Uses of GBIF in scientific research

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

List of publications

  • Chang, Y., Chuang, T.

    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

  • Guo, W., Lambertini, C., Li, X., Meyerson, L., Brix, H.

    Invasion of Old World Phragmites australis in the New World: precipitation and temperature patterns combined with human influences redesign the invasive niche.

    (Journal name unavailable from Mendeley API. To be updated soon...)

    After its introduction into North America, Euro-Asian Phragmites australis became an aggressive invasive wetland grass along the Atlantic coast of North America. Its distribution range has since expanded to the middle, south and southwest of North America, where invasive P. australis has replaced millions of hectares of native plants in inland and tidal wetlands. Another P. australis invasion from the Mediterranean region is simultaneously occurring in the Gulf region of the USA and some countries in South America. Here, we analysed the occurrence records of the two Old World invasive lineages of P. australis (Haplotype M and Med) in both their native and introduced ranges using environmental niche models (ENMs) to assess (i) whether a niche shift accompanied the invasions in the New World; (ii) the role of biologically relevant climatic variables and human influence in the process of invasion; and (iii) the current potential distribution of these two lineages. We detected local niche shifts along the East Coast of North America and the Gulf Coast of the USA for Haplotype M and around the Mississippi Delta and Florida of the USA for Med. The new niche of introduced Haplotype M accounts for temperature fluctuations and increased precipitation. The introduced Med lineage has enlarged its original subtropical niche to the tropics-subtropics, invading regions with a high annual mean temperature (> c. 10 °C) and high precipitation in the driest period. Human influence is an important factor for both niches. We suggest that an increase in precipitation in the 20(th) century, global warming and human-made habitats have shaped the invasive niches of the two lineages in the New World. However, as the invasions are on-going and human and natural disturbances occur concomitantly, the future distribution ranges of the two lineages may diverge from the potential distribution ranges detected in this study. This article is protected by copyright. All rights reserved.

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

  • He, K., Jiang, X.

    Mitochondrial phylogeny reveals cryptic genetic diversity in the genus Niviventer (Rodentia, Muroidea).

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Abstract Niviventer is a muroid genus with 17 species widely distributed in East and Southeast Asia. These animals are important components of both extant and fossil small mammal communities, and they are among the most common infectious agents in humans. In this study, we employed partitioned Bayesian and relaxed clock divergence dating analyses and included the Niviventer mitochondrial cytochrome b genes of from GenBank (n = 223). Although the intra-generic relationships were not fully resolved, we recognized four major clades/subclades that could support further division of the genus. Paraphyletic and polyphyletic species were discovered, and 21 putative species were recognized through species delimitation analysis, which indicated an imperfect taxonomy and the existent of cryptic species. Molecular dating supported Niviventer origination in the late Miocene, and relatively higher diversification rates were observed in the late Pliocene and the Pleistocene, which might correlate with climate fluctuations.

    Keywords: cryptic species, delimitation, niviventer, species, species-level paraphyly

  • Liu, J., Möller, M., Provan, J., Gao, L., Poudel, R., Li, D.

    Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot.

    The New phytologist.

    The interplay of orographic uplift and climatic changes in the Himalaya-Hengduan Mountains region (HHM) have had a key role in speciation and population demography. To gain further insight into these processes, we investigated their effects on Taxus wallichiana by combining molecular phylogeography and species distribution modeling. Molecular data were obtained from 43 populations of T. wallichiana. Nineteen climatic variables were analyzed alongside genetic discontinuities. Species distribution modeling was carried out to predict potential past distribution ranges. Two distinct lineages were identified, which diverged c. 4.2 (2.0-6.5) million years ago (Ma), a timescale that corresponds well with the recent uplift of the Qinghai-Tibet Plateau and subsequent climatic changes of the region. Correlations with climatic variables also suggest that ecological factors may have further reinforced the separation of the two lineages. Both lineages experienced population expansion during the last glaciation. The high genetic divergence, long-term isolation and ecological differentiation suggest a scenario of cryptic speciation in T. wallichiana associated with geological and climatic changes in the HHM. Our findings also challenge the notion of general population 'contraction' during the last glaciation in the HHM.

    Keywords: distribution modeling, ecological differentiation, himalaya-hengduan mountains region, population demography, speciation, species, taxus wallichiana

  • Wang, W., McKay, B., Dai, C., Zhao, N., Zhang, R., Qu, Y., Song, G., Li, S., Liang, W., Yang, X., Pasquet, E., Lei, F.

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

  • Xu, Z., Feng, Z., Yang, J., Zheng, J., Zhang, F.

    Nowhere to Invade: Rumex crispus and Typha latifolia Projected to Disappear under Future Climate Scenarios.

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Future climate change has been predicted to affect the potential distribution of plant species. However, only few studies have addressed how invasive species may respond to future climate change despite the known effects of plant species invasion on nutrient cycles, ecosystem functions, and agricultural yields. In this study, we predicted the potential distributions of two invasive species, Rumex crispus and Typha latifolia, under current and future (2050) climatic conditions. Future climate scenarios considered in our study include A1B, A2, A2A, B1, and B2A. We found that these two species will lose their habitat under the A1B, A2, A2A, and B1 scenarios. Their distributions will be maintained under future climatic conditions related to B2A scenarios, but the total area will be less than 10% of that under the current climatic condition. We also investigated variations of the most influential climatic variables that are likely to cause habitat loss of the two species. Our results demonstrate that rising mean annual temperature, variations of the coldest quarter, and precipitation of the coldest quarter are the main factors contributing to habitat loss of R. crispus. For T. latifolia, the main factors are rising mean annual temperature, variations in temperature of the coldest quarter, mean annual precipitation, and precipitation of the coldest quarter. These results demonstrate that the warmer and wetter climatic conditions of the coldest season (or month) will be mainly responsible for habitat loss of R. crispus and T. latifolia in the future. We also discuss uncertainties related to our study (and similar studies) and suggest that particular attention should be directed toward the manner in which invasive species cope with rapid climate changes because evolutionary change can be rapid for species that invade new areas.

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

  • Zhu, G., Gao, Y., Zhu, L.

    Delimiting the coastal geographic background to predict potential distribution of Spartina alterniflora

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Ecological niche modeling is an important tool in studying biological invasion; however, the geographic background on niche model transferability received scant attention. The salt marsh grass Spartina alterniflora, natively distributed along the eastern coasts of the Americas, is considered a global invasive species. In this study, we first compared the climate space among geographically separated populations. The classic niche model approaches involving the calibration of native range climate envelop of S. alterniflora and transferring worldwide were then used to predict potential invasion. Niche models based on two geographic backgrounds were compared, namely a large squared area delimited by a bounding box containing all known occurrences, which is usually used in former studies and a small coastal area defined as the geographic space available to the species. Both area-based models showed good performance in native range predictions, however, when models were transferred, niche model calibrated on the coastal area showed higher predictability in capturing the introduced occurrences. Given the potential substantial effect of geographic background on niche model transferability, caution is warranted when interpreting low-niche model transferability with niche differentiation and when predicting other (coastal) species’ invasion.

    Keywords: Coastal species, Ecological niche modeling, Geographic background, Model transferability, Niche conservatism

  • Zhu, G., Rédei, D., Kment, P., Bu, W.

    Effect of geographic background and equilibrium state on niche model transferability: predicting areas of invasion of Leptoglossus occidentalis

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Niche conservatism providing support for using ecological niche modeling in biological invasions has been widely noticed, however, the equilibrium state and geographic background effect on niche model transferability has received scant attention. The western conifer seed bug, Leptoglossus occidentalis, native to western North America, has expanded its range eastward and has become an invasive pest in Europe and Asia. Niche models calibrated on the ranges of a small native population and two large expanding populations were compared. We found that the climate niche of L. occidentalis is conserved during its steady expansion in North America and rapid spread in Europe. Models based on the small western native range successfully captured the eastern expanding and introduced European populations, whereas the large area-based models varied with the presumed state of equilibrium. The equilibrium state based model succeeded but the non-equilibrium based model failed to predict the range in Europe. Our study estimates global invasion risk zones for L. occidentalis and suggests that, based on niche conservatism, modeling based on a reasonable geographic distribution at a climatic equilibrium of a species could guarantee the transferability of niche model prediction. Caution is warranted in interpreting low niche model transferability with niche differentiation and forwarding message for management strategy.

    Keywords: Biological invasion, Ecological niche modeling (ENM), Equilibrium, Geographic background, Niche conservatism, Transferability

  • Bystriakova, N., Peregrym, M., Erkens, R., Bezsmertna, O., Schneider, H.

    Sampling bias in geographic and environmental space and its effect on the predictive power of species distribution models

    Systematics and Biodiversity(3) 305-315.

    Despite ever-growing popularity of species distribution models (SDM), their performance under conditions of spatially biased data has rarely been studied in detail. Here we explore the effect of a known spatial bias on the predictive ability of Maxent models, using five species of the genus Asplenium with variable reproductive modes. The models were trained and tested on western and central European presence-only distributional data, first with random background and then with target-group background. Then we tested the models on an independent Ukrainian dataset of the same species, using the area under the curve (AUC) value as test statistic.We carried out a principal components analysis (PCA) on the collection localities of the individual species to explore the properties of their ecological niches. In all but one species, spatial bias in the distributional data resulted in poor performance of theMaxent models (trained on the European dataset and tested on the Ukrainian dataset). In all species correction for sampling bias resulted in significantly wider predicted climatic niches. Based on the results of the PCA, spatial bias resulted in environmental bias of variable degree.We argue that species reproductive biology should be taken into account when distributional data are analysed in terms of their suitability for species distribution modelling. The reported results will inform biodiversity conservation assessments, particularly those using data from natural history collections.

    Keywords: Asplenium, climate, environmental bias, Europe, Maxent, model performance, multivariate analysis, spatial bias, Ukraine

  • Chen, D., Zhang, X., Kang, H., Sun, X., Yin, S., Du, H., Yamanaka, N., Gapare, W., Wu, H., Liu, C.

    Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations.

    PLoS ONE 7(10) e47268.

    The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N(ST = )0.751> G(ST = )0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu's F(S) indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.

    Keywords: Asplenium, climate, environmental bias, Europe, Maxent, model performance, multivariate analysis, spatial bias, Ukraine