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

  • Assis J, Zupan M, Nicastro K, Zardi G, McQuaid C, Serrão E (2015)

    Oceanographic Conditions Limit the Spread of a Marine Invader along Southern African Shores.

    PloS one 10(6) e0128124.

    Invasive species can affect the function and structure of natural ecological communities, hence understanding and predicting their potential for spreading is a major ecological challenge. Once established in a new region, the spread of invasive species is largely controlled by their dispersal capacity, local environmental conditions and species interactions. The mussel Mytilus galloprovincialis is native to the Mediterranean and is the most successful marine invader in southern Africa. Its distribution there has expanded rapidly and extensively since the 1970s, however, over the last decade its spread has ceased. In this study, we coupled broad scale field surveys, Ecological Niche Modelling (ENM) and Lagrangian Particle Simulations (LPS) to assess the current invaded distribution of M. galloprovincialis in southern Africa and to evaluate what prevents further spread of this species. Results showed that all environmentally suitable habitats in southern Africa have been occupied by the species. This includes rocky shores between Rocky Point in Namibia and East London in South Africa (approx. 2800 km) and these limits coincide with the steep transitions between cool-temperate and subtropical-warmer climates, on both west and southeast African coasts. On the west coast, simulations of drifting larvae almost entirely followed the northward and offshore direction of the Benguela current, creating a clear dispersal barrier by advecting larvae away from the coast. On the southeast coast, nearshore currents give larvae the potential to move eastwards, against the prevalent Agulhas current and beyond the present distributional limit, however environmental conditions prevent the establishment of the species. The transition between the cooler and warmer water regimes is therefore the main factor limiting the northern spread on the southeast coast; however, biotic interactions with native fauna may also play an important role.

  • Chefaoui R, Assis J, Duarte C, Serrão E (2015)

    Large-Scale Prediction of Seagrass Distribution Integrating Landscape Metrics and Environmental Factors: The Case of Cymodocea nodosa (Mediterranean–Atlantic)

    Estuaries and Coasts.

    Understanding the factors that affect seagrass meadows encompassing their entire range of distribution is challenging yet important for their conservation. Here, we predict the realized and potential distribution for the species Cymodocea nodosa modelling its environmental niche in the Mediterranean and adjacent Atlantic coastlines. We use a combination of environmental variables and landscape metrics to perform a suite of predictive algorithms which enables examination of the niche and find suitable habitats for the species. The most relevant environmental variables defining the distribution of C. nodosa were sea surface temperature (SST) and salinity. We found suitable habitats at SST from 5.8 °C to 26.4 °C and salinity ranging from 17.5 to 39.3. Optimal values of mean winter wave height ranged between 1.2 and 1.5 m, while waves higher than 2.5 m seemed to limit the presence of the species. The influence of nutrients and pH, despite having weight on the models, was not so clear in terms of ranges that confine the distribution of the species. Landscape metrics able to capture variation in the coastline enhanced significantly the accuracy of the models, despite the limitations caused by the scale of the study. We found potential suitable areas not occupied by the seagrass mainly in coastal regions of North Africa and the Adriatic coast of Italy. The present study describes the realized and potential distribution of a seagrass species, providing the first global model of the factors that can be shaping the environmental niche of C. nodosa throughout its range. We identified the variables constraining its distribution as well as thresholds delineating its environmental niche. Landscape metrics showed promising prospects for the prediction of coastal species dependent on the shape of the coast. By contrasting predictive approaches, we defined the variables affecting the distributional areas that seem unsuitable for C. nodosa as well as those suitable habitats not occupied by the species. These findings are encouraging for its use in future studies on climate-related marine range shifts and meadow restoration projects of these fragile ecosystems.

    Keywords: Coastal morphology, Cymodocea nodosa, Environmental niche, Landscape metrics, Seagrass, Species distribution modelling

  • Fernández M, Navarro L, Apaza-Quevedo A, Gallegos S, Marques A, Zambrana-Torrelio C et al. (2015)

    Challenges and opportunities for the Bolivian Biodiversity Observation Network

    Biodiversity 1-13.

    Pragmatic methods to assess the status of biodiversity at multiple scales are required to support conservation decision-making. At the intersection of several major biogeographic zones, Bolivia has extraordinary potential to develop a monitoring strategy aligned with the objectives of the Group on Earth Observations Biodiversity Observation Network (GEO BON). Bolivia, a GEO Observer since 2005, is already working on the adequacy of national earth observations towards the objectives of the Global Earth Observation System of Systems (GEOSS). However, biodiversity is still an underrepresented component in this initiative. The integration of biodiversity into Bolivia’s GEO framework would confirm the need for a country level biodiversity monitoring strategy, fundamental to assess the progress towards the 2020 Aichi targets. Here we analyse and discuss two aspects of the process of developing such a strategy: (1) identification of taxonomic, temporal and spatial coverage of biodiversity data to detect both ava...

    Keywords: Bolivia, GEO BON, baseline, big data integration, biodiversity, monitoring

  • Paterson R, Kumar L, Taylor S, Lima N (2015)

    Future climate effects on suitability for growth of oil palms in Malaysia and Indonesia

    Scientific Reports 5 14457.

    The production of palm oil (PO) is highly profitable. The economies of the principal producers, Malaysia and Indonesia, and others, benefit considerably. Climate change (CC) will most likely have an impact on the distribution of oil palms (OP) (Elaeis guineensis). Here we present modelled CC projections with respect to the suitability of growing OP, in Malaysia and Indonesia. A process-oriented niche model of OP was developed using CLIMEX to estimate its potential distribution under current and future climate scenarios. Two Global Climate Models (GCMs), CSIRO-Mk3.0 and MIROC-H, were used to explore the impacts of CC under the A1B and A2 scenarios for 2030, 2070 and 2100. Decreases in climatic suitability for OP in the region were gradual by 2030 but became more pronounced by 2100. These projections imply that OP growth will be affected severely by CC, with obvious implications to the economies of (a) Indonesia and Malaysia and (b) the PO industry, but with potential benefits towards reducing CC. A possible remedial action is to concentrate research on development of new varieties of OP that are less vulnerable to CC.

    Keywords: Bolivia, GEO BON, baseline, big data integration, biodiversity, monitoring

  • Silva-Rocha I, Salvi D, Sillero N, Mateo J, Carretero M (2015)

    Snakes on the Balearic islands: an invasion tale with implications for native biodiversity conservation.

    PloS one 10(4) e0121026.

    Biological invasions are a major conservation threat for biodiversity worldwide. Islands are particularly vulnerable to invasive species, especially Mediterranean islands which have suffered human pressure since ancient times. In the Balearic archipelago, reptiles represent an outstanding case with more alien than native species. Moreover, in the last decade a new wave of alien snakes landed in the main islands of the archipelago, some of which were originally snake-free. The identification of the origin and colonization pathways of alien species, as well as the prediction of their expansion, is crucial to develop effective conservation strategies. In this study, we used molecular markers to assess the allochthonous status and the putative origin of the four introduced snake species (Hemorrhois hippocrepis, Malpolon monspessulanus, Macroprotodon mauritanicus and Rhinechis scalaris) as well as ecological niche models to infer their patterns of invasion and expansion based on current and future habitat suitability. For most species, DNA sequence data suggested the Iberian Peninsula as the potential origin of the allochthonous populations, although the shallow phylogeographic structure of these species prevented the identification of a restricted source-area. For all of them, the ecological niche models showed a current low habitat suitability in the Balearic, which is however predicted to increase significantly in the next few decades under climate change scenarios. Evidence from direct observations and spatial distribution of the first-occurrence records of alien snakes (but also lizards and worm lizards) suggest the nursery trade, and in particular olive tree importation from Iberian Peninsula, as the main pathway of introduction of alien reptiles in the Balearic islands. This trend has been reported also for recent invasions in NE Spain, thus showing that olive trees transplantation may be an effective vector for bioinvasion across the Mediterranean. The combination of molecular and ecological tools used in this study reveals a promising approach for the understanding of the complex invasion process, hence guiding conservation management actions.

    Keywords: Bolivia, GEO BON, baseline, big data integration, biodiversity, monitoring

  • 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

  • van Kleunen M, Dawson W, Essl F, Pergl J, Winter M, Weber E et al. (2015)

    Global exchange and accumulation of non-native plants

    Nature 525(7567) 100-103.

    All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch1, 2 is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage3. So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.

    Keywords: Biodiversity, Biogeography, Invasive species, Macroecology

  • Brito J, Godinho R, Martínez-Freiría F, Pleguezuelos J, Rebelo H, Santos X et al. (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 et al. (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