Uses of GBIF in scientific research

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

List of publications

  • Horvitz N, Wang R, Wan F, Nathan R (2017)

    Pervasive human-mediated large-scale invasion: analysis of spread patterns and their underlying mechanisms in 17 of China's worst invasive plants

    Journal of Ecology 105(1) 85-94.

    Biological invasions constitute a major component of human-induced environmental change and have become a world-wide problem threatening global biodiversity and incurring massive economic costs. Consequently, research on biological invasions proliferates, placing a major emphasis on species traits and habitat characteristics associated with successful invasion. Yet, the mechanisms underlying rapid spread and the resulting patterns remain largely unexplored. Using data collected since 1980 and earlier at the county level all over China, we studied the contribution of potential dispersal vectors – railroads, rail stations, roads, general human activity, rivers and winds – to the spread of 17 of China's worst invasive plant species. Focusing on long-distance dispersal events, we calculated the minimal arrival speed for the first record of each species in each county. We also developed and applied a new method to account for observation bias due to the proximity to roads, using observational data of 776 native (non-invasive) plant species throughout China. We found that human-related vectors are accountable for the vast spread of all 17 invasive plant species we examined. Spread patterns were characterized by long jumps of tens to hundreds of kilometres and extremely fast average spread rates of roughly 2–4 km per year, and a very broad range (0·1–128·2 km per year) with high variability between years. These rates are much higher than those expected from classic dispersal vectors such as water, wind or animals. Commonly used fat-tailed dispersal kernels did not fit the observed distribution of long jumps for any species. Synthesis. We found pervasive empirical evidence for the overriding role of humans in the large-scale spread of invasive plants from multiple taxa. The observed spread patterns differ significantly from those portrayed in the literature, emphasizing the need to develop new frameworks to explore large-scale spread in general and invasive spread in particular. With public data sets of invasive species observations becoming increasingly more available, the time is ripe to go beyond exploration of species traits and habitat suitability and to examine the actual patterns and the mechanisms of large-scale invasive spread, even at a scale of thousands of kilometres over land.

    Keywords: Introduction, dispersal vectors, invasion ecology, invasive species, invasive spread, jump dispersal, long-distance dispersal, minimal arrival speed, plant dispersal, spread pattern


  • Liu D, Wang R, Gordon D, Sun X, Chen L, Wang Y (2017)

    Predicting Plant Invasions Following China’s Water Diversion Project

    Environmental Science & Technology 51(3) 1450-1457.

    China’s South to North Water Diversion (SNWD) project connects portions of the Yangtze River in the south to the Yellow River system in the north, overcoming biogeographic barriers to water movement. The diversion will supply potable water to over 110 million people and provide multiple other socioeconomic benefits. However, an inadvertent negative impact of this connection includes creation of conduits for species invasions. Alligator weed (Alternanthera philoxeroides), water hyacinth (Eichhornia crassipes), and water lettuce (Pistia stratiotes) are the only aquatic plant species on China’s shortlists for special control. These species are mainly invasive in the Yangtze River basin. If these species are able to invade the SNWD and further spread via the SNWD, they have the potential to alter water supply, including water quantity and quality, as well as local ecology and agriculture, threatening the goals of the diversion. Understanding the full potential for these species to invade northern China is cri...

    Keywords: Introduction, dispersal vectors, invasion ecology, invasive species, invasive spread, jump dispersal, long-distance dispersal, minimal arrival speed, plant dispersal, spread pattern


  • Yang L, Hu H, Xie C, Lai S, Yang M, He X et al. (2017)

    Molecular phylogeny, biogeography and ecological niche modelling of Cardiocrinum (Liliaceae): insights into the evolutionary history of endemic genera distributed across the Sino-Japanese floristic region.

    Annals of botany 119(1) 59-72.

    BACKGROUND AND AIMS The patterns of evolutionary assembly in the Sino-Japanese floristic region (SJFR) remain largely unknown due to a lack of integrative multidimensional studies throughout the region. To address this issue, we elucidated the evolutionary history of Cardiocrinum (Liliaceae), a genus containing four taxa distributed across the SJFR. METHODS Fifty-four populations were sampled throughout the geographical range of Cardiocrinum to assess genetic structure, analyse phylogenetic relationships and reconstruct ancestral area based on six chloroplast DNA (cpDNA) fragments and three low copy nuclear genes (LCNG). Ecological niche modelling was used to examine the potential range shifts of Cardiocrinum in response to climatic change. KEY RESULTS The molecular data showed high genetic similarity in the cpDNA (98·37 %) and LCNG (94·53 %) sequences. The biogeographical analyses revealed that the ancestor of Cardiocrinum diversified during the late Miocene (approx. 7·32 Mya) in Central China. The ancestor of the C. giganteum lineage dispersed westward to the Himalayas and south-west China with the split between C. giganteum and C. giganteum var. yunnanense occurring around 4·11 Mya consistent with the period of orogeny of the Hengduan Mountains. Some populations of the C. cathayanum lineage dispersed eastward to south Japan via the land bridge approx. 4·97 Mya, providing opportunities for allopatric speciation of C. cordatum The predicted suitable habitats of Cardiocrinum have become smaller and more fragmented since the Last Glacial Maximum. CONCLUSIONS Our study provides evidence of a biogeographical pattern of dispersal from Central China to the Himalayas in the west and Japan in the east for genera distributed across the SJFR, and highlights that the orogeny of the Hengduan Mountains and fluctuations of the sea level of the East China Sea played important roles in promoting species divergence.

    Keywords: Biogeography, Cardiocrinum, Sino-Japanese Floristic Region, ecological niche modelling, phylogeny, species divergence


  • Bellot S, Cusimano N, Luo S, Sun G, Zarre S, Gröger A et al. (2016)

    Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales

    Genome Biology and Evolution 8(7) 2214-2230.

    Cynomoriaceae, one of the last unplaced families of flowering plants, comprises one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence. Cynomorium has large genomes of 13.70-13.61 (Italy) to 13.95-13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.

    Keywords: Chondriome, Cynomorium, Mediterranean-Irano-Turanian, horizontal gene transfer, parasitic plants, plastome


  • Cao B, Bai C, Zhang L, Li G, Mao M (2016)

    Modeling habitat distribution of Cornus officinalis with Maxent modeling and fuzzy logics in China

    Journal of Plant Ecology rtw009.

    AimsPredicting suitable habitat distribution is an effective way to protect rare or endangered medicinal plants. Cornus officinalis is a perennial tree growing in forest edge and its air-dried pericarp is one of the traditional Chinese medicines (TCM) with significant medicinal values. In recent years, C. officinalis has undergone severe degeneration of its natural habitat owing to growing market demands and unprecedented damage to the forests. Moreover, the degeneration of suitable habitat has threatened the supply of medicinal materials, and even led to the extinction of some engendered medicinal plant species. In this case, there is a great risk to introduce and cultivate medicinal plants if planners determine the suitable cultivation regions based on personal subjective experience alone. Therefore, predicting suitable potential habitat distribution of medicinal plants (e.g. C. officinalis) and revealing the environmental factors determining such distribution patterns are important to habitat conservation and environmental restoration. MethodsIn this paper, we report the results of a study on the habitat distribution of C. officinalis using maximum entropy (Maxent) modeling and fuzzy logics together with loganin content and environmental variables. The localities of 106 C. officinalis in China were collected by our group and other researchers and used as occurrence data. The loganin content of 234 C. officinalis germplasm resources were tested by high-performance liquid chromatography (HPLC) and used as content data. 79 environmental variables were selected and processed with multi-collinearity test by using Pearson Correlation Coefficient (r) to determine a set of independent variables. The chosen variables were then processed in the fuzzy linear model according to the cell values (maximum, minimum) of localities with estimated loganin content. The SDMtoolbox was used to spatially rarefy occurrence data and prepare bias files. Furthermore, combined Maxent modeling and fuzzy logics were used to predict the suitable habitat of C. officinalis. The modeling result was validated using null-model method. Important findingsAs a result, six environmental factors including tmin3, prec3, bio4, alt, bio12 and bio3 were determined as key influential factors that mostly affected both the habitat suitability and active ingredient of C. officinalis. The highly suitable regions of C. officinalis mainly "core distribution zone" of the east-central China. The statistically significant AUC value indicated that combined Maxent modeling and fuzzy logics could be used to predict the suitable habitat distribution of medicinal plants. Furthermore, our results confirm that ecological factors played critical roles in assessing suitable geographical regions as well as active ingredient of plants, highlighting the need for effective habitat rehabilitation and resource conservation.

    Keywords: Cornus officinalis, Maxent modeling, fuzzy logics, habitat distribution, medicinal plant


  • Duan R, Kong X, Huang M, Varela S, Ji X (2016)

    The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China

    Many studies predict that climate change will cause species movement and turnover, but few studies have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change will cause a major shift in the spatial patterns of amphibian diversity. Suitable habitats for over 90% of species will be located in the north of the current range, for over 95% of species in higher altitudes, and for over 75% of species in the west of the current range. The distributions of species predicted to move westwards, southwards and to higher altitudes will contract, while the ranges of the species not showing these trends will expand. Amphibians will lose 20% of their original ranges on average; the distribution outside current ranges will increase by 15%. Climate change will likely modify the spatial configuration of climatically suitable areas. Changes in area and fragmentation of climatically suitable patches are related, which means that species may be simultaneously affected by different stressors as a consequence of climate change.

    Keywords: Amphibians, Climate impacts, Dispersal, Distribution, Fragmentation, MaxEnt, Range shifts, Turnover


  • Escobar L, Qiao H, Phelps N, Wagner C, Larkin D (2016)

    Realized niche shift associated with the Eurasian charophyte Nitellopsis obtusa becoming invasive in North America

    Scientific Reports 6 29037.

    Nitellopsis obtusa (starry stonewort) is a dioecious green alga native to Europe and Asia that has emerged as an aquatic invasive species in North America. Nitellopsis obtusa is rare across large portions of its native range, but has spread rapidly in northern-tier lakes in the United States, where it can interfere with recreation and may displace native species. Little is known about the invasion ecology of N. obtusa, making it difficult to forecast future expansion. Using ecological niche modeling we investigated environmental variables associated with invasion risk. We used species records, climate data, and remotely sensed environmental variables to characterize the species’ multidimensional distribution. We found that N. obtusa is exploiting novel ecological niche space in its introduced range, which may help explain its invasiveness. While the fundamental niche of N. obtusa may be stable, there appears to have been a shift in its realized niche associated with invasion in North America. Large portions of the United States are predicted to constitute highly suitable habitat for N. obtusa. Our results can inform early detection and rapid response efforts targeting N. obtusa and provide testable estimates of the physiological tolerances of this species as a baseline for future empirical research.

    Keywords: Amphibians, Climate impacts, Dispersal, Distribution, Fragmentation, MaxEnt, Range shifts, Turnover


  • Escobar L, Qiao H, Peterson A (2016)

    Forecasting Chikungunya spread in the Americas via data-driven empirical approaches.

    Parasites & vectors 9(1) 112.

    BACKGROUND: Chikungunya virus (CHIKV) is endemic to Africa and Asia, but the Asian genotype invaded the Americas in 2013. The fast increase of human infections in the American epidemic emphasized the urgency of developing detailed predictions of case numbers and the potential geographic spread of this disease. METHODS: We developed a simple model incorporating cases generated locally and cases imported from other countries, and forecasted transmission hotspots at the level of countries and at finer scales, in terms of ecological features. RESULTS: By late January 2015, >1.2 M CHIKV cases were reported from the Americas, with country-level prevalences between nil and more than 20 %. In the early stages of the epidemic, exponential growth in case numbers was common; later, however, poor and uneven reporting became more common, in a phenomenon we term "surveillance fatigue." Economic activity of countries was not associated with prevalence, but diverse social factors may be linked to surveillance effort and reporting. CONCLUSIONS: Our model predictions were initially quite inaccurate, but improved markedly as more data accumulated within the Americas. The data-driven methodology explored in this study provides an opportunity to generate descriptive and predictive information on spread of emerging diseases in the short-term under simple models based on open-access tools and data that can inform early-warning systems and public health intelligence.

    Keywords: Entomology, Infectious Diseases, Parasitology, Tropical Medicine


  • Guan B, Chen W, Gong X, Wu T, Cai Q, Liu Y et al. (2016)

    Landscape connectivity of Cercidiphyllum japonicum, an endangered species and its implications for conservation

    Ecological Informatics 33 51-56.

    Cercidiphyllum japonicum, a Tertiary relict, recolonized areas north of the Yangtze River after the last glacial; however, little is known about its specific colonization corridors. Together with distribution models, the least cost path (LCP) analysis has been used to reveal the landscape connectivity of species. In this study, we utilized the categorical LCP method, combining the species distribution with genetic data from cpDNA and nuclear markers, to identify the possible dispersal routes of C. japonicum after the LGM. Across time periods and genetic markers, the results revealed that the species generally spread from the western edge of the Sichuan Basin, while the highest degree of dispersal potential corresponds with the year 2080 and the cpDNA haplotype. Furthermore, shifts in the species' range and the indication of an area of low genetic divergence further support the existence of a dispersal corridor. Overall, we believe that a dispersal route from the western edge of the Sichuan Basin through the Qinling Mountains and further to the northeast could exist, and therefore, the results are an important supplement to the evolutionary history of C. japonicum. In the future, we believe species distribution models (SDM) and connectivity assessment in relation to climate change will provide increasingly useful information and new implications for prioritizing the conservation of the endangered species.

    Keywords: Dispersal corridors, Genetic landscape, Least cost path, Shared haplotypes, Species distribution models


  • 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