Uses of GBIF in scientific research

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

List of publications

  • Deblauwe V, Droissart V, Bose R, Sonké B, Blach-Overgaard A, Svenning J et al. (2016)

    Remotely sensed temperature and precipitation data improve species distribution modelling in the tropics

    Global Ecology and Biogeography.

    Aim Species distribution modelling typically relies completely or partially on climatic variables as predictors, overlooking the fact that these are themselves predictions with associated uncertainties. This is particularly critical when such predictors are interpolated between sparse station data, such as in the tropics. The goal of this study is to provide a new set of satellite-based climatic predictor data and to evaluate its potential to improve modelled species–climate associations and transferability to novel geographical regions. Location Rain forests areas of Central Africa, the Western Ghats of India and South America. Methods We compared models calibrated on the widely used WorldClim station-interpolated climatic data with models where either temperature or precipitation data from WorldClim were replaced by data from CRU, MODIS, TRMM and CHIRPS. Each predictor set was used to model 451 plant species distributions. To test for chance associations, we devised a null model with which to compare the accuracy metric obtained for every species. Results Fewer than half of the studied rain forest species distributions matched the climatic pattern better than did random distributions. The inclusion of MODIS temperature and CHIRPS precipitation estimates derived from remote sensing each allowed for a better than random fit for respectively 40% and 22% more species than models calibrated on WorldClim. Furthermore, their inclusion was positively related to a better transferability of models to novel regions. Main conclusions We provide a newly assembled dataset of ecologically meaningful variables derived from MODIS and CHIRPS for download, and provide a basis for choosing among the plethora of available climate datasets. We emphasize the need to consider the method used in the production of climate data when working on a region with sparse meteorological station data. In this context, remote sensing data should be the preferred choice, particularly when model transferability to novel climates or inferences on causality are invoked.

    Keywords: Association test, CHIRPS, GLM, MODIS, MaxEnt, TRMM, WorldClim, ecological niche model, habitat suitability, null model


  • Sanín M, Kissling W, Bacon C, Borchsenius F, Galeano G, Svenning J et al. (2016)

    The Neogene rise of the tropical Andes facilitated diversification of wax palms ( Ceroxylon : Arecaceae) through geographical colonization and climatic niche separation

    Botanical Journal of the Linnean Society.

    he tropical Andes are a biodiversity hotspot, partly due to their rich and complex floristic composition. A fundamental question regarding this outstanding biodiversity is what role the Andean orogeny has played in species diversification. Ceroxylon is a genus of endemic Andean palms that stands out in the palm family (Arecaceae) due to its adaptation to cold, mountainous environments. Here, we reconstruct the biogeography and climatic preference of this lineage to test the hypothesis that Andean uplift allowed diversification by providing suitable habitats along climatic and elevational gradients. Ancestral areas were reconstructed under a model allowing for founder-event speciation and climatic niches were inferred from climatic variables at present-day occurrences of all species. Niche evolution in a phylogenetic framework was evaluated by testing differences between the climatic niches of clades. Our analyses identified four main clades, with a general pattern of diversification through geographical colonization from south to north after the Pliocene uplift of the northern Andes. Adaptation to low temperatures was conserved at the generic level, with climatic niche differentiation among clades along elevational temperature gradients. We conclude that the Neogene Andean uplift has facilitated the diversification of this iconic plant group via opportunities for geographical migration and separation within its climatic niche

    Keywords: Miocene, Neotropics, cold adaptation, niche shift, phylogenetic niche conservatism, range expansion


  • Zhang J, Nielsen S, Chen Y, Georges D, Qin Y, Wang S et al. (2016)

    Extinction risk of North American seed plants elevated by climate and land-use change

    Journal of Applied Ecology.

    Climate and land-use change are expected to substantially alter future plant species distributions leading to higher extinction rates. However, little is known about how plant species ranges, richness and phylogenetic diversity of continents will be affected by these dynamics. We address this gap here by examining the patterns of species' distributions and phylogenetic relationships for 7465 seed plant taxa in North America. An ensemble of species distribution models was used to estimate the potential suitable habitat of species under different sets of climate, land-use and dispersal constraint scenarios. We then evaluated the vulnerability and extinction risk of individual species to changes in climate and land use, and examined whether rare, endangered and evolutionarily distinct species were disproportionally threatened by climate and land-use change. We show that ~2000 species may lose >80% of their suitable habitats under the A1b emission scenario for the 2080s, while ~100 species may experience >80% range expansions (a 20 : 1 ratio of loss to gain). When considering >50% range retraction and expansion, the ratio of loss to gain was 13 : 1. A greater loss of species diversity is expected at low latitudes, while larger gains are expected at high latitudes. Evolutionarily distinct species are predicted to have significantly higher extinction risks than extant species. This suggests a disproportionate future loss of phylogenetic diversity for the North American flora. Synthesis and applications. Our study provides continental-scale evidence of plant species extinction risk caused by future climate and land-use change, and highlights the importance of integrating phylogenetic measures into conservation risk assessments. This work provides insight into the status, trends and threats for a large share of North America's plant species by identifying risks and prioritizing conservation in a rapidly changing world.

    Keywords: Miocene, Neotropics, cold adaptation, niche shift, phylogenetic niche conservatism, range expansion


  • Alter S, Meyer M, Post K, Czechowski P, Gravlund P, Gaines C et al. (2015)

    Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100.

    Molecular ecology 24(7) 1510-22.

    Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.

    Keywords: Animals, Arctic Regions, Atlantic Ocean, Biological, Climate Change, DNA, Ecosystem, Fossils, Genetic Variation, Haplotypes, Mitochondrial, Mitochondrial: genetics, Models, Molecular Sequence Data, Phylogeography, Population Dynamics, Sequence Analysis, Whales, Whales: genetics


  • Kelbert P, Droege G, Barker K, Braak K, Cawsey E, Coddington J et al. (2015)

    B-HIT - A Tool for Harvesting and Indexing Biodiversity Data.

    PloS one 10(11) e0142240.

    With the rapidly growing number of data publishers, the process of harvesting and indexing information to offer advanced search and discovery becomes a critical bottleneck in globally distributed primary biodiversity data infrastructures. The Global Biodiversity Information Facility (GBIF) implemented a Harvesting and Indexing Toolkit (HIT), which largely automates data harvesting activities for hundreds of collection and observational data providers. The team of the Botanic Garden and Botanical Museum Berlin-Dahlem has extended this well-established system with a range of additional functions, including improved processing of multiple taxon identifications, the ability to represent associations between specimen and observation units, new data quality control and new reporting capabilities. The open source software B-HIT can be freely installed and used for setting up thematic networks serving the demands of particular user groups.

    Keywords: Animals, Arctic Regions, Atlantic Ocean, Biological, Climate Change, DNA, Ecosystem, Fossils, Genetic Variation, Haplotypes, Mitochondrial, Mitochondrial: genetics, Models, Molecular Sequence Data, Phylogeography, Population Dynamics, Sequence Analysis, Whales, Whales: genetics


  • Li X, Dong F, Lei F, Alström P, Zhang R, Ödeen A et al. (2015)

    Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of White Wagtail Motacilla alba (Aves: Passeriformes)

    Journal of Avian Biology.

    We studied the phylogeography and population history of the White Wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of White Wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in Central and South Europe; and clade SE was distributed in Central and East Asia. The deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of East Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. The recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.

    Keywords: Animals, Arctic Regions, Atlantic Ocean, Biological, Climate Change, DNA, Ecosystem, Fossils, Genetic Variation, Haplotypes, Mitochondrial, Mitochondrial: genetics, Models, Molecular Sequence Data, Phylogeography, Population Dynamics, Sequence Analysis, Whales, Whales: genetics


  • Moreno-Amat E, Mateo R, Nieto-Lugilde D, Morueta-Holme N, Svenning J, García-Amorena I (2015)

    Impact of model complexity on cross-temporal transferability in Maxent species distribution models: An assessment using paleobotanical data

    Ecological Modelling 312 308-317.

    Maximum entropy modeling (Maxent) is a widely used algorithm for predicting species distributions across space and time. Properly assessing the uncertainty in such predictions is non-trivial and requires validation with independent datasets. Notably, model complexity (number of model parameters) remains a major concern in relation to overfitting and, hence, transferability of Maxent models. An emerging approach is to validate the cross-temporal transferability of model predictions using paleoecological data. In this study, we assess the effect of model complexity on the performance of Maxent projections across time using two European plant species (Alnus glutinosa (L.) Gaertn. and Corylus avellana L.) with an extensive late Quaternary fossil record in Spain as a study case. We fit 110 models with different levels of complexity under present time and tested model performance using AUC (area under the receiver operating characteristic curve) and AICc (corrected Akaike Information Criterion) through the standard procedure of randomly partitioning current occurrence data. We then compared these results to an independent validation by projecting the models to mid-Holocene (6000 years before present) climatic conditions in Spain to assess their ability to predict fossil pollen presence–absence and abundance. We find that calibrating Maxent models with default settings result in the generation of overly complex models. While model performance increased with model complexity when predicting current distributions, it was higher with intermediate complexity when predicting mid-Holocene distributions. Hence, models of intermediate complexity resulted in the best trade-off to predict species distributions across time. Reliable temporal model transferability is especially relevant for forecasting species distributions under future climate change. Consequently, species-specific model tuning should be used to find the best modeling settings to control for complexity, notably with paleoecological data to independently validate model projections. For cross-temporal projections of species distributions for which paleoecological data is not available, models of intermediate complexity should be selected.

    Keywords: Alnus glutinosa, Corylus avellana, Model validation, Pollen fossil, Species distribution model, β-Multiplier


  • Padonou E, Teka O, Bachmann Y, Schmidt M, Lykke A, Sinsin B (2015)

    Using species distribution models to select species resistant to climate change for ecological restoration of bowé in West Africa

    African Journal of Ecology n/a-n/a.

    Bowalization is a particular form of land degradation and leads to lateral expansion of ferricrete horizons. The process occurs only in tropical regions. In this study, the most adapted and resistant species towards climate change were identified on bowé. The 15 most common bowé species of the subhumid and semi-arid climate zones of Benin were submitted together with significant environmental variables (elevation, current bioclimatic variables, soil types) to three ecological niche modelling programmes (Maxent, Domain and GARP). For future prediction (2050), IPCC4/CIAT and IPCC5/CMIP5 climate data were applied. Asparagus africanus, Andropogon pseudapricus and Combretum nigricans were identified as the most resistant species for ecological restoration of bowé in the semi-arid climate zone and Asparagus africanus, Detarium microcarpum and Lannea microcarpa in the subhumid climate zone. The ‘Pull’ strategies were identified as appropriate for ecological restoration of bowé in Benin.

    Keywords: Benin, Bowé, climate change, ecological restoration, resistant species, subhumid and semi-arid climate zones


  • Pellissier L, Eidesen P, Ehrich D, Descombes P, Schönswetter P, Tribsch A et al. (2015)

    Past climate-driven range shifts and population genetic diversity in arctic plants

    Journal of Biogeography.

    Aim High intra-specific genetic diversity is necessary for species adaptation to novel environments under climate change, but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here, we investigated the relationship between range shift since the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses. Location: The circumpolar Arctic and northern temperate alpine ranges. Methods: We estimated the climatic niches of 30 cold-adapted plant species using range maps coupled with species distribution models and hindcasted species suitable areas to reconstructions of the mid-Holocene and LGM climates. We computed the species-specific migration distances from the species glacial refugia to their current distribution and correlated distances to extant genetic diversity in 1295 populations. Differential responses among species were related to life-history traits. Results: We found a negative association between inferred migration distances from refugia and genetic diversities in 25 species, but only 11 had statistically significant negative slopes. The relationships between inferred distance and population genetic diversity were steeper for insect-pollinated species than wind-pollinated species, but the difference among pollination system was marginally independent from phylogenetic autocorrelation. Main conclusion: The relationships between inferred migration distances and genetic diversities in 11 species, independent from current isolation, indicate that past range shifts were associated with a genetic bottleneck effect with an average of 21% loss of genetic diversity per 1000 km−1. In contrast, the absence of relationship in many species also indicates that the response is species specific and may be modulated by plant pollination strategies or result from more complex historical contingencies than those modelled here.

    Keywords: Arctic plants, Last Glacial Maximum, climate change, climatic niche, migration, species distribution models


  • Sandel B, Gutiérrez A, Reich P, Schrodt F, Dickie J, Kattge J (2015)

    Estimating themissing species bias in plant trait measurements

    Journal of Vegetation Science 26(5) 828-838.

    Aim Do plant trait databases represent a biased sample of species, and if so, can that bias be corrected? Ecologists are increasingly collecting and analysing data on plant functional traits, and contributing them to large plant trait databases. Many applications of such databases involve merging trait measurements with other data such as species distributions in vegetation plots; a process that invariably produces matrices with incomplete trait and species data. Typically, missing data are simply ignored and it is assumed that the missing species are missing at random. Methods Here, we argue that this assumption is unlikely to be valid and propose an approach for estimating the strength of the bias regarding which species are represented in trait databases. The method leverages the fact that, within a given database, some species have many measurements of a trait and others have few (high vs low measurement intensity). In the absence of bias, there should be no relationship between measurement intensity and trait values. We demonstrate the method using five traits that are part of the TRY database, a global archive of plant traits. Our method also leads naturally to a correction for this bias, which we validate and apply to two examples. Results Specific leaf area and seed mass were strongly positively biased (frequently measured species had higher trait values than rarely measured species), leaf nitrogen per unit mass and maximum height were moderately negatively biased, and maximum photosynthetic capacity per unit leaf area was weakly negatively biased. The bias-correction method yielded greatly improved estimates in the validation tests for the two most biased traits. Further, in our two applications, ecological interpretations were shown to be sensitive to uncorrected bias in the data. Conclusions Species inclusion in trait databases appears to be strongly biased in some cases, and failure to correct this can lead to incorrect conclusions.

    Keywords: Bias, Leaf nitrogen, Maximum height, Missing data, Photosynthesis rate, Plant functional trait, Seed mass, Specific leaf area