Uses of GBIF in scientific research

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

List of publications

  • Abdi, A.

    Integrating Open Access Geospatial Data to Map the Habitat Suitability of the Declining Corn Bunting (Miliaria calandra)

    (Journal name unavailable from Mendeley API. To be updated soon...)

    The efficacy of integrating open access geospatial data to produce habitat suitability maps for the corn bunting (Miliaria calandra) was investigated. Landsat Enhanced Thematic Mapper Plus (ETM+), Shuttle Radar Topography Mission (SRTM) and Corine (Coordination of Information on the Environment) land cover data for the year 2000 (CLC2000) were processed to extract explanatory variables and divided into three sets; Satellite (ETM+, SRTM), CLC2000 and Combined (CLC2000 + Satellite). Presence-absence data for M. calandra, collected during structured surveys for the Catalan Breeding Bird Atlas, were provided by the Catalan Ornithological Institute. The dataset was partitioned into an equal number of presence and absence points by dividing it into five groups, each composed of 88 randomly selected presence points to match the number of absences. A logistic regression model was then built for each group. Models were evaluated using area under the curve (AUC) of the receiver operating characteristic (ROC). Results of the five groups were averaged to produce mean Satellite, CLC2000 and Combined models. The mean AUC values were 0.69, 0.81 and 0.90 for the CLC2000, Satellite and the Combined model, respectively. The probability of M. calandra presence had the strongest positive correlation with land surface temperature, modified soil adjusted vegetation index, coefficient of variation for ETM+ band 5 and the fraction of non-irrigated arable land.

    Keywords: agricultural intensification, Corine land cover, corn bunting, Landsat, Miliaria calandra, open access data, open source geospatial software, species distribution modeling


  • Bartomeus, I., Park, M., Gibbs, J., Danforth, B., Lakso, A., Winfree, R.

    Biodiversity ensures plant-pollinator phenological synchrony against climate change

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Climate change has the potential to alter the phenological synchrony between interacting mutualists, such as plants and their pollinators. However, high levels of biodiversity might buffer the negative effects of species-specific phenological shifts and maintain synchrony at the community level, as predicted by the bio- diversity insurance hypothesis. Here, we explore how biodiversity might enhance and stabilise phenological synchrony between a valuable crop, apple and its native pollinators. We combine 46 years of data on apple flowering phenology with historical records of bee pollinators over the same period. When the key apple pollinators are considered altogether, we found extensive synchrony between bee activity and apple peak bloom due to complementarity among bee species’ activity periods, and also a stable trend over time due to differential responses to warming climate among bee species. A simulation model confirms that high biodiversity levels can ensure plant–pollinator phenological synchrony and thus pollination function. Keywords

    Keywords: bees, crop pollination, ecosystem function, ecosystem services, phenology, pollination, response diversity, stabilising mechanism


  • Cárdenas, P., Rapp, H., Klitgaard, A., Best, M., Thollesson, M., Tendal, O.

    Taxonomy, biogeography and DNA barcodes of Geodia species (Porifera, Demospongiae, Tetractinellida) in the Atlantic boreo-arctic region

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Geodia species north of 60°N in the Atlantic appeared in the literature for the first time when Bowerbank described Geodia barretti and G. macandrewii in 1858 from western Norway. Since then, a number of species have been based on material from various parts of the region: G. simplex, Isops phlegraei, I. pallida, I. sphaeroides, Synops pyriformis, G. parva, G. normani, G. atlantica, Sidonops mesotriaena (now called G. hentscheli), and G. simplicissima. In addition to these 12 nominal species, four species described from elsewhere are claimed to have been identified in material from the northeast Atlantic, namely G. nodastrella and G. cydonium (and its synonyms Cydonium muelleri and Geodia gigas). In this paper, we revise the boreo-arctic Geodia species using morphological, molecular, and biogeographical data. We notably compare northwest and northeast Atlantic specimens. Biological data (reproduction, biochemistry, microbiology, epibionts) for each species are also reviewed. Our results show that there are six valid species of boreo-arctic Atlantic Geodia while other names are synonyms or mis-identifications. Geodia barretti, G. atlantica, G. macandrewii, and G. hentscheli are well established and widely distributed. The same goes for Geodia phlegraei, but this species shows a striking geographical and bathymetric variation, which led us to recognize two species, G. phlegraei and G. parva (here resurrected). Some Geodia are arctic species (G. hentscheli, G. parva), while others are typically boreal (G. atlantica, G. barretti, G. phlegraei, G. macandrewii). No morphological differences were found between specimens from the northeast and northwest Atlantic, except for G. parva. The Folmer cytochrome oxidase subunit I (COI) fragment is unique for every species and invariable over their whole distribution range, except for G. barretti which had two haplotypes. 18S is unique for four species but cannot discriminate G. phlegraei and G. parva. Two keys to the boreo-arctic Geodia are included, one based on external morphology, the other based on spicule morphology.

    Keywords: amphi-Atlantic, atlantica, barretti, Geodiidae, hentscheli, macandrewii, parva, phlegraei, sponge ground


  • Foote, A., Kaschner, K., Schultze, S., Garilao, C., Ho, S., Post, K., Higham, T., Stokowska, C., van der Es, H., Embling, C., Gregersen, K., Johansson, F., Willerslev, E., Gilbert, M.

    Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts

    Nature communications 4 1677.

    The climatic changes of the glacial cycles are thought to have been a major driver of population declines and species extinctions. However, studies to date have focused on terrestrial fauna and there is little understanding of how marine species responded to past climate change. Here we show that a true Arctic species, the bowhead whale (Balaena mysticetus), shifted its range and tracked its core suitable habitat northwards during the rapid climate change of the Pleistocene–Holocene transition. Late Pleistocene lineages survived into the Holocene and effective female population size increased rapidly, concurrent with a threefold increase in core suitable habitat. This study highlights that responses to climate change are likely to be species specific and difficult to predict. We estimate that the core suitable habitat of bowhead whales will be almost halved by the end of this century, potentially influencing future population dynamics.

    Keywords: amphi-Atlantic, atlantica, barretti, Geodiidae, hentscheli, macandrewii, parva, phlegraei, sponge ground


  • Humphreys, A., Linder, H.

    Evidence for recent evolution of cold tolerance in grasses suggests current distribution is not limited by (low) temperature.

    The New phytologist.

    Temperature is considered an important determinant of biodiversity distribution patterns. Grasses (Poaceae) occupy among the warmest and coldest environments on earth but the role of cold tolerance evolution in generating this distribution is understudied. We studied cold tolerance of Danthonioideae (c. 280 species), a major constituent of the austral temperate grass flora. We determined differences in cold tolerance among species from different continents grown in a common winter garden and assessed the relationship between measured cold tolerance and that predicted by species ranges. We then used temperatures in current ranges and a phylogeny of 81% of the species to study the timing and mode of cold tolerance evolution across the subfamily. Species ranges generally underestimate cold tolerance but are still a meaningful representation of differences in cold tolerance among species. We infer cold tolerance evolution to have commenced at the onset of danthonioid diversification, subsequently increasing in both pace and extent in certain lineages. Interspecific variation in cold tolerance is better accounted for by spatial than phylogenetic distance. Contrary to expectations, temperature - low temperature in particular - appears not to limit the distribution of this temperate clade. Competition, time or dispersal limitation could explain its relative absence from northern temperate regions.

    Keywords: cold tolerance, danthonioideae, distribution, frost tolerance, grasses, niche evolution, poaceae, temperature


  • Jansson, R., Rodríguez-Castañeda, G., Harding, L.

    What can multiple phylogenies say about the latitudinal diversity gradient? A new look at the tropical conservatism, out of the tropics, and diversification rate hypotheses

    (Journal name unavailable from Mendeley API. To be updated soon...)

    We reviewed published phylogenies and selected 111 ones representing mammals, birds, insects and flowering plants. We then mapped the latitudinal range of all taxa to test the relative importance of the tropical conservatism, out-of-the-tropics and diversification rate hypotheses in generating latitudinal diversity gradients. Most clades originated in the tropics, with diversity peaking in the zone of origin. Transitions of lineages between latitudinal zones occurred at 16–22% of the tree nodes. The most common type of transition was range expansions of tropical lineages to encompass also temperate latitudes. Thus, adaptation to new climatic conditions may not represent a major obstacle for many clades. These results contradict predictions of the tropical conservatism hypothesis (i.e., few clades colonizing extratropical latitudes), but support the out-of-the-tropics model (i.e., tropical originations and subsequent latitudinal range expansions). Our results suggest no difference in diversification between tropical and temperate sister lineages; thus, diversity of tropical clades was not explained by higher diversification rates in this zone. Moreover, lineages with latitudinal stasis diversified more compared to sister lineages entering a new latitudinal zone. This preserved pre-existing diversity differences between latitudinal zones and can be considered a new mechanism for why diversity tends to peak in the zone of origin.

    Keywords: ancestral area reconstruction, evolutionary time, latitudinal zone transitions, sister group analysis, tropical origination


  • Johansson, V., Ranius, T., Snäll, T.

    Epiphyte metapopulation persistence after drastic habitat decline and low tree regeneration: time-lags and effects of conservation actions

    Journal of Applied Ecology 50(2) 414-422.

    1. Old trees have declined in Europe due to agricultural intensification and forestry. For shade-intolerant epiphytic species occurring on old trees in semi-open landscapes, host tree numbers have further decreased because of shading by developing secondary woodland. Moreover, in this habitat, regeneration that could replace the extant old trees is low. This suggests that epiphytic species associated with old trees are declining. However, for species with low extinction rates, the decline may be slow and hard to elucidate. 2. We investigated the persistence of five old-oak-associated epiphytic lichens with different traits by simulating metapopulation dynamics using Bayesian incidence function models for dynamic landscapes. With an oak-rich landscape as a reference, we investigated effects of (i) drastic habitat decline, (ii) conservation actions such as clearing around trees or increased regeneration rate, (iii) low tree regeneration and (iv) clearing and increased regeneration after 100 years of low regeneration. 3. After drastic habitat decline, the number of occupied trees continued to decrease, display- ing long time-lags before reaching new metapopulation equilibriums. Lichen extinction risks increased with decreasing habitat and were highest for species that only colonise very old trees or have large dispersal propagules. In landscapes with low tree densities, conservation actions had only minor effects on lichen extinction risks. 4. Low tree regeneration rates increased lichen extinction risks, but species declines were slow. Conservation actions that increased regeneration after 100 years of low regeneration decreased the extinction risks to very low levels. 5. Synthesis and applications. Due to low rates of local extinction, epiphytes display long time-lags to reach new equilibriums after habitat loss. Thus, we should expect ongoing declines in epiphyte metapopulations in landscapes where old trees have recently declined. Slow extinction gives an opportunity to improve persistence by conservation actions, but the success depends on species traits and the current density of old trees. In landscapes with many old but few young trees, epiphytes may persist if conservation actions quickly address the need to increase tree regeneration rates. The best conservation approach for long-term persistence of epiphytic lichens is to ensure regular tree regeneration in landscapes with a cur- rent high density of old trees.

    Keywords: colonisation, extinction, lichens, management, Quercus, species traits, tree age structure


  • Peter Linder, H., Antonelli, A., Humphreys, A., Pirie, M., Wüest, R.

    What determines biogeographical ranges? Historical wanderings and ecological constraints in the danthonioid grasses

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Aim We sought to understand the variables that limit the distribution range of a clade (here the danthonioid grasses). We tested time, area of origin, habitat suitability, disjunction width and nature, and wind direction as possible range determinants. Location Global, but predominantly the Southern Hemisphere. Methods We mapped the range of the subfamily Danthonioideae, and used 39,000 locality records and an ensemble modelling approach to define areas with suitable danthonioid habitat. We used a well-sampled, dated phylogeny to estimate the number and direction of historical dispersal events, based on parsimony optimization. We tested for the impact of wind direction on dispersal rate using a likelihood approach, and for the effects of barrier width with a regression approach. Results We found 17 geographically isolated areas with suitable habitats for danthonioids. All currently suitable Southern Hemisphere areas have been occupied, but three apparently suitable areas in the Northern Hemisphere have not. We infer that southern Africa was first occupied in the Oligocene and that dispersal to the other areas was initiated in the middle Miocene. Inferred dispersal rate was correlated with the width of the disjunctions, up to a distance of 5000 km. There was no support for wind direction having influenced differences in dispersal rate. Main conclusions The current range of the Danthonioideae can be predicted ecologically (areas with suitable habitat) and historically (the width of the disjunctions separating the areas with suitable habitat and the area of origin). The direction of dispersal is dictated by the area of origin and by serendipity: there is no evidence for general patterns of dispersal, for example for dispersal occurring more frequently over land than over sea or in an easterly versus a westerly direction around the Southern Hemisphere. Thus the range and range-filling of Danthonioideae can be accounted for by surprisingly few variables: habitat suitability, distance between suitable areas, and area of origin.

    Keywords: Areas of endemism, biogeography, Danthonioideae, dispersal rate, lag time, long-distance dispersal, ocean width, Poaceae, West Wind Drift


  • Seth, H., Gräns, A., Sandblom, E., Olsson, C., Wiklander, K., Johnsson, J., Axelsson, M.

    Metabolic scope and interspecific competition in sculpins of greenland are influenced by increased temperatures due to climate change.

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Ongoing climate change has led to an increase in sea surface temperatures of 2-4°C on the west coast of Greenland. Since fish are ectothermic, metabolic rate increases with ambient temperature. This makes these animals particularly sensitive to changes in temperature; subsequently any change may influence their metabolic scope, i.e. the physiological capacity to undertake aerobically challenging activities. Any temperature increase may thus disrupt species-specific temperature adaptations, at both the molecular level as well as in behavior, and concomitant species differences in the temperature sensitivity may shift the competitive balance among coexisting species. We investigated the influence of temperature on metabolic scope and competitive ability in three species of marine sculpin that coexist in Greenland coastal waters. Since these species have different distribution ranges, we hypothesized that there should be a difference in their physiological response to temperature; hence we compared their metabolic scope at three temperatures (4, 9 and 14°C). Their competitive ability at the ambient temperature of 9°C was also tested in an attempt to link physiological capacity with behaviour. The Arctic staghorn sculpin, the species with the northernmost distribution range, had a lower metabolic scope in the higher temperature range compared to the other two species, which had similar metabolic scope at the three temperatures. The Arctic staghorn sculpin also had reduced competitive ability at 9°C and may thus already be negatively affected by the current ocean warming. Our results suggest that climate change can have effects on fish physiology and interspecific competition, which may alter the species composition of the Arctic fish fauna.

    Keywords: Areas of endemism, biogeography, Danthonioideae, dispersal rate, lag time, long-distance dispersal, ocean width, Poaceae, West Wind Drift


  • Chen, D., Zhang, X., Kang, H., Sun, X., Yin, S., Du, H., Yamanaka, N., Gapare, W., Wu, H., Liu, C.

    Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations.

    PLoS ONE 7(10) e47268.

    The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N(ST = )0.751> G(ST = )0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu's F(S) indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.

    Keywords: Areas of endemism, biogeography, Danthonioideae, dispersal rate, lag time, long-distance dispersal, ocean width, Poaceae, West Wind Drift