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

  • 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

  • Feuda, R., Bannikova, A., Zemlemerova, E., Di Febbraro, M., Loy, A., Hutterer, R., Aloise, G., Zykov, A., Annesi, F., Colangelo, P., 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

  • Sakalli, A., 2015.

    How can effect the synergy of climate change, soil units and vegetation groups the potential global distribution of plants up to 2300: a modelling study for prediction of potential global distribution and migration of the N 2 fixing species Alnus spp.

    Biogeosciences Discuss 12 815-864.

    Plant migration is a well known adaptation strategy of plant groups or species with evidence from historical to present observation and monitoring studies. Importance of N 2 -fixing plants has increased in last decades. Alnus (alder) is an important plant group because of its nitrogen fixation ability. Alders are generally distributed in humid 5 locations of boreal, temperate and tropical climate zones, where the nitrogen fixation is an important nitrogen source for other plants. To model the nitrogen fixation by alder, data about the global distribution of alder is absolutely required. In this study a new method and model are presented to predict the distribution of N 2 -fixing genus on global scale and its migration in the future by using climate change scenarios. Three linear functions were defined for the determination of climate niche of alders. The distribution and migration model (Alnus-Distribution-Model (ADM)) was improved with the aid of the soil units from FAO-Unesco Soil Database, and vegetation types from Schmithüsen’s biogeographical atlas. The model was also developed to predict the impact of climate change on alder distribution by using climate data from experiments performed by the Community Climate System Model version 4 (CCSM4) including the representative concentration pathways (RCPs) mitigation scenarios, and extensions of the scenarios beyond 2100 to 2300. The model covered basic approaches to understand the combine e ect of climate, soil and vegetation on plant distribution and migration in the current time and future.

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

  • Strona, G., Fattorini, S., Montano, S., Seveso, D., Galli, P., San-Miguel-Ayanz, J., 2015.

    ECo: A new measure evaluating the degree of consistency between environmental factors and spatial arrangement of species assemblages

    Ecological Indicators 52 66-74.

    We introduce a measure of Environmental Consistency (ECo), which assesses the probability of reducing homogeneity in the environmental factors within a species’ distribution by randomly displacing its occurrences. ECo is computed by applying null model analysis to a species incidence matrix where each locality is associated with a set of environmental values. Environmental homogeneity is measured, for each species, as the average multiparametric distance between any pair of localities where the species occurs. ECo can account for the effect of species interactions and resource availability by using different null models that permit or forbid occurrence displacements altering species local abundance or species prevalence. ECo provides researchers with a flexible statistical framework to address a wide range of ecological and biogeographical issues. We investigated in depth the properties and the potentialities of ECo, showing how it integrates the concepts of Eltonian and Grinnelian niches. We demonstrate that a close relationship exists between niche breadth at species level and environmental consistency of species assemblages. In addition, we provide evidence that ecological consistency is closely related to species range. A software to compute ECo is freely available at

    Keywords: Biodiversity, Environmental layers, European trees, Fish, Species-area matrix, Terrestrial vertebrates

  • Teso, M., Ferrero, C., Trejo, A., Quijano, M., Lamas, E., Alegría, J., 2015.

    In situ conservation of CWR in Spain: present and future

    Crop Wild Relative,(10) 24-26.

    One of the tasks carried out under the frame of the PGR Secure project was the development of national strategies for the preservation of CWR across Europe. These national strategies have produced lists of prioritized CWR, inventories and also studied the in situ and ex situ conservation status of the CWR selected, as well as generated proposals for better conservation and better access to them (Fitzgerald, 2013; Rubio Teso et al., 2013; Panella et al., 2014).

    Keywords: Biodiversity, Environmental layers, European trees, Fish, Species-area matrix, Terrestrial vertebrates

  • Bruno, G., Gasca, E., Monaco, C., 2014.

    The efficient management of Park resources: Natural and cultural data in the Alpi Marittime Park area

    Information Systems 42 78-88.

    Natural and cultural resource management has been widely promoted in recent years as an approach for pursuing biological conservation, cultural development and socioeconomic objectives. Parks are natural providers of such resources, due to the activities of periodical observations of species in their territory and of inventories of cultural heritage within its boundaries. However, the management and the exploitation of natural and cultural resources is often critical, due to the difficulty of collecting data in a standard and interoperable form and integrating it with other available information. This paper presents an approach to address the issue of natural and cultural data management to solve the problems of data heterogeneity, standard consistency and lack of a common data repository. In this paper, we firstly define a model to represent natural and cultural data according to specific international standards, and then we show how the resources of the Alpi Marittime Natural Park can be mapped onto it through the model. Finally, we report how we implemented and used the model in a real application in order to demonstrate the potential of our approach.

    Keywords: Collection, Database, Standards, cultural and natural resources

  • Candela, L., Castelli, D., Coro, G., Lelii, L., Mangiacrapa, F., Marioli, V., Pagano, P., 2014.

    An infrastructure-oriented approach for supporting biodiversity research

    Ecological Informatics Forthcoming.

    During the last years, considerable progresses have beenmade in developing on-line species occurrence data- bases. These are crucial in environmental and agricultural challenges, e.g., they are a basic element in the gener- ation of species distribution models. Unfortunately, their exploitation is still difficult and time consuming for many scientists. No database currently exists that can claim to host, and make available in a seamless way, all the species occurrence data needed by the ecology scientific community. Occurrence data are scattered among several databases and information systems. It is not easy to retrieve records from them, because of differences in the adopted protocols, formats and granularity. Once collected, datasets have to be selected, homogenised and pre-processed before being ready-to-use in scientific analysis and modelling. This paper introduces a set of facilities offered by the D4Science Data Infrastructure to support these phases of the scientific process. It also ex- emplifies howthey contribute to reduce the time spent in data quality assessment and curation thus improving the overall performance of the scientific investigation.

    Keywords: Data integration, Data processing, Data sharing, Species occurrence data

  • Candela, L., Faveri, F., Lelii, L., Mangiacrapa, F., Marioli, V., Pagano, P., 2014.

    Accessing biodiversity databases: a domain specific query language and a unifying data model


    Species data are scattered among several databases and information systems. During the last years, considerable progresses have been made in developing on-line species databases. However, there is no single database that can claim to host, and make available in a seamless way, all the species data needed by the communities willing to have access to such typology of data. In this report we present a domain specific query language and a unifying data model for species data that characterise a mediator service specifically conceived to act as a single access point to the plethora of existing species databases.

    Keywords: Distributed Information Retrieval, Domain Specific Query Language, Species Data Integration, Species Data Model

  • Casazza, G., Giordani, P., Benesperi, R., Foggi, B., Viciani, D., Filigheddu, R., Farris, E., Bagella, S., Pisanu, S., Mariotti, M., 2014.

    Climate change hastens the urgency of conservation for range-restricted plant species in the central-northern Mediterranean region

    Biological Conservation 179 129-138.

    With the consensus that human activities are leading to dangerous interference in Earth’s climate, there has been growing policy pressure for clear quantification and attribution of the resulting biological impacts. Despite the exceptional diversity in the Mediterranean biome, largely due to the number of rare and endemic plant species, the effect of future climate change on present Mediterranean plant species has only been examined in a few studies. In this study we presented an analysis of the potential effects of climate change on 22 plant species whose range is restricted to central-northern Mediterranean region. We used species distribution modelling to test whether projected climate change may affect the current suitability of species’ habitat; to evaluate possible future threats due to climate change; and to test any relationship between extinction risk and ecological and life-history predictors. The studied species were predicted to lose some 50% of their current range by 2020. Similarly, the probability of occurrence in known localities was predicted to drop drastically by 2020. Our results support a relationship between biological characteristics and range contractions. Although the Mediterranean species were projected to lose a lower amount of habitat than Alpine ones, species with restricted geographic range seem to be more prone to climate change effects than widespread ones. Our results emphasize the need for imme- diate monitoring and conservation actions and suggest that rare species might be useful for monitoring the conservation status of habitat in relationship to the effects of global warming in the Mediterranean region.

    Keywords: Distribution models, Extinction risk, Projected threat, Rare species

  • Creemers, R., Denoël, M., Campos, J., Vences, M., Crochet, P., Gonçalves, J., de Pous, P., Kuzmin, S., Speybroeck, J., Toxopeus, B., Corti, C., Vieites, D., Ficetola, G., Bonardi, A., Crnobrnja Isailović, J., Rodríguez, A., Lymberakis, P., Sindaco, R., Sillero, N., 2014.

    Updated distribution and biogeography of amphibians and reptiles of Europe

    Amphibia-Reptilia 35(1) 1-31.

    A precise knowledge of the spatial distribution of taxa is essential for decision-making processes in land management and biodiversity conservation, both for present and under future global change scenarios. This is a key base for several scientific disciplines (e.g. macro-ecology, biogeography, evolutionary biology, spatial planning, or environmental impact assessment) that rely on species distribution maps. An atlas summarizing the distribution of European amphibians and reptiles with 50 × 50 km resolution maps based on ca. 85 000 grid records was published by the Societas Europaea Herpetologica (SEH) in 1997. Since then, more detailed species distribution maps covering large parts of Europe became available, while taxonomic progress has led to a plethora of taxonomic changes including new species descriptions. To account for these progresses, we compiled information from different data sources: published in books and websites, ongoing national atlases, personal data kindly provided to the SEH, the 1997 European Atlas, and the Global Biodiversity Information Facility (GBIF). Databases were homogenised, deleting all information except species names and coordinates, projected to the same coordinate system (WGS84) and transformed into a 50 × 50 km grid. The newly compiled database comprises more than 384 000 grid and locality records distributed across 40 countries. We calculated species richness maps as well as maps of Corrected Weighted Endemism and defined species distribution types (i.e. groups of species with similar distribution patterns) by hierarchical cluster analysis using Jaccard’s index as association measure. Our analysis serves as a preliminary step towards an interactive, dynamic and online distributed database system (NA2RE system) of the current spatial distribution of European amphibians and reptiles. The NA2RE system will serve as well to monitor potential temporal changes in their distributions. Grid maps of all species are made available along with this paper as a tool for decision-making and conservation-related studies and actions. We also identify taxonomic and geographic gaps of knowledge that need to be filled, and we highlight the need to add temporal and altitudinal data for all records, to allow tracking potential species distribution changes as well as detailed modelling of the impacts of land use and climate change on European amphibians and reptiles.

    Keywords: European herpetofauna, IUCN red list, biogeography, conservation, distribution atlas, distribution types, endemism, species richness