Uses of GBIF in scientific research

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

List of publications

  • 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


  • Zhao, Y., Hosoya, T., 2014.

    Enumeration of Remarkable Japanese Discomycetes (8): Notes on Two Hymenoscyphus Species New to Japan

    40(4) 125-131.

    Two Hymenoscyphus species new to Japan are described and illustrated: Hymenoscy-phus menthae and H. ginkgonis (Helotiaceae, Helotiales), the latter with characteristic spore pig-mentation and substratal stroma.

    Keywords: Hymenoscyphus ginkonis, Hymenoscyphus menthae, mycobiota, stroma, taxonomy


  • Grossmann, M., Lindsay, D., Fuentes, V., 2013.

    A redescription of the post-larval physonect siphonophore stage known as Mica micula Margulis 1982, from Antarctica, with notes on its distribution and identity

    Marine Ecology 34 63-70.

    The samples obtained during the 2008 Collaborative East-Antarctic MARine Census (CEAMARC) campaign in the Southern Ocean on the TR/V Umitaka Maru contained many specimens of the physonect post-larval stage known as Mica micula, in varying stages of development, allowing us to complement the existing descriptions. M. micula appears to be endemic to the Southern Ocean, and its possible position in the family Pyrostephidae, in particular the species Pyrostephos vanhoeffeni, is discussed. For the first time, the definitive nectophores were observed, but they were still too underdeveloped to be assigned conclusively to any known physonect species.

    Keywords: antarctic, collaborative east-antarctic, marine census, mica micula, post-larval, pyrostephidae, stage


  • Hosoya, T., Hosaka, K., Saito, Y., Degawa, Y., Suzuki, R., 2013.

    Naemacyclus culmigenus, a newly reported potential pathogen to Miscanthus sinensis, new to Japan

    Mycoscience 54(6) 433-437.

    Keywords: antarctic, collaborative east-antarctic, marine census, mica micula, post-larval, pyrostephidae, stage


  • Jaruwattanaphan, T., Matsumoto, S., Watano, Y., 2013.

    Reconstructing Hybrid Speciation Events in the Pteris cretica Group (Pteridaceae) in Japan and Adjacent Regions

    Systematic Botany 38(1) 15-27.

    Polyploidy, hybridization, and agamospory have been considered important mechanisms in fern speciation. By integrating the methods of cytology, molecular phylogeny, and morphology, we examined the origins of polyploid species in the Pteris cretica group, which comprises five agamosporous taxa and six sexual species. Phylogenetic analysis was conducted using both cpDNA (rbcL and trnV-trnM) and a low-copy nuclear gene (gapCp). The combined results of cytology and the phylogenetic trees suggested that the sexual diploid P. kidoi had played a central role in the diversification of polyploid species in the P. cretica group. Some triploid clones of agamosporous P. cretica var. cretica originated through hybridization between the diploid cytotype of P. cretica var. cretica and the sexual diploid P. kidoi. The sexual polyploid species, P. henryi, P. multifida, P. ryukyuensis, and P. yamatensis, and the hexaploid race of P. deltodon have arisen through allopolyploidization between their respective ancestral parent species and P. kidoi. Additionally, the agamosporous triploid P. nipponica and P. cretica var. albolineata might have originated through hybridization between P. cretica var. cretica and an unknown ancestral diploid parent of P. ryukyuensis. Agamosporous P. cretica var. cretica harbored considerable genetic variation within both the diploid and triploid cytotypes. Because we could not find clear genetic differences between the diploid and triploid P. cretica, both cytotypes might be autopolyploids, or alternatively have originated through hybridization among the same members of ancestral sexual species.

    Keywords: Agamospory, cpDNA, gapCp, polyploidy, reticulate evolution, single strand conformation polymorphism (SSCP)


  • Oldham, P., Hall, S., Forero, O., 2013.

    Biological Diversity in the Patent System

    PLoS ONE 8(11) e78737.

    Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI) established by the Global Biodiversity Information Facility (GBIF) and Encyclopedia of Life (EOL). We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8–1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on Intellectual Property and Genetic Resources, Traditional Knowledge and Folklore at the World Intellectual Property Organization.

    Keywords: Agamospory, cpDNA, gapCp, polyploidy, reticulate evolution, single strand conformation polymorphism (SSCP)


  • Saeki, I., Kitazawa, A., Abe, A., Minemoto, K., Koike, F., 2013.

    Phylogeography of a rare orchid, Vexillabium yakushimense: comparison of populations in central Honshu and the Nansei Island chain, Japan

    Plant Systematics and Evolution 300(1) 1-12.

    Vexillabium yakushimense is a rare, terrestrial orchid which occurs in east and southeast Asia. In spite of its inconspicuous appearance, several new populations were discovered in central Honshu, Japan. Because these populations are geographically isolated at its northern range limit of distribution, they were suspected to have distinctive genetic characteristics. Given this hypothesis, we quantified the genetic variation of V. yakushimense for populations of central Honshu, and the Nansei Island chain, which represent the most southern locality in Japan. Leaves were collected from nine populations in central Honshu (n = 48) and two populations from the Nansei Island chain (n = 29). We examined genetic variation using cpDNA (1,205 bp) and ITS (511 bp) markers. Based on the cpDNA variation, a total of seven haplotypes were recovered; populations in central Honshu were clearly differentiated from those in the Nansei Island chain. Relatively high allelic richness and haplotype diversity were found in the pooled population of central Honshu. These populations likely maintained an adequate population size for a long period despite a markedly different ecological niche compared to that in the Nansei Island chain. In contrast to cpDNA, little variation was detected in ITS. Further studies on geographic occurrences, reproductive biology and mycorrhizal association are encouraged for its conservation.

    Keywords: Biogeography, Chloroplast DNA, Disjunct distribution, Endangered species, Genetic diversity


  • Chen, D., Zhang, X., Kang, H., Sun, X., Yin, S., Du, H., Yamanaka, N., Gapare, W., Wu, H., Liu, C., 2012.

    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: Biogeography, Chloroplast DNA, Disjunct distribution, Endangered species, Genetic diversity


  • Hosoya, T., Zhao, Y., Han, J., Saito, Y., Kakishima, M., 2012.

    Enumeration of Remarkable Japanese Discomycetes (6): Notes on Two Inoperculate Discomycetes new to Japan and One Operculate Discomycete

    Bulletin of the National Museum of Nature and Science: series B 38(4) 139-146.

    Three remarkable discomycetes (two inoperculate and one operculate) are described and illustrated: Hymenoscyphus immutabilis (Helotiaceae, Helotiales), Lachnum rachidicola (Lachnaceae, Helotiales) and Sphaerosporella brunnea (Pyronemataceae, Pezizales). The first two species are documented for the first time in Japan. Detailed microscopic description is provided for Sphaerosporella brunnea for the first time for Japanese material.

    Keywords: hymenoscyphus immutabilis, lachnum rachidicola, mycobiota, sphaerosporella