Uses of GBIF in scientific research

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

List of publications

  • Creemers, R., Denoël, M., Campos, J., Vences, M., Crochet, P., Gonçalves, J., de Pous, P., Kuzmin, S., Speybroeck, J., Toxopeus, B., Corti, C., Vieites, D., Ficetola, G., Bonardi, A., Crnobrnja Isailović, J., Rodríguez, A., Lymberakis, P., Sindaco, R., Sillero, N., 2014.

    Updated distribution and biogeography of amphibians and reptiles of Europe

    Amphibia-Reptilia 35(1) 1-31.

    A precise knowledge of the spatial distribution of taxa is essential for decision-making processes in land management and biodiversity conservation, both for present and under future global change scenarios. This is a key base for several scientific disciplines (e.g. macro-ecology, biogeography, evolutionary biology, spatial planning, or environmental impact assessment) that rely on species distribution maps. An atlas summarizing the distribution of European amphibians and reptiles with 50 × 50 km resolution maps based on ca. 85 000 grid records was published by the Societas Europaea Herpetologica (SEH) in 1997. Since then, more detailed species distribution maps covering large parts of Europe became available, while taxonomic progress has led to a plethora of taxonomic changes including new species descriptions. To account for these progresses, we compiled information from different data sources: published in books and websites, ongoing national atlases, personal data kindly provided to the SEH, the 1997 European Atlas, and the Global Biodiversity Information Facility (GBIF). Databases were homogenised, deleting all information except species names and coordinates, projected to the same coordinate system (WGS84) and transformed into a 50 × 50 km grid. The newly compiled database comprises more than 384 000 grid and locality records distributed across 40 countries. We calculated species richness maps as well as maps of Corrected Weighted Endemism and defined species distribution types (i.e. groups of species with similar distribution patterns) by hierarchical cluster analysis using Jaccard’s index as association measure. Our analysis serves as a preliminary step towards an interactive, dynamic and online distributed database system (NA2RE system) of the current spatial distribution of European amphibians and reptiles. The NA2RE system will serve as well to monitor potential temporal changes in their distributions. Grid maps of all species are made available along with this paper as a tool for decision-making and conservation-related studies and actions. We also identify taxonomic and geographic gaps of knowledge that need to be filled, and we highlight the need to add temporal and altitudinal data for all records, to allow tracking potential species distribution changes as well as detailed modelling of the impacts of land use and climate change on European amphibians and reptiles.

    Keywords: European herpetofauna, IUCN red list, biogeography, conservation, distribution atlas, distribution types, endemism, species richness

  • Kougioumoutzis, K., Tiniakou, A., Georgiou, O., Georgiadis, T., 2014.

    Contribution To the Flora of the South Aegean Volcanic Arc: Kimolos Island (Kiklades, Greece)

    Edinburgh Journal of Botany 71(02) 135-160.

    The island of Kimolos, located in the western Kiklades in Greece, constitutes together with Milos, Polyaegos, Anafi and the Santorini island group the central part of the South Aegean Volcanic Arc. The flora of Kimolos consists of 443 taxa, 70 of which are under a statute of protection, 30 are Greek endemics and 225 are reported here for the first time. We show that Kimolos has the highest percentage of Greek endemics in the South Aegean Volcanic Arc. The known distribution of the endemics Sedum eriocarpum subsp. eriocarpum and Anthemis rigida subsp. liguliflora is expanded, being reported for the first time for the phytogeographical region of the Kiklades. The floristic cross-correlation between Kimolos and other parts of the South Aegean Volcanic Arc by means of Sørensen’s index revealed that its phytogeographical affinities are somewhat stronger to Anafi than to neighbouring Milos.

    Keywords: biodiversity, endemism, phytogeography, volcanic flora

  • Kougioumoutzis, K., Tiniakou, A., 2014.

    Ecological factors driving plant species diversity in the South Aegean Volcanic Arc and other central Aegean islands

    Plant Ecology & Diversity 1-14.

    Background: The South Aegean Volcanic Arc (SAVA), one of the most notable geological structures of the Mediterranean Sea, is floristically well known. Nevertheless, the factors that contribute to shaping the plant species richness of the SAVA remain unclear. Aims: To investigate the factors that affect plant species richness and identify plant diversity hotspots in the SAVA and other central Aegean islands. Methods: We used stepwise multiple regression to test the relationship between a number of environmental factors and plant species richness in the SAVA, as well as the residuals from the species–area linear regressions of native, Greek and Cycladian endemic taxa as indicators of relative species richness. Results: The area was confirmed to be the most powerful single explanatory variable of island species richness, while geodiversity, maximum elevation and mean annual precipitation explained a large proportion of variance for almost all the species richness measures. Anafi, Amorgos and Folegandros were found to be endemic plant diversity hotspots. Conclusions: We have demonstrated that geodiversity is an important factor in shaping plant species diversity in the Cyclades, while mean annual precipitation, human population density and maximum elevation were significant predictors of the Greek endemics present in the Cyclades. Finally, Anafi was found to be a plant diversity hotspot in the South Aegean Sea.

    Keywords: Aegean archipelago, South Aegean Volcanic Arc, endemism, environmental diversity, geodiversity, human impact, island species–area relationship, species richness

  • Simaiakis, S., Strona, G., 2014.

    Patterns and processes in the distribution of European centipedes (Chilopoda)

    Journal of Biogeography n/a-n/a.

    Aim To identify consistent biogeographical modules, and examine species diversity and distribution patterns of centipede assemblages. Location Europe, including Turkey and Macaronesia. Methods A dataset was compiled, detailing the occurrence of 585 species of centipedes in 56 countries. Cluster analysis using UPGMA (unweighted pair-group method with arithmetic averages) was used to identify biogeographical modules. To cope with potential issues resulting from the use of political geographical entities, the robustness of the modules was tested using two different randomization approaches. Potential centres of diversity and dispersal for the taxa were hypothesized using two different approaches, based on nestedness analysis using NODF and on investigation of species diversity gradients, respectively. Results The Mediterranean region was found to be the most species-rich area. Cluster analysis identified four major biogeographical modules, namely Eastern Mediterranean, Western Mediterranean, Balkan Peninsula with eastern–central Europe, and north-western Europe. The robustness of these modules was supported by two randomization approaches. Both the analysis of nestedness and of species diversity gradients consistently identified the Balkan Peninsula as a potential centre of diversity for centipedes in Europe. Main conclusions The arrangement of the centipede fauna into four biogeographical modules is consistent with European topography and environmental heterogeneity, with high mountain ranges acting as dispersal barriers, limiting the species overlap between modules. Common palaeogeographical history may explain the high degree of nestedness observed in the central and north-western European modules, whereas the high number of singletons and endemics is responsible for the low degree of nestedness in southern Europe. The identification of the Balkan Peninsula as a potential centre of diversity is in agreement with its high environmental heterogeneity and its known role as a Pleistocene glacial refugium.

    Keywords: Balkan Peninsula, biogeographical modules, centre of diversity, endemism, nestedness, presence–absence matrix, randomization process, singletons

  • Vilaça, S., Biosa, D., Zachos, F., Iacolina, L., Kirschning, J., Alves, P., Paule, L., Gortazar, C., Mamuris, Z., Jędrzejewska, B., Borowik, T., Sidorovich, V., Kusak, J., Costa, S., Schley, L., Hartl, G., Apollonio, M., Bertorelle, G., Scandura, M., 2014.

    Mitochondrial phylogeography of the European wild boar: the effect of climate on genetic diversity and spatial lineage sorting across Europe

    Journal of Biogeography 41(5) 987-998.

    Aim: Climate changes in the past had a deep impact on the evolutionary history of many species and left genetic signatures that are often still detectable today. We investigated the geographical pattern of mitochondrial DNA divesity in the European wild boar (Sus scrofa). Our final aims were to clarify the influence of present and past climatic conditions, infer the geographical posi- tion of glacial refugia, and suggest post-glacial spatial dynamics. Location: Europe. Methods: D-loop sequences were obtained for 763 individuals from Portugal to western Russia. Phylogenetic, multivariate and interpolation methods were used to describe the genetic and geographical patterns. Climatic suitability during the Last Glacial Maximum (LGM) was predicted using MaxEnt. The effect of present and past suitability on the observed patterns of diversity was evaluated by multiple linear regression. Results: We confirmed the existence of a ubiquitous mitochondrial clade in Europe (E1), an endemic clade in Italy (E2) and a few East Asian haplotypes (A), presumably introgressed from domestic pigs. No Near Eastern haplotypes were detected. Genetic divergence was not simply related to geographical distance. A clear south–north decreasing gradient of diversity was observed, with maximum levels in putative glacial refugia. Latitudinal variation in climatic conditions during the LGM was shown to be a good predictor of current genetic diversity. Moreover, an unexpected similarity between Iberia and east- ern Europe was observed, while central European populations showed a higher affinity to the Italian gene pool. Main conclusions: The current distribution of mitochondrial genetic diversity was highly influenced by past climatic events, especially those related to the LGM, and is consistent with a major contribution of the Italian peninsula and the Balkans to the post-glacial recolonization of northern areas. More recent processes, such as restocking and extensive hunting, probably acted at rather local scales, without great impact on the global pattern of mitochondrial diversity.

    Keywords: Climate change, Last Glacial Maximum, Sus scrofa, genetic differentiation, glacial refugia, mtDNA, phylogeography

  • Gatto, F., Katsanevakis, S., Vandekerkhove, J., Zenetos, A., Cardoso, A., 2013.

    Evaluation of online information sources on alien species in Europe: the need of harmonization and integration.

    Environmental Management 51(6) 1137-46.

    Europe is severely affected by alien invasions, which impact biodiversity, ecosystem services, economy, and human health. A large number of national, regional, and global online databases provide information on the distribution, pathways of introduction, and impacts of alien species. The sufficiency and efficiency of the current online information systems to assist the European policy on alien species was investigated by a comparative analysis of occurrence data across 43 online databases. Large differences among databases were found which are partially explained by variations in their taxonomical, environmental, and geographical scopes but also by the variable efforts for continuous updates and by inconsistencies on the definition of "alien" or "invasive" species. No single database covered all European environments, countries, and taxonomic groups. In many European countries national databases do not exist, which greatly affects the quality of reported information. To be operational and useful to scientists, managers, and policy makers, online information systems need to be regularly updated through continuous monitoring on a country or regional level. We propose the creation of a network of online interoperable web services through which information in distributed resources can be accessed, aggregated and then used for reporting and further analysis at different geographical and political scales, as an efficient approach to increase the accessibility of information. Harmonization, standardization, conformity on international standards for nomenclature, and agreement on common definitions of alien and invasive species are among the necessary prerequisites.

    Keywords: Animals, Databases, Europe, Factual, Fresh Water, Fungi, Internet, Introduced Species, Plants, Seawater

  • Katsanevakis, S., Gatto, F., Zenetos, A., Cardoso, A., 2013.

    How many marine aliens in Europe?

    Management of Biological Invasions 4(1) 37-42.

    Keywords: biological invasions, easin, european seas, information system, non-indigenous species

  • Vences, M., Hauswaldt, J., Steinfartz, S., Rupp, O., Goesmann, A., Künzel, S., Orozco-terWengel, P., Vieites, D., Nieto-Román, S., Haas, S., Laugsch, C., Gehara, M., Bruchmann, S., Pabijan, M., Ludewig, A., Rudert, D., Angelini, C., Borkin, L., Crochet, P., Crottini, A., Dubois, A., Ficetola, G., Galán, P., Geniez, P., Hachtel, M., Jovanovic, O., Litvinchuk, S., Lymberakis, P., Ohler, A., Smirnov, N., 2013.

    Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana

    Molecular Phylogenetics and Evolution 68(3) 657-70.

    We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.

    Keywords: biological invasions, easin, european seas, information system, non-indigenous species

  • Garcia-Porta, J., Litvinchuk, S., Crochet, P., Romano, A., Geniez, P., Lo-Valvo, M., Lymberakis, P., Carranza, S., 2012.

    Molecular phylogenetics and historical biogeography of the west-palearctic common toads (Bufo bufo species complex)

    Molecular Phylogenetics and Evolution 63(1) 113-30.

    In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a widespread Eurasiatic group. We investigate this issue by applying a multiproxy approach combining information from molecular phylogenies, a multiple correspondence analysis of allozyme data and species distribution models. Our study includes 304 specimens from 164 populations, covering most of the distributional range of the Bufo bufo species complex in the Western Palearctic. The phylogenies (ML and Bayesian analyses) were based on a total of 1988 bp of mitochondrial DNA encompassing three genes (tRNAval, 16S and ND1). A dataset with 173 species of the family Bufonidae was assembled to estimate the separation of the two pan-Eurasiatic species complexes of Bufo and to date the main biogeographic events within the Bufo bufo species complex. The allozyme study included sixteen protein systems, corresponding to 21 presumptive loci. Finally, the distribution models were based on maximum entropy. Our distribution models show that Eastern and Western species complexes are greatly isolated by the Central Asian Deserts, and our dating estimates place this divergence during the Middle Miocene, a moment in which different sources of evidence document a major upturn of the aridification rate of Central Asia. This climate-driven process likely separated the Eastern and Western species. At the level of the Western Palearctic, our dating estimates place most of the deepest phylogenetic structure before the Pleistocene, indicating that Pleistocene glaciations did not have a major role in splitting the major lineages. At a shallow level, the glacial dynamics contributed unevenly to the genetic structuring of populations, with a strong influence in the European-Caucasian populations, and a more relaxed effect in the Iberian populations.

    Keywords: Animals, Bayes Theorem, Biological Evolution, Bufo bufo, Bufo bufo: classification, Bufo bufo: genetics, DNA, Genetic, Isoenzymes, Isoenzymes: genetics, Mitochondrial, Mitochondrial: genetics, Models, Phylogeny, Phylogeography, Sequence Analysis

  • Kozub, N., Sozinov, I., Xynias, I., Sozinov, A., 2011.

    Allelic variation at high-molecular-weight glutenin subunit loci in Aegilops biuncialis Vis.

    Russian Journal of Genetics 47(9) 1078-1083.

    Alleles at the high molecular weight glutenin subunit loci GluU1 and GluMb1 were analyzed in the tetraploid species Aegilops biuncialis (UUMbMb). The material for the investigation included the collection of 39 accessions of Ae. biuncialis from Ukraine (the Crimea), one Hellenic accession, one accession of unknown origin, F2 seeds from different crosses, as well as samples from natural populations from the Crimea. Ae. umbellulata and Ae. comosa accessions were used to allocate components of the HMW glutenin subunit patterns of Ae. biuncialis to U or Mb genomes. Eight alleles were identified at the GluU1 locus and ten alleles were revealed at the GluMb1 locus. Among alleles at the GluMb1 locus of Ae. biuncialis there were two alleles controlling the ytype subunit only and one allele encoding the xsubunit only

    Keywords: Animals, Bayes Theorem, Biological Evolution, Bufo bufo, Bufo bufo: classification, Bufo bufo: genetics, DNA, Genetic, Isoenzymes, Isoenzymes: genetics, Mitochondrial, Mitochondrial: genetics, Models, Phylogeny, Phylogeography, Sequence Analysis