Uses of GBIF in scientific research

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

List of publications

  • Onstein, R., Carter, R., Xing, Y., Richardson, J., Linder, H., 2015.

    Do Mediterranean-type ecosystems have a common history? - insights from the Buckthorn family (Rhamnaceae).

    Evolution; international journal of organic evolution.

    Mediterranean-type ecosystems (MTEs) are remarkable in their species-richness and endemism, but the processes which have led to this diversity remain enigmatic. Here, we hypothesize that continent-dependent speciation and extinction rates have led to disparity in diversity between the five MTEs of the world: the Cape, California, Mediterranean Basin, Chile and Western Australia. To test this hypothesis, we built a phylogenenetic tree for 280 Rhamnaceae species, estimated divergence times using eight fossil calibrations and use Bayesian methods and simulations to test for differences in diversification rates. Rhamnaceae lineages in MTEs generally show higher diversification rates than elsewhere, but speciation and extinction dynamics show a pattern of continent-dependence. We detected high speciation and extinction rates in California and significantly lower extinction rates in the Cape and Western Australia. The independent colonization of four out of five MTEs may have occurred conterminously in the Oligocene/Early Miocene, but colonization of the Mediterranean Basin happened later, in the Late Miocene. This suggests that the in situ radiations of these clades were initiated before the onset of winter-rainfall in these regions. These results indicate independent evolutionary histories of Rhamnaceae in MTEs, possibly related to the intensity of climate oscillations and the geological history of the regions. This article is protected by copyright. All rights reserved.

    Keywords: Californian Floristic Province, Cape, Western Australia, diversification rate, extinction, speciation


  • Wisz, M., Broennimann, O., Grønkjær, P., Møller, P., Olsen, S., Swingedouw, D., Hedeholm, R., Nielsen, E., Guisan, A., Pellissier, L., 2015.

    Arctic warming will promote Atlantic–Pacific fish interchange

    Nature Climate Change.

    Throughout much of the Quaternary Period, inhospitable environmental conditions above the Arctic Circle have been a formidable barrier separating most marine organisms in the North Atlantic from those in the North Pacific1, 2. Rapid warming has begun to lift this barrier3, potentially facilitating the interchange of marine biota between the two seas4. Here, we forecast the potential northward progression of 515 fish species following climate change, and report the rate of potential species interchange between the Atlantic and the Pacific via the Northwest Passage and the Northeast Passage. For this, we projected niche-based models under climate change scenarios and simulated the spread of species through the passages when climatic conditions became suitable. Results reveal a complex range of responses during this century, and accelerated interchange after 2050. By 2100 up to 41 species could enter the Pacific and 44 species could enter the Atlantic, via one or both passages. Consistent with historical and recent biodiversity interchanges5, 6, this exchange of fish species may trigger changes for biodiversity and food webs in the North Atlantic and North Pacific, with ecological and economic consequences to ecosystems that at present contribute 39% to global marine fish landings.

    Keywords: Californian Floristic Province, Cape, Western Australia, diversification rate, extinction, speciation


  • Beck, J., Böller, M., Erhardt, A., Schwanghart, W., 2014.

    Spatial bias in the GBIF database and its effect on modeling species' geographic distributions

    Ecological Informatics 19 10-15.

    Species distribution modelling, in combination with databases of specimen distribution records, is advocated as a solution to the problem of distributional data limitation in biogeography and ecology. The global biodiversity information facility (GBIF), a portal that collates digitized collection and survey data, is the largest online provider of distribution records. However, all distributional databases are spatially biased due to uneven effort of sampling, data storage and mobilization. Such bias is particularly pronounced in GBIF, where nation-wide differences in funding and data sharing lead to huge differences in contribution to GBIF. We use a common Eurasian butterfly (Aglais urticae) as an exemplar taxon to provide evidence that range model quality is decreasing due to the spatial clustering of distributional records in GBIF. Furthermore, we show that such loss of model quality would go unnoticed with standard methods of model quality evaluation. Using evaluations of model predictions of the Swiss distribution of the species, we compare distribution models of full data with data where a subsampling procedure removes spatial bias at the cost of record numbers, but not of spatial extent of records. We show that data with less spatial bias produce better predictive models even though they are based on less input data. Our subsampling routine may therefore be a suitable method to reduce the impact of spatial bias to species distribution models. Our results warn of automatized applications of species distribution models to distributional databases (as has been advocated and implemented), as internal model evaluation did not show the decline of model quality with increased spatial bias (but rather the opposite) while expert evaluation clearly did.

    Keywords: AUC, CSCF, Ecological niche modelling, Lepidoptera, Maxent, Small tortoiseshell


  • Colombo, M., Damerau, M., Hanel, R., Salzburger, W., Matschiner, M., 2014.

    Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes.

    Journal of evolutionary biology.

    According to theory, adaptive radiation is triggered by ecological opportunity that can arise through the colonization of new habitats, the extinction of antagonists, or the origin of key innovations. In the course of an adaptive radiation, diversification and morphological evolution are expected to slow down after an initial phase of rapid adaptation to vacant ecological niches, followed by speciation. Such 'early bursts' of diversification are thought to occur because niche space becomes increasingly filled over time. The diversification of Antarctic notothenioid fishes into over 120 species has become one of the prime examples of adaptive radiation in the marine realm, and has likely been triggered by an evolutionary key innovation in the form of the emergence of antifreeze glycoproteins. Here, we test, using a novel time-calibrated phylogeny of 49 species and five traits that characterize notothenioid body size and shape as well as buoyancy adaptations and habitat preferences, whether the notothenioid adaptive radiation is compatible with an early burst scenario. Extensive Bayesian model comparison shows that phylogenetic age estimates are highly dependent on model choice, and that models with unlinked gene trees are generally better supported and result in younger age estimates. We find strong evidence for elevated diversification rates in Antarctic notothenioids compared to outgroups, yet no sign of rate heterogeneity in the course of the radiation, except that the notothenioid family Artedidraconidae appears to show secondarily elevated diversification rates. We further observe an early burst in trophic morphology, suggesting that the notothenioid radiation proceeds in stages similar to other prominent examples of adaptive radiation. This article is protected by copyright. All rights reserved.

    Keywords: adaptive radiation, early burst, geometric morphometrics, incomplete lineage, sorting, species tree


  • Elmendorf, S., Henry, G., Hollister, R., Fosaa, A., Gould, W., Hermanutz, L., Hofgaard, A., Jónsdóttir, I., Jorgenson, J., Lévesque, E., Magnusson, B., Molau, U., Myers-Smith, I., Oberbauer, S., Rixen, C., Tweedie, C., Walker, M., 2014.

    Experiment, monitoring, and gradient methods used to infer climate change effects on plant communities yield consistent patterns

    Proceedings of the National Academy of Sciences 112(2) 201410088.

    SignificanceMethodological constraints can limit our ability to quantify potential impacts of climate warming. We assessed the consistency of three approaches in estimating warming effects on plant community composition: manipulative warming experiments, repeat sampling under ambient temperature change (monitoring), and space-for-time substitution. The three approaches showed agreement in the direction of change (an increase in the relative abundance of species with a warmer thermal niche), but differed in the magnitude of change estimated. Experimental and monitoring approaches were similar in magnitude, whereas space-for-time comparisons indicated a much stronger response. These results suggest that all three approaches are valid, but experimental warming and long-term monitoring are best suited for forecasting impacts over the coming decades. Inference about future climate change impacts typically relies on one of three approaches: manipulative experiments, historical comparisons (broadly defined to include monitoring the response to ambient climate fluctuations using repeat sampling of plots, dendroecology, and paleoecology techniques), and space-for-time substitutions derived from sampling along environmental gradients. Potential limitations of all three approaches are recognized. Here we address the congruence among these three main approaches by comparing the degree to which tundra plant community composition changes (i) in response to in situ experimental warming, (ii) with interannual variability in summer temperature within sites, and (iii) over spatial gradients in summer temperature. We analyzed changes in plant community composition from repeat sampling (85 plant communities in 28 regions) and experimental warming studies (28 experiments in 14 regions) throughout arctic and alpine North America and Europe. Increases in the relative abundance of species with a warmer thermal niche were observed in response to warmer summer temperatures using all three methods; however, effect sizes were greater over broad-scale spatial gradients relative to either temporal variability in summer temperature within a site or summer temperature increases induced by experimental warming. The effect sizes for change over time within a site and with experimental warming were nearly identical. These results support the view that inferences based on space-for-time substitution overestimate the magnitude of responses to contemporary climate warming, because spatial gradients reflect long-term processes. In contrast, in situ experimental warming and monitoring approaches yield consistent estimates of the magnitude of response of plant communities to climate warming.

    Keywords: climate change, space-for-time substitution, thermophilization, tundra, warming experiment


  • Ficetola, G., Rondinini, C., Bonardi, A., Katariya, V., Padoa-Schioppa, E., Angulo, A., 2014.

    An evaluation of the robustness of global amphibian range maps

    Journal of Biogeography 41(2) 211-221.

    Aim Maps of species ranges are among the most frequently used distribution data in biodiversity studies. As with any biological data, range maps have some level of measurement error, but this error is rarely quantified. We assessed the error associated with amphibian range maps by comparing them with point locality data. Location Global. Methods The maps published by the Global Amphibian Assessment were assessed against two data sets of species point localities: the Global Biodiversity Information Facility (GBIF), and a refined data set including recently published, high-quality presence data from both GBIF and other sources. Range fit was measured as the proportion of presence records falling within the range polygon(s) for each species. Results Using the high-quality point data provided better fit measures than using the raw GBIF data. Range fit was highly variable among continents, being highest for North American and European species (a fit of 84–94%), and lowest for Asian and South American species (a fit of 57–64%). At the global scale, 95% of amphibian point records were inside the ranges published in maps, or within 31 km of the range edge. However, differences among continents were striking, and more points were found far from range edges for South American and Asian species. Main conclusions The Global Amphibian Assessment range maps represent the known distribution of most amphibians well; this study provides measures of accuracy that can be useful for future research using amphibian maps as baseline data. Nevertheless, there is a need for greater investment in the continuous updating and improvement of maps, particularly in the megadiverse areas of tropical Asia and South America.

    Keywords: alpha-hulls, amphibians, conservation biogeography, data quality, gbif, mea-, point data, range size, species distribution range, surement error, wallacean


  • Forasiepi, A., Soibelzon, L., Gomez, C., Sánchez, R., Quiroz, L., Jaramillo, C., Sánchez-Villagra, M., 2014.

    Carnivorans at the Great American Biotic Interchange: new discoveries from the northern neotropics

    Die Naturwissenschaften(2011).

    We report two fossil procyonids, Cyonasua sp. and Chapalmalania sp., from the late Pliocene of Venezuela (Vergel Member, San Gregorio Formation) and Colombia (Ware Formation), respectively. The occurrence of these pre-Holocene procyonids outside Argentina and in the north of South America provides further information about the Great American Biotic Interchange (GABI). The new specimens are recognized in the same monophyletic group as procyonids found in the southern part of the continent, the "Cyonasua group," formed by species of Cyonasua and Chapalmalania. The phylogenetic analysis that includes the two new findings support the view that procyonids dispersed from North America in two separate events (initially, previous to the first major migration wave-GABI 1-and then within the last major migration wave-GABI 4-). This involved reciprocal lineage migrations from North to South America, and included the evolution of South American endemic forms.

    Keywords: Pliocene, neotropics, procyonidae, south america


  • Gross, A., Holdenrieder, O., Pautasso, M., Queloz, V., Sieber, T., 2014.

    Hymenoscyphus pseudoalbidus, the causal agent of European ash dieback

    Molecular Plant Pathology 15(1) 5-21.

    The ascomycete Hymenoscyphus pseudoalbidus (anamorph Chalara fraxinea) causes a lethal disease known as ash dieback on Fraxinus excelsior and Fraxinus angustifolia in Europe. The pathogen was probably introduced from East Asia and the disease emerged in Poland in the early 1990s; the subsequent epidemic is spreading to the entire native distribution range of the host trees. This pathogen profile represents a comprehensive review of the state of research from the discovery of the pathogen and points out knowledge gaps and research needs. TAXONOMY: Members of the genus Hymenoscyphus (Helotiales, Leotiomycetidae, Leotiomycetes, Ascomycota) are small discomycetes which form their ascomata on dead plant material. A phylogeny based on the internal transcribed spacers (ITSs) of the rDNA indicated the avirulent Hymenoscyphus albidus, a species native to Europe, as the closest relative of H. pseudoalbidus. SYMPTOMS: Hymenoscyphus pseudoalbidus causes necrotic lesions on leaves, twigs and stems, eventually leading to wilting and dieback of girdled shoots. Bark lesions are characterized by a typical dark- to cinnamon-brown discoloration. LIFE CYCLE: Hymenoscyphus pseudoalbidus is heterothallic and reproduces sexually on ash petioles in the litter once a year. Ascospores are wind dispersed and infect ash leaves during the summer. The asexual spores only serve as spermatia. TOOLS AND TECHNIQUES: The most important techniques for fungal handling, such as detection, isolation, culturing, storage, crossing and ascocarp production, are briefly described. MANAGEMENT: Once the disease is established, management is hardly possible. The occurrence of a small fraction of partially tolerant trees constitutes hope for resistance breeding in the future. Healthy-looking trees should be preserved.

    Keywords: The ascomycete Hymenoscyphus pseudoalbidus (anamor, and the subsequent epidemic is spreading to the en


  • Kostikova, A., Litsios, G., Burgy, S., Milani, L., Pearman, P., Salamin, N., 2014.

    Scale-dependent adaptive evolution and morphological convergence to climatic niche in Californian eriogonoids (Polygonaceae)

    Journal of Biogeography 41(7) 1326-1337.

    Aim: Macroevolutionary patterns and processes change substantially depending on levels of taxonomic and ecological organization, and the resolution of environmental and spatial variability. In comparative methods, the resolution of environmental and spatial variability often defines the number of selective regimes used to test whether phenotypic characteristics are adaptively correlated with the environment. Here, we examine how investigator choice of the number of selective regimes, determined by varying the resolution of among-species variability in the species climatic niche (hereafter called ‘ecological scale’), influences trait morphological diversification among Eriogonoideae species. We assess whether adaptive or neutral processes drive the evolution of several morphological traits in these species. Location: South-western North America. Methods We applied a phylogenetic framework of three evolutionary models to four morphological traits and the climatic niches of Eriogonoideae (in the buckwheat family, Polygonaceae). We tested whether morphological traits evolve in relation to climate by adaptive or neutral process, and whether the resulting patterns of morphological variability are conserved or convergent across the clade. We inspected adaptive models of evolution under different levels of resolution of among-species variability of the climatic niche. Results: We show that morphological traits and climate niches of Eriogonoideae species are not phylogenetically conserved. Further, adaptive evolution of phenotypic traits is specific to climatic niche occupancy across this clade. Finally, the likely evolutionary process and the level of detectable niche conservatism change depending on the resolution of environmental variability of the climatic niche. Main conclusions: Our study demonstrates the need to consider both the resolution of environmental variability and alternative evolutionary models to understand the morphological diversification that accompanies divergent adaptive evolution of lineages to climatic conditions.

    Keywords: Adaptive evolution, Eriogonoideae, climatic niche, convergent evolution, morphological evolution, niche conservatism, phylogeny, scale, south-western North America


  • Kostikova, A., Salamin, N., Pearman, P., 2014.

    The role of climatic tolerances and seed traits in reduced extinction rates of temperate polygonaceae

    Evolution 68(7) 1856-70.

    The latitudinal diversity gradient (LDG) is one of the most striking and consistent biodiversity patterns across taxonomic groups. We investigate the species richness gradient in the buckwheat family, Polygonaceae, which exhibits a reverse LDG and is, thus, decoupled from dominant gradients of energy and environmental stability that increase toward the tropics and confound mechanistic interpretations. We test competing age and evolutionary diversification hypotheses, which may explain the diversification of this plant family over the past 70 million years. Our analyses show that the age hypothesis, which posits that clade richness is positively correlated with the ecological and evolutionary time since clade origin, fails to explain the richness gradient observed in Polygonaceae. However, an evolutionary diversification hypothesis is highly supported, with diversification rates being 3.5 times higher in temperate clades compared to tropical clades. We demonstrate that differences in rates of speciation, migration, and molecular evolution insufficiently explain the observed patterns of differential diversification rates. We suggest that reduced extinction rates in temperate clades may be associated with adaptive responses to selection, through which seed morphology and climatic tolerances potentially act to minimize risk in temporally variable environments. Further study is needed to understand causal pathways among these traits and factors correlated with latitude.

    Keywords: adaptation, climate tolerance, dispersal, distribution model, diversification