Uses of GBIF in scientific research

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

List of publications

  • Byrne M, Gall M, Wolfe K, Agüera A (2016)

    From pole to pole: the potential for the Arctic seastar Asterias amurensis to invade a warming Southern Ocean

    Global Change Biology.

    Due to climatic warming, Asterias amurensis, a keystone boreal predatory seastar that has established extensive invasive populations in southern Australia, is a potential high-risk invader of the sub-Antarctic and Antarctic. To assess the potential range expansion of A. amurensis to the Southern Ocean as it warms, we investigated the bioclimatic envelope of the adult and larval life stages. We analysed the distribution of adult A. amurensis with respect to present day and future climate scenarios using habitat temperature data to construct species distribution models (SDM). To integrate the physiological response of the dispersive phase we determined the thermal envelope of larval development to assess their performance in present day and future thermal regimes and the potential for success of A. amurensis in poleward latitudes. The SDM indicated that the thermal 'niche' of the adult stage correlates with a 0-17 °C and 1-22.5 °C range, in winter and summer, respectively. As the ocean warms the range of A. amurensis in Australia will contract, while more southern latitudes will have conditions favorable for range expansion. Successful fertilisation occurred from 3-23.8 °C. By day 12, development to the early larval stage was successful from 5.5-18 °C. Although embryos were able to reach the blastula stage at 2 °C, they had arrested development and high mortality. The optimal thermal range for survival of pelagic stages was 3.5-19.2 °C with a lower and upper critical limit of 2.6 °C and 20.3 °C, respectively. Our data predict that A. amurensis faces demise in its current invasive range while more favourable conditions at higher latitudes would facilitate invasion of both larval and adult stages to the Southern Ocean. Our results show that vigilance is needed to reduce the risk that this ecologically important Arctic carnivore may invade the Southern Ocean and Antarctica. This article is protected by copyright. All rights reserved.

    Keywords: Antarctica, asteroid, climate change, introduced species, larva, ocean warming, southern migration, thermal tolerance


  • Coro G, Magliozzi C, Vanden Berghe E, Bailly N, Ellenbroek A, Pagano P (2016)

    Estimating absence locations of marine species from data of scientific surveys in OBIS

    Ecological Modelling 323 61-76.

    Estimating absence locations of a species is important in conservation biology and conservation planning. For instance, using reliable absence as much as presence information, species distribution models can enhance their performance and produce more accurate predictions of the distribution of a species. Unfortunately, estimating reliable absence locations is difficult and often requires a deep knowledge of the species’ distribution and of its abiotic and biotic environmental preferences and tolerance. In this paper, we propose a methodology to reconstruct reliable absence information from presence-only information, and the conditions that those presence-only data have to meet to make this possible. Large species occurrence data collections (otherwise called occurrence datasets) contain high quality and expert-reviewed species observation records from scientific surveys. These surveys can be used to retrieve species presence locations, but they also record places where the species in their target list were not observed. Although these absences could be simply due to sampling variation, it is possible to intersect many of these reports to estimate true absence locations, i.e. those due to habitat unsuitability or geographical hindrances. In this paper, we present a method to generate reliable absence locations of this type for marine species, using scientific surveys reports contained in the Ocean Biogeographic Information System (OBIS), an authoritative species occurrence dataset. Our method spatially aggregates information from surveys focussing on the same target species. It detects absence locations for a given species as those locations in which repeated surveys (that included the species of interest in their target list) reported information only on other species. We qualitatively demonstrate the reliability of our method using distribution records of the Atlantic cod as a case study. Additionally, we quantitatively estimate its performance using another authoritative large species occurrence dataset, the Global Biodiversity Information Facility (GBIF). We also demonstrate that our approach has higher accuracy and presents complementary behaviour with respect to another method using environmental envelopes. Our process can support species distribution models (as well as other types of models, e.g. climate change models) by providing reliable data to presence/absence approaches. It can manage regional as well as global scale scenarios and runs within a collaborative e-Infrastructure (D4Science) that publishes it as-a-Service, allowing biologists to reproduce, repeat and share experimental results.

    Keywords: Absence locations, Ecological niche modelling, Marine biodiversity, Occurrence data, Scientific surveys, Species distribution maps


  • 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


  • Greve M, Lykke A, Fagg C, Gereau R, Lewis G, Marchant R et al. (2016)

    Realising the potential of herbarium records for conservation biology

    South African Journal of Botany 105 317-323.

    One of the major challenges in ecosystem conservation is obtaining baseline data, particularly for regions that have been poorly inventoried, such as regions of the African continent. Here we use a database of African herbarium records and examples from the literature to show that, although herbarium records have traditionally been collected to build botanical reference “libraries” for taxonomic and inventory purposes, they provide valuable and useful information regarding species, their distribution in time and space, their traits, phenological characteristics, associated species and their physical environment. These data have the potential to provide invaluable information to feed into evidence-based conservation decisions.

    Keywords: Biological collections, Database, Historical records, Label information, Long-term data collections, Trait


  • Janssens S, Vandelook F, De Langhe E, Verstraete B, Smets E, Vandenhouwe I et al. (2016)

    Evolutionary dynamics and biogeography of Musaceae reveal a correlation between the diversification of the banana family and the geological and climatic history of Southeast Asia.

    The New phytologist.

    Tropical Southeast Asia, which harbors most of the Musaceae biodiversity, is one of the most species-rich regions in the world. Its high degree of endemism is shaped by the region's tectonic and climatic history, with large differences between northern Indo-Burma and the Malayan Archipelago. Here, we aim to find a link between the diversification and biogeography of Musaceae and geological history of the Southeast Asian subcontinent. The Musaceae family (including five Ensete, 45 Musa and one Musella species) was dated using a large phylogenetic framework encompassing 163 species from all Zingiberales families. Evolutionary patterns within Musaceae were inferred using ancestral area reconstruction and diversification rate analyses. All three Musaceae genera - Ensete, Musa and Musella - originated in northern Indo-Burma during the early Eocene. Musa species dispersed from 'northwest to southeast' into Southeast Asia with only few back-dispersals towards northern Indo-Burma. Musaceae colonization events of the Malayan Archipelago subcontinent are clearly linked to the geological and climatic history of the region. Musa species were only able to colonize the region east of Wallace's line after the availability of emergent land from the late Miocene onwards.

    Keywords: Biological collections, Database, Historical records, Label information, Long-term data collections, Trait


  • Lens F, Vos R, Charrier G, van der Niet T, Merckx V, Baas P et al. (2016)

    Scalariform-to-simple transition in vessel perforation plates triggered by differences in climate during the evolution of Adoxaceae

    Annals of Botany mcw151.

    Background and Aims Angiosperms with simple vessel perforations have evolved many times independently of species having scalariform perforations, but detailed studies to understand why these transitions in wood evolution have happened are lacking. We focus on the striking difference in wood anatomy between two closely related genera of Adoxaceae, Viburnum and Sambucus, and link the anatomical divergence with climatic and physiological insights. Methods After performing wood anatomical observations, we used a molecular phylogenetic framework to estimate divergence times for 127 Adoxaceae species. The conditions under which the genera diversified were estimated using ancestral area reconstruction and optimization of ancestral climates, and xylem-specific conductivity measurements were performed. Key Results Viburnum, characterized by scalariform vessel perforations (ancestral), diversified earlier than Sambucus, having simple perforations (derived). Ancestral climate reconstruction analyses point to cold temperate preference for Viburnum and warm temperate for Sambucus. This is reflected in the xylem-specific conductivity rates of the co-occurring species investigated, showing that Viburnum lantana has rates much lower than Sambucus nigra. Conclusions The lack of selective pressure for high conductive efficiency during early diversification of Viburnum and the potentially adaptive value of scalariform perforations in frost-prone cold temperate climates have led to retention of the ancestral vessel perforation type, while higher temperatures during early diversification of Sambucus have triggered the evolution of simple vessel perforations, allowing more efficient long-distance water transport.

    Keywords: Adoxaceae, Baileyan wood trends, Sambucus, Viburnum, ancestral area and climate reconstruction, molecular dating, vessel perforation plate transition, wood anatomy


  • Ma H, Ge D, Shenbrot G, Pisano J, Yang Q, Zhang Z (2016)

    Hypsodonty of Dipodidae (Rodentia) in Correlation with Diet Preferences and Habitats

    Journal of Mammalian Evolution 1-10.

    The evolution of molar teeth from low-crowned (brachyodont) to high-crowned (hypsodont) has traditionally been recognized as a response to increasing tooth wear due to endogenous (e.g., fiber, silica) and/ or exogenous (e.g., dust, grit) properties of ingested food. Recent work indicates that the mean hypsodonty level of large herbivorous land mammalian communities is a strong predictor of precipitation in their habitats. For small mammals, however, the research is still in an early stage. This study performed comparative studies of hypsodonty on 26 extant dipodid species with and without consideration of phylogeny. The results confirm the role of diet in shaping the cheek tooth crown height in Dipodidae. The significant relationship of investigated environmental variables with hypsodonty may be partly due to phylogenetic effects. Nonetheless, the mean hypsodonty of dipodid communities has significant relationship with regional climatic variables. Hence, the hypsodonty of dipodids also has great potential to be a regional climate proxy.

    Keywords: Climate, DietHabitat, Dipodidae, Hypsodonty, Phylogeny


  • Pârâu L, Strubbe D, Mori E, Menchetti M, Ancillotto L, Kleunen A et al. (2016)

    Rose-ringed Parakeet Populations and Numbers in Europe: A Complete Overview

    The Open Ornithology Journal 9(1) 1-13.

    Purpose: Alien species are considered one of the major causes contributing to the current loss of biodiversity. Over the past few decades, a large and increasing number of alien species have become invasive in many parts of the world. Their impacts range from competition for resources with native species to damage of urban infrastructure. In Europe, over a thousand alien species are now established, of which 74 are birds. Among 12 established alien parrot species in Europe, Introduction: The Rose-ringed Parakeet (RRP) Psittacula krameri (Scopoli, 1769) is the most abundant and widespread. Since the 1960's, RRPs have established more than 100 wild populations in several European countries. For Western Europe, long-term demographic data indicate the species has grown considerably in number, although some populations have failed to persist. Data: Is scarce and dispersed for countries in Central, Eastern and Northern Europe. Therefore, here we present detailed demographic data of RRP for 90 populations in 10 European countries. Furthermore, we present information on the status of the species in another 27 European countries, for which previously no data were published. Conclusion: Our synthesis reveals a positive demographic trend across the continent, although locally, some populations appear to have reached carrying capacity.

    Keywords: Demography, Europe, Invasive alien species, Parrots, Population, Psittaciformes


  • Roger N, Moerman R, Carvalheiro L, Aguirre-Guitiérrez J, Jacquemart A, Kleijn D et al. (2016)

    Impact of pollen resources drift on common bumblebees in NW Europe

    Global Change Biology.

    Several bee species are experiencing significant population declines. As bees exclusively rely on pollen for development and survival, such declines could be partly related to changes in their host plant abundance and quality. Here, we investigate whether generalist bumblebee species, with stable population trends over the past years, adapted their diets in response to changes in the distribution and chemical quality of their pollen resources. We selected five common species of bumblebee in NW Europe for which we had a precise description of their pollen diet through two time periods (‘prior to 1950’ and ‘2004–2005’). For each species, we assessed whether the shift in their pollen diet was related with the changes in the suitable area of their pollen resources. Concurrently, we evaluated whether the chemical composition of pollen resources changed over time and experimentally tested the impact of new major pollen species on the development of B. terrestris microcolonies. Only one species (i.e. B. lapidarius) significantly included more pollen from resources whose suitable area expanded. This opportunist pattern could partly explain the expansion of B. lapidarius in Europe. Regarding the temporal variation in the chemical composition of the pollen diet, total and essential amino acid contents did not differ significantly between the two time periods while we found significant differences among plant species. This result is driven by the great diversity of resources used by bumblebee species in both periods. Our bioassay revealed that the shift to new major pollen resources allowed microcolonies to develop, bringing new evidence on the opportunist feature of bumblebee in their diets. Overall, this study shows that the response to pollen resource drift varies among closely related pollinators, and a species-rich plant community ensures generalist species to select a nutrient-rich pollen diet.

    Keywords: bumblebee, diet performance, floral resources, food choices, land-use change, pollen


  • Stropp J, Ladle R, M. Malhado A, Hortal J, Gaffuri J, H. Temperley W et al. (2016)

    Mapping ignorance: 300 years of collecting flowering plants in Africa

    Global Ecology and Biogeography.

    Aim Spatial and temporal biases in species-occurrence data can compromise broad-scale biogeographical research and conservation planning. Although spatial biases have been frequently scrutinized, temporal biases and the overall quality of species-occurrence data have received far less attention. This study aims to answer three questions: (1) How reliable are species-occurrence data for flowering plants in Africa? (2) Where and when did botanical sampling occur in the past 300 years? (3) How complete are plant inventories for Africa? Location Africa. Methods By filtering a publicly available dataset containing 3.5 million records of flowering plants, we obtained 934,676 herbarium specimens with complete information regarding species name, date and location of collection. Based on these specimens, we estimated inventory completeness for sampling units (SUs) of 25 km × 25 km. We then tested whether the spatial distribution of well-sampled SUs was correlated with temporal parameters of botanical sampling. Finally, we determined whether inventory completeness in individual countries was related to old or recently collected specimens. Results Thirty-one per cent of SUs contained at least one specimen, whereas only 2.4% of SUs contained a sufficient number of specimens to reliably estimate inventory completeness. We found that the location of poorly sampled areas remained almost unchanged for half a century. Moreover, there was pronounced temporal bias towards old specimens in South Africa, the country that holds half of the available data for the continent. There, high inventory completeness stems from specimens collected several decades ago. Main conclusions Despite the increasing availability of species occurrence data for Africa, broad-scale biogeographical research is still compromised by the uncertain quality and spatial and temporal biases of such data. To avoid erroneous inferences, the quality and biases in species-occurrence data should be critically evaluated and quantified prior to use. To this end, we propose a quantification method based on inventory completeness using easily accessible species-occurrence data.

    Keywords: Africa, GBIF, data quality, flowering plants, inventory completeness, spatial and temporal biases, species-occurrence data