Uses of GBIF in scientific research

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

List of publications

  • Dufresnes C, Litvinchuk S, Leuenberger J, Ghali K, Zinenko O, Stöck M et al. (2016)

    Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog ( Hyla orientalis )

    Molecular Ecology.

    Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated to glacial refugia, i.e. areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and Southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modeling, to understand what shaped the genetic variation of this species. We documented an important diversity center around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and Eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity, and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important center of intraspecific diversity in the Palearctic with implications for conservation.


  • Díaz S, Kattge J, Cornelissen J, Wright I, Lavorel S, Dray S et al. (2015)

    The global spectrum of plant form and function

    Nature.

    Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today’s terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Three-quarters of trait variation is captured in a two-dimensional global spectrum of plant form and function. One major dimension within this plane reflects the size of whole plants and their parts; the other represents the leaf economics spectrum, which balances leaf construction costs against growth potential. The global plant trait spectrum provides a backdrop for elucidating constraints on evolution, for functionally qualifying species and ecosystems, and for improving models that predict future vegetation based on continuous variation in plant form and function.


  • Feuda R, Bannikova A, Zemlemerova E, Di Febbraro M, Loy A, Hutterer R et al. (2015)

    Tracing the evolutionary history of the mole, Talpa europaea , through mitochondrial DNA phylogeography and species distribution modelling

    Biological Journal of the Linnean Society 114(3) 495-512.

    Our understanding of the effect of Pleistocene climatic changes on the biodiversity of European mammals mostly comes from phylogeographical studies of non-subterranean mammals, whereas the influence of glaciation cycles on subterranean mammals has received little attention. The lack of data raises the question of how and to what extent the current amount and distribution of genetic variation in subterranean mammals is the result of Pleistocene range contractions/expansions. The common mole (Talpa europaea) is a strictly subterranean mammal, widespread across Europe, and represents one of the best candidates for studying the influence of Quaternary climatic oscillation on subterranean mammals. Cytochrome b sequences, as obtained from a sampling covering the majority of the distribution area, were used to evaluate whether Pleistocene climate change influenced the evolution of T. europaea and left a trace in the genetic diversity comparable to that observed in non-subterranean small mammals. Subsequently, we investigated the occurrence of glacial refugia by comparing the results of phylogeographical analysis with species distribution modelling. We found three differentiated mitochondrial DNA lineages: two restricted to Spain and Italy and a third that was widespread across Europe. Phylogenetic inferences and the molecular clock suggest that the Spanish moles represent a highly divergent and ancient lineage, highlighting for the first time the paraphyly of T. europaea. Furthermore, our analyses suggest that the genetic break between the Italian and the European lineages predates the last glacial phase. Historical demography and spatial principal component analysis further suggest that the Last Glacial Maximum left a signature both in the Italian and in the European lineages. Genetic data combined with species distribution models support the presence of at least three putative glacial refugia in southern Europe (France, Balkan Peninsula and Black Sea) during thelast glacial maximum that likely contributed to post-glacial recolonization of Europe. By contrast, the Italian lineage remained trapped in the Italian peninsula and, according to the pattern observed in other subterranean mammals, did not contribute to the recolonization of northern latitudes

    Keywords: Europe, Last Glacial Maximum, SDM, cytochrome b, glacial refugia, historical demography, paraphyly, phylogenetics, sPCA


  • Loskutov I, Melnikova S, Bagmet L (2015)

    Eco-geographical assessment of Avena L. wild species at the VIR herbarium and genebank collection

    Genetic Resources and Crop Evolution.

    On the bases of analysis of the collecting sites of 1160 herbarium specimens and 1640 genebank accessions of wild Avena L. species from the world collection of the Vavilov Institute of Plant Genetic Resources maps of areas of the species were produced data base. A comparison of the climate conditions of the Mediterranean, Southwestern Asiatic and Abyssinian centers of diversity with those of the oat species distribution areas shows that all oat species mostly prefer the moderately hot, semi-arid and dry climate. An analysis of the range of soils in the areas of wild oat species distribution has shown that the collected accessions, preferred different types of soil. When considering the soil diversity within the areas of natural distribution of wild oat species, it could be established that the majority of diploid and tetraploid taxa prefer to grow on mountain or plain cinnamon soils; the hexaploid taxa favorites were the mountain forest brown or red-brown soils, as well as subtropical desert soils. An analysis of the database of geographic distribution on wild oat species showed a full picture of oat species diversity, and a basis to make plans concerning further collecting activities or a basis for selecting potential sources of novel genes that can improve some valuable traits and characters to use them for practical purposes.

    Keywords: Avena, Climate, Collecting sites, Data base, Genebank accessions, Herbarium specimens, Types of soils, Wild species


  • Orlov A, Cotton C (2015)

    New data on the rare deep-sea skate Amblyraja jenseni (Rajidae) from the North Atlantic Ocean

    Journal of Ichthyology 55(4) 478-496.

    In this study we present the most complete description of color variation, morphometric and meristic characters for the rare deep-sea North Atlantic Jensen’s skate Amblyraja jenseni, based on analyses of a wide range of accessible material. Comparisons of external morphological characters of male and female specimens of varying sizes and from different regions of the North Atlantic indicated regional morphological differences likely due to prolonged geographic isolation of local populations of this species. The vast majority of individuals exhibited a “dark” coloration, with a less common “light” coloration observed particularly among skates from the waters of the northeast and northwest Atlantic. Only dark-colored skates were found in the waters of the Mid-Atlantic Ridge. We also provide new data on the habitat, vertical distribution and size of the Jensen’s skate.

    Keywords: Amblyraja jenseni, Jensen’s skate, North Atlantic, color, dimorphism, external morphology, meristics, morphometrics


  • Orlova-Bienkowskaja M, Ukrainsky A, Brown P (2015)

    Harmonia axyridis (Coleoptera: Coccinellidae) in Asia: a re-examination of the native range and invasion to southeastern Kazakhstan and Kyrgyzstan

    Biological Invasions.

    Harmonia axyridis (Pallas) is an invasive ladybird spreading in several continents. It is native to East Asia, but its range in Asia has until now been poorly understood. The most complete map of the range of Harmonia axyridis in Asia has been compiled (432 localities). Harmonia axyridis occurs in the south-east of West Siberia, the south of East Siberia, the south of Russian Far East, the east of Kazakhstan, the north of Kyrgyzstan, Mongolia, China, North Korea, South Korea, Japan, and the north of Vietnam. Southeastern Kazakhstan and the north of Kyrgyzstan are not a part of the native range: the large Balkhash Desert is situated between this mountainous region and the nearest part of the native range (Altai mountains). The analysis of dates and places of findings indicates that Harmonia axyridis appeared in southeastern Kazakhstan and Kyrgyzstan after the construction of the Turkestan-Siberian Railway. It is hypothesized that the beetles crossed the desert along this railway.

    Keywords: Coccinellidae, Harlequin ladybird, Harmonia axyridis, Invasive species, Multicolored Asian lady beetle, Native range


  • Ware C, Berge J, Jelmert A, Olsen S, Pellissier L, Wisz M et al. (2015)

    Biological introduction risks from shipping in a warming Arctic

    Journal of Applied Ecology.

    1.Several decades of research on invasive marine species have yielded a broad understanding of the nature of species invasion mechanisms and associated threats globally. However, this is not true of the Arctic, a region where ongoing climatic changes may promote species invasion. Here we evaluated risks associated with non-indigenous propagule loads discharged with ships’ ballast water to the high-Arctic archipelago, Svalbard, as a case study for the wider Arctic. 2.We sampled and identified transferred propagules using traditional and DNA barcoding techniques. We then assessed the suitability of the Svalbard coast for non-indigenous species under contemporary and future climate scenarios using ecophysiological models based on critical temperature and salinity reproductive thresholds. 3.Ships discharging ballast water in Svalbard carried high densities of zooplankton (mean 1522 ± 335 SE individuals m−3), predominately comprised of indigenous species. Ballast water exchange did not prevent non-indigenous species introduction. Non-indigenous coastal species were present in all except one of 16 ballast water samples (mean 144 ± 67 SE individuals m−3), despite five of the eight ships exchanging ballast water en route. 4.Of a total of 73 taxa, 36 species including 23 non-indigenous species were identified. Of those 23, sufficient data permitted evaluation of the current and future colonization potential for eight widely-known invaders. With the exception of one of these species, modelled suitability indicated that the coast of Svalbard is unsuitable presently; under the 2100 RCP 8.5 climate scenario, however, modelled suitability will favour colonization for six species. 5.Synthesis and applications. We show that current ballast water management practices do not prevent non-indigenous species from being transferred to the Arctic. Consequences of these shortcomings will be shipping-route dependent, but will likely magnify over time: our models indicate future conditions will favour the colonization of non-indigenous species Arctic-wide. Invasion threats will be greatest where shipping transfers organisms across biogeographic realms, and for these shipping routes ballast water treatment technologies may be required to prevent impacts. Our results also highlight critical gaps in our understanding of ballast water management efficacy and prioritization. Thereby, our study provides an agenda for research and policy development.

    Keywords: Arctic, ballast water exchange, climate change, ecophysiological thresholds, habitat suitability, invasion, marine non-indigenous species, regeneration niche, shipping, zooplankton


  • van Kleunen M, Dawson W, Essl F, Pergl J, Winter M, Weber E et al. (2015)

    Global exchange and accumulation of non-native plants

    Nature 525(7567) 100-103.

    All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch1, 2 is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage3. So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.

    Keywords: Biodiversity, Biogeography, Invasive species, Macroecology


  • Artyukova E, Kozyrenko M, Boltenkov E, Gorovoy P (2014)

    One or three species in Megadenia (Brassicaceae): insight from molecular studies

    Genetica 142(4) 337-50.

    Megadenia Maxim. is a small genus of the Brassicaceae endemic to East Asia with three disjunct areas of distribution: the eastern edge of the Qinghai-Tibetan Plateau, the Eastern Sayan Mountains in southern Siberia, and Chandalaz Ridge in the southern Sikhote-Alin Mountains. Although distinct species (M. pygmaea Maxim., M. bardunovii Popov, and M. speluncarum Vorob., Vorosch. and Gorovoj) have been described from each area, they have lately been reduced to synonymy with M. pygmaea due to high morphological similarity. Here, we present the first molecular study of Megadenia. Using the sequences of 11 noncoding regions from the cytoplasmic (chloroplast and mitochondrial) and nuclear genomes, we assessed divergence within the genus and explored the relationships between Megadenia and Biscutella L. Although M. bardunovii, M. speluncarum, and M. pygmaea were found to be indiscernible with regard to the nuclear and mitochondrial markers studied, our data on the plastid genome revealed their distinctness and a clear subdivision of the genus into three lineages matching the three described species. All of the phylogenetic analyses of the chloroplast DNA sequences provide strong support for the inclusion of Megadenia and Biscutella in the tribe Biscutelleae. A dating analysis shows that the genus Megadenia is of Miocene origin and diversification within the genus, which has led to the three extant lineages, most likely occurred during the Early-Middle Pleistocene, in agreement with the vicariance pattern. Given the present-day distribution, differences in habitat preferences and in some anatomical traits, and lack of a direct genealogical relationship, M. pygmaea, M. bardunovii, and M. speluncarum should be treated as distinct species or at least subspecies.

    Keywords: Biodiversity, Biogeography, Invasive species, Macroecology


  • Borisanova A, Chernyshev A, Neretina T, Stupnikova A (2014)

    Description and phylogenetic position of the first abyssal solitary kamptozoan species from the Kuril-Kamchatka trench area: Loxosomella profundorum sp. nov. (Kamptozoa: Loxosomatidae)

    Deep Sea Research Part II: Topical Studies in Oceanography Forthcoming.

    One of two orders of a small phylum Kamptozoa, Solitaria, consisting of one family Loxosomatidae of about 140 species, has never been recorded deeper than 700m. All known for the north-western Pacific loxosomatids (about 17 species) occur in shallow waters. The first abyssal solitary kamptozoan, Loxosomella profundorum sp. nov. is described herein. It was collected during the German–Russian deep-sea expedition KuramBio aboard RV Sonne in the summer of 2012 in the abyssal plain adjacent to the Kuril-Kamchatka Trench. It is the deepest finding of Kamptozoa to date. The new species was found living on the anthozoan polyp Corallimorpharia. L. profundorum sp. nov. is a largest solitary kamptozoan species, up to 4mm in length, with a stalk of up to 3.5 mm, with 10–12 tentacles, with two conspicuous lateral papillae, and a row of glandular cells in its stalk. A preliminary molecular phylogenetic analysis based on partial 18S rDNA indicated that L. profundorum sp. nov. is a sister clade to the clade, which includes other Loxosomella and two species of Loxomitra.

    Keywords: Abyssal, Biodiversity, Biogeography, Corallimorpharia, Entoprocta, Kuril-Kamchatka Trench, Loxosomella, New species