Uses of GBIF in scientific research

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

List of publications

  • 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

  • Henk D, Shahar-Golan R, Devi K, Boyce K, Zhan N, Fedorova N et al. (2012)

    Clonality Despite Sex: The Evolution of Host-Associated Sexual Neighborhoods in the Pathogenic Fungus Penicillium marneffei

    PLoS Pathogens 8(10) e1002851.

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

  • Lai K, Cheng Y, Chen Y, Li Y, Shao K (2012)

    Applying cluster analysis and Google Maps in the study of large-scale species occurrence data

    Biodiversity Science 20(1) 76-85.

    The primary species occurrence data include the data on animal and plant specimens in museums and herbaria, as well as species observations. TaiBIF (Taiwan Biodiversity Information Facility) data portal has integrated 26 datasets so far, resulting in more than 1.5 million species occurrence data; 85% of them are geo-referenced. This study utilizes more than 8,800 Cyprinidae occurrence data from 11 datasets and uses three different types of clustering algorithms—grid-based, partition-based, and density-based—to produce different spatial visualization results. It aims to resolve the problems of efficacy and poor visualization when large scales of species occurrence data are presented in Google Maps. The study also explores the compara- tive differences between the results obtained from the three clustering algorithms and the expert opinion range maps of Cyprinidae. It hopes to identify a quick and efficient way to present species distribution data, in turn help researchers to extract knowledge from large amount of data so that the knowledge can be tapped as important reference for ecological conservation efforts.

    Keywords: biodiversity informatics, cluster analysis, species occurrence data, visualization

  • Wu T, Lee P, Lin R, Wu J, Walther B (2012)

    Modeling the Distribution of Rare or Cryptic Bird Species of Taiwan

    Taiwania 57(4) 342-358.

    For the study of the macroecology and conservation of Taiwan’s birds, there was an urgent need to develop distribution models of bird species whose distribution had never before been modeled. Therefore, we here model the distributions of 27 mostly rare and cryptic breeding bird species using a statistical approach which has been shown to be especially reliable for modeling species with a low sample size of presence localities, namely the maximum entropy (Maxent) modeling technique. For this purpose, we began with a dedicated attempt to collate as much high-quality distributional data as possible, assembling databases from several scientific reports, contacting individual data recorders and searching publicly accessible database, the internet and the available literature. This effort resulted in 2022 grid cells of 1 × 1 km size being associated with a presence record for one of the 27 species. These records and 10 pre-selected environmental variables were then used to model each species’ probability distribution which we show here with all grid cells below the lowest presence threshold being converted to zeros. We then in detail discuss the interpretation and applicability of these distributions, whereby we pay close attention to habitat requirements, the intactness and fragmentation of their habitat, the general detectability of the species and data reliability. This study is another one in an ongoing series of studies which highlight the usefulness of using large electronic databases and modern analytical methods to help with the monitoring and assessment of Taiwan’s bird species.

    Keywords: biogeography, conservation status, gis, rarity, taiwan avifauna