Uses of GBIF in scientific research

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

List of publications

  • 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

  • Jermakowicz E, Wróblewska A, Brzosko E, Mirski P, Hirse T (2015)

    Phylogeographical structure of the boreal-montane orchid Malaxis monophyllos as a result of multi-directional gene flow

    Botanical Journal of the Linnean Society 178(1) 138-154.

    We investigated the phylogeographical structure of the boreal-montane orchid Malaxis monophyllos in its Eurasian geographical range. We analysed four sequences of plastid DNA (trnL, trnL–trnF, rps16 and accD-psaI), resulting in 19 haplotypes and revealing a high level of intraspecific diversity (HD = 0.702 and π = 0.196 × 10−2), but showing a lack of phylogeographical structure. This pattern might be caused by multiple phenomena and processes, e.g. broad-fronted recolonization with accompanying multi-directional gene flow between populations and expansion from at least two refugial areas. Despite the lack of phylogeographical structure, three centres of haplotype diversity were indicated in the European part of the range of M. monophyllos. According to these data, alpine and lowland glacial refugia located between the ice sheets in the European Alps and the Scandinavian glaciers seem most likely to be in Europe. Moreover, models of climatically suitable areas during the Last Glacial Maximum (LGM) confirmed the Alps as a possible refuge, and indicated an opportunity for the persistence of M. monophyllos populations in Beringia and parts of Siberia. Using two models [Model for Interdisciplinary Research on Climate (MIROC) and Community Climate System Model (CCSM)], we predicted a significant reduction in climatically suitable areas for M. monophyllos in the future (2080). Our study also demonstrated that the biological features of M. monophyllos, including breeding system and dispersal mode, seem to be crucial in understanding its phylogeographical pattern. Our results also highlighted the importance of anthropogenic habitats as reservoirs of genetic diversity and alternative habitats for this species in the context of declining natural populations

    Keywords: Orchidaceae, anthropogenic habitats, cpDNA, plastid DNA diversity centres, species distribution models

  • Wasof S, Lenoir J, Aarrestad P, Alsos I, Armbruster W, Austrheim G et al. (2015)

    Disjunct populations of European vascular plant species keep the same climatic niches

    Global Ecology and Biogeography.

    Aim Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been separated for thousands of years. Location European Alps and Fennoscandia. Methods Of the studied pool of 888 terrestrial vascular plant species occurring in both the Alps and Fennoscandia, we used two complementary approaches to test and quantify climatic-niche shifts for 31 species having strictly disjunct populations and 358 species having either a contiguous or a patchy distribution with distant populations. First, we used species distribution modelling to test for a region effect on each species' climatic niche. Second, we quantified niche overlap and shifts in niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) within a bi-dimensional climatic space. Results Only one species (3%) of the 31 species with strictly disjunct populations and 58 species (16%) of the 358 species with distant populations showed a region effect on their climatic niche. Niche overlap was higher for species with strictly disjunct populations than for species with distant populations and highest for arctic–alpine species. Climatic niches were, on average, wider and located towards warmer and wetter conditions in the Alps. Main conclusion Climatic niches seem to be generally conserved between populations that are separated between the Alps and Fennoscandia and have probably been so for 10,000–15,000 years. Therefore, the basic assumption of species distribution models that a species' climatic niche is constant in space and time – at least on time scales 104 years or less – seems to be largely valid for arctic–alpine plants.

    Keywords: Alpine plants, arctic plants, climatic niche, disjunct distribution, distant populations, niche conservatism, niche optimum, niche overlap, niche width, species distribution modelling

  • Cornwell W, Westoby M, Falster D, FitzJohn R, O'Meara B, Pennell M et al. (2014)

    Functional distinctiveness of major plant lineages

    Journal of Ecology 102(2) 345-356.

    1. Plant traits vary widely across species and underpin differences in ecological strategy. Despite centuries of interest, the contributions of different evolutionary lineages to modern-day functional diversity remain poorly quantified. 2. Expanding data bases of plant traits plus rapidly improving phylogenies enable for the first time a data-driven global picture of plant functional diversity across the major clades of higher plants. We mapped five key traits relevant to metabolism, resource competition and reproductive strategy onto a phylogeny across 48324 vascular plant species world-wide, along with climate and biogeo- graphic data. Using a novel metric, we test whether major plant lineages are functionally distinctive. We then highlight the trait–lineage combinations that are most functionally distinctive within the present-day spread of ecological strategies. 3. For some trait–clade combinations, knowing the clade of a species conveys little information to neo- and palaeo-ecologists. In other trait–clade combinations, the clade identity can be highly reveal- ing, especially informative clade–trait combinations include Proteaceae, which is highly distinctive, representing the global slow extreme of the leaf economic spectrum. Magnoliidae and Rosidae con- tribute large leaf sizes and seed masses and have distinctively warm, wet climatic distributions. 4. Synthesis. This analysis provides a shortlist of the most distinctive trait–lineage combinations along with their geographic and climatic context: a global view of extant functional diversity across the tips of the vascular plant phylogeny.

    Keywords: Kolmogorov–Smirnov Importance index, determinants of plant community diversity and stru, functional traits, geographic and climatic distributions, leaf nitrogen, leaf size, maximum adult height, phylogenetic tree, seed mass, specific leaf area

  • Obermayer W, Randlane T (2012)

    Morphological and chemical studies on Platismatia erosa (Parmeliaceae) from Tibet, Nepal and Bhutan

    The Bryologist 115(1) 51-60.

    The occurrence of Platismatia erosa in Tibet and adjacent regions is reported. The shape of (hitherto rarely found) apothecia and pycnospores (the latter observed for the first time) are illustrated and compared with those of European material of P. glauca. TLC analyses of P. erosa samples revealed two substances, hitherto unknown in Platismatia, namely pannaric acid and jackinic acid, the latter also found in fruiting material of Platismatia glauca from Europe. Two chemotypes of P. erosa are recognized: chemotype I with caperatic acid as main fatty acid, and chemotype II (found only once) with jackinic acid as main aliphatic substance.

    Keywords: Lichen, Platismatia glauca, chemotypes, conidia, taxonomy

  • Gugger P, González-Rodríguez A, Rodríguez-Correa H, Sugita S, Cavender-Bares J (2010)

    Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of ‘rear edge’ populations

    New Phytologist online.

    Summary * •Poleward Pleistocene plant migration has been an important process structuring modern temperate and boreal plant communities, but the contribution of equatorward migration remains poorly understood. Paleobotanical evidence suggests Miocene or Pleistocene origin for temperate ‘sky island’ plant taxa in Mexico. These ‘rear edge’ populations situated in a biodiversity hotspot may be an important reserve of genetic diversity in changing climates. * •We used mtDNA sequences, cpDNA sequences and chloroplast microsatellites to test hypotheses of Miocene vs Pleistocene colonization of temperate Douglas-fir in Mexico, explore geographic patterns of molecular variation in relation to Pleistocene climate history using ecological niche models, and assess the taxonomic and conservation implications. * •We found strong evidence for Pleistocene divergence of Douglas-fir in Mexico (958 thousand yr before present (ka) with the 90% highest posterior density interval ranging from 1.6 million yr before present (Ma) to 491 ka), consistent with the southward Pleistocene migration hypothesis. Genetic diversity was high and strongly partitioned among populations. Spatial patterns of molecular variation and ecological niche models suggest a complex late Pleistocene history involving periods of isolation and expansion along mountain corridors. * •These results highlight the importance of southward Pleistocene migration in establishing modern high-diversity plant communities and provide critical insights into proposals to conserve the unique biodiversity of Mexican Douglas-fir and associated taxa.

    Keywords: Mexico, Pseudotsuga menziesii, cpDNA, cpSSR, ecological niche modeling, mtDNA, phylogeography, rear edge