Uses of GBIF in scientific research

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

List of publications

  • Ningthoujam, S., Choudhury, M., Potsangbam, K., Chetia, P., Nahar, L., Sarker, S., Basar, N., Talukdar, A., 2014.

    NoSQL Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources

    Phytochemical Analysis 25(6) 495-507.

    INTRODUCTION: Sharing traditional knowledge with the scientific community could refine scientific approaches to phytochemical investigation and conservation of ethnomedicinal plants. As such, integration of traditional knowledge with scientific data using a single platform for sharing is greatly needed. However, ethnomedicinal data are available in heterogeneous formats, which depend on cultural aspects, survey methodology and focus of the study. Phytochemical and bioassay data are also available from many open sources in various standards and customised formats. OBJECTIVE: To design a flexible data model that could integrate both primary and curated ethnomedicinal plant data from multiple sources. MATERIALS AND METHODS: The current model is based on MongoDB, one of the Not only Structured Query Language (NoSQL) databases. Although it does not contain schema, modifications were made so that the model could incorporate both standard and customised ethnomedicinal plant data format from different sources. RESULTS: The model presented can integrate both primary and secondary data related to ethnomedicinal plants. Accommodation of disparate data was accomplished by a feature of this database that supported a different set of fields for each document. It also allowed storage of similar data having different properties. CONCLUSION: The model presented is scalable to a highly complex level with continuing maturation of the database, and is applicable for storing, retrieving and sharing ethnomedicinal plant data. It can also serve as a flexible alternative to a relational and normalised database. Copyright © 2014 John Wiley & Sons, Ltd.

    Keywords: ethnomedicinal plants, mongodb, nosql databases


  • Polgar, G., Zane, L., Babbucci, M., Barbisan, F., Patarnello, T., Rüber, L., Papetti, C., 2014.

    Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus)

    Molecular Phylogenetics and Evolution 73 161-176.

    This study provides a first description of the phylogeographic patterns and evolutionary history of two species of the mudskipper genus Periophthalmus. These amphibious gobies are distributed throughout the whole Indo-Pacific region and Atlantic coast of Africa, in peritidal habitats of soft-bottom coastal ecosystems. Three sequence datasets of two widely distributed species, Periophthalmus argentilineatus and P. kalolo, were obtained by amplifying and sequencing two mtDNA markers (D-loop and 16S rDNA) and the nDNA rag1 region. The three datasets were then used to perform phylogeographic, demographic and population genetic analyses. Our results indicate that tectonic events and past climatic oscillations strongly contributed to shape present genetic differentiation, phylogeographic and demographic patterns. We found support for the monophyly of P. kalolo, and only shallow genetic differentiation between East-African and Indo-Malayan populations of this species. However, our collections of the morphospecies P. argentilineatus include three molecularly distinct lineages, one of them more closely related to P. kalolo. The presence of Miocenic timings for the most recent common ancestors of some of these morphologically similar clades, suggests the presence of strong stabilising selection in mudskippers' habitats. At population level, demographic analyses and palaeoecological records of mangrove ecosystems suggest that Pleistocene bottlenecks and expansion plus secondary contact events of the studied species were associated with recurrent sea transgressions during interglacials, and sea regressions or stable regimes during glacials, respectively.

    Keywords: Bayesian analyses, Fish morphology, Mangrove habitat, Molecular evolution, Periophthalmus argentilineatus, Periophthalmus kalolo


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

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

    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


  • Record, S., Charney, N., Zakaria, R., Ellison, A., 2013.

    Projecting global mangrove species and community distributions under climate change

    Ecosphere 4(3) art34.

    Given the multitude of ecosystem services provided by mangroves, it is important to understand their potential responses to global climate change. Extensive reviews of the literature and manipulative experiments suggest that mangroves will be impacted by climate change, but few studies have tested these predictions over large scales using statistical models. We provide the first example of applying species and community distribution models (SDMs and CDMs, respectively) to coastal mangroves worldwide. Species distributions were modeled as ensemble forecasts using BIOMOD. Distributions of mangrove communities with high species richness were modeled in threeways: as the sum of the separate SDM outputs, as binary hotspots (with .3 species) using a generalized linear model, and continuously using a general boosted model. Individual SDMs were projected for 12 species with sufficient data and CDMs were projected for 30 species into 2080 using global climate model outputs and a range of sea-level rise projections. Species projected to shift their ranges polewards by at least 2 degrees of latitude consistently experience a decrease in the amount of suitable coastal area available to them. Central America and the Caribbean are forecast to lose more mangrove species than other parts of the world.We found that the extent and grain size, at which continuous CDMoutputs are examined, independent of the grain size at which the models operate, can dramatically influence the number of pseudo-absences needed for optimal parameterization. The SDMs and CDMs presented here provide a first approximation of how mangroves will respond to climate change given simple correlative relationships between occurrence records and environmental data. Additional, precise georeferenced data on mangrove localities and concerted efforts to collect data on ecological processes across large-scale climatic gradients will enable future research to improve upon these correlative models.

    Keywords: climate envelope, community, global, mangal, sea-level rise, species richness


  • Harris, J., Yong, D., Sheldon, F., Boyce, A., Eaton, J., Bernard, H., Biun, A., Langevin, A., Martin, T., Wei, D., 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


  • Jalonen, R., Zonneveld, M., Thomas, E., Gaisberger, H., Vinceti, B., Thong, H., Loo, J., 2012.

    Identifying Tree Populations for Conservation Action through Geospatial Analyses

    Asia and the Pacific Workshop - Multinational and Transboundary Conservation of Valuable and Endangered Forest Tree Species 98-101.

    Rapid development of information and communication technologies has made it possible to easily collect georeferenced information on species and their environment, and to use it for analyzing biological diversity, its distribution and threats to it. Such analyses can importantly inform development of conservation strategies and priorities, especially across countries or species distribution ranges (Guarino et al. 2002). Data for spatial analyses on species or genetic diversity and its distribution are collected in specifically designed studies, obtained from existing records of species occurrence, or both. Observations may be complemented by species distribution modelling, where the potential occurrence of a species is predicted based on its documented geographic distribution and climate in those areas. Results on the distribution of diversity, documented or modelled, can then be compared, for example, with existing protected areas, rates of forest degradation, threats of environmental changes, or socio-economic indicators, to identify priority tree populations and tailor strategies for their conservation and sustainable use (Pautasso 2009). In this paper recent case studies on spatial biodiversity analyses across the tropics are presented, demonstrating how such analyses can help to identify most unique or most threatened populations of a tree species for conservation actions. Insights on initiating collaborative research on diversity and distributions of important Asian tree species are also discussed.

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


  • Chong, V., Lee, P., Lau, C., 2010.

    Diversity, extinction risk and conservation of Malaysian fishes.

    Journal of fish biology 76(9) 2009-66.

    A total of 1951 species of freshwater and marine fishes belonging to 704 genera and 186 families are recorded in Malaysia. Almost half (48%) are currently threatened to some degree, while nearly one third (27%) mostly from the marine and coral habitats require urgent scientific studies to evaluate their status. Freshwater habitats encompass the highest percentage of threatened fish species (87%) followed by estuarine habitats (66%). Of the 32 species of highly threatened (HT) species, 16 are freshwater and 16 are largely marine-euryhaline species. Fish extinctions in Malaysia are confined to two freshwater species, but both freshwater and marine species are being increasingly threatened by largely habitat loss or modification (76%), overfishing (27%) and by-catch (23%). The most important threat to freshwater fishes is habitat modification and overfishing, while 35 species are threatened due to their endemism. Brackish-water, euryhaline and marine fishes are threatened mainly by overfishing, by-catch and habitat modification. Sedimentation (pollution) additionally threatens coral-reef fishes. The study provides recommendations to governments, fish managers, scientists and stakeholders to address the increasing and unabated extinction risks faced by the Malaysian fish fauna.

    Keywords: Animals, Biodiversity, Biological, Conservation of Natural Resources, Ecosystem, Endangered Species, Extinction, Fishes, Fishes: classification, Fresh Water, Malaysia, Risk Management, Seawater, Water Pollution