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

  • German D (2017)

    What is Cochlearia venusta (Cruciferae)?

    Phytotaxa 297(3) 295.

    Available material on the improperly known Cruciferae (Brassicaceae) species, Cochlearia venusta (Pseudosempervivum venustum), is revised and identified. The taxon is found to be conspecific with the eastern Anatolian endemic Noccaea bornmuelleri, previously long known as Thlaspi bornmuelleri (based on Syrenopsis bornmuelleri). The 10-years younger S. bornmuelleri is reduced to synonymy of C. venusta and a combination Noccaea venusta is validated. Original material of both names is briefly discussed; a lectotype (instead of holotype) is recognized for S. bornmuelleri and that is designated for C. venusta.

    Keywords: Brassicaceae, Eudicots, nomenclature, taxonomy

  • Hens H, Jäkäläniemi A, Tali K, Efimov P, Kravchenko A, Kvist L (2017)

    Genetic structure of a regionally endangered orchid, the dark red helleborine (Epipactis atrorubens) at the edge of its distribution

    Genetica 1-13.

    The genetic structure and diversity of species is determined by both current population dynamics and historical processes. Population genetic structure at the edge of the distribution is often expected to differ substantially from populations at the centre, as these edge populations are often small and fragmented. In addition, populations located in regions that have experienced repeated glaciations throughout the Pleistocene, may still carry imprints from the genetic consequences of frequent distribution shifts. Using chloroplast DNA sequences and nuclear microsatellite markers we studied the genetic structure of Epipactis atrorubens at the northern edge of its distribution. Contrary to populations in the centre of the distribution, populations at the northern range are regionally endangered as they are small and disjunct. Sequence data of 2 chloroplast loci and allelic data from 6 nuclear microsatellite markers were obtained from 297 samples from Finland, Estonia and Russia. We sought for genetic indicators of past population processes, such as post-glacial colonisation history of E. atrorubens. As expected, we observed low genetic variation, in terms of numbers of substitutions, haplotypes and alleles, and significant levels of differentiation, especially pronounced in the chloroplast DNA. These features suggest that the edge populations could be prone to extinction.

    Keywords: Genetic diversity, Microsatellites, Population differentiation, intergenic spacer, rbcL-accD, trnK

  • 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.

    Keywords: Genetic diversity, Microsatellites, Population differentiation, intergenic spacer, rbcL-accD, trnK

  • Fedosov V, Pisarenko O, Bakalin V (2016)

    Venturiella sinensis (Erpodiaceae, Bryophyta), a new species and a new family for the moss flora of Russia

    Arctoa 25(1) 364-368.

    Venturiella sinensis (Venturi) Müll. Hal., the species with temperate amphipacific distribution was recently found on Mt. Sinyaya (the East Manchurian Mountains, south of Primorskij Territory, the Russian Far East). The description and illustrations of the species based on the Russian specimen are provided, its ecology and distribution are considered. Though the present record of the species is not surprising, it provides a remarkable extension of the Russian moss flora as the first representative of the generally tropic family Erpodiaceae. The Manchurian mountains represent the easternmost distribution limit of several species of vascular plants and liverworts with generally southern distribution.

    Keywords: Erpodiaceae, Far East, Manchuria, Primorskij Territory, Russia, flora, rare species

  • Hantemirova E, Heinze B, Knyazeva S, Musaev A, Lascoux M, Semerikov V (2016)

    A new Eurasian phylogeographical paradigm? Limited contribution of southern populations to the recolonization of high latitude populations in Juniperus communis L. (Cupressaceae)

    Journal of Biogeography.

    Aim The aims of this population genetics study of the common juniper across Eurasia were to (1) assess the contribution of southern mountain ranges to the post-glacial recolonization of high latitudes and (2) test whether recent expansion or high gene flow could explain the low genetic differentiation in Northern Eurasia. Location Northern Eurasia and mountain regions of Central Europe and Asia. Methods Six hundred and twenty-two individuals were sampled in 42 populations. Two chloroplast DNA (cpDNA) fragments were investigated (trnT-trnL and 16S-trnA). Analyses of the distribution of haplotypes across the continent included a suite of phylogeographical and phylogenetic tests. Putative geographical distribution in the past was reconstructed using environmental niche modelling. Results Eighty-four haplotypes clustered into four main clades (GL1-GL4). The largest clade, GL3, corresponds to populations from the Alps, northern Europe, Western Caucasus and Siberia. These populations were moderately differentiated (28%) compared to the total range (76%) and Fu's Fs statistic was negative, indicating a population expansion. Some haplotypes within GL3 form subclades with a restricted geographical distribution, suggesting a local origin of the mutation and limited dispersal. In line with these findings, modelling of ecological niches found no significant reduction in the expected range during the LGM. Remarkably, populations from the eastern part of North Caucasus, the Himalayas, Tien Shan and south Siberia were distinctly different from populations in the rest of the range. Main conclusions As in Siberian larch species, the pattern of genetic diversity at cpDNA across the natural range of J. communis suggests that colonization of northern Europe and Siberia started from a limited area and predated the last glaciation. It is likely that juniper survived the subsequent glacial epoch at high latitudes in cryptic refugia serving as secondary centres of recolonization. Southern mountain refugia contribution to the recolonization of high latitudes was, at best, limited.

    Keywords: Cupressaceae, Eurasia, chloroplast DNA, common juniper, glacial cycles, phylogeography

  • Marques I, Draper D, López-Herranz M, Garnatje T, Segarra-Moragues J, Catalán P et al. (2016)

    Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

    Scientific Reports 6 36283.

    Apart from the overwhelming cases of allopolyploidization, the impact of speciation through homoploid hybridization is becoming more relevant than previously thought. Much less is known, however, about the impact of climate changes as a driven factor of speciation. To investigate these issues, we selected Festuca picoeuropeana, an hypothetical natural hybrid between the diploid species F. eskia and F. gautieri that occurs in two different mountain ranges (Cantabrian Mountains and Pyrenees) separated by more than 400 km. To unravel the outcomes of this mode of speciation and the impact of climate during speciation we used a multidisciplinary approach combining genome size and chromosome counts, data from an extensive nuclear genotypic analysis, plastid sequences and ecological niche models (ENM). Our results show that the same homoploid hybrid was originated independently in the two mountain ranges, being currently isolated from both parents and producing viable seeds. Parental species had the opportunity to contact as early as 21000 years ago although niche divergence occurs nowadays as result of a climate-driven shift. A high degree of niche divergence was observed between the hybrid and its parents and no recent introgression or backcrossed hybrids were detected, supporting the current presence of reproductive isolation barriers between these species.

    Keywords: Cupressaceae, Eurasia, chloroplast DNA, common juniper, glacial cycles, phylogeography

  • Maurin O, Muasya A, Catalan P, Shongwe E, Viruel J, Wilkin P et al. (2016)

    Diversification into novel habitats in the Africa clade of Dioscorea (Dioscoreaceae): erect habit and elephant’s foot tubers

    BMC Evolutionary Biology 16(1) 238.

    Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct group of species with a pachycaul or “elephant’s foot” structure that is partially to fully exposed above the substrate. In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have led to modification of reproductive organs and mode of dispersal. The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology and climate, where the fynbos, thicket, succulent karoo and forest biomes meet. Diversification out of forest is associated with major shifts in morphology of the perennial tuber (specifically an increase in size and orientation which presumably led them to become pachycaul) and rotation of stem (from twining to non-twining). The iconic elephant's foot morphology, observed in grasslands and thicket biomes, where its corky bark may offer protection against fire and herbivory, evolved since mid Miocene. A shift in pollination trait is observed within the forest, but entry into open habitat does not show association with reproductive morphology, except in the seed wing, which has switched from winged all round the seed margin to just at the base or at the apex of it, or has been even replaced by an elaiosome.

    Keywords: Biogeography, Dioscoreales, Fire adaptation, Habitat transition, Pachycaul, Southern Africa, Yams, “elephant’s foot”

  • Pierce S, Negreiros D, Cerabolini B, Kattge J, Díaz S, Kleyer M et al. (2016)

    A global method for calculating plant CSR ecological strategies applied across biomes world-wide

    Functional Ecology.

    Competitor, stress-tolerator, ruderal (CSR) theory is a prominent plant functional strategy scheme previously applied to local floras. Globally, the wide geographic and phylogenetic coverage of available values of leaf area (LA), leaf dry matter content (LDMC) and specific leaf area (SLA) (representing, respectively, interspecific variation in plant size and conservative vs. acquisitive resource economics) promises the general application of CSR strategies across biomes, including the tropical forests hosting a large proportion of Earth's diversity. We used trait variation for 3068 tracheophytes (representing 198 families, six continents and 14 biomes) to create a globally calibrated CSR strategy calculator tool and investigate strategy–environment relationships across biomes world-wide. Due to disparity in trait availability globally, co-inertia analysis was used to check correspondence between a ‘wide geographic coverage, few traits’ data set and a ‘restricted coverage, many traits’ subset of 371 species for which 14 whole-plant, flowering, seed and leaf traits (including leaf nitrogen content) were available. CSR strategy/environment relationships within biomes were investigated using fourth-corner and RLQ analyses to determine strategy/climate specializations. Strong, significant concordance (RV = 0·597; P < 0·0001) was evident between the 14 trait multivariate space and when only LA, LDMC and SLA were used. Biomes such as tropical moist broadleaf forests exhibited strategy convergence (i.e. clustered around a CS/CSR median; C:S:R = 43:42:15%), with CS-selection associated with warm, stable situations (lesser temperature seasonality), with greater annual precipitation and potential evapotranspiration. Other biomes were characterized by strategy divergence: for example, deserts varied between xeromorphic perennials such as Larrea divaricata, classified as S-selected (C:S:R = 1:99:0%) and broadly R-selected annual herbs (e.g. Claytonia perfoliata; R/CR-selected; C:S:R = 21:0:79%). Strategy convergence was evident for several growth habits (e.g. trees) but not others (forbs). The CSR strategies of vascular plants can now be compared quantitatively within and between biomes at the global scale. Through known linkages between underlying leaf traits and growth rates, herbivory and decomposition rates, this method and the strategy–environment relationships it elucidates will help to predict which kinds of species may assemble in response to changes in biogeochemical cycles, climate and land use.

    Keywords: Comparative ecology, Grime’s CSR triangle, community assembly, plant economics spectrum, plant functional type, survival strategy, universal adaptive strategy theory

  • Skirina IF, Salokhin AV, Tsarenko NA S (2016)

    New locations of protected lichens of Sakhalin island

    Turczaninowia 19(2).

    In this work floristic findings of protected, rare and poorly studied lichens of Sakhalin island are presented. Information is based on expedition research in 2014–2015. From 19 species included in this paper – Biatora chrysantha, Coenogonium pineti, Diplotomma alboatrum, Evernia esorediosa, Hypogymnia fujisanensis and Thelotrema foveolare are provided first time for the study area; Rinodina polyspora is the new species for the south of the Russian Far East. New locations on Sakhalin island are pointed out for the Anzia colpodes, Coccocarpia erythroxyli, Hypogymnia fragillima, H. hypotrypa, Lethariella togashii, Nephromopsis laii, N. laureri, N. ornata, Rinodina degeliana, Sticta limbata, S. fuliginosa and Tetramelas geophilus. All of these lichen species are epiphytic ones excepting Coenogonium pineti, which is epibryophytic. 7 lichen species are protected. 5 species are included in Red Book of Russia and Red Book of Sakhalin region: Coccocarpia erythroxyli, Hypogymnia fragillima, Nephromopsis laureri, N. ornata and Sticta limbata. Two species, Nephromopsis laii and Hypogymnia hypotrypa are included in Red Book of Sakhalin region. For each species labels are cited, data about substrate and community distribution and frequency of occurrence are given. Brief information about distribution of studied lichen species on Sakhalin island, in Russia and general distribution is presented. Photos of several lichen species are given. Key words: lichens, floristic find, Russian Far East.

    Keywords: Comparative ecology, Grime’s CSR triangle, community assembly, plant economics spectrum, plant functional type, survival strategy, universal adaptive strategy theory

  • Wang H, Oskolski A, Jacques F, Wang Y, Zhou Z (2016)

    Lignified woods of Pinus (Pinaceae) from the late Miocene of central Yunnan, China, and their biogeographic and paleoclimatic implications


    Two new species, Pinus uniseriata and P. nanfengensis, were described on the basis of lignified fossil woods from the late Miocene of the Xianfeng Basin (central Yunnan, southwestern China). The woods of both species are characterized by gradual transition from early wood to late wood, predominantly uniseriate pitting in the tracheid walls, the absence of axial parenchyma and traumatic resin canals, the presence of axial and radial resin ducts, uniseriate rays, smooth to slightly pitted ray tracheids and pinoid/taxodioid pits in cross-field pits. They differ in that P. uniseriata wood has unisetiate marginal ray tracheids and taxodioid (occasionally cupressoid) pits whereas P. nanfengensis wood has ray tracheids usually arranged as biseriate, as well as pinoid and taxodioid cross-field pits. The fossil woods showed a considerable anatomical similarity to extant species P. bungeana and P. roxburghii, respectively, which are now absent from central Yunnan. Pinus uniseriata is the first macrofossil record for subsection Gerardianae. Pinus nanfengensis is the first fossil record of the subsection Pinaster outside Europe.

    Keywords: Central Yunnan, Fossil wood, Late Miocene, Paleoclimate, Pinus, Southwestern China