Uses of GBIF in scientific research

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

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

  • 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

  • Tangjitman K, Trisonthi C, Wongsawad C J (2015)

    Potential impact of climatic change on medicinal plants used in the Karen women’s health care in northern Thailand

    Songklanakarin Journal of Science and Technology 37(3) 369-379.

    Global climate change can be expected to drive losses in plant diversity. To exemplifying this issue , the potential impact of climate change on nine medicinal plants relating to Karen women’s healthcare in northern Thailand was investigated using species distribution models. Climatic and non-climatic variables were used to develop the distributi on models. The green- house gas emissions scenarios, A1B (medium-high emission) and A2 (high emission) were used to examin e the potential future species distribution for year 2050 and 2080. It was shown that a combination of climatic and non-climatic factors had strong effects on the distribution of medicinal plant species. Eight plant species were predicted to reduce suitable area in northern Thailand whereas one species is predicted to increase suitable area. Following IUCN Red Lis t criteria, seven of the studied plant species were categorized as critically endangered under A1B or A2 scenarios by 2080. T he importance of planning for climate change effects on the availability of wild-collected plant for rural population s was pointed ou

    Keywords: ethnobotany, global warming, rural livelihoods, sp

  • Ware C, Berge J, Jelmert A, Olsen S, Pellissier L, Wisz M et al. (2015)

    Biological introduction risks from shipping in a warming Arctic

    Journal of Applied Ecology.

    1.Several decades of research on invasive marine species have yielded a broad understanding of the nature of species invasion mechanisms and associated threats globally. However, this is not true of the Arctic, a region where ongoing climatic changes may promote species invasion. Here we evaluated risks associated with non-indigenous propagule loads discharged with ships’ ballast water to the high-Arctic archipelago, Svalbard, as a case study for the wider Arctic. 2.We sampled and identified transferred propagules using traditional and DNA barcoding techniques. We then assessed the suitability of the Svalbard coast for non-indigenous species under contemporary and future climate scenarios using ecophysiological models based on critical temperature and salinity reproductive thresholds. 3.Ships discharging ballast water in Svalbard carried high densities of zooplankton (mean 1522 ± 335 SE individuals m−3), predominately comprised of indigenous species. Ballast water exchange did not prevent non-indigenous species introduction. Non-indigenous coastal species were present in all except one of 16 ballast water samples (mean 144 ± 67 SE individuals m−3), despite five of the eight ships exchanging ballast water en route. 4.Of a total of 73 taxa, 36 species including 23 non-indigenous species were identified. Of those 23, sufficient data permitted evaluation of the current and future colonization potential for eight widely-known invaders. With the exception of one of these species, modelled suitability indicated that the coast of Svalbard is unsuitable presently; under the 2100 RCP 8.5 climate scenario, however, modelled suitability will favour colonization for six species. 5.Synthesis and applications. We show that current ballast water management practices do not prevent non-indigenous species from being transferred to the Arctic. Consequences of these shortcomings will be shipping-route dependent, but will likely magnify over time: our models indicate future conditions will favour the colonization of non-indigenous species Arctic-wide. Invasion threats will be greatest where shipping transfers organisms across biogeographic realms, and for these shipping routes ballast water treatment technologies may be required to prevent impacts. Our results also highlight critical gaps in our understanding of ballast water management efficacy and prioritization. Thereby, our study provides an agenda for research and policy development.

    Keywords: Arctic, ballast water exchange, climate change, ecophysiological thresholds, habitat suitability, invasion, marine non-indigenous species, regeneration niche, shipping, zooplankton