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

  • 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

  • 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)