Uses of GBIF in scientific research

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

List of publications

  • 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 http://forest.jrc.ec.europa.eu/download/software/eco.

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


  • van Kleunen, M., Dawson, W., Essl, F., Pergl, J., Winter, M., Weber, E., Kreft, H., Weigelt, P., Kartesz, J., Nishino, M., Antonova, L., Barcelona, J., Cabezas, F., Cárdenas, D., Cárdenas-Toro, J., Castaño, N., Chacón, E., Chatelain, C., Ebel, A., Figueiredo, E., Fuentes, N., Groom, Q., Henderson, L., Kupriyanov, A., Masciadri, S., Meerman, J., Morozova, O., Moser, D., Nickrent, D., Patzelt, A., Pelser, P., Baptiste, M., Poopath, M., Schulze, M., Seebens, H., Shu, W., Thomas, J., Velayos, M., Wieringa, J., Pyšek, P., 2015.

    Global exchange and accumulation of non-native plants

    Nature advance on.

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


  • Brito, J., Godinho, R., Martínez-Freiría, F., Pleguezuelos, J., Rebelo, H., Santos, X., Vale, C., Velo-Antón, G., Boratyński, Z., Carvalho, S., Ferreira, S., Gonçalves, D., Silva, T., Tarroso, P., Campos, J., Leite, J., Nogueira, J., Alvares, F., Sillero, N., Sow, A., Fahd, S., Crochet, P., Carranza, S., 2014.

    Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel

    Biological Reviews of the Cambridge Philosophical Society 89(1) 215-31.

    Deserts and arid regions are generally perceived as bare and rather homogeneous areas of low diversity. The Sahara is the largest warm desert in the world and together with the arid Sahel displays high topographical and climatic heterogeneity, and has experienced recent and strong climatic oscillations that have greatly shifted biodiversity distribution and community composition. The large size, remoteness and long-term political instability of the Sahara-Sahel, have limited knowledge on its biodiversity. However, over the last decade, there have been an increasing number of published scientific studies based on modern geomatic and molecular tools, and broad sampling of taxa of these regions. This review tracks trends in knowledge about biodiversity patterns, processes and threats across the Sahara-Sahel, and anticipates needs for biodiversity research and conservation. Recent studies are changing completely the perception of regional biodiversity patterns. Instead of relatively low species diversity with distribution covering most of the region, studies now suggest a high rate of endemism and larger number of species, with much narrower and fragmented ranges, frequently limited to micro-hotspots of biodiversity. Molecular-based studies are also unravelling cryptic diversity associated with mountains, which together with recent distribution atlases, allows identifying integrative biogeographic patterns in biodiversity distribution. Mapping of multivariate environmental variation (at 1 km × 1 km resolution) of the region illustrates main biogeographical features of the Sahara-Sahel and supports recently hypothesised dispersal corridors and refugia. Micro-scale water-features present mostly in mountains have been associated with local biodiversity hotspots. However, the distribution of available data on vertebrates highlights current knowledge gaps that still apply to a large proportion of the Sahara-Sahel. Current research is providing insights into key evolutionary and ecological processes, including causes and timing of radiation and divergence for multiple taxa, and associating the onset of the Sahara with diversification processes for low-mobility vertebrates. Examples of phylogeographic patterns are showing the importance of allopatric speciation in the Sahara-Sahel, and this review presents a synthetic overview of the most commonly hypothesised diversification mechanisms. Studies are also stressing that biodiversity is threatened by increasing human activities in the region, including overhunting and natural resources prospection, and in the future by predicted global warming. A representation of areas of conflict, landmines, and natural resources extraction illustrates how human activities and regional insecurity are hampering biodiversity research and conservation. Although there are still numerous knowledge gaps for the optimised conservation of biodiversity in the region, a set of research priorities is provided to identify the framework data needed to support regional conservation planning.

    Keywords: Africa, Sahara, Sahel, biodiversity, climate change, conservation, deserts, distribution, diversification, phylogeography


  • Capinha, C., Rocha, J., Sousa, C., 2014.

    Macroclimate determines the global range limit of Aedes aegypti

    EcoHealth 11(3) 420-8.

    Aedes aegypti is the main vector of dengue and a number of other diseases worldwide. Because of the domestic nature of this mosquito, the relative importance of macroclimate in shaping its distribution has been a controversial issue. We have captured here the worldwide macroclimatic conditions occupied by A. aegypti in the last century. We assessed the ability of this information to predict the species' observed distribution using supra-continental spatially-uncorrelated data. We further projected the distribution of the colonized climates in the near future (2010-2039) under two climate-change scenarios. Our results indicate that the macroclimate is largely responsible for setting the maximum range limit of A. aegypti worldwide and that in the near future, relatively wide areas beyond this limit will receive macroclimates previously occupied by the species. By comparing our projections, with those from a previous model based strictly on species-climate relationships (i.e., excluding human influence), we also found support for the hypothesis that much of the species' range in temperate and subtropical regions is being sustained by artificial environments. Altogether, these findings suggest that, if the domestic environments commonly exploited by this species are available in the newly suitable areas, its distribution may expand considerably in the near future.

    Keywords: Aedes aegypti, Climate change, Dengue, Global distribution, Urban disease-vectors


  • 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


  • DeSoto, L., Varino, F., Andrade, J., Gouveia, C., Campelo, F., Trigo, R., Nabais, C., 2014.

    Different growth sensitivity to climate of the conifer Juniperus thurifera on both sides of the Mediterranean Sea

    International Journal of Biometeorology.

    Mediterranean plants cope with cold wet winters and dry hot summers, with a drought gradient from northwest to southeast. Limiting climatic conditions have become more pronounced in the last decades due to the warming trend and rainfall decrease. Juniperus thurifera L., a long-lived conifer tree endemic to the western Mediterranean region, has a disjunct distribution in Europe and Africa, making it a suitable species to study sensitivity to climate in both sides of the Mediterranean Basin. Tree-ring width chronologies were built for three J. thurifera stands at Spain (Europe) and three in Morocco (Africa) and correlated with monthly temperature and precipitation. The temporal stability of climate-growth relationships was assessed using moving correlations; the drought effect on growth was calculated using the monthly standardized precipitation-evapotranspiration index (SPEI) at different temporal scales. In the wettest stands, increasing spring temperature and summer precipitation enhanced growth, while in the driest stands, growth was enhanced by higher spring precipitation and lower summer temperature. The climate-growth correlations shifted during the twentieth century, especially since the 1970s. Particularly noticeable is the recent negative correlation with previous autumn and winter precipitation in the wettest stands of J. thurifera, probably related with an effect of cloud cover or flooding on carbon storage depletion for next year growth. The driest stands were affected by drought at long time scales, while the wettest stands respond to drought at short time scales. This reveals a different strategy to cope with drought conditions, with populations from drier sites able to cope with short periods of water deficit.

    Keywords: climate change, dendrochronology, juniper, mediterranean basin, tree ring


  • Early, R., Sax, D., 2014.

    Climatic niche shifts between species' native and naturalized ranges raise concern for ecological forecasts during invasions and climate change

    Global Ecology and Biogeography Forthcoming.

    Aim: Correlative models that forecast extinction risk from climate change and invasion risks following species introductions, depend on the assumption that species' current distributions reflect their climate tolerances (‘climatic equilibrium’). This assumption has rarely been tested with independent distribution data, and studies that have done so have focused on species that are widespread or weedy in their native range. We use independent data to test climatic equilibrium for a broadly representative group of species, and ask whether there are any general indicators that can be used to identify when equilibrium occurs. Location: Europe and contiguous USA. Methods: We contrasted the climate conditions occupied by 51 plant species in their native (European) and naturalized (USA) distributions by applying kernel smoothers to species' occurrence densities. We asked whether species had naturalized in climate conditions that differ from their native ranges, suggesting climatic disequilibrium in the native range, and whether characteristics of species' native distributions correspond with climatic equilibrium. Results: A large proportion of species' naturalized distributions occurred outside the climatic conditions occupied in their native ranges: for 22 species, the majority of their naturalized ranges fell outside their native climate conditions. Our analyses revealed large areas in Europe that species do not occupy, but which match climatic conditions occupied in the USA, suggesting a high degree of climatic disequilibrium in the native range. Disequilibrium was most severe for species with native ranges that are small and occupy a narrow range of climatic conditions. Main conclusions: Our results demonstrate that the direct effects of climate on species distributions have been widely overestimated, and that previous large-scale validations of the equilibrium assumption using species' native and naturalized distributions are not generally applicable. Non-climatic range limitations are likely to be the norm, rather than the exception, and pose added risks for species under climate change.

    Keywords: biotic interactions, conservation planning, conservatism, ecological niche model, niche, niche shift, plant invasions, species distribution model


  • Tarroso, P., Pereira, R., Martínez-Freiría, F., Godinho, R., Brito, J., 2014.

    Hybridization at an ecotone: ecological and genetic barriers between three Iberian vipers

    Molecular Ecology 23(5) 1108-23.

    The formation of stable genetic boundaries between emerging species is often diagnosed by reduced hybrid fitness relative to parental taxa. This reduced fitness can arise from endogenous and/or exogenous barriers to gene flow. Although detecting exogenous barriers in nature is difficult, we can estimate the role of ecological divergence in driving species boundaries by integrating molecular and ecological niche modelling tools. Here, we focus on a three-way secondary contact zone between three viper species (Vipera aspis, V. latastei and V. seoanei) to test for the contribution of ecological divergence to the development of reproductive barriers at several species traits (morphology, nuclear DNA and mitochondrial DNA). Both the nuclear and mitochondrial data show that all taxa are genetically distinct and that the sister species V. aspis and V. latastei hybridize frequently and backcross over several generations. We find that the three taxa have diverged ecologically and meet at a hybrid zone coincident with a steep ecotone between the Atlantic and Mediterranean biogeographical provinces. Integrating landscape and genetic approaches, we show that hybridization is spatially restricted to habitats that are suboptimal for parental taxa. Together, these results suggest that niche separation and adaptation to an ecological gradient confer an important barrier to gene flow among taxa that have not achieved complete reproductive isolation.

    Keywords: Iberian Peninsula, Speciation, Vipera, ecological niche, hybridization, natural selection


  • Tarroso, P., Carrión, J., Dorado-Valiño, M., Queiroz, P., Santos, L., Valdeolmillos-Rodríguez, A., Célio Alves, P., Brito, J., Cheddadi, R., 2014.

    Spatial climate dynamics in the Iberian Peninsula since 15 000 Yr BP

    Climate of the Past Discussions 10(5) 3901-3930.

    The evolution of the climate in the Iberian Peninsula since the last glacial maximum is associated with distributional shifts of multiple species. We rely on this dynamic relationship between past climate and biodiversity patterns to quantify climate change 5 using fossil pollen records widespread throughout the Iberian Peninsula and modern spatial distribution of plant taxa and climate.We have reconstructed spatial layers (1 ka interval) of January minimum temperature, July maximum temperature and minimum annual precipitation using a method based on probability density functions and cover- ing the time period between 15 and 3ka. A functional principal component analysis was 10 used in order to summarise the spatial evolution of climate. Using a clustering method we have identified areas that share similar climate evolutions during the studied time period. The spatial reconstructions show a highly dynamic pattern in accordance with the main climatic trends. The four cluster areas we found exhibit different climate evolution over the studied period. The clustering scheme and patterns of change between 15 millenia are coherent with the existence of multiple refugial areas in the Iberian Peninsula.

    Keywords: Iberian Peninsula, Speciation, Vipera, ecological niche, hybridization, natural selection


  • Tingley, R., Vallinoto, M., Sequeira, F., Kearney, M., 2014.

    Realized niche shift during a global biological invasion

    Proceedings of the National Academy of Sciences of the United States of America 1-6.

    Accurate forecasts of biological invasions are crucial for managing invasion risk but are hampered by niche shifts resulting from evolved environmental tolerances (fundamental niche shifts) or the presence of novel biotic and abiotic conditions in the invaded range (realized niche shifts). Distinguishing between these kinds of niche shifts is impossible with traditional, correlative approaches to invasion forecasts, which exclusively consider the realized niche. Here we overcome this challenge by combining a physiologically mechanistic model of the fundamental niche with correlative models based on the realized niche to study the global invasion of the cane toad Rhinella marina. We find strong evidence that the success of R. marina in Australia reflects a shift in the species' realized niche, as opposed to evolutionary shifts in range-limiting traits. Our results demonstrate that R. marina does not fill its fundamental niche in its native South American range and that areas of niche unfilling coincide with the presence of a closely related species with which R. marina hybridizes. Conversely, in Australia, where coevolved taxa are absent, R. marina largely fills its fundamental niche in areas behind the invasion front. The general approach taken here of contrasting fundamental and realized niche models provides key insights into the role of biotic interactions in shaping range limits and can inform effective management strategies not only for invasive species but also for assisted colonization under climate change.

    Keywords: Iberian Peninsula, Speciation, Vipera, ecological niche, hybridization, natural selection