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.


  • 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


  • 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

    Palaeoworld.

    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


  • Wauchope H, Shaw J, Varpe , Lappo E, Boertmann D, Lanctot R et al. (2016)

    Rapid climate-driven loss of breeding habitat for Arctic migratory birds

    Global Change Biology.

    Millions of birds migrate to and from the Arctic each year, but rapid climate change in the High North could strongly affect where species are able to breed, disrupting migratory connections globally. We modelled the climatically suitable breeding conditions of 24 Arctic specialist shorebirds and projected them to 2070 and to the mid-Holocene climatic optimum, the world's last major warming event ~6000 years ago. We show that climatically suitable breeding conditions could shift, contract and decline over the next 70 years, with 66–83% of species losing the majority of currently suitable area. This exceeds, in rate and magnitude, the impact of the mid-Holocene climatic optimum. Suitable climatic conditions are predicted to decline acutely in the most species rich region, Beringia (western Alaska and eastern Russia), and become concentrated in the Eurasian and Canadian Arctic islands. These predicted spatial shifts of breeding grounds could affect the species composition of the world's major flyways. Encouragingly, protected area coverage of current and future climatically suitable breeding conditions generally meets target levels; however, there is a lack of protected areas within the Canadian Arctic where resource exploitation is a growing threat. Given that already there are rapid declines of many populations of Arctic migratory birds, our results emphasize the urgency of mitigating climate change and protecting Arctic biodiversity.

    Keywords: Beringia, flyway, maxent, mid-Holocene, protected areas, shorebirds, species distribution modelling, waders


  • 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.

    Keywords: Beringia, flyway, maxent, mid-Holocene, protected areas, shorebirds, species distribution modelling, waders


  • 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