Uses of GBIF in scientific research

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

List of publications

  • Coro G, Magliozzi C, Vanden Berghe E, Bailly N, Ellenbroek A, Pagano P (2016)

    Estimating absence locations of marine species from data of scientific surveys in OBIS

    Ecological Modelling 323 61-76.

    Estimating absence locations of a species is important in conservation biology and conservation planning. For instance, using reliable absence as much as presence information, species distribution models can enhance their performance and produce more accurate predictions of the distribution of a species. Unfortunately, estimating reliable absence locations is difficult and often requires a deep knowledge of the species’ distribution and of its abiotic and biotic environmental preferences and tolerance. In this paper, we propose a methodology to reconstruct reliable absence information from presence-only information, and the conditions that those presence-only data have to meet to make this possible. Large species occurrence data collections (otherwise called occurrence datasets) contain high quality and expert-reviewed species observation records from scientific surveys. These surveys can be used to retrieve species presence locations, but they also record places where the species in their target list were not observed. Although these absences could be simply due to sampling variation, it is possible to intersect many of these reports to estimate true absence locations, i.e. those due to habitat unsuitability or geographical hindrances. In this paper, we present a method to generate reliable absence locations of this type for marine species, using scientific surveys reports contained in the Ocean Biogeographic Information System (OBIS), an authoritative species occurrence dataset. Our method spatially aggregates information from surveys focussing on the same target species. It detects absence locations for a given species as those locations in which repeated surveys (that included the species of interest in their target list) reported information only on other species. We qualitatively demonstrate the reliability of our method using distribution records of the Atlantic cod as a case study. Additionally, we quantitatively estimate its performance using another authoritative large species occurrence dataset, the Global Biodiversity Information Facility (GBIF). We also demonstrate that our approach has higher accuracy and presents complementary behaviour with respect to another method using environmental envelopes. Our process can support species distribution models (as well as other types of models, e.g. climate change models) by providing reliable data to presence/absence approaches. It can manage regional as well as global scale scenarios and runs within a collaborative e-Infrastructure (D4Science) that publishes it as-a-Service, allowing biologists to reproduce, repeat and share experimental results.

    Keywords: Absence locations, Ecological niche modelling, Marine biodiversity, Occurrence data, Scientific surveys, Species distribution maps

  • Katsanevakis S, Tempera F, Teixeira H (2016)

    Mapping the impact of alien species on marine ecosystems: the Mediterranean Sea case study

    Diversity and Distributions.

    Aim To develop a standardized, quantitative method for mapping cumulative impacts of invasive alien species on marine ecosystems. Location The methodology is applied in the Mediterranean Sea but is widely applicable. Methods A conservative additive model was developed to account for the Cumulative IMPacts of invasive ALien species (CIMPAL) on marine ecosystems. According to this model, cumulative impact scores are estimated on the basis of the distributions of invasive species and ecosystems, and both the reported magnitude of ecological impacts and the strength of such evidence. In the Mediterranean Sea case study, the magnitude of impact was estimated for every combination of 60 invasive species and 13 habitats, for every 10 × 10 km cell of the basin. Invasive species were ranked based on their contribution to the cumulative impact score across the Mediterranean. Results The CIMPAL index showed strong spatial heterogeneity. Spatial patterns varied depending on the pathway of initial introduction of the invasive species in the Mediterranean Sea. Species introduced by shipping gave the highest impact scores and impacted a much larger area than those introduced by aquaculture and the Suez Canal. Overall, invasive macroalgae had the highest impact among all taxonomic groups. These results represent the current best estimate of the spatial variation in impacts of invasive alien species on ecosystems, in the Mediterranean Sea. Main Conclusions A framework for mapping cumulative impacts of invasive alien species was developed. The application of this framework in the Mediterranean Sea provided a baseline that can be built upon with future improved information. Such analysis allows the identification of hotspots of highly impacted areas, and prioritization of sites, pathways and species for management actions.

    Keywords: CIMPAL, biological invasions, cumulative impacts, indicators, invasive alien species, pathways

  • Badieritakis E, Thanopoulos R, Fantinou A, Emmanouel N (2015)

    A qualitative and quantitative study of thrips (Thysanoptera) on alfalfa and records of thrips species on cultivated and wild Medicago species of Greece

    Biologia 70(4).

    Foliage and litter samples of twelve Medicago species (medics) (Fabaceae) were collected for the study of Thysanoptera from mainland and insular Greece between 2007-2013. The species composition, population dynamics and spatial distribution of thrips were also evaluated based on two similarly managed experimental plots, except the number of cuttings, within an alfalfa hay field in Kopais Valley (Central Greece) between 2007-2008. Nine thrips species were recorded from nine medics, two of which (Pseudodendrothrips mori and Sericothrips bicornis) are new to the Greek fauna. Eight species of Thysanoptera were recorded on alfalfa and five species in the rest of the medics, among which Medicago strasseri is an endemic shrub of Crete. Data regarding the quantitative part of the study demonstrated that Frankliniella occidentalis, which was the most abundant thrips species in both plots, presented a seasonal pattern of population fluctuation and also tended to aggregate. The mean population density of this species significantly differed between the above-mentioned plots, but no such a difference was estimated for the larvae of Thripidae.

    Keywords: Greece, Medicago, Thysanoptera, population dynamics, spatial distribution

  • Crowl A, Visger C, Mansion G, Hand R, Wu H, Kamari G et al. (2015)

    Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the Eastern Mediterranean

    Ecology and Evolution.

    At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low-copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation and species tree analyses. Niche modeling, ancestral range estimation, and diversification analyses were conducted to provide further insights into patterns of endemism and diversification through time. Diversification of the Roucela clade appears to have been primarily the result of vicariance driven by the breakup of an ancient landmass. We found geologic events such as the formation of the mid-Aegean trench and the Messinian Salinity Crisis to be historically important in the evolutionary history of this group. Contrary to numerous past studies, the onset of the Mediterranean climate has not promoted diversification in the Roucela complex and, in fact, may be negatively affecting these species. This study highlights the diversity and complexity of historical processes driving plant evolution in the Mediterranean Basin.

    Keywords: Aegean Archipelago, Campanulaceae, Mediterranean, Roucela clade, continental islands, drabifolia complex, endemism

  • Creemers R, Denoël M, Campos J, Vences M, Crochet P, Gonçalves J et al. (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 et al. (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