Uses of GBIF in scientific research

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

List of publications

  • Cadima, X., van Zonneveld, M., Scheldeman, X., Castañeda, N., Patiño, F., Beltran, M., Van Damme, P., 2014.

    Endemic wild potato (Solanum spp.) biodiversity status in Bolivia: Reasons for conservation concerns

    Journal for Nature Conservation 22(2) 113-131.

    Crop wild relatives possess important traits, therefore ex situ and in situ conservation efforts are essential to maintain sufficient options for crop improvement. Bolivia is a centre of wild relative diversity for several crops, among them potato, which is an important staple worldwide and the principal food crop in this country. Despite their relevance for plant breeding, limited knowledge exists about their in situ conservation status. We used Geographic Information Systems (GIS) and distribution modelling with the software Maxent to better understand geographic patterns of endemic wild potato diversity in Bolivia. In combination with threat layers, we assessed the conservation status of all endemic species, 21 in total. We prioritised areas for in situ conservation by using complementary reserve selection and excluded 25% of the most-threatened collection sites because costs to implement conservation measures at those locations may be too high compared to other areas. Some 70% (15 of 21 species) has a preliminary vulnerable status or worse according to IUCN red list distribution criteria. Our results show that four of these species would require special conservation attention because they were only observed in <15 locations and are highly threatened by human accessibility, fires and livestock pressure. Although highest species richness occurs in south-central Bolivia, in the departments Santa Cruz and Chuquisaca, the first priority area for in situ conservation according to our reserve selection exercise is central Bolivia, Cochabamba; this area is less threatened than the potato wild relatives’ hotspot in south-central Bolivia. Only seven of the 21 species were observed in protected areas. To improve coverage of potato wild relatives’ distribution by protected areas, we recommend starting inventories in parks and reserves with high modelled diversity. Finally, to improve ex situ conservation, we targeted areas for germplasm collection of species with <5 accessions conserved in genebanks.

    Keywords: Crop wild relatives, Ex situ conservation, IUCN red listing, In situ conservation, Potato breeding material, Reserve selection, Species distribution modelling, Threat assessment

  • Hustad, V., Kučera, V., Rybáriková, N., Lizoň, P., Gaisler, J., Baroni, T., Miller, A., 2014.

    Geoglossum simile of North America and Europe: distribution of a widespread earth tongue species and designation of an epitype

    Mycological Progress.

    Geoglossum simile is a distinctive species of the earth tongue class Geoglossomycetes, first described in 1873. The taxonomic standing of this species has long been disputed, resulting in nearly 70 years of potential misdiagnoses. Although G. simile was originally described from North America, it has subsequently been reported from several European countries as well as Asia, Australasia, and India. In this study, we report the first records of G. simile from Slovakia and the Czech Republic, examine the morphological and molecular diversity of Northern Hemisphere collections, discuss the taxonomic history and current status of the species, and designate a recent North American collection as the epitype of this widely distributed and conservationally significant species.

    Keywords: ascomycota, conservation, fungal, geoglossomycetes, phylogenetics, systematics

  • Kalwij, J., Steyn, C., le Roux, P., 2014.

    Repeated monitoring as an effective early detection means: first records of naturalised Solidago gigantea Aiton (Asteraceae) in southern Africa

    South African Journal of Botany 93 204-206.

    Early detectionofemerginginvasive plants depends onmaximizingthe probability of detecting newpopulations. Repeated surveys along a gradient of environmental conditions or in areas exposed to high propagule pressure provide a potentially efficient strategy for early detection of alien species. The long-termmonitoring of such an area resulted in the documentation of the first naturalised Solidago gigantea Aiton (Asteraceae) population for southern Africa. This population consisted of c. 45 individuals growing in two locations on unmanaged grassland in the Drakensberg Mountains at an elevation of 1619 m a.s.l. Solidago gigantea readily invades unmanaged European grasslands, altering biomass and transforming habitats. Moreover, since goldenrods (Solidago spp) are perennial species reproducing through a large number of wind-dispersed seeds and belowground rootstocks, these species appearwell pre-adapted to the fire-prone grassland biome of South Africa. We therefore suggest early-stage eradication of S. gigantea before it potentially becomes an unmanageable and costly invasive species in this region. This study supports long-termmonitoring programmes as an effectivemeans for early detection of new invasive species.

    Keywords: Colonisation, Emerging invaders, Goldenrod, Management, Non-native species, Weed risk assessment

  • Kolesik, P., Butterill, P., 2014.

    New gall midges (Diptera: Cecidomyiidae) from Papua New Guinea

    Austral Entomology Forthcoming.

    Two new species of gall midges that feed on trees in Papua New Guinea are described. The larvae of Schizomyia novoguineensis Kolesik sp. nov. transform the flowers of Macaranga aleuritoides (Euphorbiaceae) into spherical galls preventing sexual reproduction of the host tree. The larvae of Rhopalomyia psychotriae Kolesik sp. nov. induce pustulate leaf galls on Psychotria ramuensis (Rubiaceae). Descriptions of adults and immature stages, and DNA sequences of the cytochrome oxidase unit I mitochondrial gene segment, are given for each of the new species.

    Keywords: COI, barcoding, insect taxonomy, primary tropical forest, secondary tropical forest

  • Lucarini, D., Gigante, D., Landucci, F., Panfili, E., Venanzoni, R., 2014.

    The anArchive taxonomic Checklist for Italian botanical data banking and vegetation analysis: Theoretical basis and advantages

    Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology 1-8.

    In recent years, research in botany was increasingly related with the use of large data-sets and data banks, in order to address emerging issues such as the severe risk of species, habitats and biodiversity loss. In this frame, the anArchive taxonomic Checklist, an online synonymized list of botanical species names, developed to support the botanical data banking and vegetation analysis, is presented and discussed here. The benefits deriving from such a supervised and referenced tool are emphasized. They include the possibility to keep track of old and new species names, pointing out the latest reviewed accepted scientific name and its synonyms, and harmonizing different taxonomic points of view. Furthermore, the list is open access and expert qualified customers can collaborate to its improvement. The basic unit of the taxonomic Checklist is an object including the taxon name at specific or, when present, infraspecific level; the taxonomic frame stops at the level of family and ranks higher than genus ar...

    Keywords: Biodiversity informatics, database, harmonization, nomenclature, plant names, synonymity

  • Metallinou, M., Vasconcelos, R., Smíd, J., Sindaco, R., Carranza, S., 2014.

    Filling in the gap: two new records and an updated distribution map for the Gulf Sand gecko Pseudoceramodactyluskhobarensis Haas, 1957.

    Biodiversity data journal 2(2) e4011.

    The genus Pseudoceramodactylus Haas, 1957 comprises a single species, the Gulf Sand gecko P. khobarensis, described from eastern Saudi Arabia (Haas 1957) and is known to be distributed across parts of the Arabian Gulf, including Kuwait, Bahrain, Qatar and the United Arab Emirates (U.A.E.) (Sindaco and Jeremčenko 2008, Valdeón et al. 2013). It has also been reported from Qeshm Island, Iran (Dakhteh et al. 2007, Sharifi et al. 2012) and a few localities are known from coastal eastern Oman (Fujita and Papenfuss 2011, Gardner 2013, Metallinou et al. 2012). Pseudoceramodactylus khobarensis are nocturnal geckos, found on moist, salt-impregnated to solid, salt-encrusted flats (sabkhas) (Fig. 1a, b, c) and are often the sole reptile dweller of such extreme environments (Arnold 1977, Gardner 2013). Their fingers are swollen with loose connective tissue and bear numerous elongated spiny scales on the underside (Arnold 1977), considered to be an adaptation to this particular substrate.

    Keywords: 12S, Arabia, DNA, Gekkonidae, Reptilia, distribution range, sabkha

  • van Zonneveld, M., Castañeda, N., Scheldeman, X., van Etten, J., Van Damme, P., 2014.

    Application of consensus theory to formalize expert evaluations of plant species distribution models

    Applied Vegetation Science 17(3) 528-542.

    Aim: Application of environmental envelope modelling (EEM) for conservation planning requires careful validation. Opinions of experts who have worked with species of interest in the field can be a valuable and independent information source to validate EEM because of their first-hand experience with species occurrence and absence. However, their use in model validation is limited because of the subjectivity of their feedback. In this study, we present a method on the basis of cultural consensus theory to formalize expert model evaluations. Methods We developed, for five tree species, distribution models with nine different variable combinations and Maxent EEM software. Species specialists validated the generated distribution maps through an online Google Earth interface with the scores from Invalid to Excellent. Experts were also asked about the commission and omission errors of the distribution models they evaluated. We weighted expert scores according to consensus theory. These values were used to obtain a final average expert score for each of the produced distribution models. The consensus-weighted expert scores were compared with un-weighted scores and correlated to four conventional model performance parameters after cross-validation with test data: Area Under Curve (AUC), maximum Kappa, commission error and omission error. Results The median consensus-weighted expert score of all species–variable combinations was close to Fair. In general, experts that reached more consensus with peers were more positive about the EEM outcomes, compared to those that had more opposite judgements. Both consensus-weighted and un-weighted scores were significantly correlated to corresponding AUC, maximum Kappa and commission error values, but not to omission errors. More than half of the experts indicated that the distribution model they considered best included areas where the species is known to be absent. One third also indicated areas of species presence that were omitted by the model. Conclusions Our results indicate that experts are fairly positive about EEM outcomes. This is encouraging, but EEM application for conservation actions remains limited according to them. Methods to formalize expert knowledge allow a wider use of this information in model validation and improvement, and they complement conventional validation methods of presence-only modelling. Online GIS and survey applications facilitate the consultation of experts.

    Keywords: cultural consensus theory, envelope modelling, expert opinion, google earth, in situ conservation, mapforgen, model validatation, online survey, species distribution modelling

  • Šmarda, P., Bureš, P., Horová, L., Leitch, I., Mucina, L., Pacini, E., Tichý, L., Grulich, V., Rotreklová, O., 2014.

    Ecological and evolutionary significance of genomic GC content diversity in monocots

    Proceedings of the National Academy of Sciences of the United States of America 111(39) E4096-102.

    Genomic DNA base composition (GC content) is predicted to significantly affect genome functioning and species ecology. Although several hypotheses have been put forward to address the biological impact of GC content variation in microbial and vertebrate organisms, the biological significance of GC content diversity in plants remains unclear because of a lack of sufficiently robust genomic data. Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monocot families and compare them with genomic characters, a suite of life history traits and climatic niche data using phylogeny-based statistics. GC content of monocots varied between 33.6% and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, highlighting their unusual genome architecture and organization. GC content showed a quadratic relationship with genome size, with the decreases in GC content in larger genomes possibly being a consequence of the higher biochemical costs of GC base synthesis. Dramatic decreases in GC content were observed in species with holocentric chromosomes, whereas increased GC content was documented in species able to grow in seasonally cold and/or dry climates, possibly indicating an advantage of GC-rich DNA during cell freezing and desiccation. We also show that genomic adaptations associated with changing GC content might have played a significant role in the evolution of the Earth's contemporary biota, such as the rise of grass-dominated biomes during the mid-Tertiary. One of the major selective advantages of GC-rich DNA is hypothesized to be facilitating more complex gene regulation.

    Keywords: Poaceae, genome size evolution, geographical stratification, phylogenetic regression, plant genome

  • Leavitt, S., Fernández-Mendoza, F., Pérez-Ortega, S., Sohrabi, M., Divakar, P., Vondrák, J., Thorsten Lumbsch, H., St.Clair, L., 2013.

    Local representation of global diversity in a cosmopolitan lichen-forming fungal species complex (Rhizoplaca, Ascomycota)

    Journal of Biogeography 40(9) 1792-1806.

    Aim The relative importance of long-distance dispersal versus vicariance in determining the distribution of lichen-forming fungi remains unresolved. Here, we examined diversity and distributions in a cosmopolitan lichen-forming fungal species complex, Rhizoplaca melanophthalma sensu lato (Ascomycota), across a broad, intercontinental geographical distribution. We sought to determine the temporal context of diversification and the impacts of past climatic fluctuations on demographic dynamics within this group. Location Antarctica, Asia, Europe, North America and South America. Methods We obtained molecular sequence data from a total of 240 specimens of R. melanophthalma s.l. collected across five continents. We assessed the monophyly of candidate species using individual gene trees and a tree from a seven-locus concatenated data set. Divergence times and relationships among candidate species were evaluated using a multilocus coalescent-based species tree approach. Speciation probabilities were estimated using the coalescent-based species delimitation program bpp. We also calculated statistics on molecular diversity and population demographics for independent lineages. Main conclusions Our analyses of R. melanophthalma s.l. collected from five continents supported the presence of six species-level lineages within this complex. Based on current sampling, two of these lineages were found to have broad intercontinental distributions, while the other four were limited to western North America. Of the six lineages, five were found on a single mountain in the western USA and the sixth occurred no more than 200 km away from this mountain. Our estimates of divergence times suggest that Pleistocene glacial cycles played an important role in species diversification within this group. At least three lineages show evidence of recent or ongoing population expansion.

    Keywords: beast, biogeography, bpp, coalescent, correspondence, cryptic species, leavitt, long-distance dispersal, rhizoplaca melanophthalma, speciation

  • Mestre, A., Aguilar-Alberola, J., Baldry, D., Balkis, H., Ellis, A., Gil-Delgado, J., Grabow, K., Klobučar, G., Kouba, A., Maguire, I., Martens, A., Mülayim, A., Rueda, J., Scharf, B., Soes, M., S. Monrós, J., Mesquita-Joanes, F., 2013.

    Invasion biology in non-free-living species: interactions between abiotic (climatic) and biotic (host availability) factors in geographical space in crayfish commensals (Ostracoda, Entocytheridae)

    Ecology and Evolution 3(16) 5237-5253.

    In invasion processes, both abiotic and biotic factors are considered essential, but the latter are usually disregarded when modeling the potential spread of exo- tic species. In the framework of set theory, interactions between biotic (B), abi- otic (A), and movement-related (M) factors in the geographical space can be hypothesized with BAM diagrams and tested using ecological niche models (ENMs) to estimate A and B areas. The main aim of our survey was to evaluate the interactions between abiotic (climatic) and biotic (host availability) factors in geographical space for exotic symbionts (i.e., non-free-living species), using ENM techniques combined with a BAM framework and using exotic Entocythe- ridae (Ostracoda) found in Europe as model organisms. We carried out an extensive survey to evaluate the distribution of entocytherids hosted by crayfish in Europe by checking 94 European localities and 12 crayfish species. Both exotic entocytherid species found, Ankylocythere sinuosa and Uncinocythere occidentalis, were widely distributed in W Europe living on the exotic crayfish species Pro- cambarus clarkii and Pacifastacus leniusculus, respectively. No entocytherids were observed in the remaining crayfish species. The suitable area for A. sinuosa was mainly restricted by its own limitations to minimum temperatures in W and N Europe and precipitation seasonality in circum-Mediterranean areas. Uncinocy- there occidentalis was mostly restricted by host availability in circum-Mediterra- nean regions due to limitations of P. leniusculus to higher precipitation seasonality and maximum temperatures. The combination of ENMs with set the- ory allows studying the invasive biology of symbionts and provides clues about biogeographic barriers due to abiotic or biotic factors limiting the expansion of the symbiont in different regions of the invasive range. The relative importance of abiotic and biotic factors on geographical space can then be assessed and applied in conservation plans. This approach can also be implemented in other systems where the target species is closely interacting with other taxa.

    Keywords: bam diagrams, biological invasions, ecological niche models, host availability