Uses of GBIF in scientific research

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

List of publications

  • Huang D, Hoeksema B, Affendi Y, Ang P, Chen C, Huang H et al. (2016)

    Conservation of reef corals in the South China Sea based on species and evolutionary diversity

    Biodiversity and Conservation.

    The South China Sea in the Central Indo-Pacific is a large semi-enclosed marine region that supports an extraordinary diversity of coral reef organisms (including stony corals), which varies spatially across the region. While one-third of the world’s reef corals are known to face heightened extinction risk from global climate and local impacts, prospects for the coral fauna in the South China Sea region amidst these threats remain poorly understood. In this study, we analyse coral species richness, rarity, and phylogenetic diversity among 16 reef areas in the region to estimate changes in species and evolutionary diversity during projected anthropogenic extinctions. Our results show that richness, rarity, and phylogenetic diversity differ considerably among reef areas in the region, and that their outcomes following projected extinctions cannot be predicted by species diversity alone. Although relative rarity and threat levels are high in species-rich areas such as West Malaysia and the Philippines, areas with fewer species such as northern Vietnam and Paracel Islands stand to lose disproportionately large amounts of phylogenetic diversity. Our study quantifies various biodiversity components of each reef area to inform conservation planners and better direct sparse resources to areas where they are needed most. It also provides a critical biological foundation for targeting reefs that should be included in a regional network of marine protected areas in the South China Sea

    Keywords: IUCN Red List, Marine biodiversity, Phylogenetic diversity, Rarity, Scleractinia, Species richness

  • Ahrends A, Hollingsworth P, Ziegler A, Fox J, Chen H, Su Y et al. (2015)

    Current trends of rubber plantation expansion may threaten biodiversity and livelihoods

    Global Environmental Change 34 48-58.

    The first decade of the new millennium saw a boom in rubber prices. This led to rapid and widespread land conversion to monoculture rubber plantations in continental SE Asia, where natural rubber production has increased >50% since 2000. Here, we analyze the subsequent spread of rubber between 2005 and 2010 in combination with environmental data and reports on rubber plantation performance. We show that rubber has been planted into increasingly sub-optimal environments. Currently, 72% of plantation area is in environmentally marginal zones where reduced yields are likely. An estimated 57% of the area is susceptible to insufficient water availability, erosion, frost, or wind damage, all of which may make long-term rubber production unsustainable. In 2013 typhoons destroyed plantations worth US$ >250 million in Vietnam alone, and future climate change is likely to lead to a net exacerbation of environmental marginality for both current and predicted future rubber plantation area. New rubber plantations are also frequently placed on lands that are important for biodiversity conservation and ecological functions. For example, between 2005 and 2010 >2500km2 of natural tree cover and 610km2 of protected areas were converted to plantations. Overall, expansion into marginal areas creates potential for loss-loss scenarios: clearing of high-biodiversity value land for economically unsustainable plantations that are poorly adapted to local conditions and alter landscape functions (e.g. hydrology, erosion) – ultimately compromising livelihoods, particularly when rubber prices fall.

    Keywords: Biodiversity, Cash crops, Deforestation, Rubber, South East Asia

  • Huang D, Roy K (2015)

    The future of evolutionary diversity in reef corals.

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 370(1662) 20140010-.

    One-third of the world's reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in conjunction with geographical distributions of living reef coral species to model how extinctions are likely to affect evolutionary diversity across different ecoregions. Based on two measures-phylogenetic diversity and phylogenetic species variability-we highlight regions with the largest losses of evolutionary diversity and hence of potential conservation interest. Notably, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle, while many regions with fewer species stand to lose much larger shares of their diversity. We also suggest that for complex ecosystems like coral reefs it is important to consider changes in phylogenetic species variability; areas with disproportionate declines in this measure should be of concern even if phylogenetic diversity is not as impacted. These findings underscore the importance of integrating evolutionary history into conservation planning for safeguarding the future diversity of coral reefs.

    Keywords: Scleractinia, coral reef, ecoregions, extinction risk, phylogenetic diversity, tree shape

  • Moonlight P, Richardson J, Tebbitt M, Thomas D, Hollands R, Peng C et al. (2015)

    Continental-scale diversification patterns in a megadiverse genus: the biogeography of Neotropical Begonia

    Journal of Biogeography 42(6) 1137-1149.

    Aim The origin of Neotropical hyperdiversity is one of the most intriguing questions in modern biogeography and is best answered through the investigation of large, pantropically distributed genera, allowing the comparison of closely related clades in different regions. We produced a dated phylogeny and reconstructed ancestral ranges of the megadiverse, Andean-centred genus Begonia to discern its dispersal history throughout the Neotropics and correlates of range evolution. Neotropical and Palaeotropical diversification rates were estimated. Location Neotropics: Central America, South America, West Indies and Mexico. Methods Plastid DNA sequence data from species representing the full geographical range and majority of sections of Neotropical Begonia were analysed with a secondarily calibrated relaxed molecular clock in order to estimate the age of crown groups and divergence times within Neotropical Begonia. Ancestral areas were reconstructed with a Bayesian approach to dispersal–vicariance analysis, a likelihood framework under a dispersal–extinction–cladogenesis model, and a Bayesian binary method. Diversification rates were estimated under a Bayesian framework. Results Biogeographical reconstruction indicated two independent trans-Atlantic colonizations of the Neotropics from Africa. Early-diverging lineages of both clades are reconstructed as having diversified in the mid-Miocene, with multiple dispersal events between the Brazilian Atlantic rain forest and the Andes, and single radiations within the West Indies and Central America plus Mexico. Main conclusions Begonia displays numerous radiations within regions, punctuated by long-distance dispersal. Successful colonization and diversification is predicted by the presence of upland habitat. Recognizing the role of chance dispersal events between available habitats is vital for understanding the formation of current biogeographical patterns.

    Keywords: Ancestral area reconstruction, Begonia, Neotropics, dispersal, diversification, historical biogeography, hybridization

  • Silva D, Macêdo A, Ascher J, De Marco P (2015)

    Range increase of a Neotropical orchid bee under future scenarios of climate change

    Journal of Insect Conservation.

    Along with other human impacts, climate change is an important driver of biological changes worldwide and is expected to severely affect species distributions. Although dramatic range shifts and contractions are predicted for many taxa occurring at higher latitudes, including bumble bees, the response of widespread tropical species is less clear due in part to scarcity of reliable occurrence data. Newly mobilized specimen records and improved species distribution models facilitate more robust assessment of future climate effects under various scenarios. Here, we predict both current and future distribution of the orchid bee Eulaema nigrita Lepeletier, 1841 (Apidae: Euglossinae), a large-bodied species widely distributed in the Neotropics whose populations within the Amazon region are believed to be controlled by cleptoparasitic Euglossini bees, such as Exaerete smaragdina Guérin-Menéville, 1844 and Aglae caerulea Lepeletier and Serville, 1825. Under both current and future scenarios of climate change, El. nigrita is expected to persist in deforested areas including those that might suffer desertification. While under current climatic conditions this species is not expected to occur in central Amazonia where the forest is still conserved, its range is expected to increase under future scenarios of climate change, especially in areas corresponding to the arc of deforestation in eastern Amazonia. The increase of human-related disturbances in this biome, as well as changes in the relationship of El. nigrita–Ex. smaragdina and El. nigrita–A. caerulea may explain the potential range increase of El. nigrita under future scenarios of climate change.

    Keywords: Amazon, Brazil, Climate change, Deforestation, Euglossini, Species distribution models

  • Watson S, Morley S, Bates A, Clark M, Day R, Lamare M et al. (2014)

    Low global sensitivity of metabolic rate to temperature in calcified marine invertebrates

    Oecologia 174(1) 45-54.

    Metabolic rate is a key component of energy budgets that scales with body size and varies with large-scale environmental geographical patterns. Here we conduct an analysis of standard metabolic rates (SMR) of marine ectotherms across a 70° latitudinal gradient in both hemispheres that spanned collection temperatures of 0-30 °C. To account for latitudinal differences in the size and skeletal composition between species, SMR was mass normalized to that of a standard-sized (223 mg) ash-free dry mass individual. SMR was measured for 17 species of calcified invertebrates (bivalves, gastropods, urchins and brachiopods), using a single consistent methodology, including 11 species whose SMR was described for the first time. SMR of 15 out of 17 species had a mass-scaling exponent between 2/3 and 1, with no greater support for a 3/4 rather than a 2/3 scaling exponent. After accounting for taxonomy and variability in parameter estimates among species using variance-weighted linear mixed effects modelling, temperature sensitivity of SMR had an activation energy (Ea) of 0.16 for both Northern and Southern Hemisphere species which was lower than predicted under the metabolic theory of ecology (Ea 0.2-1.2 eV). Northern Hemisphere species, however, had a higher SMR at each habitat temperature, but a lower mass-scaling exponent relative to SMR. Evolutionary trade-offs that may be driving differences in metabolic rate (such as metabolic cold adaptation of Northern Hemisphere species) will have important impacts on species abilities to respond to changing environments.

    Keywords: Amazon, Brazil, Climate change, Deforestation, Euglossini, Species distribution models

  • Wijedasa, L., Shee, Z. Q., Chia E (2014)

    Conservation status and lectotypfication of Alangium ridleyi (Cornaceae) in Singapore | Lahiru Wijedasa -

    Gardens’ Bulletin Singapore 66(2) 233 - 239.

    Alangium ridleyi King is lectotypied and the conservation status updated from Nationally Extinct to Endangered in Singapore and Endangered in Peninsula Malaysia

    Keywords: Alangium ridleyi King, Endangered, lectotypicatio

  • Polgar G, Jaafar Z, Konstantinidis P (2013)

    A New Species Of Mudskipper, Boleophthalmus Poti (Teleostei: Gobiidae: Oxudercinae) From The Gulf Of Papua, Papua New Guinea, And A Key To The Genus

    The Raffles Bulletin of Zoology 61(1) 311-321.

    Boleophthalmus poti, new species, is described from the Gulf of Papua, Papua New Guinea. It is distinguished from its congeners by a combination of characters, including: un-notched, fl attened and horizontally disposed dentary teeth; pelvic-disc length ~10% of SL; D1 base length ~15% of SL; D2 base length ~40% of SL; ~5 interdorsal scale rows; ~110 lateral-scale rows; and the shape and colour pattern of the fi rst and second dorsal fi ns.

    Keywords: amphibious gobies, boleophthalmus, fly river delta, oxudercine gobies, taxonomy

  • Harris J, Yong D, Sheldon F, Boyce A, Eaton J, Bernard H et al. (2012)

    Using diverse data sources to detect elevational range changes of birds on Mount Kinabalu, Malaysian Borneo

    The Raffles Bulletin of Zoology(25) 197-247.

    Few empirical studies have measured the effects of climate change on tropical biodiversity, and this paucity has contributed to uncertainty in predicting the severity of climate change on tropical organisms. With regards to elevational changes, most studies have either re-sampled historical systematic survey sites or analyzed time series of occurrence data at long-term study sites. Such data sources are unavailable for most tropical mountains, so other methods of detecting elevational changes must be sought. Here we combine data from published checklists, recent fi eld work, peer-reviewed literature, unpublished reports, birdwatchers’ trip reports, databases of birdwatchers’ observations, audio recordings, and photographs to compare historical (pre-1998) and current (post-2006) bird distributions on Mt. Kinabalu in Sabah, Malaysian Borneo. Records were carefully checked by experts on Bornean birds. More species are now known from Mt. Kinabalu, but historical data provided elevational range estimates for more species than current data because of extensive mountain-wide collections and surveys. Most elevational comparisons for this study had to be limited to the 1450–1900 m elevational band, where most of the recent work has been done. Information was compiled into an annotated list of 342 species from 200–4095 m. We present this list to encourage refi nement of the dataset and future work on elevational distributions on the mountain. Of 58 species with suffi cient data from 1450 m to the summit, 38 appear to have shifted their ranges (24 species upslope and 14 downslope). A total of 22 resident species have recently been observed above their published maximum elevation for Borneo. Some species that have shifted upwards, such as Chalcophaps indica and Pellorneum pyrrogenys, are now common or breeding at elevations above their published maximum. Fifteen species appear to have declined on the mountain, probably as a result of habitat loss outside the protected area. Several of the upslope shifts are probably attributable to climate change, but many downslope shifts may be artifacts of incomplete recent sampling. The upward shifts agree with the few other tropical range comparisons that have been published. Our approach demonstrates the viability of combining diverse data sources (of varying accuracy and bias) to detect distributional shifts from climate change.

    Keywords: checklist, citizen science, climate change, habitat loss, range limit

  • Gaikwad J, Wilson P, Ranganathan S (2011)

    Ecological niche modeling of customary medicinal plant species used by Australian Aborigines to identify species-rich and culturally valuable areas for conservation

    Ecological Modelling 222(18) 3437–3443.

    Customary medicinal plant species used by Australian Aborigines are disappearing rapidly with its associated knowledge, due to the loss of habitats. Conservation and protection of these species is important as they represent sources of novel therapeutic phytochemical compounds and are culturally valuable. Information on the spatial distribution and use of customary medicinal plants is often inadequate and fragmented, posing limitations on the identification and conservation of species-rich areas and culturally valuable habitats. In this study, the habitat suitability modeling program, MaxEnt, was used to predict the potential ecological niches of 431 customary medicinal plant species, based on bioclimatic variables. Specimen locality records were obtained from the Global Biodiversity Information Facility (GBIF) data portal and from Australia's Virtual Herbarium (AVH). Ecological niche models of 414 predicted species, which had 30 or more occurrence points, were used to produce maps indicating areas that were ecologically suitable for multiple species (concordance of high predicted ecological suitability) and having cultural values. For the concordance map, individual species niche models were thresholded and summed. To derive a map of culturally valuable areas, customary medicinal uses from Customary Medicinal Knowledgebase (CMKb) ( were used to weight individual species models, resulting in a value within each grid cell reflecting its cultural worth. Even though the available information is scarce and fragmented, our approach provides an opportunity to infer areas predicted to be suitable for multiple species (i.e. concordance hotspots) and to estimate the cultural value of a particular geographical area. Our results also indicate that to conserve bio-cultural diversity, comprehensive information and active participation of Aboriginal communities is indispensable.

    Keywords: australian aborigines, customary medicinal plants, ecological niche modeling