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

  • 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

  • Pichler U, Hauser M, Wolf M, Bernardi M, Gadermaier G, Weiss R et al. (2015)

    Pectate lyase pollen allergens: sensitization profiles and cross-reactivity pattern.

    PloS one 10(5) e0120038.

    BACKGROUND: Pollen released by allergenic members of the botanically unrelated families of Asteraceae and Cupressaceae represent potent elicitors of respiratory allergies in regions where these plants are present. As main allergen sources the Asteraceae species ragweed and mugwort, as well as the Cupressaceae species, cypress, mountain cedar, and Japanese cedar have been identified. The major allergens of all species belong to the pectate lyase enzyme family. Thus, we thought to investigate cross-reactivity pattern as well as sensitization capacities of pectate lyase pollen allergens in cohorts from distinct geographic regions. METHODS: The clinically relevant pectate lyase pollen allergens Amb a 1, Art v 6, Cup a 1, Jun a 1, and Cry j 1 were purified from aqueous pollen extracts, and patients' sensitization pattern of cohorts from Austria, Canada, Italy, and Japan were determined by IgE ELISA and cross-inhibition experiments. Moreover, we performed microarray experiments and established a mouse model of sensitization. RESULTS: In ELISA and ELISA inhibition experiments specific sensitization pattern were discovered for each geographic region, which reflected the natural allergen exposure of the patients. We found significant cross-reactivity within Asteraceae and Cupressaceae pectate lyase pollen allergens, which was however limited between the orders. Animal experiments showed that immunization with Asteraceae allergens mainly induced antibodies reactive within the order, the same was observed for the Cupressaceae allergens. Cross-reactivity between orders was minimal. Moreover, Amb a 1, Art v 6, and Cry j 1 showed in general higher immunogenicity. CONCLUSION: We could cluster pectate lyase allergens in four categories, Amb a 1, Art v 6, Cup a 1/Jun a 1, and Cry j 1, respectively, at which each category has the potential to sensitize predisposed individuals. The sensitization pattern of different cohorts correlated with pollen exposure, which should be considered for future allergy diagnosis and therapy.

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

  • Mimura M, Mishima M, Lascoux M, Yahara T (2014)

    Range shift and introgression of the rear and leading populations in two ecologically distinct Rubus species

    BMC Evolutionary Biology 14(1) 209.

    Background:The margins of a species¿ range might be located at the margins of a species¿ niche, and in such cases, can be highly vulnerable to climate changes. They, however, may also undergo significant evolutionary change due to drastic population dynamics; e.g., changes in population size and distribution, which may increase the chance of contact among species. Such species interactions induced by climate changes could then regulate or facilitate further responses to climatic changes. We hypothesized that climate change-induced species contacts and subsequent genetic exchanges due to differences in population dynamics take place at the species boundaries. We sampled two closely related Rubus species, one temperate (Rubus palmatus) and the other subtropical (R. grayanus) near their joint species boundaries in southern Japan. Coalescent analysis, based on molecular data and ecological niche modelling during the Last Glacial Maximum (LGM), were used to infer past population dynamics. At the contact zones on Yakushima (Yaku Island), where the two species are parapatrically distributed, we tested hybridization along altitudinal gradients.ResultsCoalescent analysis suggested that the southernmost populations of R. palmatus predated the LGM (~20,000 ya). Conversely, populations at the current northern limit of R. grayanus diverged relatively recently and likely represent young outposts of a northbound range shift. These population dynamics were partly supported by the ensemble forecasting of six different species distribution models. Both past and ongoing hybridizations were detected near and on Yakushima. Backcrosses and advanced-generation hybrids likely generated the clinal hybrid zones along altitudinal gradients on the island where the two species are currently parapatrically distributed.ConclusionsClimate oscillations during the Quaternary Period and the response of a species in range shifts likely led to repeated contacts with the gene pools of ecologically distinct relatives. Such species interactions, induced by climate changes, may bring new genetic material to the marginal populations where species tend to experience more extreme climatic conditions at the margins of the species distribution.

    Keywords: Climate change, Colonizer, Introgression, Isolation with migration, Phylogeography, Species boundaries

  • Phartyal S, Kondo T, Fuji A, Hidayati S, Walck J (2014)

    A comprehensive view of epicotyl dormancy in Viburnum furcatum: combining field studies with laboratory studies using temperature sequences

    Seed Science Research 24(04) 281-292.

    Seeds with epicotyl dormancy reside in soil up to 15 months (or longer), being exposed to a sequence of temperatures, before seedlings completely emerge (i.e. with both roots and shoots). Heretofore, few studies have examined precise temperatures, especially in sequences, for promotion of radicle and cotyledon emergence and how they relate to environ- mental cues in nature. Viburnum is the best known genus to exhibit epicotyl dormancy and, as such, we investigated the Japanese V. furcatum, hypothesizing a similar kind and level of dormancy. The under- developed embryos in mature seeds in October were spatulate shaped, unlike those in other Viburnum species, and they elongated from late June to August of the following year. Radicles emerged after embryo growth until mid-October, followed by cotyledons from mid-April to mid-May. Temperatures required for embryo growth, radicle and cotyledon emergence in the laboratory approximated closely those in the field. Embryo elongation and radicle emergence occurred at warmtemperature regimes, and gibberellic acid (GA3) did not substitute for this warm temperature require- ments. Following a 120-d cold stratification of seeds with an emerged radicle, shoots emerged from seeds at 10, 15, 15/5, 20/10 and 25/158C. We identified that seeds of V. furcatum have deep simple epicotyl morphophysiological dormancy like the majority of other Viburnum species. For propagation of the species from seeds, the nearly 2-year period for seedling emergence could be shortened to 8 months: start fresh seeds at 25/158C(60 d) and then move them through a sequence of 15/58C (30 d) ! 08C (120 d) ! 20/108C (30 d).

    Keywords: Viburnum, cotyledon emergence, epicotyl dormancy, morphophysiological dormancy, radicle emergence, temperature sequences