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

  • 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


  • 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


  • 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


  • Katsanevakis S, Tempera F, Teixeira H (2016)

    Mapping the impact of alien species on marine ecosystems: the Mediterranean Sea case study

    Diversity and Distributions.

    Aim To develop a standardized, quantitative method for mapping cumulative impacts of invasive alien species on marine ecosystems. Location The methodology is applied in the Mediterranean Sea but is widely applicable. Methods A conservative additive model was developed to account for the Cumulative IMPacts of invasive ALien species (CIMPAL) on marine ecosystems. According to this model, cumulative impact scores are estimated on the basis of the distributions of invasive species and ecosystems, and both the reported magnitude of ecological impacts and the strength of such evidence. In the Mediterranean Sea case study, the magnitude of impact was estimated for every combination of 60 invasive species and 13 habitats, for every 10 × 10 km cell of the basin. Invasive species were ranked based on their contribution to the cumulative impact score across the Mediterranean. Results The CIMPAL index showed strong spatial heterogeneity. Spatial patterns varied depending on the pathway of initial introduction of the invasive species in the Mediterranean Sea. Species introduced by shipping gave the highest impact scores and impacted a much larger area than those introduced by aquaculture and the Suez Canal. Overall, invasive macroalgae had the highest impact among all taxonomic groups. These results represent the current best estimate of the spatial variation in impacts of invasive alien species on ecosystems, in the Mediterranean Sea. Main Conclusions A framework for mapping cumulative impacts of invasive alien species was developed. The application of this framework in the Mediterranean Sea provided a baseline that can be built upon with future improved information. Such analysis allows the identification of hotspots of highly impacted areas, and prioritization of sites, pathways and species for management actions.

    Keywords: CIMPAL, biological invasions, cumulative impacts, indicators, invasive alien species, pathways


  • Londei T (2016)

    Piapiacs ( Ptilostomus afer Linnaeus, 1766) and yellow-billed oxpeckers ( Buphagus africanus Linnaeus, 1766) avoid proximity when on African buffaloes ( Syncerus caffer Sparrman, 1779)

    African Journal of Ecology.

    Many African bird species (totalling 96 according to Dean & MacDonald, 1981) show feeding associations with mammals. However, little attention, if any, has been paid to interspecific interactions among birds attending the same mammal. Moreover, except for the red-billed oxpecker (Buphagus erythrorhyncus Stanley, 1814) and yellow-billed oxpecker (Buphagus africanus Linnaeus, 1766), which are obligate ectoparasite gleaners, there are only suggestions for any of the other species about the extent of their dependence on mammals (Dean & MacDonald, 1981). The piapiac (Ptilostomus afer Linnaeus, 1766) is a savannah corvid of sub-Saharan Africa north of the equator, ranging west-eastwards from Senegal to extreme W Kenya (Madge, 2009). Considering its wide distribution, consistent numbers and conspicuous behaviour, it is an understudied species. It is frequently seen on the backs of slowly moving herbivorous mammals, which serve as lookouts not only to catch the insects which the mammal flushes from the ground, but also as feeding substrate for the mammal's ectoparasites. Analysis of stomach contents has been very scarce for the piapiac. Among the 181 specimens listed in the Global Biodiversity Information Facility (http://www.gbif.org/; accessed 25 March 2016), only five specimens (four of which collected in 2 days in the same area) had stomach contents reported, which were all insects, mainly grasshoppers. However, Wilson (1981) found ‘ticks’ in the one piapiac stomach he examined. The piapiac may be second to only the oxpeckers in its apparent (although still understudied) morphological specializations to use grazing mammals for foraging. Interestingly, the piapiac prefers balancing on, rather than clinging to, the mammal's body (Fig. 1). This may be the reason why elephants (Loxodonta africana Blumenbach, 1797) more easily tolerate piapiacs on their sensitive skin (see, e.g. Mundy & Haynes, 1996) and why oxpeckers and not piapiacs are usually found on the sloping back of giraffes (Giraffa camelopardalis Linnaeus, 1758). The search for a stable perch may also explain why piapiacs would especially be attracted to domestic ungulates, quieter animals than their wild counterparts. The suggestion of a partial niche overlap and consequent competition between piapiacs and oxpeckers prompted this study. I chose the African buffalo (Syncerus caffer Sparrman, 1779) as the associated mammal because of its apparent attractiveness for both the piapiacs and the oxpeckers, its abundance in the study area and it being the closest wild African relative of the domestic cattle to which the oxpeckers often become detrimental through wound-feeding (e. g., Weeks, 2000).

    Keywords: CIMPAL, biological invasions, cumulative impacts, indicators, invasive alien species, pathways


  • Marta S, Lacasella F, Gratton P, Cesaroni D, Sbordoni V (2016)

    Deciphering range dynamics: effects of niche stability areas and post-glacial colonization on alpine species distribution

    Journal of Biogeography.

    Aim Niche stability areas (NSAs) are portions of the species range where climate conditions remain suitable through time. They represent the core of species ranges. Their distribution and extent, coupled with dispersal and colonization, shape the realized range of species. In this study, we quantified the roles of survival within NSAs and post-glacial dispersal in determining the current distribution of two groups of alpine butterflies (two taxa in the Erebia tyndarus species complex; three taxa in the Parnassius apollo–P. phoebus species complex). Location Holarctic. Methods NSAs were identified for each taxon by combining current and past potential distributions models, estimated using different modelling techniques and general circulation models. We then (1) assessed the distributional bias towards NSAs by comparing actual occurrence records with randomized occupancies of the current potential range and (2) quantified post-glacial dispersal by examining the distribution of distances from each occurrence record to the nearest NSA. Results In almost all taxa, realized distributions are biased towards NSAs. However, while Erebia's present range is strongly dominated by NSAs, some populations of Parnassius are found very far from NSAs, suggesting more effective colonization of the available geographical space. Main conclusions Our study highlights the relative roles of survival within NSAs and post-glacial dispersal in shaping the ranges of different alpine butterflies during the Holocene. Results suggest that Erebia was unable to disperse far from NSAs, thus experiencing increasing range fragmentation. Parnassius populations, on the other hand, coupled local survival with northward dispersal. As NSAs allowed the long-term survival of the species, acting as sources for recolonization, and tend to preserve most of each species’ genetic diversity, identifying NSAs and understanding their importance in determining the current distribution of species represents a pivotal task for the conservation of biological diversity.

    Keywords: Erebia, Parnassius, alpine species, butterflies, climate change, hindcasting, interglacial refugia, niche stability areas, species distribution modelling, species–climate equilibrium


  • Pârâu L, Strubbe D, Mori E, Menchetti M, Ancillotto L, Kleunen A et al. (2016)

    Rose-ringed Parakeet Populations and Numbers in Europe: A Complete Overview

    The Open Ornithology Journal 9(1) 1-13.

    Purpose: Alien species are considered one of the major causes contributing to the current loss of biodiversity. Over the past few decades, a large and increasing number of alien species have become invasive in many parts of the world. Their impacts range from competition for resources with native species to damage of urban infrastructure. In Europe, over a thousand alien species are now established, of which 74 are birds. Among 12 established alien parrot species in Europe, Introduction: The Rose-ringed Parakeet (RRP) Psittacula krameri (Scopoli, 1769) is the most abundant and widespread. Since the 1960's, RRPs have established more than 100 wild populations in several European countries. For Western Europe, long-term demographic data indicate the species has grown considerably in number, although some populations have failed to persist. Data: Is scarce and dispersed for countries in Central, Eastern and Northern Europe. Therefore, here we present detailed demographic data of RRP for 90 populations in 10 European countries. Furthermore, we present information on the status of the species in another 27 European countries, for which previously no data were published. Conclusion: Our synthesis reveals a positive demographic trend across the continent, although locally, some populations appear to have reached carrying capacity.

    Keywords: Demography, Europe, Invasive alien species, Parrots, Population, Psittaciformes


  • Stropp J, Ladle R, M. Malhado A, Hortal J, Gaffuri J, H. Temperley W et al. (2016)

    Mapping ignorance: 300 years of collecting flowering plants in Africa

    Global Ecology and Biogeography.

    Aim Spatial and temporal biases in species-occurrence data can compromise broad-scale biogeographical research and conservation planning. Although spatial biases have been frequently scrutinized, temporal biases and the overall quality of species-occurrence data have received far less attention. This study aims to answer three questions: (1) How reliable are species-occurrence data for flowering plants in Africa? (2) Where and when did botanical sampling occur in the past 300 years? (3) How complete are plant inventories for Africa? Location Africa. Methods By filtering a publicly available dataset containing 3.5 million records of flowering plants, we obtained 934,676 herbarium specimens with complete information regarding species name, date and location of collection. Based on these specimens, we estimated inventory completeness for sampling units (SUs) of 25 km × 25 km. We then tested whether the spatial distribution of well-sampled SUs was correlated with temporal parameters of botanical sampling. Finally, we determined whether inventory completeness in individual countries was related to old or recently collected specimens. Results Thirty-one per cent of SUs contained at least one specimen, whereas only 2.4% of SUs contained a sufficient number of specimens to reliably estimate inventory completeness. We found that the location of poorly sampled areas remained almost unchanged for half a century. Moreover, there was pronounced temporal bias towards old specimens in South Africa, the country that holds half of the available data for the continent. There, high inventory completeness stems from specimens collected several decades ago. Main conclusions Despite the increasing availability of species occurrence data for Africa, broad-scale biogeographical research is still compromised by the uncertain quality and spatial and temporal biases of such data. To avoid erroneous inferences, the quality and biases in species-occurrence data should be critically evaluated and quantified prior to use. To this end, we propose a quantification method based on inventory completeness using easily accessible species-occurrence data.

    Keywords: Africa, GBIF, data quality, flowering plants, inventory completeness, spatial and temporal biases, species-occurrence data


  • Ancillotto L, Strubbe D, Menchetti M, Mori E (2015)

    An overlooked invader? Ecological niche, invasion success and range dynamics of the Alexandrine parakeet in the invaded range

    Biological Invasions.

    Parrots and parakeets (Aves, Psittaciformes) are prominent among avian invaders, as more than 16 % of living species are currently breeding with at least one population outside their native range. Most studies have been carried out on ring-necked and monk parakeets, as they are the most successful invasive parrots globally. Recently, however, reports of invasive Alexandrine parakeet Psittacula eupatria have increased. Here, we summarize the current knowledge on the current occurrence of Alexandrine parakeets outside the natural range and assess the degree of niche conservatism during the invasion process. Our results show that Alexandrine parakeets have established invasive populations predominantly in Europe, parts of the Middle east and Far Eastern countries such as Japan and Singapore. During the ongoing invasion of Europe, the Alexandrine parakeet considerably expanded its niche into colder climates with respect to those occupied in the native range. Our results offer some support to the hypothesis that interspecific facilitation with previously established ring-necked parakeets Psittacula krameri may contribute to niche expansion and invasion success of congeneric Alexandrine parakeets. Species Distribution Models including both native and invaded range occurrence data predict a high invasion risk across multiple parts of the globe where the species is currently not yet present, thus indicating a high potential for the species for further invasion success and range expansion.

    Keywords: Interspecific facilitation, Niche conservatism, Psittaciformes, Psittacula eupatria, Range expansion