Uses of GBIF in scientific research

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

List of publications

  • De Pooter D, Appeltans W, Bailly N, Bristol S, Deneudt K, Eliezer M et al. (2017)

    Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

    Biodiversity Data Journal 5 e10989.

    The Ocean Biogeographic Information System (OBIS) is the world’s most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.

    Keywords: Darwin Core Archive, data standardisation, ecosystem data, environmental data, oceanographic data, sample event, species occurrence, telemetry data


  • Figuerola B, Barnes D, Brickle P, Brewin P (2017)

    Bryozoan diversity around the Falkland and South Georgia Islands: Overcoming Antarctic barriers

    Marine Environmental Research 126 81-94.

    There are a number of remote archipelagos distributed between 45 and 60 °S. The biota of these islands provide useful information to describe and understand patterns in biodiversity and biogeography as well as potential impacts of climate change on marine ecosystems. They are in key locations either side of the Polar Front but also have limited influence from human activities. Here we investigate one taxon, bryozoans, on South Atlantic shelf habitats of the Falkland (FI) and the sub-Antarctic island of South Georgia (SG). We present new data on spatial distribution in these islands, as well as an analysis of the bryozoological similarities between these and neighbouring regions. A total of 85 species of cheilostome bryozoans (351 samples) were found, belonging to 33 genera, including 18 potentially new genera and 23 new species. Remarkably 65% and 41% of species were reported for the first time at FI and SG, respectively. The highest and the lowest value of species richness and species/genus ratio were found at East (EFI) and West Falkland (WFI), respectively, likely showing a tendency for stronger intrageneric competition. New data from this study were jointly analysed with data from the literature and existing databases, revealing new bathymetric ranges in 32 species. The biogeographic affinities of the bryozoans found give further evidence of the hypothesis of sequential separation of Gondwana and support the changing concept that although the Polar Front acts as a circumpolar biogeographic barrier it is not as impermeable as originally thought. Potential dispersal mechanisms are also discussed.

    Keywords: Benthos, Biodiversity, Biogeography, Marine ecology, Southern ocean, Spatial patterns


  • Fitt R, Lancaster L (2017)

    Range shifting species reduce phylogenetic diversity in high latitude communities via competition

    Journal of Animal Ecology.

    Under anthropogenic climate change, many species are expanding their ranges to higher latitudes and altitudes, resulting in novel species interactions. The consequences of these range shifts for native species, patterns of local biodiversity, and community structure in high latitude ecosystems are largely unknown but critical to understand in light of widespread poleward expansions by many warm-adapted generalists. Using niche modelling, phylogenetic methods, and field and laboratory studies, we investigated how colonisation of Scotland by a range expanding damselfly, Ischnura elegans, influences patterns of competition and niche shifts in native damselfly species, and changes in phylogenetic community structure. Colonization by I. elegans was associated with reduced population density and niche shifts in the resident species least related to I. elegans (Lestes sponsa), reflecting enhanced competition. Furthermore, communities colonized by I. elegans exhibited phylogenetic underdispersion, reflecting patterns of relatedness and competition. Our results provide a novel example of a potentially general mechanism whereby climate change-mediated range shifts can reduce phylogenetic diversity within high latitude communities, if colonising species are typically competitively superior to members of native communities that are least-closely-related to the coloniser.

    Keywords: Benthos, Biodiversity, Biogeography, Marine ecology, Southern ocean, Spatial patterns


  • Kennedy M, Lang P, Grimaldo J, Martins S, Bruce A, Moore I et al. (2017)

    Niche-breadth of freshwater macrophytes occurring in tropical southern African rivers predicts species global latitudinal range

    Aquatic Botany 136 21-30.

    The study tested the hypothesis that measurement, using multivariate Principal Components Analysis (PCA), of the niche-breadth of river macrophyte species in southern tropical Africa, may predict their larger-scale biogeographical range. Two measures of niche-breadth were calculated for 44 riverine macrophyte species, from 20 families commonly occurring in Zambia, using an approach based on PCA ordination with 16 bio-physico-chemical input variables. These included altitude, stream order, stream flow, pH, conductivity and soluble reactive phosphate concentration (SRP). In the absence of additional chemical water quality data for Zambian rivers, invertebrate-based measures of general water quality were also used. These were benthic macroinvertebrate Average Score per Taxon (ASPT), and individual abundance of nine macroinvertebrate families with differing water quality tolerance, indicated by their Sensitivity Weightings within the Zambian Invertebrate Scoring System (ZISS). Macrophyte large-scale latitudinal range was derived from world geopositional records held by online databases, and additional records held by the authors. The two niche-breadth metrics divided the species into narrow-niche and intermediate/broad-niche categories, showing significant variation (from one or both of correlation and ANOVA test outcomes) in altitude, stream flow, conductivity, SRP, pH and ASPT, but not stream order. Macrophyte alpha-diversity (as a measure of number of individual niches co-existing per habitat) showed no significant relationship with individual species niche-breadth. Narrow-niche species included a higher proportion of Afrotropical endemics than did species with broader niche size. There were significant predictive relationships between macrophyte niche-breadth and latitudinal range of the target species at global and Afrotropical scales, but not for the Neotropics.

    Keywords: Africa, Aquatic plants, Benthic macroinvertebrates, Freshwater ecology, Latitudinal distribution, Niche analysis, Rivers


  • Martin A, Harvey W (2017)

    The Global Pollen Project: A New Tool for Pollen Identification and the Dissemination of Physical Reference Collections

    Methods in Ecology and Evolution.

    1.The study of fossil and modern pollen assemblages provides essential information about vegetation dynamics in space and time. A major methodological component of these studies is the identification of pollen grains to plant family, genus and species. This identification is achieved through the use of pollen keys and reference collections of physical specimens, which are regional in scope, disparate, and incomplete, slowing the identification process. Reference material is also held in museums and research institutions, where access can be limited. Identification is particularly challenging for those new to the field, such as graduate students. 2.To aid the identification of pollen grains, and provide virtual access to reference material, we present a new online tool: The Global Pollen Project (https://globalpollenproject.org). The project aims to enable people to share and identify pollen grains and through this, will create an open, free, and accessible reference library for pollen identification. 3.The online tool has been developed as an open, peer-reviewed database of global pollen, where content and expertise is crowdsourced from across the world. The tool enables: (a) the submission and identification of unknown pollen grains; (b) the submission and digitisation of existing “physical” reference collections; and (c) the availability of a free public database of pollen images and their metadata, for use in scientific research and education. The tool connects to external services, including the Global Biodiversity Information Facility and Neotoma Palaeoecology Database, to provide botanical descriptions and occurrence data for each taxon, alongside pollen images and metadata. 4.The database currently holds information for over 1,500 species, from Europe, the Americas, and Asia. As the collection grows, we envision easier pollen identification, and greater use of the database for novel research on pollen morphology and other characteristics, especially when linked to other palaeoecological databases, such as Neotoma.

    Keywords: Africa, Aquatic plants, Benthic macroinvertebrates, Freshwater ecology, Latitudinal distribution, Niche analysis, Rivers


  • Pellegrini A, Anderegg W, Paine C, Hoffmann W, Kartzinel T, Rabin S et al. (2017)

    Convergence of bark investment according to fire and climate structures ecosystem vulnerability to future change

    Ecology Letters.

    Fire regimes in savannas and forests are changing over much of the world. Anticipating the impact of these changes requires understanding how plants are adapted to fire. In this study, we test whether fire imposes a broad selective force on a key fire-tolerance trait, bark thickness, across 572 tree species distributed worldwide. We show that investment in thick bark is a pervasive adaptation in frequently burned areas across savannas and forests in both temperate and tropical regions where surface fires occur. Geographic variability in bark thickness is largely explained by annual burned area and precipitation seasonality. Combining environmental and species distribution data allowed us to assess vulnerability to future climate and fire conditions: tropical rainforests are especially vulnerable, whereas seasonal forests and savannas are more robust. The strong link between fire and bark thickness provides an avenue for assessing the vulnerability of tree communities to fire and demands inclusion in global models.

    Keywords: Bark thickness, fire ecology, forest, functional traits, global change, savanna


  • Phillips J, Magos Brehm J, van Oort B, Asdal , Rasmussen M, Maxted N (2017)

    Climate change and national crop wild relative conservation planning

    Ambio 1-14.

    Climate change is likely to be one of the most important factors affecting our future food security. To mitigate negative impacts, we will require our crops to be more genetically diverse. Such diversity is available in crop wild relatives (CWRs), the wild taxa relatively closely related to crops and from which diverse traits can be transferred to the crop. Conservation of such genetic resources resides within the nation where they are found; therefore, national-level conservation recommendations are fundamental to global food security. We investigate the potential impact of climate change on CWR richness in Norway. The consequences of a 1.5 and 3.0 °C temperature rise were studied for the years 2030, 2050, 2070, 2080 and then compared to the present climate. The results indicate a pattern of shifting CWR richness from the south to the north, with increases in taxa turnover and in the numbers of threatened taxa. Recommendations for in situ and ex situ conservation actions over the short and long term for the priority CWRs in Norway are presented. The methods and recommendations developed here can be applied within other nations and at regional and global levels to improve the effectiveness of conservation actions and help ensure global food security.

    Keywords: Agriculture, Ex situ conservation, Food security, Genetic diversity, In situ conservation, Plant genetic resources


  • Rocchini D, Garzon-Lopez C, Marcantonio M, Amici V, Bacaro G, Bastin L et al. (2017)

    Anticipating species distributions: Handling sampling effort bias under a Bayesian framework

    Science of The Total Environment.

    Keywords: Anticipation, Bayesian theorem, Species distribution modeling, Uncertainty, sampling effort bias


  • Smeraldo S, Di Febbraro M, Ćirović D, Bosso L, Trbojević I, Russo D (2017)

    Species distribution models as a tool to predict range expansion after reintroduction: A case study on Eurasian beavers (Castor fiber)

    Journal for Nature Conservation.

    Species Distribution Models (SDMs) may provide important information for the follow-up phase of reintroduction operations by identifying the main areas most likely to be colonized by the reintroduced species. We used SDMs to identify the potential distribution of Eurasian beavers (Castor fiber) reintroduced to Serbia and Bosnia and Herzegovina in 2004–2006 after being historically driven to extinction by overhunting. Models were also used to carry out a gap analysis to assess the degree of protection granted by the national reserve networks to the potentially expanding population. Distances from hydrographic network, broadleaved forest, main watercourses and farmland were the main factors influencing model performance. We estimated that suitable habitat covers 14.0% (31,000 km2) of the whole study area. In Serbia, in 2004–2013 beavers expanded their range at a mean colonization speed of 70.9 ± 12.8 km/year (mean ± SD). Only 2.89% of and 9.72% of beaver’s suitable habitat lie within the national network of protected areas of Bosnia and Serbia respectively. We detected new potential areas where beavers will likely settle in the near future, advising on where further monitoring should be focused. We also identified low suitability areas to be targeted with appropriate management to improve their conditions as well as important regions falling outside reserve boundaries where protection should be granted.

    Keywords: Bosnia and Herzegovina, Conservation gap analyses, Habitat suitability, Riparian habitats, Serbia


  • Taylor N, Kell S, Holubec V, Parra-Quijano M, Chobot K, Maxted N (2017)

    A systematic conservation strategy for crop wild relatives in the Czech Republic

    Diversity and Distributions 23(4) 448-462.

    Aim To create a crop wild relative (CWR) conservation strategy for the Czech Republic: the first national CWR conservation strategy for Central and Eastern Europe. Location Czech Republic. Methods We generated a CWR checklist for the Czech Republic and then prioritized taxa, using widely adopted criteria modified with input from local experts, to create a national CWR inventory. For 204 priority CWR species, we collated 206,760 presence records. We carried out spatial analyses to identify patterns in species richness, gaps in existing conservation actions, complementary conservation networks and collecting strategies to increase representativeness of gene bank accessions. We considered both specific and genetic conservation, using geographic and ecogeographic proxies for the latter. Results Passive in situ conservation of CWR in the Czech Republic is comprehensive at present, with all but one priority CWR species being contained in protected areas. Active in situ CWR conservation could be focussed within 11 ca. 10-km-by-10-km grid cells containing 94% of priority species, or their overlapping protected areas. To augment the genetic coverage of the in situ conservation network, active CWR conservation is encouraged within 11 supplementary areas. Meanwhile, there are huge gaps in ex situ collections, with no known conserved material for 134 of the 204 priority species. Furthermore, existing accessions are generally unrepresentative of genetic diversity. Main conclusions In the Czech Republic, active in situ conservation of priority CWR should be instigated within the 22 recommended grid cell areas or their 14 overlapping protected areas. For ex situ conservation, strategic and targeted collection of germplasm would markedly increase the value of gene bank collections. Diversity of priority Czech CWR is concentrated in South Moravia, making this a particularly important CWR area for the country and for Europe.

    Keywords: Bosnia and Herzegovina, Conservation gap analyses, Habitat suitability, Riparian habitats, Serbia