Uses of GBIF in scientific research

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

List of publications

  • Bacon C, Look S, Gutiérrez-Pinto N, Antonelli A, Tan H, Kumar P et al. (2016)

    Species limits, geographical distribution and genetic diversity in Johannesteijsmannia (Arecaceae)

    Botanical Journal of the Linnean Society.

    Four species are recognized in the understorey palm genus Johannesteijsmannia (Arecaceae), all of which occur in close geographical proximity in the Malay Peninsula. We hypothesize that overlapping distributions are maintained by a lack of gene flow among species and that segregation along morphological trait or environmental axes confers ecological divergence and, hence, defines species limits. Although some species have sympatric distributions, differentiation was detected among species in morphological and genetic data, corroborating current species delimitation. Differences in niche breadth were not found to explain the overlapping distribution and co-existence of Johannesteijsmannia spp. Four species formed over the last 3 Mya, showing that diversity accumulated within a short time frame and wide range expansion has not occurred, potentially due to a lack of time for dispersal or the evolution of traits to facilitate movement. An assessment of genetic diversity is presented and, as expected, the widest distribution in the genus harbours the highest genetic diversity.

    Keywords: Malesia, Palmae, niche, phylogenetics, speciation

  • Benedict J, Smith S, Specht C, Collinson M, Leong-Škorničková J, Parkinson D et al. (2016)

    Species diversity driven by morphological and ecological disparity: a case study of seeds of Zingiberales (bananas, gingers, and relatives).

    AoB PLANTS plw063.

    Phenotypic variation can be attributed to genetic heritability as well as biotic and abiotic factors. Across Zingiberales, there is a high variation in the number of species per clade and in phenotypic diversity. Factors contributing to this phenotypic variation have never been studied in a phylogenetic or ecological context. Seeds of 166 species from all eight families in Zingiberales were analyzed for 51 characters using synchrotron based 3D X-ray tomographic microscopy to determine phylogenetically informative characters and to understand the distribution of morphological disparity within the order. All families are distinguishable based on seed characters. Non-metric multidimensional scaling analyses show Zingiberaceae occupy the largest seed morphospace relative to the other families, and environmental analyses demonstrate that Zingiberaceae inhabit both temperate and tropical regions, while other Zingiberales are almost exclusively tropical. Temperate species do not cluster in morphospace nor do they share a common suite of character states. This suggests that the diversity seen is not driven by adaptation to temperate niches; rather, the morphological disparity seen likely reflects an underlying genetic plasticity that allowed Zingiberaceae to repeatedly colonize temperate environments. The notable morphoanatomical variety in Zingiberaceae seeds may account for their extraordinary ecological success and high species diversity as compared to other Zingiberales.

    Keywords: Cannaceae, Costaceae, Heliconiaceae, Lowiaceae, Marantaceae, Musaceae, Strelitziaceae, Zingiberaceae

  • 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

  • Moyes C, Shearer F, Huang Z, Wiebe A, Gibson H, Nijman V et al. (2016)

    Predicting the geographical distributions of the macaque hosts and mosquito vectors of Plasmodium knowlesi malaria in forested and non-forested areas.

    Parasites & vectors 9(1) 242.

    BACKGROUND: Plasmodium knowlesi is a zoonotic pathogen, transmitted among macaques and to humans by anopheline mosquitoes. Information on P. knowlesi malaria is lacking in most regions so the first step to understand the geographical distribution of disease risk is to define the distributions of the reservoir and vector species. METHODS: We used macaque and mosquito species presence data, background data that captured sampling bias in the presence data, a boosted regression tree model and environmental datasets, including annual data for land classes, to predict the distributions of each vector and host species. We then compared the predicted distribution of each species with cover of each land class. RESULTS: Fine-scale distribution maps were generated for three macaque host species (Macaca fascicularis, M. nemestrina and M. leonina) and two mosquito vector complexes (the Dirus Complex and the Leucosphyrus Complex). The Leucosphyrus Complex was predicted to occur in areas with disturbed, but not intact, forest cover (> 60 % tree cover) whereas the Dirus Complex was predicted to occur in areas with 10-100 % tree cover as well as vegetation mosaics and cropland. Of the macaque species, M. nemestrina was mainly predicted to occur in forested areas whereas M. fascicularis was predicted to occur in vegetation mosaics, cropland, wetland and urban areas in addition to forested areas. CONCLUSIONS: The predicted M. fascicularis distribution encompassed a wide range of habitats where humans are found. This is of most significance in the northern part of its range where members of the Dirus Complex are the main P. knowlesi vectors because these mosquitoes were also predicted to occur in a wider range of habitats. Our results support the hypothesis that conversion of intact forest into disturbed forest (for example plantations or timber concessions), or the creation of vegetation mosaics, will increase the probability that members of the Leucosphyrus Complex occur at these locations, as well as bringing humans into these areas. An explicit analysis of disease risk itself using infection data is required to explore this further. The species distributions generated here can now be included in future analyses of P. knowlesi infection risk.

    Keywords: Entomology, Infectious Diseases, Parasitology, Tropical Medicine

  • Oliveira U, Paglia A, Brescovit A, de Carvalho C, Silva D, Rezende D et al. (2016)

    The strong influence of collection bias on biodiversity knowledge shortfalls of Brazilian terrestrial biodiversity

    Diversity and Distributions 22(12) 1232-1244.

    Aim The knowledge of biodiversity facets such as species composition, distribution and ecological niche is fundamental for the construction of biogeographic hypotheses and conservation strategies. However, the knowledge on these facets is affected by major shortfalls, which are even more pronounced in the tropics. This study aims to evaluate the effect of sampling bias and variation in collection effort on Linnean, Wallacean and Hutchinsonian shortfalls and diversity measures as species richness, endemism and beta-diversity. Location Brazil. Methods We have built a database with over 1.5 million records of arthropods, vertebrates and angiosperms of Brazil, based on specimens deposited in scientific collections and on the taxonomic literature. We used null models to test the collection bias regarding the proximity to access routes. We also tested the influence of sampling effort on diversity measures by regression models. To investigate the Wallacean shortfall, we modelled the geographic distribution of over 4000 species and compared their observed distribution with models. To quantify the Hutchinsonian shortfall, we used environmental Euclidean distance of the records to identify regions with poorly sampled environmental conditions. To estimate the Linnean shortfall, we measured the similarity of species composition between regions close to and far from access routes. Results We demonstrated that despite the differences in sampling effort, the strong collection bias affects all taxonomic groups equally, generating a pattern of spatially biased sampling effort. This collection pattern contributes greatly to the biodiversity knowledge shortfalls, which directly affects the knowledge on the distribution patterns of diversity. Main conclusions The knowledge on species richness, species composition and endemism in the Brazilian biodiversity is strongly biased spatially. Despite differences in sampling effort for each taxonomic group, roadside bias affected them equally. Species composition similarity decreased with the distance from access routes, suggesting collection surveys at sites far from roads could increase the probability of sampling new geographic records or new species.

    Keywords: Hutchinsonian shortfall, Linnean shortfall, Wallacean shortfall, beta-diversity, endemism, species distribution models, species richness

  • Zeng Y, Low B, Yeo D (2016)

    Novel methods to select environmental variables in MaxEnt: A case study using invasive crayfish

    Ecological Modelling 341 5-13.

    The popularity of MaxEnt in species distribution modeling has been driven by several factors including its high degree of accuracy, and flexibility to tailor efforts to species-specific situations. Although many recent studies have identified the importance of adjusting mathematical transformation (feature class) and regularization of coefficient values, collectively known as tuning, few studies have addressed the need to customize the variables used in species distribution modeling, and use unselected variable sets. This study presents two novel methods to select for environmental variables in MaxEnt. The first involves selecting from a priori determined environmental variable sets (pre-selected based on ecological or biological knowledge), and the second utilizes a reiterative process of model formation and stepwise removal of least contributing variables. Both methods were tested on eight known species of invasive crayfish, with results reinforcing the need for species-specific environmental variable sets. While the reiterative process generally performs better than the a priori selected variables, selection of method can be based on information availability. These techniques appear to outperform the current practice of utilizing unselected variable sets and is especially important considering the increasing application of species distribution modeling (across spatial and temporal barriers) in conservation and management efforts whereby inaccurate predictions might have adverse effects.

    Keywords: A priori, Distribution, Ecological niche, Species distribution model, Stepwise removal, Tuning

  • 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