Uses of GBIF in scientific research

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

List of publications

  • Adriaens, T., Sutton-Croft, M., Owen, K., Brosens, D., van Valkenburg, J., Kilbey, D., Groom, Q., Ehmig, C., Thürkow, F. V, , P., Schneider K (2015)

    Trying to engage the crowd in recording invasive alien species in Europe: experiences from two smartphone applications in northwest Europe

    Management of Biological Invasions 6(2) 215-225.

    New technologies such as smartphone appli cation software (apps) are increasingly used to reach a wider audience on the subject of invasive alien species (IAS) and to involve the public in recording them. In this paper we pr esent two of the more recent smartphone app lications for IAS recording in northwest Europe, the RINSE That’s Invasive! app and the KORINA app. We present an overview of available smartphone apps for IAS recording in Europe and addr ess issues of data integra tion, data openness, data quality, data harmonisation and da tabase interoperability. Finally, we make some recommendations for future app design

    Keywords: biological recording, citizen science, early war

  • 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

  • Castañeda-Álvarez N, de Haan S, Juárez H, Khoury C, Achicanoy H, Sosa C et al. (2015)

    Ex situ conservation priorities for the wild relatives of potato (solanum L. Section petota).

    PloS one 10(4) e0122599.

    Crop wild relatives have a long history of use in potato breeding, particularly for pest and disease resistance, and are expected to be increasingly used in the search for tolerance to biotic and abiotic stresses. Their current and future use in crop improvement depends on their availability in ex situ germplasm collections. As these plants are impacted in the wild by habitat destruction and climate change, actions to ensure their conservation ex situ become ever more urgent. We analyzed the state of ex situ conservation of 73 of the closest wild relatives of potato (Solanum section Petota) with the aim of establishing priorities for further collecting to fill important gaps in germplasm collections. A total of 32 species (43.8%), were assigned high priority for further collecting due to severe gaps in their ex situ collections. Such gaps are most pronounced in the geographic center of diversity of the wild relatives in Peru. A total of 20 and 18 species were assessed as medium and low priority for further collecting, respectively, with only three species determined to be sufficiently represented currently. Priorities for further collecting include: (i) species completely lacking representation in germplasm collections; (ii) other high priority taxa, with geographic emphasis on the center of species diversity; (iii) medium priority species. Such collecting efforts combined with further emphasis on improving ex situ conservation technologies and methods, performing genotypic and phenotypic characterization of wild relative diversity, monitoring wild populations in situ, and making conserved wild relatives and their associated data accessible to the global research community, represent key steps in ensuring the long-term availability of the wild genetic resources of this important crop.

    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

  • Khoury C, Heider B, Castañeda-Álvarez N, Achicanoy H, Sosa C, Miller R et al. (2015)

    Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas].

    Frontiers in plant science 6 251.

    Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.

    Keywords: Crop Improvement, Crop diversity, Crop wild relatives, Food security, Gap analysis, Plant Genetic Resources

  • Kriticos D, Brunel S, Ota N, Fried G, Oude Lansink A, Panetta F et al. (2015)

    Downscaling Pest Risk Analyses: Identifying Current and Future Potentially Suitable Habitats for Parthenium hysterophorus with Particular Reference to Europe and North Africa

    PLOS ONE 10(9) e0132807.

    Pest Risk Assessments (PRAs) routinely employ climatic niche models to identify endangered areas. Typically, these models consider only climatic factors, ignoring the ‘Swiss Cheese’ nature of species ranges due to the interplay of climatic and habitat factors. As part of a PRA conducted for the European and Mediterranean Plant Protection Organization, we developed a climatic niche model for Parthenium hysterophorus, explicitly including the effects of irrigation where it was known to be practiced. We then downscaled the climatic risk model using two different methods to identify the suitable habitat types: expert opinion (following the EPPO PRA guidelines) and inferred from the global spatial distribution. The PRA revealed a substantial risk to the EPPO region and Central and Western Africa, highlighting the desirability of avoiding an invasion by P. hysterophorus. We also consider the effects of climate change on the modelled risks. The climate change scenario indicated the risk of substantial further spread of P. hysterophorus in temperate northern hemisphere regions (North America, Europe and the northern Middle East), and also high elevation equatorial regions (Western Brazil, Central Africa, and South East Asia) if minimum temperatures increase substantially. Downscaling the climate model using habitat factors resulted in substantial (approximately 22–53%) reductions in the areas estimated to be endangered. Applying expert assessments as to suitable habitat classes resulted in the greatest reduction in the estimated endangered area, whereas inferring suitable habitats factors from distribution data identified more land use classes and a larger endangered area. Despite some scaling issues with using a globally conformal Land Use Systems dataset, the inferential downscaling method shows promise as a routine addition to the PRA toolkit, as either a direct model component, or simply as a means of better informing an expert assessment of the suitable habitat types.

    Keywords: Crop Improvement, Crop diversity, Crop wild relatives, Food security, Gap analysis, Plant Genetic Resources

  • Käffer M, Koch N, Aptroot A, de A. Martins S (2015)

    New records of corticolous lichens for South America and Brazil

    Plant Ecology and Evolution 148(1) 111-118.

    Background and aims – The corticolous microlichens are the greatest group of lichens in the world and also the least known. For this reason intensive studies on this group are seriously needed. Based on this necessity, the main objective of this paper is to present new records of corticolous microlichen species for South America, Brazil, the Southern region of Brazil and the state of Rio Grande do Sul. Methods – The species were collected in three different forest types: native Araucaria forest, Atlantic rainforest and riparian forests from the Pampa Biome. Key results – A total of 43 new records of corticolous microlichen species are here presented. Six species are new reports for South America: Cryptothelium cecidiogenum Aptroot & Lücking, Distopyrenis composita R.C.Harris, Graphis pseudocinerea Lücking & Umaña, Herpothallon echinatum Aptroot, Lücking & Will-Wolf, Lecanora thysanophora R.C.Harris and Psoroglaena stigonemoides (Orange) Henssen. Two species are new records for Brazil: Pyrenula dissimulans (Müll.Arg.) R.C.Harris and Rinodina conradii Körb., while four are new occurrences for the state of Rio Grande do Sul: Graphis elongata Zenker, Graphis furcata Fée, Graphis longula Kremp. and Haematomma africanum (Steiner) Dodge. Thirty-one new records are as well reported here for the Southern region of Brazil. Conclusion – The high number of new crustose species records of this study greatly contributes to the current knowledge on lichens. Additionally, our study highlights the importance of conserving all kinds of forest environments, since they are important areas for lichen establishment and dispersion.


  • Lin Y, Deng D, Lin W, Lemmens R, Crossman N, Henle K et al. (2015)

    Uncertainty analysis of crowd-sourced and professionally collected field data used in species distribution models of Taiwanese moths

    Biological Conservation 181 102-110.

    The purposes of this study are to extract the names of species and places for a citizen-science monitoring program, to obtain crowd-sourced data of acceptable quality, and to assess the quality and the uncertainty of predictions based on crowd-sourced data and professional data. We used Natural Language Processing to extract names of species and places from text messages in a citizen science project. Bootstrap and Maximum Entropy methods were used to assess the uncertainty in the model predictions based on crowd-sourced data from the EnjoyMoths project in Taiwan. We compared uncertainty in the predictions obtained from the project and from the Global Biodiversity Information Facility (GBIF) field data for seven focal species of moth. The proximity to locations of easy access and the Ripley K method were used to test the level of spatial bias and randomness of the crowd-sourced data against GBIF data. Our results show that extracting information to identify the names of species and their locations from crowd-sourced data performed well. The results of the spatial bias and randomness tests revealed that the crowd-sourced data and GBIF data did not differ significantly in respect to both spatial bias and clustering. The prediction models developed using the crowd-sourced dataset were the most effective, followed by those that were developed using the combined dataset. Those that performed least well were based on the small sample size GBIF dataset. Our method demonstrates the potential for using data collected by citizen scientists and the extraction of information from vast social networks. Our analysis also shows the value of citizen science data to improve biodiversity information in combination with data collected by professionals.

    Keywords: Citizen science, Large-scale monitoring program, Natural language, Prediction of species distribution, Social media, Uncertainty, Volunteer survey

  • Sevink J, Verstraten JM, Kooijman AM, Loayza-Muro RA, Hoitinga L P (2015)

    Rare Moss-Built Microterraces in a High-Altitude, Acid Mine Drainage-Polluted Stream (Cordillera Negra, Peru) - Springer

    Water, Air, & Soil Pollution.

    The Rio Santiago in the Cordillera Negra of Peru is severely contaminated by acid mine drainage in its headwaters. In a strongly acid stream, at about 3800 m above sea level (masl), microterraces were found with terrace walls built up of dead moss, with encrustations and interstitial fine, creamy sediment. The stream water was turbid due to the presence of similar suspended sediment, which also occurred as a thin basal layer in inter-rim basins. The moss was identified as the rare bryophyte Anomobryum prostratum (Müll. Hal.) Besch. Chemical and mineralogical analyses show that green, living parts of the moss are gradually coated by Al/Fe (hydr)oxides, inducing their senescence and death. The necromass is covered by creamy crusts through precipitation of schwertmannite-type material from the stream water and simultaneous ‘capture’ of fine sediment. The latter consists of a mixture of precipitate and fine detrital primary minerals. These processes are held responsible for the formation of the microterraces, which regarding their composition and environment seem to be unique. Remarkable is the high As content of the creamy crusts and sediment, attributed to strong sorption of As, whereas its solute concentration is relatively low. This calls for more attention to suspended fine sediment in the assessment of environmental risks of stream water use. Lastly, the results raise serious doubts about the use of aquatic bryophytes as bioindicator for chemical pollution in acid mine drainage-polluted streams.

    Keywords: Acid mine drainage, Arsenic, Bryophyte Microterraces, Schwertmannite

  • Verheijen L, Aerts R, Bönisch G, Kattge J, Van Bodegom P (2015)

    Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology.

    The New phytologist.

    Plant functional types (PFTs) aggregate the variety of plant species into a small number of functionally different classes. We examined to what extent plant traits, which reflect species' functional adaptations, can capture functional differences between predefined PFTs and which traits optimally describe these differences. We applied Gaussian kernel density estimation to determine probability density functions for individual PFTs in an n-dimensional trait space and compared predicted PFTs with observed PFTs. All possible combinations of 1-6 traits from a database with 18 different traits (total of 18 287 species) were tested. A variety of trait sets had approximately similar performance, and 4-5 traits were sufficient to classify up to 85% of the species into PFTs correctly, whereas this was 80% for a bioclimatically defined tree PFT classification. Well-performing trait sets included combinations of correlated traits that are considered functionally redundant within a single plant strategy. This analysis quantitatively demonstrates how structural differences between PFTs are reflected in functional differences described by particular traits. Differentiation between PFTs is possible despite large overlap in plant strategies and traits, showing that PFTs are differently positioned in multidimensional trait space. This study therefore provides the foundation for important applications for predictive ecology.

    Keywords: kernel density estimation, plant functional types, plant strategies, plant traits, trade-offs, trait variation

  • Werner G, Cornwell W, Cornelissen J, Kiers E (2015)

    Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism

    Proceedings of the National Academy of Sciences 112(33) 201424030.

    Understanding the origins and evolutionary trajectories of symbiotic partnerships remains a major challenge. Why are some symbioses lost over evolutionary time whereas others become crucial for survival? Here, we use a quantitative trait reconstruction method to characterize different evolutionary stages in the ancient symbiosis between legumes (Fabaceae) and nitrogen-fixing bacteria, asking how labile is symbiosis across different host clades. We find that more than half of the 1,195 extant nodulating legumes analyzed have a high likelihood (>95%) of being in a state of high symbiotic persistence, meaning that they show a continued capacity to form the symbiosis over evolutionary time, even though the partnership has remained facultative and is not obligate. To explore patterns associated with the likelihood of loss and retention of the N2-fixing symbiosis, we tested for correlations between symbiotic persistence and legume distribution, climate, soil and trait data. We found a strong latitudinal effect and demonstrated that low mean annual temperatures are associated with high symbiotic persistence in legumes. Although no significant correlations between soil variables and symbiotic persistence were found, nitrogen and phosphorus leaf contents were positively correlated with legumes in a state of high symbiotic persistence. This pattern suggests that highly demanding nutrient lifestyles are associated with more stable partnerships, potentially because they "lock" the hosts into symbiotic dependency. Quantitative reconstruction methods are emerging as a powerful comparative tool to study broad patterns of symbiont loss and retention across diverse partnerships.

    Keywords: cooperation, deep history, persistence, reconstruction, symbiosis