Uses of GBIF in scientific research

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

List of publications

  • Beatty, G., Lennon, J., O'Sullivan, C., Provan, J., 2015.

    The not-so-Irish spurge: Euphorbia hyberna (Euphorbiaceae) and the Littletonian plant ‘steeplechase’

    Biological Journal of the Linnean Society 114(2) 249-259.

    The disjunct distributions of the Lusitanian flora, which are found only in south-west Ireland and northern Iberia, and are generally absent from intervening regions, have been of great interest to biogeographers. There has been much debate as to whether Irish populations represent relicts that survived the Last Glacial Maximum (LGM; approximately 21 kya), or whether they recolonized from southern refugia subsequent to the retreat of the ice and, if so, whether this occurred directly (i.e. the result of long distance dispersal) or successively (i.e. in the manner of a ‘steeplechase’, with the English Channel and Irish Sea representing successive ‘water-jumps’ that have to be successfully crossed). In the present study, we used a combined palaeodistribution modelling and phylogeographical approach to determine the glacial history of the Irish spurge, Euphorbia hyberna, the sole member of the Lusitanian flora that is also considered to occur naturally in south-western England. Our findings suggest that the species persisted through the LGM in several southern refugia, and that northern populations are the result of successive recolonization of Britain and Ireland during the postglacial Littletonian warm stage, akin to the ‘steeplechase’ hypothesis

    Keywords: Last Glacial Maximum, Lusitanian flora, palaeodistribution modelling, phylogeography


  • Kandel, K., Huettmann, F., Suwal, M., Ram Regmi, G., Nijman, V., Nekaris, K., Lama, S., Thapa, A., Sharma, H., Subedi, T., 2015.

    Rapid multi-nation distribution assessment of a charismatic conservation species using open access ensemble model GIS predictions: Red panda (Ailurus fulgens) in the Hindu-Kush Himalaya region

    Biological Conservation 181 150-161.

    The red panda (Ailurus fulgens) is a globally threatened species living in the multi-national Hindu-Kush Himalaya (HKH) region. It has a declining population trend due to anthropogenic pressures. Human-driven climate change is expected to have substantial impacts. However, quantitative and transparent information on the ecological niche (potential as well as realized) of this species across the vast and complex eight nations of the HKH region is lacking. Such baseline information is not only crucial for identifying new populations but also for restoring locally-extinct populations, for understanding its bio-geographical evolution, as well as for prioritizing regions and an efficient management. First we compiled, and made publicly available through an institutional repository (dSPACE), the best known ‘presence only’ red panda dataset with ISO compliant metadata. This was done through the International Centre for Integrated Mountain Development (ICIMOD.org) data-platform to the Global Biodiversity Information Facility (GBIF.org). We used data mining and machine learning algorithms such as high-performance commercial Classification and Regression Trees, Random Forest, TreeNet, and Multivariate Adaptive Regression Splines implementations. We averaged all these Geographic Information System (GIS) models for the first produced ensemble model for this species in the HKH region. Our predictive model is the first of its kind and allows to assess the red panda distribution based on empirical open access data, latest methods and the major signals and drivers of the ecological niche. It allows to assess and fine-tune earlier habitat area estimates. Our models promote ‘best professional practices’. It can readily be used by the red panda Recovery Team, the red panda Action Plan, etc. because they are robust, transparent, publicly available, fit for use, and have a good accuracy, as judged by several independent assessment metrics (Receiver Operating Characteristics (ROC-AUC) curves, expert opinion, assessed by known absence regions, 95% confidence intervals and new field data).

    Keywords: Ensemble model GIS prediction, Hindu-Kush Himalaya (HKH), Machine learning, Open access GBIF data, Red panda (Ailurus fulgens)


  • Onstein, R., Carter, R., Xing, Y., Richardson, J., Linder, H., 2015.

    Do Mediterranean-type ecosystems have a common history? - insights from the Buckthorn family (Rhamnaceae).

    Evolution; international journal of organic evolution.

    Mediterranean-type ecosystems (MTEs) are remarkable in their species-richness and endemism, but the processes which have led to this diversity remain enigmatic. Here, we hypothesize that continent-dependent speciation and extinction rates have led to disparity in diversity between the five MTEs of the world: the Cape, California, Mediterranean Basin, Chile and Western Australia. To test this hypothesis, we built a phylogenenetic tree for 280 Rhamnaceae species, estimated divergence times using eight fossil calibrations and use Bayesian methods and simulations to test for differences in diversification rates. Rhamnaceae lineages in MTEs generally show higher diversification rates than elsewhere, but speciation and extinction dynamics show a pattern of continent-dependence. We detected high speciation and extinction rates in California and significantly lower extinction rates in the Cape and Western Australia. The independent colonization of four out of five MTEs may have occurred conterminously in the Oligocene/Early Miocene, but colonization of the Mediterranean Basin happened later, in the Late Miocene. This suggests that the in situ radiations of these clades were initiated before the onset of winter-rainfall in these regions. These results indicate independent evolutionary histories of Rhamnaceae in MTEs, possibly related to the intensity of climate oscillations and the geological history of the regions. This article is protected by copyright. All rights reserved.

    Keywords: Californian Floristic Province, Cape, Western Australia, diversification rate, extinction, speciation


  • Orlova-Bienkowskaja, M., Ukrainsky, A., Brown, P., 2015.

    Harmonia axyridis (Coleoptera: Coccinellidae) in Asia: a re-examination of the native range and invasion to southeastern Kazakhstan and Kyrgyzstan

    Biological Invasions.

    Harmonia axyridis (Pallas) is an invasive ladybird spreading in several continents. It is native to East Asia, but its range in Asia has until now been poorly understood. The most complete map of the range of Harmonia axyridis in Asia has been compiled (432 localities). Harmonia axyridis occurs in the south-east of West Siberia, the south of East Siberia, the south of Russian Far East, the east of Kazakhstan, the north of Kyrgyzstan, Mongolia, China, North Korea, South Korea, Japan, and the north of Vietnam. Southeastern Kazakhstan and the north of Kyrgyzstan are not a part of the native range: the large Balkhash Desert is situated between this mountainous region and the nearest part of the native range (Altai mountains). The analysis of dates and places of findings indicates that Harmonia axyridis appeared in southeastern Kazakhstan and Kyrgyzstan after the construction of the Turkestan-Siberian Railway. It is hypothesized that the beetles crossed the desert along this railway.

    Keywords: Coccinellidae, Harlequin ladybird, Harmonia axyridis, Invasive species, Multicolored Asian lady beetle, Native range


  • Allen, L., May, R., Ortega, J., Burdekin, O., 2014.

    A preliminary geographic distribution map of Elachistocleis muiraquitan Nunes de Almeida & Toledo, 2012 (Amphibia: Anura: Microhylidae)

    Check List 10(2) 388-391.

    Elachistocleis muiraquitan was recently described from fifteen specimens found at two sites in Acre state, northwestern Brazil. Prior to the description of E. muiraquitan, individuals fitting the description of this species found in southeastern Peru and northwestern Bolivia were identified as Elachistocleis bicolor, a species associated with markedly different habitat and environmental conditions. Here, we re-identified these specimens and also propose the first map of E. muiraquitan’s potential distribution, based on known localities along with climatic and environmental parameters.

    Keywords: Coccinellidae, Harlequin ladybird, Harmonia axyridis, Invasive species, Multicolored Asian lady beetle, Native range


  • Amirkia, V., Heinrich, M., 2014.

    Alkaloids as drug leads – A predictive structural and biodiversity-based analysis

    Phytochemistry Letters Forthcoming.

    The process of drug discovery and development particularly that of natural products, has evolved markedly over the last 30 years into increasingly formulaic approaches. As a major class of natural products initially discovered and used as early as 4000 years ago, alkaloids and the species they are derived from have been used worldwide as a source of remedies to treat a wide variety of illnesses. Yet, a tremendously wide discrepancy between their historical significance and their occurrence in modern drug development exists. Are alkaloids underrepresented in modern medicine? The physicochemical features of 27,683 alkaloids from the Dictionary of Natural Products were cross- referenced to pharmacologically significant and other metrics from various databases including the European Bioinformatics Institute’s ChEMBL and Global Biodiversity Information Facility’s GBIF. For the first time we show that market/developmental performance of a class of compounds is linked to its biodiversity distributions, as defined by the GBIF dataset. The potential of such a large-scale data analysis is analyzed against both prevalent rules used to guide drug discovery processes and the larger context of natural product development.

    Keywords: Biodiversity, Drug discovery, Drug-likeness, Modeling, Natural products, Secondary metabolites, alkaloid development


  • Antunes Carvalho, F., Filer, D., Renner, S., 2014.

    Taxonomy in the electronic age and an e-monograph of the papaya family (Caricaceae) as an example

    Cladistics Forthcoming.

    The need for taxonomists to take full advantage of biodiversity informatics has been clear for at least 10 years. Significant progress has been made in providing access to taxonomic resources online, including images of specimens (especially types), ori- ginal species descriptions, and georeferenced collection data. However, in spite of persuasive calls for e-monography, there are few, if any, completed project, even though monographic research is the only mechanism for reducing synonymous names, which are estimated to comprise 50% of all published names. Caricaceae is an economically important family of flowering plants from Africa and the Neotropics, best known for the fruit crop papaya. There is a large amount of information on the family, espe- cially on chemistry, crop improvement, genomics, and the sex chromosomes of papaya, but up-to-date information on the 230 names and which species they might belong to was not available. A dynamically updated e-monograph of the Caricaceae now brings together all information on this family, including keys, species descriptions, and specimen data relating the 230 names to 34 species and one hybrid. This may be the first taxonomic monograph of a plant family completely published online. The curated information will be continuously updated to improve the monograph’s comprehensiveness and utility.

    Keywords: Biodiversity, Drug discovery, Drug-likeness, Modeling, Natural products, Secondary metabolites, alkaloid development


  • Ashford, O., Davies, A., Jones, D., 2014.

    Deep-sea benthic megafaunal habitat suitability modelling: A global-scale maximum entropy model for xenophyophores

    Deep Sea Research Part I: Oceanographic Research Papers 94 31-44.

    Xenophyophores are a group of exclusively deep-sea agglutinating rhizarian protozoans, at least some of which are foraminifera. They are an important constituent of the deep-sea megafauna that are sometimes found in sufficient abundance to act as a significant source of habitat structure for meiofaunal and macrofaunal organisms. This study utilised maximum entropy modelling (Maxent) and a high-resolution environmental database to explore the environmental factors controlling the presence of Xenophyophorea and two frequently sampled xenophyophore species that are taxonomically stable: Syringammina fragilissima and Stannophyllum zonarium. These factors were also used to predict the global distribution of each taxon. Areas of high habitat suitability for xenophyophores were highlighted throughout the world's oceans, including in a large number of areas yet to be suitably sampled, but the Northeast and Southeast Atlantic Ocean, Gulf of Mexico and Caribbean Sea, the Red Sea and deep-water regions of the Malay Archipelago represented particular hotspots. The two species investigated showed more specific habitat requirements when compared to the model encompassing all xenophyophore records, perhaps in part due to the smaller number and relatively more clustered nature of the presence records available for modelling at present. The environmental variables depth, oxygen parameters, nitrate concentration, carbon-chemistry parameters and temperature were of greatest importance in determining xenophyophore distributions, but, somewhat surprisingly, hydrodynamic parameters were consistently shown to have low importance, possibly due to the paucity of well-resolved global hydrodynamic datasets. The results of this study (and others of a similar type) have the potential to guide further sample collection, environmental policy, and spatial planning of marine protected areas and industrial activities that impact the seafloor, particularly those that overlap with aggregations of these conspicuously large single-celled eukaryotes.

    Keywords: Maxent, Stannophyllum zonarium, Syringammina fragilissima, Xenophyophorea, species distribution modelling


  • Beatty, G., Provan, J., 2014.

    Phylogeographical analysis of two cold-tolerant plants with disjunct Lusitanian distributions does not support in situ survival during the last glaciation

    Journal of Biogeography 41(11) 2185-2193.

    Aim: We used a combination of modelling and genetic approaches to investigate whether Pinguicula grandiflora and Saxifraga spathularis, two species that exhibit disjunct Lusitanian distributions, may have persisted through the Last Glacial Maximum (LGM, c. 21 ka) in separate northern and southern refugia. Location: Northern and eastern Spain and south-western Ireland. Methods: Palaeodistribution modelling using Maxent was used to identify putative refugial areas for both species at the LGM, as well as to estimate their distributions during the Last Interglacial (LIG, c. 120 ka). Phylogeographical analysis of samples from across both species' ranges was carried out using one chloroplast and three nuclear loci for each species. Results: The palaeodistribution models identified very limited suitable habitat for either species during the LIG, followed by expansion during the LGM. A single, large refugium across northern Spain and southern France was postulated for P. grandiflora. Two suitable regions were identified for S. spathularis: one in northern Spain, corresponding to the eastern part of the species' present-day distribution in Iberia, and the other on the continental shelf off the west coast of Brittany, south of the limit of the British–Irish ice sheet. Phylogeographical analyses indicated extremely reduced levels of genetic diversity in Irish populations of P. grandiflora relative to those in mainland Europe, but comparable levels of diversity between Irish and mainland European populations of S. spathularis, including the occurrence of private hapotypes in both regions. Main conclusions: Modelling and phylogeographical analyses indicate that P. grandiflora persisted through the LGM in a southern refugium, and achieved its current Irish distribution via northward dispersal after the retreat of the ice sheets. Although the results for S. spathularis are more equivocal, a similar recolonization scenario also seems the most likely explanation for the species' current distribution.

    Keywords: Large-flowered butterwort, Last Glacial Maximum, Lusitanian flora, Pinguicula grandiflora, Saxifraga spathularis, St. Patrick’s cabbage, palaeodistribution modelling, phylogeography, refugia


  • Borges, L., Sivrikaya, H., Cragg, S., 2014.

    First records of the warm water shipworm Teredo bartschi Clapp, 1923 (Bivalvia, Teredinidae) in Mersin, southern Turkey and in Olhão, Portugal

    Bioinvasion Records 3(1) 25-28.

    Bivalves of the family Teredinidae are among the most destructive wood-boring species in the sea. We report the first occurrences of the warm-water shipworm Teredo bartschi in Mersin, Turkey, and Olhão, Portugal. The colonisation of the site in Mersin is likely to have occurred by rafting adults originating from the Red Sea, which passed through the Suez Canal (lessepsian migrants). T. bartschi might have been introduced in Olhão Harbour, Portugal, either by rafting adults with larvae transported by currents or by larvae transported by ships in ballast water. These seem to be the first published records of established T. bartschi populations in the Mediterranean and in northeast Atlantic.

    Keywords: mediterranean sea, northeast atlantic ocean, shipworms, teredinids, teredo bartschi