Uses of GBIF in scientific research

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

List of publications

  • Pironon, S., Villellas, J., Morris, W., Doak, D., García, M., 2015.

    Do geographic, climatic or historical ranges differentiate the performance of central versus peripheral populations?

    Global Ecology and Biogeography n/a-n/a.

    Aim The ‘centre–periphery hypothesis’ (CPH) predicts that species performance (genetics, physiology, morphology, demography) will decline gradually from the centre towards the periphery of the geographic range. This hypothesis has been subjected to continuous debate since the 1980s, essentially because empirical studies have shown contrasting patterns. Moreover, it has been proposed that species performance might not be higher at the geographic range centre but rather at the environmental optimum or at sites presenting greater environmental stability in time. In this paper we re-evaluate the CPH by disentangling the effects of geographic, climatic and historical centrality/marginality on the demography of three widely distributed plant species and the genetic diversity of one of them. Location Europe and North America. Methods Based on a species distribution modelling approach, we test whether demographic parameters (vital rates, stochastic population growth rates, density) of three plant species of contrasting life-forms, and the genetic diversity of one of them, are higher at their geographic range centres, climatic optima or projected glacial refugia. Results While geographic, climatic and historical centre–periphery gradients are often not concordant, overall, none of them explain well the distribution of species demographic performance, whereas genetic diversity responds positively only to a historical centrality, related to post-glacial range dynamics. Main conclusions To our knowledge, this is the first assessment of the response of species performance to three centrality gradients, considering all the components of different species life cycles and genetic diversity information across continental distributions. Our results are inconsistent with the idea that geographically, climatically or historically marginal populations generally perform worse than central ones. We particularly emphasize the importance of adopting an interdisciplinary approach in order to understand the relative effects of contemporary versus historical and geographic versus ecological factors on the distribution of species performance.

    Keywords: Abundant-centre model, Last Glacial Maximum, central–marginal hypothesis, climatic niche, genetic diversity, latitude, plant demography, population performance, species distribution models


  • Vårhammar, A., Wallin, G., McLean, C., Dusenge, M., Medlyn, B., Hasper, T., Nsabimana, D., Uddling, J., 2015.

    Photosynthetic temperature responses of tree species in Rwanda: evidence of pronounced negative effects of high temperature in montane rainforest climax species.

    The New phytologist.

    The sensitivity of photosynthetic metabolism to temperature has been identified as a key uncertainty for projecting the magnitude of the terrestrial feedback on future climate change. While temperature responses of photosynthetic capacities have been comparatively well investigated in temperate species, the responses of tropical tree species remain unexplored. We compared the responses of seedlings of native cold-adapted tropical montane rainforest tree species with those of exotic warm-adapted plantation species, all growing in an intermediate temperature common garden in Rwanda. Leaf gas exchange responses to carbon dioxide (CO2 ) at different temperatures (20-40°C) were used to assess the temperature responses of biochemical photosynthetic capacities. Analyses revealed a lower optimum temperature for photosynthetic electron transport rates than for Rubisco carboxylation rates, along with lower electron transport optima in the native cold-adapted than in the exotic warm-adapted species. The photosynthetic optimum temperatures were generally exceeded by daytime peak leaf temperatures, in particular in the native montane rainforest climax species. This study thus provides evidence of pronounced negative effects of high temperature in tropical trees and indicates high susceptibility of montane rainforest climax species to future global warming.

    Keywords: Africa, leaf energy balance, maximum rate of electron transport (Jmax), optimum temperature (Topt), stomatal conductance (gs), the maximum carboxylation rate of oxygenase (Vcmax, tropical montane rainforest


  • 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


  • Leidenberger, S., De Giovanni, R., Kulawik, R., Williams, A., Bourlat, S., 2014.

    Mapping present and future potential distribution patterns for a meso-grazer guild in the Baltic Sea

    Journal of Biogeography Forthcoming.

    pute the extent and intensity of change in species’ potential distributions. Indi- vidual ecological niche models were generated under present conditions and then projected into a future climate change scenario (2050) for a food web consisting of a guild of meso-grazers (Idotea spp.), their host algae (Fucus vesi- culosus and Fucus radicans) and their fish predator (Gasterosteus aculeatus). We used occurrence data from the Global Biodiversity Information Facility (GBIF), literature and museum collections, together with five environmental layers at a resolution of 5 and 30 arc-minutes. Results Habitat suitability for Idotea balthica and Idotea chelipes in the Baltic Sea seems to be mostly determined by temperature and ice cover rather than by salinity. 2050 predictions for all modelled species show a northern/north- eastern shift in the Baltic Sea. The distribution ranges for Idotea granulosa and G. aculeatus are predicted to become patchier in the Baltic than in the rest of northern Europe, where the species will gain more suitable habitats. Main conclusions For the Baltic Sea, climate-induced changes resulted in a gain of suitable habitats for F. vesiculosus, I. chelipes and I. balthica, whereas lower habitat suitability was predicted for I. granulosa, F. radicans and G. aculeatus. The predicted north-eastern shift of I. balthica and I. chelipes into the dis- tribution area of F. radicans in the Baltic Sea may result in increased grazing pressure. Such additional threats to isolated Baltic populations can lead to a higher extinction risk for the species, especially as climate changes are likely to be very rapid.

    Keywords: Baltic Sea, climate change, e-Science, ecological niche modelling, food web, fucus radicans, fucus vesiculosus, gasterosteus aculeatus, idotea, workflows


  • Lembrechts, J., Milbau, A., Nijs, I., 2014.

    Alien Roadside Species More Easily Invade Alpine than Lowland Plant Communities in a Subarctic Mountain Ecosystem

    PLoS ONE 9(2) e89664.

    Effects of roads on plant communities are not well known in cold-climate mountain ecosystems, where road building and development are expected to increase in future decades. Knowledge of the sensitivity of mountain plant communities to disturbance by roads is however important for future conservation purposes. We investigate the effects of roads on species richness and composition, including the plant strategies that are most affected, along three elevational gradients in a subarctic mountain ecosystem. We also examine whether mountain roads promote the introduction and invasion of alien plant species from the lowlands to the alpine zone. Observations of plant community composition were made together with abiotic, biotic and anthropogenic factors in 60 T-shaped transects. Alpine plant communities reacted differently to road disturbances than their lowland counterparts. On high elevations, the roadside species composition was more similar to that of the local natural communities. Less competitive and ruderal species were present at high compared with lower elevation roadsides. While the effects of roads thus seem to be mitigated in the alpine environment for plant species in general, mountain plant communities are more invasible than lowland communities. More precisely, relatively more alien species present in the roadside were found to invade into the surrounding natural community at high compared to low elevations. We conclude that effects of roads and introduction of alien species in lowlands cannot simply be extrapolated to the alpine and subarctic environment.

    Keywords: Baltic Sea, climate change, e-Science, ecological niche modelling, food web, fucus radicans, fucus vesiculosus, gasterosteus aculeatus, idotea, workflows


  • Mathew, C., Güntsch, A., Obst, M., Vicario, S., Haines, R., Williams, A., de Jong, Y., Goble, C., 2014.

    A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control

    Biodiversity Data Journal 2(2) e4221.

    The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.

    Keywords: biodiversity informatics, data cleaning, e-Science, service oriented architecture, web services, workflows


  • Mimura, M., Mishima, M., Lascoux, M., Yahara, T., 2014.

    Range shift and introgression of the rear and leading populations in two ecologically distinct Rubus species

    BMC Evolutionary Biology 14(1) 209.

    Background:The margins of a species¿ range might be located at the margins of a species¿ niche, and in such cases, can be highly vulnerable to climate changes. They, however, may also undergo significant evolutionary change due to drastic population dynamics; e.g., changes in population size and distribution, which may increase the chance of contact among species. Such species interactions induced by climate changes could then regulate or facilitate further responses to climatic changes. We hypothesized that climate change-induced species contacts and subsequent genetic exchanges due to differences in population dynamics take place at the species boundaries. We sampled two closely related Rubus species, one temperate (Rubus palmatus) and the other subtropical (R. grayanus) near their joint species boundaries in southern Japan. Coalescent analysis, based on molecular data and ecological niche modelling during the Last Glacial Maximum (LGM), were used to infer past population dynamics. At the contact zones on Yakushima (Yaku Island), where the two species are parapatrically distributed, we tested hybridization along altitudinal gradients.ResultsCoalescent analysis suggested that the southernmost populations of R. palmatus predated the LGM (~20,000 ya). Conversely, populations at the current northern limit of R. grayanus diverged relatively recently and likely represent young outposts of a northbound range shift. These population dynamics were partly supported by the ensemble forecasting of six different species distribution models. Both past and ongoing hybridizations were detected near and on Yakushima. Backcrosses and advanced-generation hybrids likely generated the clinal hybrid zones along altitudinal gradients on the island where the two species are currently parapatrically distributed.ConclusionsClimate oscillations during the Quaternary Period and the response of a species in range shifts likely led to repeated contacts with the gene pools of ecologically distinct relatives. Such species interactions, induced by climate changes, may bring new genetic material to the marginal populations where species tend to experience more extreme climatic conditions at the margins of the species distribution.

    Keywords: Climate change, Colonizer, Introgression, Isolation with migration, Phylogeography, Species boundaries


  • Pigott, D., Golding, N., Mylne, A., Huang, Z., Henry, A., Weiss, D., Brady, O., Kraemer, M., Smith, D., Moyes, C., Bhatt, S., Gething, P., Horby, P., Bogoch, I., Brownstein, J., Mekaru, S., Tatem, A., Khan, K., Hay, S., 2014.

    Mapping the zoonotic niche of Ebola virus disease in Africa

    eLife 3:e04395.

    Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.

    Keywords: Climate change, Colonizer, Introgression, Isolation with migration, Phylogeography, Species boundaries


  • Abdi, A., 2013.

    Integrating Open Access Geospatial Data to Map the Habitat Suitability of the Declining Corn Bunting (Miliaria calandra)

    ISPRS International Journal of Geo-Information 2(4) 935-954.

    The efficacy of integrating open access geospatial data to produce habitat suitability maps for the corn bunting (Miliaria calandra) was investigated. Landsat Enhanced Thematic Mapper Plus (ETM+), Shuttle Radar Topography Mission (SRTM) and Corine (Coordination of Information on the Environment) land cover data for the year 2000 (CLC2000) were processed to extract explanatory variables and divided into three sets; Satellite (ETM+, SRTM), CLC2000 and Combined (CLC2000 + Satellite). Presence-absence data for M. calandra, collected during structured surveys for the Catalan Breeding Bird Atlas, were provided by the Catalan Ornithological Institute. The dataset was partitioned into an equal number of presence and absence points by dividing it into five groups, each composed of 88 randomly selected presence points to match the number of absences. A logistic regression model was then built for each group. Models were evaluated using area under the curve (AUC) of the receiver operating characteristic (ROC). Results of the five groups were averaged to produce mean Satellite, CLC2000 and Combined models. The mean AUC values were 0.69, 0.81 and 0.90 for the CLC2000, Satellite and the Combined model, respectively. The probability of M. calandra presence had the strongest positive correlation with land surface temperature, modified soil adjusted vegetation index, coefficient of variation for ETM+ band 5 and the fraction of non-irrigated arable land.

    Keywords: Corine land cover, Landsat, Miliaria calandra, agricultural intensification, corn bunting, open access data, open source geospatial software, species distribution modeling


  • Bartomeus, I., Park, M., Gibbs, J., Danforth, B., Lakso, A., Winfree, R., 2013.

    Biodiversity ensures plant-pollinator phenological synchrony against climate change

    Ecology Letters 16(11) 1331-8.

    Climate change has the potential to alter the phenological synchrony between interacting mutualists, such as plants and their pollinators. However, high levels of biodiversity might buffer the negative effects of species-specific phenological shifts and maintain synchrony at the community level, as predicted by the biodiversity insurance hypothesis. Here, we explore how biodiversity might enhance and stabilise phenological synchrony between a valuable crop, apple and its native pollinators. We combine 46 years of data on apple flowering phenology with historical records of bee pollinators over the same period. When the key apple pollinators are considered altogether, we found extensive synchrony between bee activity and apple peak bloom due to complementarity among bee species' activity periods, and also a stable trend over time due to differential responses to warming climate among bee species. A simulation model confirms that high biodiversity levels can ensure plant-pollinator phenological synchrony and thus pollination function.

    Keywords: bees, crop pollination, ecosystem function, ecosystem services, phenology, pollination, response diversity, stabilising mechanism