Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from Portugal.
For all researches, please visit our "Peer-reviewed publications" page.

List of publications

  • Almada F, Francisco S, Lima C, FitzGerald R, Mirimin L, Villegas-Ríos D et al. (2017)

    Historical gene flow constraints in a northeastern Atlantic fish: phylogeography of the ballan wrasse Labrus bergylta across its distribution range

    Royal Society Open Science 4(2) 160773.

    The distribution and demographic patterns of marine organisms in the north Atlantic were largely shaped by climatic changes during the Pleistocene, when recurrent glacial maxima forced them to move south or to survive in northern peri-glacial refugia. These patterns were also influenced by biological and ecological factors intrinsic to each species, namely their dispersion ability. The ballan wrasse (Labrus bergylta), the largest labrid fish along Europe's continental margins, is a target for fisheries and aquaculture industry. The phylogeographic pattern, population structure, potential glacial refugia and recolonization routes for this species were assessed across its full distribution range, using mitochondrial and nuclear markers. The existence of a marked population structure can reflect both recolonization from three distinct glacial refugia and current and past oceanographic circulation patterns. Although isolated in present times, shared haplotypes between continental and Azores populations and historical exchange of migrants in both directions point to a common origin of L. bergylta. This situation is likely to be maintained and/or accentuated by current circulation patterns in the north Atlantic, and may lead to incipient speciation in the already distinct Azorean population. Future monitoring of this species is crucial to evaluate how this species is coping with current environmental changes.

    Keywords: Azorean distinctiveness, Labridae, cleaner fish, glacial refugia, incipient speciation, population structure


  • Araújo R, Assis J, Aguillar R, Airoldi L, Bárbara I, Bartsch I et al. (2016)

    Status, trends and drivers of kelp forests in Europe: an expert assessment

    Biodiversity and Conservation 25(7) 1319-1348.

    A comprehensive expert consultation was conducted in order to assess the status, trends and the most important drivers of change in the abundance and geographical distribution of kelp forests in European waters. This consultation included an on-line questionnaire, results from a workshop and data provided by a selected group of experts working on kelp forest mapping and eco-evolutionary research. Differences in status and trends according to geographical areas, species identity and small-scale variations within the same habitat where shown by assembling and mapping kelp distribution and trend data. Significant data gaps for some geographical regions, like the Mediterranean and the southern Iberian Peninsula, were also identified. The data used for this study confirmed a general trend with decreasing abundance of some native kelp species at their southern distributional range limits and increasing abundance in other parts of their distribution (Saccharina latissima and Saccorhiza polyschides). The expansion of the introduced species Undaria pinnatifida was also registered. Drivers of observed changes in kelp forests distribution and abundance were assessed using experts’ opinions. Multiple possible drivers were identified, including global warming, sea urchin grazing, harvesting, pollution and fishing pressure, and their impact varied between geographical areas. Overall, the results highlight major threats for these ecosystems but also opportunities for conservation. Major requirements to ensure adequate protection of coastal kelp ecosystems along European coastlines are discussed, based on the local to regional gaps detected in the study.

    Keyword: Kelp forests Expert consultation Status and tempor


  • Boavida J, Assis J, Silva I, Serrão E, Martin C, Bongaerts P et al. (2016)

    Overlooked habitat of a vulnerable gorgonian revealed in the Mediterranean and Eastern Atlantic by ecological niche modelling

    Scientific Reports 6 36460.

    Factors shaping the distribution of mesophotic octocorals (30–200 m depth) remain poorly understood, potentially leaving overlooked coral areas, particularly near their bathymetric and geographic distributional limits. Yet, detailed knowledge about habitat requirements is crucial for conservation of sensitive gorgonians. Here we use Ecological Niche Modelling (ENM) relating thirteen environmental predictors and a highly comprehensive presence dataset, enhanced by SCUBA diving surveys, to investigate the suitable habitat of an important structuring species, Paramuricea clavata, throughout its distribution (Mediterranean and adjacent Atlantic). Models showed that temperature (11.5–25.5 °C) and slope are the most important predictors carving the niche of P. clavata. Prediction throughout the full distribution (TSS 0.9) included known locations of P. clavata alongside with previously unknown or unreported sites along the coast of Portugal and Africa, including seamounts. These predictions increase the understanding of the potential distribution for the northern Mediterranean and indicate suitable hard bottom areas down to >150 m depth. Poorly sampled habitats with predicted presence along Algeria, Alboran Sea and adjacent Atlantic coasts encourage further investigation. We propose that surveys of target areas from the predicted distribution map, together with local expert knowledge, may lead to discoveries of new P. clavata sites and identify priority conservation areas.

    Keyword: Kelp forests Expert consultation Status and tempor


  • Caperta A, Castro S, Loureiro J, Róis A, Conceição S, Costa J et al. (2016)

    Biogeographical, ecological and ploidy variation in related asexual and sexual Limonium taxa ( Plumbaginaceae )

    Botanical Journal of the Linnean Society.

    Limonium is a widespread genus of halophytes and taxa found on the Atlantic coast include sexual diploids of the L. ovalifolium complex, agamospermous tetraploids of the L. binervosum complex and the triploid L. algarvense. In this study, we investigated: (1) cytotype distribution and diversity within and among populations in an overlapping region of diploid and polyploid Limonium spp. in south-western Iberia and north-western Morocco; and (2) patterns of geographical parthenogenesis and ecological preferences across a latitudinal gradient on the Atlantic coast. We show here for the first time that L. nydeggeri and L. algarvense are found further south in Morocco than previously reported. Genome size and ploidy estimates showed that the distribution of these species is not random at the overlapping region studied: tetraploid apomicts tend to be found at higher latitudes than the sexual diploids and L. algarvense grows in sympatry at the southern boundaries of the diploids. Natural populations showed a constancy in ploidy in these complexes. However, we report for the first time the occurrence of mixed-ploidy populations of L. ovalifolium s.l., euploid triploids in L. algarvense and aneuploids in the L. binervosum complex. On the Atlantic coasts, L. algarvense followed by L. ovalifolium complexes occur significantly more frequently in thermomediterranean and dry ombrotype habitats than the L. binervosum complex. Significant differences were also observed among taxa in the frequency of occurrences on the most common lithological groups. In conclusion, this work presents the first biogeographical insights for the group based in a coarse-scale analysis of data and it provides evidence of ecological differentiation between the studied Limonium complexes.

    Keywords: agamospecies, apomixis, biogeography, chromosome base numbers, cytotypes, ecological characteristics, geographical distribution, habitat, polyploidy


  • Gilles D, Zaiss R, Blach-Overgaard A, Catarino L, Damen T, Deblauwe V et al. (2016)

    RAINBIO: a mega-database of tropical African vascular plants distributions

    PhytoKeys 74 1-18.

    The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

    Keywords: Herbarium specimens, biodiversity assessmen, cultivated species, digitization, georeferencing, habit, native species, taxonomic backbone, tropical forests


  • Henriques Antão L, Connolly S, Magurran A, Soares A, Dornelas M (2016)

    Prevalence of multimodal species abundance distributions is linked to spatial and taxonomic breadth

    Global Ecology and Biogeography.

    Aim Species abundance distributions (SADs) are a synthetic measure of biodiversity and community structure. Although typically described by unimodal logseries or lognormal distributions, empirical SADs can also exhibit multiple modes. However, we do not know how prevalent multimodality is, nor do we have an understanding of the factors leading to this pattern. Here we quantify the prevalence of multimodality in SADs across a wide range of taxa, habitats and spatial extents. Location Global. Methods We used the second-order Akaike information criterion for small sample sizes (AICc) and likelihood ratio tests (LRTs) to test whether models with more than one mode accurately describe the empirical abundance frequency distributions of the underlying communities. We analysed 117 empirical datasets from intensely sampled communities, including taxa ranging from birds, plants, fish and invertebrates, from terrestrial, marine and freshwater habitats. Results We find evidence for multimodality in 14.5% of the SADs when using AICc and LRT. This is a conservative estimate, as AICc alone estimates a prevalence of multimodality of 22%. We additionally show that the pattern is more common in data encompassing broader spatial scales and greater taxonomic breadth, suggesting that multimodality increases with ecological heterogeneity. Main conclusions We suggest that higher levels of ecological heterogeneity, underpinned by larger spatial extent and higher taxonomic breadth, can yield multimodal SADs. Our analysis shows that multimodality occurs with a prevalence that warrants its systematic consideration when assessing SAD shape and emphasizes the need for macroecological theories to include multimodality in the range of SADs they predict.

    Keywords: Community structure, Poisson lognormal mixture, diversity patterns, lognormal, logseries, spatial scale, taxonomic breadth


  • Jaffé R, Pope N, Acosta A, Alves D, Arias M, De la Rúa P et al. (2016)

    Beekeeping practices and geographic distance, not land use, drive gene flow across tropical bees

    Molecular Ecology.

    Across the globe, wild bees are threatened by ongoing natural habitat loss, risking the maintenance of plant biodiversity and agricultural production. Despite the ecological and economic importance of wild bees and the fact that several species are now managed for pollination services worldwide, little is known about how land use and beekeeping practices jointly influence gene flow. Using stingless bees as a model system, containing wild and managed species that are presumed to be particularly susceptible to habitat degradation, here we examine the main drivers of tropical bee gene flow. We employ a novel landscape genetic approach to analyse data from 135 populations of 17 stingless bee species distributed across diverse tropical biomes within the Americas. Our work has important methodological implications, as we illustrate how a maximum-likelihood approach can be applied in a meta-analysis framework to account for multiple factors, and weight estimates by sample size. In contrast to previously held beliefs, gene flow was not related to body size or deforestation, and isolation by geographic distance (IBD) was significantly affected by management, with managed species exhibiting a weaker IBD than wild ones. Our study thus reveals the critical importance of beekeeping practices in shaping the patterns of genetic differentiation across bee species. Additionally, our results show that many stingless bee species maintain high gene flow across heterogeneous landscapes. We suggest that future efforts to preserve wild tropical bees should focus on regulating beekeeping practices to maintain natural gene flow and enhancing pollinator-friendly habitats, prioritizing species showing a limited dispersal ability.

    Keywords: beekeeping, dispersal, land use, landscape genetics, pollination, stingless bees


  • Leite Y, Costa L, Loss A, Rocha R, Batalha-Filho H, Bastos A et al. (2016)

    Neotropical forest expansion during the last glacial period challenges refuge hypothesis.

    Proceedings of the National Academy of Sciences of the United States of America 1513062113-.

    The forest refuge hypothesis (FRH) has long been a paradigm for explaining the extreme biological diversity of tropical forests. According to this hypothesis, forest retraction and fragmentation during glacial periods would have promoted reproductive isolation and consequently speciation in forest patches (ecological refuges) surrounded by open habitats. The recent use of paleoclimatic models of species and habitat distributions revitalized the FRH, not by considering refuges as the main drivers of allopatric speciation, but instead by suggesting that high contemporary diversity is associated with historically stable forest areas. However, the role of the emerged continental shelf on the Atlantic Forest biodiversity hotspot of eastern South America during glacial periods has been ignored in the literature. Here, we combined results of species distribution models with coalescent simulations based on DNA sequences to explore the congruence between scenarios of forest dynamics through time and the genetic structure of mammal species cooccurring in the central region of the Atlantic Forest. Contrary to the FRH predictions, we found more fragmentation of suitable habitats during the last interglacial (LIG) and the present than in the last glacial maximum (LGM), probably due to topography. We also detected expansion of suitable climatic conditions onto the emerged continental shelf during the LGM, which would have allowed forests and forest-adapted species to expand. The interplay of sea level and land distribution must have been crucial in the biogeographic history of the Atlantic Forest, and forest refuges played only a minor role, if any, in this biodiversity hotspot during glacial periods.

    Keywords: Atlantic Forest, Quaternary, continental shelf, last glacial maximum, sea level


  • Lessmann J, Guayasamin J, Casner K, Flecker A, Funk W, Ghalambor C et al. (2016)

    Freshwater vertebrate and invertebrate diversity patterns in an Andean-Amazon basin: implications for conservation efforts

    Neotropical Biodiversity 2(1) 99-114.

    The Napo Basin in Ecuador is an important drainage of the Amazon Basin, the most biodiverse ecosystem for freshwater species. At the same time, this basin has conspicuous information gaps on its biodiversity patterns and human threats. Here, we estimated the diversity distribution patterns of freshwater vertebrates and invertebrates in the Napo Basin, as a tool for present and future management and conservation efforts. Also, we assessed the spatial congruence of the diversity patterns observed between aquatic vertebrates and invertebrates. For this, we compiled occurrence records for 481 freshwater vertebrate species (amphibians, birds, mammals, reptiles, and fish), and 54 invertebrate families obtained across an altitudinal gradient of the basin (200–4500 m). Using these occurrence records and environmental variables, we modeled the distribution of each vertebrate species and invertebrate family. Then, we stacked these distributions to build species richness maps for vertebrates, and a family richness m...

    Keywords: Ecuador, Napo Basin, aquatic invertebrate families, freshwater tropical ecosystems, vertebrate species


  • Marques I, Draper D, López-Herranz M, Garnatje T, Segarra-Moragues J, Catalán P et al. (2016)

    Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

    Scientific Reports 6 36283.

    Apart from the overwhelming cases of allopolyploidization, the impact of speciation through homoploid hybridization is becoming more relevant than previously thought. Much less is known, however, about the impact of climate changes as a driven factor of speciation. To investigate these issues, we selected Festuca picoeuropeana, an hypothetical natural hybrid between the diploid species F. eskia and F. gautieri that occurs in two different mountain ranges (Cantabrian Mountains and Pyrenees) separated by more than 400 km. To unravel the outcomes of this mode of speciation and the impact of climate during speciation we used a multidisciplinary approach combining genome size and chromosome counts, data from an extensive nuclear genotypic analysis, plastid sequences and ecological niche models (ENM). Our results show that the same homoploid hybrid was originated independently in the two mountain ranges, being currently isolated from both parents and producing viable seeds. Parental species had the opportunity to contact as early as 21000 years ago although niche divergence occurs nowadays as result of a climate-driven shift. A high degree of niche divergence was observed between the hybrid and its parents and no recent introgression or backcrossed hybrids were detected, supporting the current presence of reproductive isolation barriers between these species.

    Keywords: Ecuador, Napo Basin, aquatic invertebrate families, freshwater tropical ecosystems, vertebrate species