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

  • Abdi, A.

    Integrating Open Access Geospatial Data to Map the Habitat Suitability of the Declining Corn Bunting (Miliaria calandra)

    (Journal name unavailable from Mendeley API. To be updated soon...)

    The efficacy of integrating open access geospatial data to produce habitat suitability maps for the corn bunting (Miliaria calandra) was investigated. Landsat Enhanced Thematic Mapper Plus (ETM+), Shuttle Radar Topography Mission (SRTM) and Corine (Coordination of Information on the Environment) land cover data for the year 2000 (CLC2000) were processed to extract explanatory variables and divided into three sets; Satellite (ETM+, SRTM), CLC2000 and Combined (CLC2000 + Satellite). Presence-absence data for M. calandra, collected during structured surveys for the Catalan Breeding Bird Atlas, were provided by the Catalan Ornithological Institute. The dataset was partitioned into an equal number of presence and absence points by dividing it into five groups, each composed of 88 randomly selected presence points to match the number of absences. A logistic regression model was then built for each group. Models were evaluated using area under the curve (AUC) of the receiver operating characteristic (ROC). Results of the five groups were averaged to produce mean Satellite, CLC2000 and Combined models. The mean AUC values were 0.69, 0.81 and 0.90 for the CLC2000, Satellite and the Combined model, respectively. The probability of M. calandra presence had the strongest positive correlation with land surface temperature, modified soil adjusted vegetation index, coefficient of variation for ETM+ band 5 and the fraction of non-irrigated arable land.

    Keywords: agricultural intensification, Corine land cover, corn bunting, Landsat, Miliaria calandra, open access data, open source geospatial software, species distribution modeling


  • Ahmadzadeh, F., Flecks, M., Carretero, M., Wolfgang, B., Ilgaz, C., Engler, J., Harris, D.

    Rapid lizard radiation lacking niche conservatism: ecological diversification within a complex landscape

    Journal of Biogeography.

    Keywords: anatolia, ancestral niche reconstruction, eastern mediterranean, lacerta, lacerta pamphylica, lacerta trilineata, lacertid lizards, media, niche divergence, niche overlap, species distribution model


  • 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.

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

    Biological reviews of the Cambridge Philosophical Society 1.

    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, biodiversity, climate change, conservation, deserts, distribution, diversification, phylogeography, Sahara, Sahel


  • Capinha, C., Larson, E., Tricarico, E., Olden, J., Gherardi, F.

    Effects of Climate Change, Invasive Species, and Disease on the Distribution of Native European Crayfishes

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Climate change will require species to adapt to new conditions or follow preferred climates to higher latitudes or elevations, but many dispersal-limited freshwater species may be unable to move due to barriers imposed by watershed boundaries. In addition, invasive nonnative species may expand into new regions under future climate conditions and contribute to the decline of native species. We evaluated future distributions for the threatened European crayfish fauna in response to climate change, watershed boundaries, and the spread of invasive crayfishes, which transmit the crayfish plague, a lethal disease for native European crayfishes. We used climate projections from general circulation models and statistical models based on Mahalanobis distance to predict climate-suitable regions for native and invasive crayfishes in the middle and at the end of the 21st century. We identified these suitable regions as accessible or inaccessible on the basis of major watershed boundaries and present occurrences and evaluated potential future overlap with 3 invasive North American crayfishes. Climate-suitable areas decreased for native crayfishes by 19% to 72%, and the majority of future suitable areas for most of these species were inaccessible relative to native and current distributions. Overlap with invasive crayfish plague-transmitting species was predicted to increase. Some native crayfish species (e.g., noble crayfish [Astacus astacus]) had no future refugia that were unsuitable for the modeled nonnative species. Our results emphasize the importance of preventing additional introductions and spread of invasive crayfishes in Europe to minimize interactions between the multiple stressors of climate change and invasive species, while suggesting candidate regions for the debatable management option of assisted colonization.

    Keywords: biotic interactions, dispersal barriers, europe, freshwater, invasive species, species distribution


  • Mateo, R., Vanderpoorten, A., Muñoz, J., Laenen, B., Désamoré, A.

    Modeling species distributions from heterogeneous data for the biogeographic regionalization of the European bryophyte flora.

    (Journal name unavailable from Mendeley API. To be updated soon...)

    The definition of biogeographic regions provides a fundamental framework for a range of basic and applied questions in biogeography, evolutionary biology, systematics and conservation. Previous research suggested that environmental forcing results in highly congruent regionalization patterns across taxa, but that the size and number of regions depends on the dispersal ability of the taxa considered. We produced a biogeographic regionalization of European bryophytes and hypothesized that (1) regions defined for bryophytes would differ from those defined for other taxa due to the highly specific eco-physiology of the group and (2) their high dispersal ability would result in the resolution of few, large regions. Species distributions were recorded using 10,000 km(2) MGRS pixels. Because of the lack of data across large portions of the area, species distribution models employing macroclimatic variables as predictors were used to determine the potential composition of empty pixels. K-means clustering analyses of the pixels based on their potential species composition were employed to define biogeographic regions. The optimal number of regions was determined by v-fold cross-validation and Moran's I statistic. The spatial congruence of the regions identified from their potential bryophyte assemblages with large-scale vegetation patterns is at odds with our primary hypothesis. This reinforces the notion that post-glacial migration patterns might have been much more similar in bryophytes and vascular plants than previously thought. The substantially lower optimal number of clusters and the absence of nested patterns within the main biogeographic regions, as compared to identical analyses in vascular plants, support our second hypothesis. The modelling approach implemented here is, however, based on many assumptions that are discussed but can only be tested when additional data on species distributions become available, highlighting the substantial importance of developing integrated mapping projects for all taxa in key biogeographically areas of Europe, and the Mediterranean peninsulas in particular.

    Keywords: biotic interactions, dispersal barriers, europe, freshwater, invasive species, species distribution


  • Vences, M., Susanne Hauswaldt, J., Steinfartz, S., Rupp, O., Goesmann, A., Künzel, S., Orozco-Terwengel, P., Vieites, D., Nieto-Roman, S., Haas, S., Laugsch, C., Gehara, M., Bruchmann, S., Pabijan, M., Ludewig, A., Rudert, D., Angelini, C., Borkin, L., Crochet, P., Crottini, A., Dubois, A., Francesco Ficetola, G., Galán, P., Geniez, P., Hachtel, M., Jovanovic, O., Litvinchuk, S., Lymberakis, P., Ohler, A., Smirnov, N.

    Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana.

    Molecular phylogenetics and evolution(May).

    We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas, whereas R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ∼3.5 mya for both species), but R. temporaria might have been been characterized by larger ancestral and current effective population sizes than R. dalmatina. The unusually high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a more recent event.

    Keywords: biotic interactions, dispersal barriers, europe, freshwater, invasive species, species distribution


  • Vieira, R., Thiel, R., Christiansen, B., Coelho, R., Denda, A., Gonçalves, J.

    The deep-sea fish Kali macrodon: a new record for the tropical eastern Atlantic off Cape Verde

    Marine Biodiversity Records 6 e4.

    A new deep-sea fish is reported for the tropical eastern Atlantic. The rare chiasmodontid Kali macrodon was caught for the first time in Cape Verdean waters during an oceanographic survey in September 2009. This record provides the fifth occur- rence for the species in the north-eastern Atlantic and represents the third specimen ever caught in tropical waters.

    Keywords: accepted 27 november 2012, cape verde, chiasmodontidae, kali macrodon, senghor seamount, submitted 9 october 2012


  • Bettencourt, E.

    Understanding Diversity for harmonious and sustainable development

    Agriculture & Forestry 57(2) 7-25.

    Diversity is as crucial for the survival of humanity as the air we breathe and the water we drink. Understanding diversity is a prerequisite for the promotion of the sustainable utilisation of crop diversity (the raw material for improving and adapting crops to meet future challenges), essential to respond to the unprecedented demands on agriculture posed by increasingly unpredictable and changing climate as well as the increasing pressure of constantly evolving pests and diseases, by providing extra source of material and knowledge. In spite of the many challenges ahead impacting in agricultural production, like the threat of genetic erosion, deforestation, changes in key climatic features (i.e. temperature increase) and food insecurity, there are a number of elements that play a crucial role in contributing to attaining the goals of harmonious and sustainable development such as the genetic diversity in germplasm collections maintained at local, national, regional and global level, that need to be harnessed, by means of understanding the diversity, for the benefit and improved well- being, ensuring food and nutrition security and healthy life for present and future generations of humankind.

    Keywords: genetic diversity, germplasm collections, sustainability, sustainable development, utilisation


  • Bosso, L., Rebelo, H., Garonna, A., Russo, D.

    Modelling geographic distribution and detecting conservation gaps in Italy for the threatened beetle Rosalia alpina

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Presence-only models can aid conservation and management of threatened, elusive species. We developed a Maxent model for the rare cerambycid beetle Rosalia longicorn Rosalia alpina L. in Italy and neighbouring regions and identified the variables best explaining the species’ occurrence on a large scale. Once successfully validated, we used the model to (a) evaluate the current degree of fragmentation of R. alpina range in Italy; and (b) quantify the amount of the Italian territory with the highest probability of beetle presence within the existing national conservation areas (Natura 2000 network, parks and reserves). Low (<0.5) probability scores of R. alpina presence corresponded to 89% of the total area considered, whereas high scores (>0.9) covered only 2.5%. R. alpina was predicted to occur mostly in broadleaved deciduous forest at 1000–1700 m a.s.l. with warm maximum spring temperatures and May and November precipitation >80 mm. We found a high degree of fragmentation; gaps were mainly covered with farmland or other unsuitable habitat. Over 52% of potential habitat is unprotected. While the Natura 2000 network protects 42% of potential habitat, parks and reserve covers less than 29%. To preserve R. alpina, we urge to create, or restore, forest corridors to bridge the otherwise impermeable gaps our model detected and grant protection to the still largely unprotected area of the Italian territory e.g. by including it in further Natura 2000 sites. Models such as ours may also help focus field surveys in selected areas to save resources and increase survey success.

    Keywords: Biodiversity, Forest management, Fragmentation, Gap analysis, Insect conservation, IUCN, Maxent, Natura 2000, Saproxylic beetles


  • Capinha, C., Brotons, L., Anastácio, P.

    Geographical variability in propagule pressure and climatic suitability explain the European distribution of two highly invasive crayfish

    Journal of Biogeography online.

    Aim:We assess the relative contribution of human, biological and climatic factors in explaining the colonization success of two highly invasive freshwater decapods: the signal crayfish (Pacifastacus leniusculus) and the red swamp crayfish (Procambarus clarkii). Location: Europe. Methods: We used boosted regression trees to evaluate the relative influence of, and relationship between, the invader's current pattern of distribution and a set of spatially explicit variables considered important to their colonization success. These variables are related to four well-known invasion hypotheses, namely the role of propagule pressure, climate matching, biotic resistance from known competitors, and human disturbance. Results: Model predictions attained a high accuracy for the two invaders (mean AUC ≥ 0.91). Propagule pressure and climatic suitability were identified as the primary drivers of colonization, but the former had a much higher relative influence on the red swamp crayfish. Climate matching was shown to have limited predictive value and climatic suitability models based on occurrences from other invaded areas had consistently higher relative explanatory power than models based on native range data. Biotic resistance and human disturbance were also shown to be weak predictors of the distribution of the two invaders. Main conclusions: These results contribute to our general understanding of the factors that enable certain species to become notable invaders. Being primarily driven by propagule pressure and climatic suitability, we expect that, given their continued dispersal, the future distribution of these problematic decapods in Europe will increasingly represent their fundamental climatic niche.

    Keywords: biotic resistance, climate matching, crayfish, freshwater invasions, human disturbance, pacifastacus leniusculus, procambarus clarkii, propagule pressure, red swamp, signal crayfish