increase representativeness of gene bank accessions. We considered both specific and genetic conservation, using geographic and ecogeographic proxies for the latter. Results Passive in situ conservation of CWR in the Czech Republic is comprehensive at present, with all but one priority CWR species being contained in protected areas. Active in situ CWR conservation could be focussed within 11 ca. 10-km-by-10-km grid cells containing 94% of priority species, or their overlapping protected areas. To augment the genetic coverage of the in situ conservation network, active CWR conservation is encouraged within 11 supplementary areas. Meanwhile, there are huge gaps in ex situ collections, with no known conserved material for 134 of the 204 priority species. Furthermore, existing accessions are generally unrepresentative of genetic diversity. Main conclusions In the Czech Republic, active in situ conservation of priority CWR should be instigated within the 22 recommended grid cell areas or their 14 overlapping protected areas. For ex situ conservation, strategic and targeted collection of germplasm would markedly increase the value of gene bank collections. Diversity of priority Czech CWR is concentrated in South Moravia, making this a particularly important CWR area for the country and for Europe.

    Keywords: Bosnia and Herzegovina, Conservation gap analyses, Habitat suitability, Riparian habitats, Serbia


  • 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