Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from Italy.
Extracted from the Mendeley GBIF Public Library.

List of publications

  • 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.

  • 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

  • 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

  • Barredo J, Strona G, de Rigo D, Caudullo G, Stancanelli G, San-Miguel-Ayanz J (2015)

    Assessing the potential distribution of insect pests: case studies on large pine weevil ( Hylobius abietis L) and horse-chestnut leaf miner ( Cameraria ohridella ) under present and future climate conditions in European forests

    EPPO Bulletin 45(2) 273-281.

    Forest insect pests represent a serious threat to European forests and their negative effects could be exacerbated by climate change. This paper illustrates how species distribution modelling integrated with host tree species distribution data can be used to assess forest vulnerability to this threat. Two case studies are used: large pine weevil (Hylobius abietis L) and horse-chestnut leaf miner (Cameraria ohridella Deschka & Dimič) both at pan-European level. The proposed approach integrates information from different sources. Occurrence data of insect pests were collected from the Global Biodiversity Information Facility (GBIF), climatic variables for present climate and future scenarios were sourced, respectively, from WorldClim and from the Research Program on Climate Change, Agriculture and Food Security (CCAFS), and distributional data of host tree species were obtained from the European Forest Data Centre (EFDAC), within the Forest Information System for Europe (FISE). The potential habitat of the target pests was calculated using the machine learning algorithm of Maxent model. On the one hand, the results highlight the potential of species distribution modelling as a valuable tool for decision makers. On the other hand, they stress how this approach can be limited by poor pest data availability, emphasizing the need to establish a harmonised open European database of geo-referenced insect pest distribution data. Évaluation de la répartition potentielle des insectes nuisibles: études de cas sur le grand charançon du pin (Hylobius abietis L.) et sur la mineuse du marronnier (Cameraria ohridella) dans les conditions climatiques actuelles et futures dans les forêts européennes Les insectes nuisibles des forêts représentent une menace sérieuse pour les forêts européennes et leurs effets négatifs pourraient être aggravés par le changement climatique. Cet article illustre l'utilisation de la modélisation de la répartition des espèces, intégrée aux données de répartition des arbres-hôtes, pour évaluer la vulnérabilité des forêts à cette menace. Deux études de cas sont utilisées, toutes deux au niveau paneuropéen, pour le grand charançon du pin (Hylobius abietis L.) et la mineuse du marronnier (Cameraria ohridella Deschka & Dimič). L'approche proposée utilise des informations de différentes sources. Les données sur la présence des insectes nuisibles proviennent du service mondial d'information sur la biodiversité (‘Global Biodiversity Information Facility’, GBIF), les variables climatiques pour le climat actuel et des scénarios futurs ont été obtenues, respectivement, à partir de WorldClim et du Programme de recherche sur le changement climatique, l'agriculture et la sécurité alimentaire (CCAFS), et les données sur la répartition des arbres-hôtes ont été obtenues auprès du Centre européen de données sur les forêts (EFDAC), qui fait partie du système d'information forestière pour l'Europe (‘Forest Information System for Europe’, FISE). L'habitat potentiel des ravageurs étudiés a été calculé en utilisant l'algorithme d'apprentissage automatique du modèle Maxent. D'une part, les résultats indiquent que la modélisation de la répartition des espèces peut devenir un outil précieux pour les décideurs. D'autre part, ils indiquent que cette approche peut être limitée par le manque de données sur les organismes nuisibles, renforçant ainsi la nécessité de créer une base de données européenne harmonisée et ouverte pour les données géo-référencées sur la répartition des insectes nuisibles.

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

  • Bradley B, Early R, Sorte C (2015)

    Space to invade? Comparative range infilling and potential range of invasive and native plants

    Global Ecology and Biogeography n/a-n/a.

    Aim Our understanding of potential ranges for native and non-native species is often based on their current geographic distributions. Non-native species have had less time than co-occurring native species to expand their ranges following introduction, so non-native ranges may under-represent suitable conditions. Therefore it is often assumed that species distribution models will predict disproportionately smaller potential ranges for non-natives than natives. We compare the distributions of native, endemic, alien and invasive plants to determine how the different range attributes of these groups might influence ecological forecasting. Location Continental USA. Methods We compared the geographic ranges of 13,575 plant species (9402 native, 2397 endemic, 1201 alien and 755 invasive) using (1) US only and (2) global distribution data from herbarium records. We calculated US longitudinal and latitudinal range extents as potential indicators of range-limiting factors, modelled potential range based on climate using principal components analysis, and calculated occupancy of potential ranges (range infilling). Results Contrary to expectations, modelled potential ranges were significantly larger for non-natives than natives, even for species with few occurrences. Distributions of native species, not invasive species, appeared strongly limited longitudinally. However, invasive plants occupied substantially less area within their climatically suitable ranges than native plants (lower range infilling). Main conclusions Invasive plant distributions were consistently broader, both climatically and geographically, than comparable native species. This suggests that invasive plant distribution models at regional scales are not underpredicting potential ranges relative to models for native species. In contrast, the comparatively limited longitudinal ranges of native species suggest a high degree of non-climatic limitation, which is likely to cause distribution models to underpredict the potential ranges of native species. Invasive plants have not achieved the degree of range infilling expected relative to natives. Thus, plants introduced to the US still have plenty of space to invade.

    Keywords: Alien, bioclimatic envelope model, dispersal, ecological niche model, equilibrium, exotic, introduced, occupancy, plant invasion

  • Carta A, Peruzzi L (2015)

    Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality in Liliaceae

    New Phytologist.

    The factors driving genome size evolution in Liliaceae were examined. In particular, we investigated whether species with larger genomes are confined to less stressful environments with a longer vegetative season. We tested our hypotheses by correlating the genome size with other plant traits and environmental variables. To determine the adaptive nature of the genome size, we also compared the performances of Brownian motion (BM) processes with those inferred by Ornstein–Uhlenbeck (OU) models of trait evolution. A positive correlation of genome size with plant size, mean temperature and habitat moisture and a negative correlation with altitude and precipitation seasonality were found. Models of trait evolution revealed a deviation from a drift process or BM. Instead, changes in genome size were significantly associated with precipitation regimes according to an OU process. Specifically, the evolutionary optima towards which the genome size evolves were higher for humid climates and lower for drier ones. Taken together, our results indicate that the genome size increase in Liliaceae is constrained by climate seasonality.

    Keywords: Liliaceae, genome size evolution, models of trait evolution, phylogenetic comparative analysis, plant–climate interactions

  • Coro G, Magliozzi C, Ellenbroek A, Pagano P (2015)

    Improving data quality to build a robust distribution model for Architeuthis dux

    Ecological Modelling 305 29-39.

    The giant squid (Architeuthis) has been reported since even before the 16th century, and has recently been observed live in its habitat for the first time. Among the species belonging to this genus, Architeuthis dux has received special attention from biologists. The distribution of this species is poorly understood, as most of our information stems from stranded animals or stomach remains. Predicting the habitat and distribution of this species, and more in general of difficult to observe species, is important from a biological conservation perspective. In this paper, we present an approach to estimate the potential distribution of A. dux at global scale, with relative high resolution (1-degree). Our approach relies on a complex preparation phase, which improves the reliability of presence, absence and environmental data correlated to the species habitat. We compare our distribution with those produced by state-of-the-art approaches (MaxEnt and AquaMaps), and use an expert-drawn map as reference. We demonstrate that our model projection is in agreement with the expert's map and is also compliant with several biological assessments of the species habitat and with recent observations. Furthermore, we show that our approach can be generalized as a paradigm that is applicable to other rare species.

    Keywords: AquaMaps, Ecological niche modelling, Maximum entropy, Neural networks, Rare species

  • Di Febbraro M, Roscioni F, Frate L, Carranza M, De Lisio L, De Rosa D et al. (2015)

    Long-term effects of traditional and conservation-oriented forest management on the distribution of vertebrates in Mediterranean forests: a hierarchical hybrid modelling approach

    Diversity and Distributions 21(10) 1141-1154.

    Aim Recently, increasing attention has been devoted to the development of sustainable forestry practices aimed at finding a balance between the maintenance and enhancement of different forest resources. However, the long-term, large-scale effects of conservation-oriented forest management on vertebrates have been poorly studied. We tested the hypothesis that conservation-oriented forest management, being conceived to mimic the dynamics of a natural forest succession more closely than does traditional forestry, causes a less severe long-term impact on the distribution of forest vertebrates. Location Molise region, Central Italy. Methods We proposed a hybrid modelling framework based on the integration of a forest dynamic model (‘LANDIS-II’) with species distribution models (SDMs). The framework was applied on four forest specialist vertebrates (tiny salamander, slow worm, Eurasian nuthatch and Leisler's bat) and included three components: forest dynamic model (FDM), SDMs and spatial pattern analysis (SPA). FDM was used to simulate spatially explicit patterns of forest succession for the current time and for 2050, imposing three alternative forestry scenarios. The simulated forest succession patterns were analysed through SPA to calculate spatialized landscape metrics that were adopted as environmental predictors for SDMs. Landscape trajectories were calculated on current and future species distributions predicted with SDMs to evaluate the effect of alternative forestry practices on their extent and fragmentation. Results Forest management mainly affected the spatial configuration rather than the extent of the species potential distributions. Conservation-oriented forest management was more favourable than traditional forestry in increasing the extent and reducing the fragmentation of the studied species’ distributions. Main conclusions Conservation-oriented forest management, by mimicking the dynamics of a natural forest succession more closely than did traditional practices, favoured elements, such as forest unevenness, species richness, aggregation of patches and variability in their distances, which emerged as fundamental characteristics for preserving the long-term persistence of forest vertebrates.

    Keywords: Mediterranean forests, conservation-oriented forest management, forest dynamic models, habitat fragmentation, species distribution models, vertebrates

  • Díaz S, Kattge J, Cornelissen J, Wright I, Lavorel S, Dray S et al. (2015)

    The global spectrum of plant form and function


    Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today’s terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Three-quarters of trait variation is captured in a two-dimensional global spectrum of plant form and function. One major dimension within this plane reflects the size of whole plants and their parts; the other represents the leaf economics spectrum, which balances leaf construction costs against growth potential. The global plant trait spectrum provides a backdrop for elucidating constraints on evolution, for functionally qualifying species and ecosystems, and for improving models that predict future vegetation based on continuous variation in plant form and function.

    Keywords: Mediterranean forests, conservation-oriented forest management, forest dynamic models, habitat fragmentation, species distribution models, vertebrates

  • Feuda R, Bannikova A, Zemlemerova E, Di Febbraro M, Loy A, Hutterer R et al. (2015)

    Tracing the evolutionary history of the mole, Talpa europaea , through mitochondrial DNA phylogeography and species distribution modelling

    Biological Journal of the Linnean Society 114(3) 495-512.

    Our understanding of the effect of Pleistocene climatic changes on the biodiversity of European mammals mostly comes from phylogeographical studies of non-subterranean mammals, whereas the influence of glaciation cycles on subterranean mammals has received little attention. The lack of data raises the question of how and to what extent the current amount and distribution of genetic variation in subterranean mammals is the result of Pleistocene range contractions/expansions. The common mole (Talpa europaea) is a strictly subterranean mammal, widespread across Europe, and represents one of the best candidates for studying the influence of Quaternary climatic oscillation on subterranean mammals. Cytochrome b sequences, as obtained from a sampling covering the majority of the distribution area, were used to evaluate whether Pleistocene climate change influenced the evolution of T. europaea and left a trace in the genetic diversity comparable to that observed in non-subterranean small mammals. Subsequently, we investigated the occurrence of glacial refugia by comparing the results of phylogeographical analysis with species distribution modelling. We found three differentiated mitochondrial DNA lineages: two restricted to Spain and Italy and a third that was widespread across Europe. Phylogenetic inferences and the molecular clock suggest that the Spanish moles represent a highly divergent and ancient lineage, highlighting for the first time the paraphyly of T. europaea. Furthermore, our analyses suggest that the genetic break between the Italian and the European lineages predates the last glacial phase. Historical demography and spatial principal component analysis further suggest that the Last Glacial Maximum left a signature both in the Italian and in the European lineages. Genetic data combined with species distribution models support the presence of at least three putative glacial refugia in southern Europe (France, Balkan Peninsula and Black Sea) during thelast glacial maximum that likely contributed to post-glacial recolonization of Europe. By contrast, the Italian lineage remained trapped in the Italian peninsula and, according to the pattern observed in other subterranean mammals, did not contribute to the recolonization of northern latitudes

    Keywords: Europe, Last Glacial Maximum, SDM, cytochrome b, glacial refugia, historical demography, paraphyly, phylogenetics, sPCA