Uses of GBIF in scientific research

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

List of publications

  • Fournier A, Sullivan A, Bump J, Perkins M, Shieldcastle M, King S (2016)

    Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail

    Journal of Applied Ecology.

    1.Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution, or movement patterns can ameliorate this limitation but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments. 2.We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional on species distribution models constructed from citizen scientist observations. To illustrate this approach, we analysed the migratory connectivity of the Virginia rail Rallus limicola, a secretive and declining migratory game bird in North America. 3.Citizen science observations enabled both estimation of sampling bias and construction of bias-corrected species distribution models. Conditioning δD assignments on these species distribution models yielded comparably high-resolution assignments. 4.Most Virginia rails wintering across five Gulf Coast sites spent the previous summer near the Great Lakes, although a considerable minority originated from the Chesapeake Bay watershed or Prairie Pothole region of North Dakota. Conversely, the majority of migrating Virginia rails from a site in the Great Lakes most likely spent the previous winter on the Gulf Coast between Texas and Louisiana. 5.Synthesis and applications. In this analysis Virginia rail migratory connectivity does not fully correspond to the administrative flyways used to manage migratory birds. This example demonstrates that with the increasing availability of citizen science data to create species distribution models, our framework can produce high-resolution estimates of migratory connectivity for many animals, including cryptic species. Empirical evidence of links between seasonal habitats will help enable effective habitat management, hunting quotas, and population monitoring and also highlight critical knowledge gaps.

    Keywords: Bayesian, Virginia rail Rallus limicola, citizen science, eBird, feathers, hydrogen isotopes, migration, migratory connectivity, species distribution model (SDM), δD animal origins

  • Jia S, Zhang M, Raab-Straube E, Thulin M (2016)

    Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia

    Biological Journal of the Linnean Society.

    Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid-late Miocene significantly affected the diversification of the genus in these areas.

    Keywords: 2016, CN, China, DE, GBIF_used, Germany, SE, Sweden, phylogenetic analysis, phylogenetics

  • Lagomarsino L, Condamine F, Antonelli A, Mulch A, Davis C (2016)

    The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae).

    The New phytologist.

    The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in driving diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 million yr. Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world's biodiversity.

    Keywords: Andes, Lobelioideae, Neotropics, biodiversity hotspot, climate change, diversification, pollination syndromes, rapid radiation

  • Nylinder S, Razafimandimbison S, Anderberg A (2016)

    From the Namib around the world: biogeography of the Inuleae-Plucheinae (Asteraceae)

    Journal of Biogeography.

    Aim We investigated the historical biogeography of the Inuleae–Plucheinae (Asteraceae), a group of arid-adapted plants with partly unresolved generic circumscriptions, in order to understand its origin and spatiotemporal evolutionary history in relation to the Cenozoic climate shifts. Location Global, with highest species diversity in the Southern Hemisphere. Methods The spatiotemporal biogeography of the Plucheinae was estimated by both a discrete method using a set of general distribution areas, and a relaxed random walk based on extant species distributions. The topology was time calibrated using a combination of secondary node ages and secondary derived rates for included loci. Results Our results indicate the median age of the Plucheinae to be approximately 15.4 Ma. The biogeographical analyses infer an ancestral origin in southern Africa, with the relaxed random walk analysis narrowing the uncertainty down to an area reaching from coastal Namibia to the western Kalahari. Africa was colonized in a (south)western–(north)eastern direction following the spread of arid habitats. Ancestral representatives of the Plucheinae colonized South America on at least three separate occasions (13.0–4.0, 4.3–3.1 and 4.1–3.7 Ma), with one subsequent spread to North America. Australia was colonized three times between 3.6 and 0.4 Ma. Madagascar and the Mascarenes were colonized at least seven times. Main conclusions The origin of the Plucheinae is estimated to the Namib region, with early speciations and radiations concurring with the timing of aridification of southern Africa, following the increase in strength of the Antarctic Circumpolar Current and subsequent formation of the Benguela Upwelling at c. 11.8 Ma. The current biogeographical distribution of the Plucheinae is best explained by several Neogene long-distance dispersal events from tropical Africa

    Keywords: Africa, Asteraceae, Namibia, arid environment, biogeography, dispersal, molecular dating

  • Sanín M, Kissling W, Bacon C, Borchsenius F, Galeano G, Svenning J et al. (2016)

    The Neogene rise of the tropical Andes facilitated diversification of wax palms ( Ceroxylon : Arecaceae) through geographical colonization and climatic niche separation

    Botanical Journal of the Linnean Society.

    he tropical Andes are a biodiversity hotspot, partly due to their rich and complex floristic composition. A fundamental question regarding this outstanding biodiversity is what role the Andean orogeny has played in species diversification. Ceroxylon is a genus of endemic Andean palms that stands out in the palm family (Arecaceae) due to its adaptation to cold, mountainous environments. Here, we reconstruct the biogeography and climatic preference of this lineage to test the hypothesis that Andean uplift allowed diversification by providing suitable habitats along climatic and elevational gradients. Ancestral areas were reconstructed under a model allowing for founder-event speciation and climatic niches were inferred from climatic variables at present-day occurrences of all species. Niche evolution in a phylogenetic framework was evaluated by testing differences between the climatic niches of clades. Our analyses identified four main clades, with a general pattern of diversification through geographical colonization from south to north after the Pliocene uplift of the northern Andes. Adaptation to low temperatures was conserved at the generic level, with climatic niche differentiation among clades along elevational temperature gradients. We conclude that the Neogene Andean uplift has facilitated the diversification of this iconic plant group via opportunities for geographical migration and separation within its climatic niche

    Keywords: Miocene, Neotropics, cold adaptation, niche shift, phylogenetic niche conservatism, range expansion

  • Edler D, Guedes T, Zizka A, Rosvall M, Antonelli A (2015)

    Infomap Bioregions: Interactive mapping of biogeographical regions from species distributions


    Biogeographical regions reveal how species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions data. However, there are no tools that make this methodology simple and efficient to use. Here we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps. Species distributions may be provided as georeferenced point occurrences or range maps, and can be of local, regional or global scale. The application uses a novel adaptive resolution method to make best use of often incomplete species distribution data. The results can be downloaded as vector graphics, shapefiles or in table format. We validate the tool by processing large datasets of publicly available species distribution data of the world's amphibians using species ranges, and mammals using point occurrences. Potential applications include ancestral range reconstructions in historical biogeography and identification of indicator species for targeted conservation.

    Keywords: Miocene, Neotropics, cold adaptation, niche shift, phylogenetic niche conservatism, range expansion

  • Fuentes-Hurtado M, Hof A, Jansson R (2015)

    Paleodistribution modeling suggests glacial refugia in Scandinavia and out-of-Tibet range expansion of the Arctic fox

    Ecology and Evolution.

    Quaternary glacial cycles have shaped the geographic distributions and evolution of numerous species in the Arctic. Ancient DNA suggests that the Arctic fox went extinct in Europe at the end of the Pleistocene and that Scandinavia was subsequently recolonized from Siberia, indicating inability to track its habitat through space as climate changed. Using ecological niche modeling, we found that climatically suitable conditions for Arctic fox were found in Scandinavia both during the last glacial maximum (LGM) and the mid-Holocene. Our results are supported by fossil occurrences from the last glacial. Furthermore, the model projection for the LGM, validated with fossil records, suggested an approximate distance of 2000 km between suitable Arctic conditions and the Tibetan Plateau well within the dispersal distance of the species, supporting the recently proposed hypothesis of range expansion from an origin on the Tibetan Plateau to the rest of Eurasia. The fact that the Arctic fox disappeared from Scandinavia despite suitable conditions suggests that extant populations may be more sensitive to climate change than previously thought.

    Keywords: Arctic fox, Fennoscandia, Out-of-Tibet hypothesis, ecological niche modeling, last glacial maximum, refugia

  • Gough L, Sverdrup-Thygeson A, Milberg P, Pilskog H, Jansson N, Jonsell M et al. (2015)

    Specialists in ancient trees are more affected by climate than generalists

    Ecology and Evolution.

    Ancient trees are considered one of the most important habitats for biodiversity in Europe and North America. They support exceptional numbers of specialized species, including a range of rare and endangered wood-living insects. In this study, we use a dataset of 105 sites spanning a climatic gradient along the oak range of Norway and Sweden to investigate the importance of temperature and precipitation on beetle species richness in ancient, hollow oak trees. We expected that increased summer temperature would positively influence all wood-living beetle species whereas precipitation would be less important with a negligible or negative impact. Surprisingly, only oak-specialist beetles with a northern distribution increased in species richness with temperature. Few specialist beetles and no generalist beetles responded to the rise of 4°C in summer as covered by our climatic gradient. The negative effect of precipitation affected more specialist species than did temperature, whereas the generalists remained unaffected. In summary, we suggest that increased summer temperature is likely to benefit a few specialist beetles within this dead wood community, but a larger number of specialists are likely to decline due to increased precipitation. In addition, generalist species will remain unaffected. To minimize adverse impacts of climate change on this important community, long-term management plans for ancient trees are important.

    Keywords: Beetles, climate gradient, coleoptera, precipitation, saproxylic, temperature

  • Hof A, Svahlin A (2015)

    The potential effect of climate change on the geographical distribution of insect pest species in the Swedish boreal forest

    Scandinavian Journal of Forest Research 1-11.

    ABSTRACTWith the expected rising temperatures, outbreaks of insect pests may be more frequent, which can have large consequences on forest ecosystems and may therefore negatively affect the forestry sector. In order to be better able to predict where, but not if, outbreaks may occur in future we investigated the potential future (2070) geographical distribution of 30 prospective insect pest species (Coleoptera and Lepidoptera) by applying species distribution modelling. We also assessed the geographical extent to which the boreal forest in Sweden may be affected. We found that numerous species may experience large increases in their potential distribution in future, which may result in outbreaks in “new” areas. It is therefore likely that more trees will be infested by pests in future, which may have large implications for the Swedish forestry sector.

    Keywords: Norway spruce, Scots pine, climate change, forestry, insects, pests, species distribution modelling

  • Kullander S, Rahman M, Norén M, Mollah A (2015)

    Why is Pseudosphromenus cupanus (Teleostei: Osphronemidae) reported from Bangladesh, Indonesia, Malaysia, Myanmar, and Pakistan?

    Zootaxa 3990(4) 575-83.

    The native distribution of the small labyrinth fish species Pseudosphromenus cupanus includes southern India and Sri Lanka. According to literature it has a range including also Pakistan, Bangladesh, Myanmar, Malaysia, and Indonesia (Sumatra) but there are no voucher specimens or reliable observations from those areas. The distribution record of P. cupanus was inflated partly by including P. dayi as a synonym. Pseudosphronemus dayi is native to the Western Ghats in India, but the origin of the aquarium importation in 1907 was reported as both Cochin (=Kochi) and Malacca (=Malaysia), the latter locality obviously in error. The basis for the Sumatra record is an obviously mislabeled sample of P. dayi from Pulau Weh close to Sumatra. The basis for reporting the species from Pakistan, Myanmar or Bangladesh could not be located. Misidentified museum specimens from Myanmar and Pakistan identified as P. cupanus were never published on. Pseudosphromenus cupanus has been considered recently to be extinct in Bangladesh, but in fact it never occurred there.

    Keywords: Asia, Freshwater, Geographical distribution, Threat status