Uses of GBIF in scientific research

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

List of publications

  • Cruz R, Baseia I, Hosaka K (2016)

    Distribution Data of Birds Nest Fungi in Japan: Nidula niveotomentosa and Crucibulum laeve

    Bulletin of the National Museum of Nature and Science. Series B, Botany 42(2) 49-55.

    Nidula niveotomentosa and Crucibulum laeve are distributed widely in temperate countries, but the true distribution in Japan has not been investigated. We hereby update the distribution record of these two species in Japan based on observation of morphological characters from recently collected samples from some areas in Japan, e.g., Chichibu, Nikko, Mt. Fuji and Mt. Daisen, as well as the distribution data from GBIF and other herbarium records. Detailed description of macro-and microscopic characters with photographs and distribution records in each prefecture in Japan are provided.

    Keywords: GBIF, herbarium, mushrooms, specimens, taxonomy


  • Krehenwinkel H, Graze M, Rödder D, Tanaka K, Baba Y, Muster C et al. (2016)

    A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna

    Journal of Biogeography.

    Aim The phylogeographical history of wide-ranging Palaearctic species is not well understood. Here, we present a range-wide phylogeographical study of the wasp spider, Argiope bruennichi (Scopoli, 1772), a highly dispersive and widely distributed Palaearctic species. We aim to identify glacial refugia and patterns of interglacial gene flow across the Palaearctic. Location Palaearctic region, including the Azores, Madeira, Europe, North Africa and Asia. Methods We conduct a range-wide phylogeographical survey. Our study is based on nuclear and mitochondrial DNA markers, as well as morphological characters. We use species distribution models to predict the species’ current range as well as its historical distribution during and shortly after the Last Glacial Maximum (LGM). Results All analysed genetic markers and morphological characters support the divergence of a lineage in eastern Asia from the remainder of the Palaearctic. Within the Western Palaearctic, a less pronounced divergence into an Azorean and a European clade is found. Species distribution models predict a pronounced loss of suitable habitat for Western Palaearctic lineages during the LGM, whereas the range of East Asian populations remained largely unaffected. Main conclusions Our results highlight the existence of non-European glacial refugia for Palaearctic species, particularly in East Asia. The current genetic structure is best explained by the recent recolonization of the Western Palaearctic from eastern Asia, or repeated interglacial contact of populations.

    Keywords: Azores, East Asia, Madeira, Palaearctic, gene flow, mitochondrial–nuclear incongruence, morphometry, palaeoclimate, phylogeography, species distribution model


  • Moyes C, Shearer F, Huang Z, Wiebe A, Gibson H, Nijman V et al. (2016)

    Predicting the geographical distributions of the macaque hosts and mosquito vectors of Plasmodium knowlesi malaria in forested and non-forested areas.

    Parasites & vectors 9(1) 242.

    BACKGROUND: Plasmodium knowlesi is a zoonotic pathogen, transmitted among macaques and to humans by anopheline mosquitoes. Information on P. knowlesi malaria is lacking in most regions so the first step to understand the geographical distribution of disease risk is to define the distributions of the reservoir and vector species. METHODS: We used macaque and mosquito species presence data, background data that captured sampling bias in the presence data, a boosted regression tree model and environmental datasets, including annual data for land classes, to predict the distributions of each vector and host species. We then compared the predicted distribution of each species with cover of each land class. RESULTS: Fine-scale distribution maps were generated for three macaque host species (Macaca fascicularis, M. nemestrina and M. leonina) and two mosquito vector complexes (the Dirus Complex and the Leucosphyrus Complex). The Leucosphyrus Complex was predicted to occur in areas with disturbed, but not intact, forest cover (> 60 % tree cover) whereas the Dirus Complex was predicted to occur in areas with 10-100 % tree cover as well as vegetation mosaics and cropland. Of the macaque species, M. nemestrina was mainly predicted to occur in forested areas whereas M. fascicularis was predicted to occur in vegetation mosaics, cropland, wetland and urban areas in addition to forested areas. CONCLUSIONS: The predicted M. fascicularis distribution encompassed a wide range of habitats where humans are found. This is of most significance in the northern part of its range where members of the Dirus Complex are the main P. knowlesi vectors because these mosquitoes were also predicted to occur in a wider range of habitats. Our results support the hypothesis that conversion of intact forest into disturbed forest (for example plantations or timber concessions), or the creation of vegetation mosaics, will increase the probability that members of the Leucosphyrus Complex occur at these locations, as well as bringing humans into these areas. An explicit analysis of disease risk itself using infection data is required to explore this further. The species distributions generated here can now be included in future analyses of P. knowlesi infection risk.

    Keywords: Entomology, Infectious Diseases, Parasitology, Tropical Medicine


  • Osawa T, Kohyama K, Mitsuhashi H (2016)

    Trade-off relationship between modern agriculture and biodiversity: Heavy consolidation work has a long-term negative impact on plant species diversity

    Land Use Policy 54 78-84.

    Human-driven land-use changes often cause a decline in biodiversity. Although traditional agricultural practices maintained biodiversity at high levels, recent land-use changes may have negative consequences on species composition. In this study, we examined the hypothesis that land consolidation, which is a major recent land-use change in agricultural areas, decreases plant species diversity over the long term (the so-called negative legacy). To test this hypothesis, we examined the relationships between consolidated areas and the occurrence of threatened plant species across Japan and at the prefecture scale. Twenty-three threatened plant species were selected, all of which were formerly common. Our results show that areas containing records of threatened plant species rarely experienced consolidation at whole-country and prefectural scales. Breakdown analysis showed that unconsolidated agricultural areas contained significantly more threatened species than consolidated agricultural areas. These results suggest that threatened plant species require unconsolidated agricultural areas (i.e., these species could not grow in consolidated areas). Thus, we propose that consolidation history could be used as an indicator of the potential for biodiversity recovery. We also suggest that consolidated agricultural areas should be used for food production rather than for the restoration of biodiversity, for reasons of cost efficiency.

    Keywords: Agricultural ecosystem, Biodiversity, Land-use change, Overuse, Red data book, Red list


  • Wepfer P, Guénard B, Economo E (2016)

    Influences of climate and historical land connectivity on ant beta diversity in East Asia

    Journal of Biogeography.

    Aim Biodiversity patterns reflect both ecological and evolutionary processes interacting with geographical variation in climate and the current and historical connectivity between land areas. We sought to disentangle these effects in explaining the organization of ant diversity across geographical areas and islands in East Asia. Location The Japanese Archipelago including the Ryukyu and Ogasawara Islands, Taiwan and coastal continental regions of Korea, China and Russia. Methods We aggregated species occurrence records from published literature, specimen databases and museum records, and compiled climatic variables for islands and politically defined continental areas. Current and historical land connections in the Last Glacial Maximum were determined using bathymetric databases. We analysed factors driving patterns of Simpson composition dissimilarity using multiple regression of distance matrices. Results Temperature was the largest driver of dissimilarity among areas, with geographical distance and historical land contiguity also being important. Current land contiguity had no detectable effect. Main conclusions We found climate to be a primary driver of ant diversity patterns on large scales, consistent with previous work on ants and other organisms. Interestingly, land connectivity during historical periods of low sea level was more important than current land connectivity in explaining faunal similarities. This implies that despite the potential overwater dispersal of ants, overland dispersal via transient land connections is a more important driver of regional-scale biogeographical pattern in East Asia.

    Keywords: East Asia, Japan, LGM, MRM, ants, beta diversity, dispersal, dissimilarity, island biogeography, land connectivity


  • Ytow N (2016)

    Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API

    Biodiversity Data Journal 4 e9787.

    Background The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. New information A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF’s ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

    Keywords: Data visualization, GBIF API, Multiple hierarchies, Tree comparison


  • Zhang D, Ye Z, Yamada K, Zhen Y, Zheng C, Bu W et al. (2016)

    Pleistocene sea level fluctuation and host plant habitat requirement influenced the historical phylogeography of the invasive species Amphiareus obscuriceps (Hemiptera: Anthocoridae) in its native range

    BMC Evolutionary Biology 16(1) 174.

    On account of repeated exposure and submergence of the East China Sea (ECS) land bridge, sea level fluctuation played an important role in shaping the population structure of many temperate species across the ECS during the glacial period. The flower bug Amphiareus obscuriceps (Poppius, 1909) (Hemiptera: Anthocoridae) is an invasive species native to the Sino-Japanese Region (SJR) of East Asia. We tested the hypothesis of the ECS land bridge acting as a dispersal corridor or filter for A. obscuriceps during the glacial period. Specifically, we tested whether and the extent to which dispersal ability and host plant habitat requirement influenced the genetic structure of A. obscuriceps during the exposure of the ECS land bridge. Phylogenetic and network analyses indicated that A. obscuriceps is composed of two major lineages, i.e., China and Japan. Divergence time on both sides of the ECS was estimated to be approximately 1.07 (0.79–1.32) Ma, which was about the same period that the sea level increased. No significant Isolation by Distance (IBD) relationship was found between Фst and Euclidean distances in the Mantel tests, which is consistent with the hypothesis that this species has a good dispersal ability. Our Last Glacial Maximum (LGM) niche modeling of plants that constitute preferred habitats for A. obscuriceps exhibited a similar habitat gap on the exposed ECS continental shelf between China and Japan, but showed a continuous distribution across the Taiwan Strait. Our results suggest that ecological properties (habitat requirement and dispersal ability), together with sea level fluctuation during the Pleistocene across the ECS, have shaped the genetic structure and demographic history of A. obscuriceps in its native area. The host plant habitat requirement could also be a key to the colonization of the A. obscuriceps species during the exposure of the ECS land bridge. Our findings will shed light on the potential role of habitat requirement in the process of biological invasion in future studies.

    Keywords: Cological niche modeling, Dispersal ability, East China Sea, Genetic structure, Habitat requirement, Land bridge, Last Glacial, Maximum


  • 剛 , 志穂美 , 健太郎 , 伸一 (2016)

    An assessment of fungi endemic to Japan

    日本菌学会会報 57(2) 77-84.

    The names of mushrooms were taken from “Colored illustrations of Mushrooms of Japan, Vol. 1 and 2” (Imazeki and Hongo 1987, 1989), and categorized as follows: 1) “endemic” (182 taxa); 2) known to be distributed in overseas countries (815); and 3) distribution range unknown (2931). The overseas distribution of mushrooms in the first category was further assessed using data from the Global Biodiversity Information Facility. The results revealed that 109 taxa were distributed overseas and not classed as endemic; however, the endemicity of 71 taxa was unclear. Therefore, these should be regarded as possible endemic mushrooms.

    Keywords: GBIF, conser vation biology, endemism, hot spot, national check list


  • Hinojosa L, Gaxiola A, Pérez M, Carvajal F, Campano M, Quattrocchio M et al. (2015)

    Non-congruent fossil and phylogenetic evidence on the evolution of climatic niche in the gondwana genus Nothofagus

    Journal of Biogeography.

    Aim We used fossil and phylogenetic evidence to reconstruct climatic niche evolution in Nothofagus, a Gondwana genus distributed in tropical and temperate latitudes. To assess whether the modern distribution of the genus can be explained by the tropical conservatism hypothesis, we tested three predictions: (1) species from all Nothofagus subgenera coexisted under mesothermal climates during the early Eocene; (2) tolerance to microthermal climates evolved during the Eocene–Oligocene cooling from an ancestor that grew under mesothermal conditions; and (3) the climatic niche in Nothofagus is phylogenetically conserved. Location Australia, New Zealand, New Caledonia, Papua-New Guinea and South America. Methods We estimated the palaeoclimate of the Early Eocene, fossil-bearing Ligorio Marquez Formation (LMF, Chile), using coexistence and leaf physiognomic analysis. We reconstructed ancestral climatic niches of Nothofagus using extant species distributions and a time-calibrated phylogeny. Finally, we used the morphological disparity index and phylogenetic generalized least squares to assess whether climatic variables follow a Brownian motion (BM) or an Ornstein–Uhlenbeck (OU) model of evolution. Results Our palaeoclimatic estimates suggest mesothermal conditions for the LMF, where macrofossils associated with subgenera Lophozonia and possibly Fuscospora, and fossil pollen of Brassospora and Fuscospora/Nothofagus were recorded. These results are not supported by our phylogenetic analysis, which instead suggests that the ancestor of Nothofagus lived under microthermal to marginally mesothermal conditions, with tolerance to mesothermal conditions evolving only in the subgenus Brassospora. Precipitation and temperature dimensions of the realized climatic niche fit with a gradual BM or constrained OU model of evolution. Main Conclusions Our results suggest that the use of phylogenetic reconstruction methods based only on present distributions of extant taxa to infer ancestral climatic niches is likely to lead to erroneous results when climatic requirements of ancestors differ from their extant descendants, or when much extinction has occurred.

    Keywords: Eocene, Gondwana, Nothofagaceae, into the tropics, niche modelling, palaeoclimate, phylogenetic signal, tropical conservatism hypothesis


  • Jordan G, Harrison P, Worth J, Williamson G, Kirkpatrick J (2015)

    Palaeoendemic plants provide evidence for persistence of open, well-watered vegetation since the Cretaceous

    Global Ecology and Biogeography.

    Aim Palaeoendemics are clades that are ancient but geographically restricted, often because they have been selected against in other areas. Ecological similarities among palaeoendemics may be indicators of ancient environments. We determine the environmental ranges of the remarkable palaeoendemic plants of Tasmania to deduce whether they indicate the long-term persistence of particular environmental conditions. Location Tasmania, Australia, a global centre of plant palaeoendemism, containing some of the world's most relictual plant lineages. Methods Palaeoendemic clades in Tasmania were identified using a scoring system of clade age divided by the square root of the number of 10 km × 10 km grid cells occupied globally. Total palaeoendemism scores for 1199 30″ grid cells were calculated by summing scores for individual clades, and modelled against climate, topography, geology and vegetation type using Random Forest models. Palaeoendemic and non-palaeoendemic species richness in climate space was measured. The global distribution of climates favoured by palaeoendemics was assessed. Results Twenty-nine phylogenetically and ecologically diverse palaeoendemic clades (51 species) were identified. High levels of palaeoendemism occurred widely in western Tasmania, but the highest scoring areas were at or slightly above the tree line in relatively undisturbed vegetation. Palaeoendemism scores were strongly predicted by constantly moist climates lacking extreme temperatures, and by open vegetation types with rare or no fire. The palaeoendemics occupied a climate space that is globally rare and very different from that of non-palaeoendemics. Main conclusions These patterns suggest the persistence since the Cretaceous of open vegetation in constantly moist areas with equable temperatures and few or no fires. This conclusion is consistent with an increasing body of fossil and phylogenetic evidence for the antiquity of open vegetation. The methods here produce quantitative values of palaeoendemism that can be compared among regions.

    Keywords: Biodiversity, endemism, fire adaptation, niche conservatism, relict, temperate rainforest, tropical conservatism hypothesis