Uses of GBIF in scientific research

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

List of publications

  • Liao C, Chen C (2017)

    Investigation of floristic similarities between Taiwan and terrestrial ecoregions in Asia using GBIF data

    Botanical Studies 58(1) 15.

    Background Floristic compositions of non-endemic plants of continental islands were related to the neighboring continents because non-endemic plant species had historically migrated to continental islands from source areas. This study attempts to identify source areas of a continental island by means of floristic analysis and to assess possible migration routes on the basis of geographical distribution ranges of plants. Large quantities of angiosperm data records were downloaded from the Global Biodiversity Information Facility (GBIF). Similarity index and cluster analysis were used to identify the floristic similarities among 22 geographical localities of Taiwan (GLTs) and 34 terrestrial ecoregions in Asia. Geographical distribution ranges of non-endemic angiosperm species in Taiwan (NEASTs) were evaluated to mirror the possible migration routes from different source areas to Taiwan. Results There are 3275 angiosperm species in Taiwan derived from the dataset of GBIF. Among them, 847 are endemic and 2428 are NEASTs. Geographical distribution ranges of the 2428 NEASTs were categorized into 7 distribution groups. They were widely distribution from equator to Siberia (27 species), tropical ecoregions (345 species), tropical and subtropical ecoregions (663 species), tropical to temperate ecoregions (591 species), subtropical ecoregions (265 species), subtropical to temperate ecoregions (387 species), and temperate ecoregions (150 species). Results of similarity indices and cluster analysis demonstrated that high floristic similarities were observed among GLTs at lowland and southern Taiwan and tropical and subtropical ecoregions in Asia. GLTs at high mountains were assumed to have floristic similarity with temperate ecoregions in Asia, whereas the assumption was not supported by our analysis. It is partly because of that angiosperms with tropical and subtropical distributions extend their ranges from low to high elevations in Taiwan. Conclusions Subtropical ecoregions at southern China and tropical ecoregions at Indochina were more important than temperate ecoregions on playing source areas of NEASTs. Geographical distribution ranges of NEASTs implied that most of the NEASTs were probably migrated from topical or subtropical ecoregions of Asian continent to Taiwan.

    Keywords: Angiosperm, Asia, Continental island, Floristic similarity, Geographical distribution, Taiwan, Terrestrial ecoregion

  • Solberg S, Chou Y (2017)

    Conservation of Indigenous Vegetables from a Hotspot in Tropical Asia: What Did We Learn from Vavilov?

    Frontiers in Plant Science 7 1982.

    Conservation biologists have allocated an Indo-Burma biodiversity hotspot among 34 regions around the world especially rich in plants, animals, and other species (Myers et al., 2000). More than 13,500 different vascular plant species, of which 7000 are endemic, have been detected in this hotspot (Tordoff et al., 2012). Ninety years ago, the Russian scientist Vavilov (1926) pointed to the richness of cultivated plant species and their crop wild relatives in certain areas around the world, of which the Tropical Asia Center was one of eight. Later, Zeven and Zhukovsky (1975) applied the term Indochinese—Indonesian region of diversity for the area, which by then had been divided by various authors into an Indochinese region including Myanmar, Laos, Cambodia, Thailand, Bangladesh, and parts of Northeastern India and Southern China, and a more southern region including Malaysia and Indonesia (Darlington, 1956; Li, 1969; Schery, 1972; Janick, 2002; Nandwani, 2014). Rice (Oryza sp.), mungbean (Vigna radiata), gourd species, and indigenous vegetables were among crops that Zeven and Zhukovsky (1975) listed in the Indochinese region of diversity.

    Keywords: Angiosperm, Asia, Continental island, Floristic similarity, Geographical distribution, Taiwan, Terrestrial ecoregion

  • 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

  • Kraemer M, Sinka M, Duda K, Mylne A, Shearer F, Barker C et al. (2015)

    The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus

    eLife 4 e08347.

    Dengue and chikungunya are increasing global public health concerns due to their rapid geographical spread and increasing disease burden. Knowledge of the contemporary distribution of their shared vectors, Aedes aegypti and Ae. albopictus remains incomplete and is complicated by an ongoing range expansion fuelled by increased global trade and travel. Mapping the global distribution of these vectors and the geographical determinants of their ranges is essential for public health planning. Here we compile the largest contemporary database for both species and pair it with relevant environmental variables predicting their global distribution. We show Aedes distributions to be the widest ever recorded; now extensive in al l continents, including North America and Europe. These maps will help define the spatial limits of current autochthonous transmission of dengue and chikungunya viruses. It is only with this kind of rigorous entomological baseline that we can hope to project future health impacts of these viruses.

    Keywords: Aedes aegypti, Aedes albopictus, arboviruses, chikungunya, dengue, ecological niche, yellow fever

  • Lin Y, Deng D, Lin W, Lemmens R, Crossman N, Henle K et al. (2015)

    Uncertainty analysis of crowd-sourced and professionally collected field data used in species distribution models of Taiwanese moths

    Biological Conservation 181 102-110.

    The purposes of this study are to extract the names of species and places for a citizen-science monitoring program, to obtain crowd-sourced data of acceptable quality, and to assess the quality and the uncertainty of predictions based on crowd-sourced data and professional data. We used Natural Language Processing to extract names of species and places from text messages in a citizen science project. Bootstrap and Maximum Entropy methods were used to assess the uncertainty in the model predictions based on crowd-sourced data from the EnjoyMoths project in Taiwan. We compared uncertainty in the predictions obtained from the project and from the Global Biodiversity Information Facility (GBIF) field data for seven focal species of moth. The proximity to locations of easy access and the Ripley K method were used to test the level of spatial bias and randomness of the crowd-sourced data against GBIF data. Our results show that extracting information to identify the names of species and their locations from crowd-sourced data performed well. The results of the spatial bias and randomness tests revealed that the crowd-sourced data and GBIF data did not differ significantly in respect to both spatial bias and clustering. The prediction models developed using the crowd-sourced dataset were the most effective, followed by those that were developed using the combined dataset. Those that performed least well were based on the small sample size GBIF dataset. Our method demonstrates the potential for using data collected by citizen scientists and the extraction of information from vast social networks. Our analysis also shows the value of citizen science data to improve biodiversity information in combination with data collected by professionals.

    Keywords: Citizen science, Large-scale monitoring program, Natural language, Prediction of species distribution, Social media, Uncertainty, Volunteer survey

  • 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

  • Chao Y, Rouhan G, Amoroso V, Chiou W (2014)

    Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)

    Annals of Botany 109-124.

    BACKGROUND AND AIMS: Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented. METHODS: A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications. KEY RESULTS: The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions. CONCLUSIONS: This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.

    Keywords: actiniopteris, allopatric speciation, biogeography, brake ferns, long-distance dispersal, mat k, morphological character evolution, onychium, parapatric speciation, phylogeny, platyzoma, pteridaceae, pteris, rbc l

  • Chang Y, Chuang T (2013)

    A study of using grey system theory and artificial neural network on the climbing ability of Buergeria robusta frog

    Open Journal of Ecology 03(02) 83-93.

    Keywords: artificial neural, buergeria robusta, ecological engineering, grey system theory, network

  • Wang W, McKay B, Dai C, Zhao N, Zhang R, Qu Y et al. (2013)

    Glacial expansion and diversification of an East Asian montane bird, the green-backed tit (Parus monticolus)

    Journal of Biogeography 40(6) 1156-1169.

    Aim We combined genetic sequence data and ecological niche modelling to resolve the impacts of past climatic fluctuations on the distribution, genetic diversification, and demographic dynamics of an East Asian montane bird, the green-backed tit (Parus monticolus). Location East Asia. Methods Phylogenetic analyses were carried out using four mitochondrial fragments and seven nuclear loci from 161 birds sampled from 29 localities spanning the entire geographical range of the green-backed tit. We used *beast to estimate the species tree and calculate divergence times. Extended Bayesian skyline plots were used to infer potential historical shifts in population size. We used MaxEnt to predict potential distributions during three periods: the present day, the Last Glacial Maximum and the Last Interglacial. Results The mitochondrial DNA (mtDNA) gene tree showed strong support for three reciprocally monophyletic groups: a south-western clade, a central clade and a Taiwanese clade. Taiwanese and Vietnamese samples had fixed differences at several nuclear loci, but the south-western and central samples shared haplotypes at all nuclear loci. The mtDNA gene tree topology differed from the species tree topology. The species tree suggested sister relationships between Taiwanese and Vietnamese operational taxonomic units (OTUs) and between south-western and central OTUs. Diversification within the green-backed tit was relatively recent, probably within the last 0.9 million years. Extended Bayesian skyline plots suggested rapid population expansion in the south-western and central phylogroups after the Last Interglacial, and this result was consistent with ecological niche models. Main conclusions Our results suggest that genetic diversification within the green-backed tit was affected by the later Pleistocene climate fluctuations. Ecological niche models indicated that the present-day vegetation distribution was, in many ways, more similar to that of the Last Glacial Maximum than it was to that of the Last Interglacial. Continental populations of the green-backed tit experienced unusual demographic and range expansion that is likely to have occurred during the cooling transition between the Last Interglacial and the Last Glacial Maximum. We found incongruence between the mtDNA gene tree and the species tree, which underscores the importance of using both mitochondrial and nuclear markers when estimating the evolutionary history of populations.

    Keywords: East Asia, Parus monticolus, birds, ecological niche modelling, green-backed tit, historical demography, phylogeography, spatial dynamics, species tree

  • Chiang Y, Huang B, Liao P (2012)

    Diversification, Biogeographic Pattern, and Demographic History of Taiwanese Scutellaria Species Inferred from Nuclear and Chloroplast DNA

    PLoS ONE 7(11) e50844.

    The ragged topography created by orogenesis generates diversified habitats for plants in Taiwan. In addition to colonization from nearby mainland China, high species diversity and endemism of plants is also present in Taiwan. Five of the seven Scutellaria species (Lamiaceae) in Taiwan, for example, are endemic to the island. Hypotheses of multiple sources or in situ radiation have arisen to explain the high endemism of Taiwanese species. In this study, phylogenetic analyses using both nuclear and chloroplast markers revealed the multiple sources of Taiwanese Scutellaria species and confirmed the rapid and recent speciation of endemic species, especially those of the ‘‘indica group’’ composed of S. indica, S. austrotaiwanensis, S. tashiroi, and S. playfairii. The common ancestors of the indica group colonized first in northern Taiwan and dispersed regionally southward and eastward. Climate changes during glacial/interglacial cycles led to gradual colonization and variance events in the ancestors of these species, resulting in the present distribution and genetic differentiation of extant populations. Population decline was also detected in S. indica, which might reflect a bottleneck effect from the glacials. In contrast, the recently speciated endemic members of the indica group have not had enough time to accumulate much genetic variation and are thus genetically insensitive to demographic fluctuations, but the extant lineages were spatially expanded in the coalescent process. This study integrated phylogenetic and population genetic analyses to illustrate the evolutionary history of Taiwanese Scutellaria of high endemism and may be indicative of the diversification mechanism of plants on continental islands.

    Keywords: East Asia, Parus monticolus, birds, ecological niche modelling, green-backed tit, historical demography, phylogeography, spatial dynamics, species tree