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

  • Balao F, Trucchi E, Wolfe T, Hao B, Lorenzo M, Baar J et al. (2017)

    Adaptive sequence evolution is driven by biotic stress in a pair of orchid species ( Dactylorhiza ) with distinct ecological optima

    Molecular Ecology.

    The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and D. fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage-specific adaptive evolution of protein-coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post-transcriptional regulation via sRNAs. Finally, Dactylorhiza incarnata appears to suffer from insufficient sRNA control over the activity of RNA-dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.

    Keywords: Abiotic stress, Defence, Ecological divergence, Positive selection, Small RNAs, Transcriptomics

  • Beech E, Rivers M, Oldfield S, Smith P (2017)

    GlobalTreeSearch – the first complete global database of tree species and country distributions

    Journal of Sustainable Forestry 10549811.2017.1310049.

    This paper presents, for the first time, an overview of all known tree species by scientific name and country level distribution, and describes an online database—GlobalTreeSearch—that provides access to this information. Based on our comprehensive analysis of published data sources and expert input, the number of tree species currently known to science is 60,065, representing 20 percent of all angiosperm and gymnosperm plant species. Nearly half of all tree species (45%) are found in just ten families, with the three most tree-rich families being Leguminosae, Rubiaceae, and Myrtaceae. Geographically, Brazil, Colombia, and Indonesia are the countries with the most tree species. The countries with the most country-endemic tree species reflect broader plant diversity trends (Brazil, Australia, China) or islands where isolation has resulted in speciation (Madagascar, Papua New Guinea, Indonesia). Nearly 58 percent of all tree species are single country-endemics. Our intention is for GlobalTreeSearch to be used as a tool for monitoring and managing tree species diversity, forests, and carbon stocks on a global, regional, and/or national level. It will also be used as the basis of the Global Tree Assessment, which aims to assess the conservation status of all of the world’s tree species by 2020.

    Keywords: Abiotic stress, Defence, Ecological divergence, Positive selection, Small RNAs, Transcriptomics

  • Carne C (2017)

    Predicting habitat suitability for the wart-biter bush cricket (Decticus verrucivorus) in Europe

    Journal of Insect Conservation 1-9.

    The wart-biter bush cricket is a relatively abundant species in mainland Europe, but has been declining at the northern edge of its range. With the predicted changes to the global climate that are expected to occur over the next century, it is probable that many species will shift their ranges polewards and to higher altitudes to track suitable climates. In this paper, a species distribution model was used to explore the effects of potential climate change scenarios on the distribution of the wart-biter bush cricket. The model predicts that suitable habitat will shift towards the north and to higher altitudes under a moderate climate change scenario, and that under severe climate change, the cricket will be left with very little suitable habitat in Europe. This highlights the threat of climate change to the species, but also the importance of maintaining the current habitat in the northern and high altitude areas of its range, as these areas may become important strongholds for the species in the future.

    Keywords: Climate change, Decticus verrucivorus, Habitat suitability, Maxent, Modelling

  • 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

  • Liedtke H, Müller H, Hafner J, Penner J, Gower D, Mazuch T et al. (2017)

    Terrestrial reproduction as an adaptation to steep terrain in African toads

    Proceedings of the Royal Society B: Biological Sciences 284(1851) 20162598.

    How evolutionary novelties evolve is a major question in evolutionary biology. It is widely accepted that changes in environmental conditions shift the position of selective optima, and advancements in phylogenetic comparative approaches allow the rigorous testing of such correlated transitions. A longstanding question in vertebrate biology has been the evolution of terrestrial life histories in amphibians and here, by investigating African bufonids, we test whether terrestrial modes of reproduction have evolved as adaptations to particular abiotic habitat parameters. We reconstruct and date the most complete species-level molecular phylogeny and estimate ancestral states for reproductive modes. By correlating continuous habitat measurements from remote sensing data and locality records with life-history transitions, we discover that terrestrial modes of reproduction, including viviparity evolved multiple times in this group, most often directly from fully aquatic modes. Terrestrial modes of reproduction are strongly correlated with steep terrain and low availability of accumulated water sources. Evolutionary transitions to terrestrial modes of reproduction occurred synchronously with or after transitions in habitat, and we, therefore, interpret terrestrial breeding as an adaptation to these abiotic conditions, rather than an exaptation that facilitated the colonization of montane habitats.

    Keywords: Bufonidae, amphibian, evolution, reproductive mode, terrestrial life history, viviparity

  • Longbottom J, Browne A, Pigott D, Sinka M, Golding N, Hay S et al. (2017)

    Mapping the spatial distribution of the Japanese encephalitis vector, Culex tritaeniorhynchus Giles, 1901 (Diptera: Culicidae) within areas of Japanese encephalitis risk

    Parasites & Vectors 10(1) 148.

    Background Japanese encephalitis (JE) is one of the most significant aetiological agents of viral encephalitis in Asia. This medically important arbovirus is primarily spread from vertebrate hosts to humans by the mosquito vector Culex tritaeniorhynchus. Knowledge of the contemporary distribution of this vector species is lacking, and efforts to define areas of disease risk greatly depend on a thorough understanding of the variation in this mosquito’s geographical distribution. Results We assembled a contemporary database of Cx. tritaeniorhynchus presence records within Japanese encephalitis risk areas from formal literature and other relevant resources, resulting in 1,045 geo-referenced, spatially and temporally unique presence records spanning from 1928 to 2014 (71.9% of records obtained between 2001 and 2014). These presence data were combined with a background dataset capturing sample bias in our presence dataset, along with environmental and socio-economic covariates, to inform a boosted regression tree model predicting environmental suitability for Cx. tritaeniorhynchus at each 5 × 5 km gridded cell within areas of JE risk. The resulting fine-scale map highlights areas of high environmental suitability for this species across India, Nepal and China that coincide with areas of high JE incidence, emphasising the role of this vector in disease transmission and the utility of the map generated. Conclusions Our map contributes towards efforts determining the spatial heterogeneity in Cx. tritaeniorhynchus distribution within the limits of JE transmission. Specifically, this map can be used to inform vector control programs and can be used to identify key areas where the prevention of Cx. tritaeniorhynchus establishment should be a priority.

    Keywords: Culex tritaeniorhynchus, Ecological surveillance, Insect vectors, Species distribution model

  • Luo X, Hu Q, Zhou P, Zhang D, Wang Q, Abbott R et al. (2017)

    Chasing ghosts: Allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor

    Molecular Ecology.

    Reconstructing the origin of a polyploid species is particularly challenging when an ancestor has become extinct. Under such circumstances the extinct donor of a genome found in the polyploid may be treated as a ‘ghost’ species in that its prior existence is recognised through the presence of its genome in the polyploid. In this study, we aimed to determine the polyploid origin of Oxyria sinensis (2n=40) for which only one congeneric species is known, i.e. diploid O. digyna (2n=14). Genomic in situ hybridization (GISH), transcriptome, phylogenetic and demographic analyses, and ecological niche modeling were conducted for this purpose. GISH revealed that O. sinensis comprised 14 chromosomes from O. digyna and 26 chromosomes from an unknown ancestor. Transcriptome analysis indicated that following divergence from O. digyna, involving genome duplication around 12 million years ago (Ma), a second genome duplication occurred approximately 6 Ma to give rise to O. sinensis. Oxyria sinensis was shown to contain homologous gene sequences divergent from those present in O. digyna in addition to a set that clustered with those in O. digyna. Coalescent simulations indicated that O. sinensis expanded its distribution approximately 6-7 Ma, possibly following the second polyploidization event, whereas O. digyna expanded its range much later. It was also indicated that the distributions of both species contracted and re-expanded during the Pleistocene climatic oscillations. Ecological niche modeling similarly suggested that both species experienced changes in their distributional ranges in response to Quaternary climatic changes. The extinction of the unknown ‘ghost’ tetraploid species implicated in the origin of O. sinensis could have resulted from superior adaptation of O. sinensis to repeated climatic changes in the region where it now occurs.

    Keywords: GISH, Oxyria, allopolyploid speciation, demographic history, ghost species, transcriptome