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

  • Ruedas L, Silva S, French J, Platt ii R, Salazar–bravo J, Mora J et al. (2017)



    A critical issue with species names derived from Linnaeus’ 10th edition of the Systema Naturae is the lack of holotypes, which in many instances has led to taxonomic confusion and uncertainty, as well as an unstable taxonomy. In the particular case of the South American cottontail, currently known as Sylvilagus brasiliensis, Linnaeus listed the type locality as “America Meridionali,” or South America. As a result, S. brasiliensis was ascribed a widespread distribution in North and South America, over an area estimated as approximately 1.09 × 107 Km2, and containing upwards of 37 named subspecies. In order to stabilize the taxonomy and initiate the process of illumination of evolutionary and biogeographic relationships among the South American cottontails, we designate herein a neotype for S. brasiliensis. Because the original description by Linnaeus was based on the posthumously published 1648 work of Georg Marcgraff, we restrict the type locality of S. brasiliensis to coastal Pernambuco State, near Recife, where Marcgraff largely was based. We select and describe a neotype from that area, speci cally from a forest fragment in the Pernambuco Endemism Center of the Atlantic Forest Biome, collected at ca. 7o50′38.4′′S, 35o6′7.3′′W, elevation: ca. 137 m. Niche modeling suggests that S. brasiliensis as thus de ned may have a much more restricted range of 500–700 Km2, in a narrow distributional band along northern Atlantic coastal Brazil. We compare the neotype of S. brasiliensis to holotype material of S. andinus and S. tapetillus and nd suf cient distinction in characters and measurements between S. brasiliensis, S. andinus, and S. tapetillus, to retain the latter two as valid species level taxa. Molecular phylogenetic analyses based on a limited number of sequences from the mitochondrial 12S rRNA and cytochrome–b genes support the distinction between S. andinus and S. brasiliensis. Genetic distances also support the lack of close relationship between the two taxa, with cytochrome–b showing a patristic distance between the two of ca. 15%, the largest interspeci c distance among Sylvilagus species previously examined for that locus. Our analysis of Lineages Through Time suggests that the vast unreported taxonomic diversity among Tropical Sylvilagus is based on high speciation rates in the genus, combined with unusually low extinction rates. Episodes of explosive speciation in Sylvilagus, hypothesized to be ecologically driven, have been coeval with cooling events at the Miocene–Pliocene transition and following the Piacenzan Warm Period (Late Pliocene) into the Pleistocene; warm periods have in contrast slowed down speciation rates. The status of all described subspecies of S. brasiliensis will require careful scrutiny and comparison with the neotype to ascertain and establish species limits. Because of a lack of specimens of Neotropical Sylvilagus in collections, our study suffers from a typological schema, however, our approach from rst principles—examination of holotypes—not only serves to establish a more stable taxonomic framework for Neotropical Sylvilagus, but also further suggests that many of the existing taxa currently subsumed as subspecies within Sylvilagus brasiliensis likely are valid species in their own right.

    Keywords: Andes, Ecuador, Neotropics, Páramo, biogeography, conservation, taxonomy

  • de Carvalho D, Sousa-Neves T, Cerqueira P, Gonsioroski G, Silva S, Silva D et al. (2017)

    Delimiting priority areas for the conservation of endemic and threatened Neotropical birds using a niche-based gap analysis

    PLOS ONE 12(2) e0171838.

    Knowledge of spatiotemporal distribution of biodiversity is still very incomplete in the tropics. This is one of the major problems preventing the assessment and effectiveness of conservation actions. Mega-diverse tropical regions are being exposed to fast and profound environmental changes, and the amount of resources available to describe the distribution of species is generally limited. Thus, the tropics is losing species at unprecedented rates, without a proper assessment of its biodiversity. Species distribution models (SDMs) can be used to fill such biogeographic gaps within a species’ range and, when allied with systematic conservation planning (e.g. analyses of representativeness, gap analysis), help transcend such data shortage and support practical conservation actions. Within the Neotropics, eastern Amazon and northern Cerrado present a high variety of environments and are some of the most interesting ecotonal areas within South America, but are also among the most threatened biogeographic provinces in the world. Here, we test the effectiveness of the current system of Protected Areas (PAs), in protecting 24 threatened and endemic bird species using SDMs. We found that taxa with wider distributions are potentially as protected as taxa with smaller ranges, and larger PAs were more efficient than smaller PAs, while protecting these bird species. Nonetheless, Cerrado PAs are mostly misallocated. We suggest six priority areas for conservation of Neotropical birds. Finally, we highlight the importance of indigenous lands in the conservation of Neotropical biodiversity, and recommend the development of community management plans to conserve the biological resources of the region.

    Keywords: Biodiversity, Birds, Brazil, Climate change, Conservation science, Ecosystems, Forests, Species diversity

  • 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