Uses of GBIF in scientific research

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

List of publications

  • Pellissier L, Eidesen P, Ehrich D, Descombes P, Schönswetter P, Tribsch A et al. (2015)

    Past climate-driven range shifts and population genetic diversity in arctic plants

    Journal of Biogeography.

    Aim High intra-specific genetic diversity is necessary for species adaptation to novel environments under climate change, but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here, we investigated the relationship between range shift since the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses. Location: The circumpolar Arctic and northern temperate alpine ranges. Methods: We estimated the climatic niches of 30 cold-adapted plant species using range maps coupled with species distribution models and hindcasted species suitable areas to reconstructions of the mid-Holocene and LGM climates. We computed the species-specific migration distances from the species glacial refugia to their current distribution and correlated distances to extant genetic diversity in 1295 populations. Differential responses among species were related to life-history traits. Results: We found a negative association between inferred migration distances from refugia and genetic diversities in 25 species, but only 11 had statistically significant negative slopes. The relationships between inferred distance and population genetic diversity were steeper for insect-pollinated species than wind-pollinated species, but the difference among pollination system was marginally independent from phylogenetic autocorrelation. Main conclusion: The relationships between inferred migration distances and genetic diversities in 11 species, independent from current isolation, indicate that past range shifts were associated with a genetic bottleneck effect with an average of 21% loss of genetic diversity per 1000 km−1. In contrast, the absence of relationship in many species also indicates that the response is species specific and may be modulated by plant pollination strategies or result from more complex historical contingencies than those modelled here.

    Keywords: Arctic plants, Last Glacial Maximum, climate change, climatic niche, migration, species distribution models

  • Wasof S, Lenoir J, Aarrestad P, Alsos I, Armbruster W, Austrheim G et al. (2015)

    Disjunct populations of European vascular plant species keep the same climatic niches

    Global Ecology and Biogeography.

    Aim Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been separated for thousands of years. Location European Alps and Fennoscandia. Methods Of the studied pool of 888 terrestrial vascular plant species occurring in both the Alps and Fennoscandia, we used two complementary approaches to test and quantify climatic-niche shifts for 31 species having strictly disjunct populations and 358 species having either a contiguous or a patchy distribution with distant populations. First, we used species distribution modelling to test for a region effect on each species' climatic niche. Second, we quantified niche overlap and shifts in niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) within a bi-dimensional climatic space. Results Only one species (3%) of the 31 species with strictly disjunct populations and 58 species (16%) of the 358 species with distant populations showed a region effect on their climatic niche. Niche overlap was higher for species with strictly disjunct populations than for species with distant populations and highest for arctic–alpine species. Climatic niches were, on average, wider and located towards warmer and wetter conditions in the Alps. Main conclusion Climatic niches seem to be generally conserved between populations that are separated between the Alps and Fennoscandia and have probably been so for 10,000–15,000 years. Therefore, the basic assumption of species distribution models that a species' climatic niche is constant in space and time – at least on time scales 104 years or less – seems to be largely valid for arctic–alpine plants.

    Keywords: Alpine plants, arctic plants, climatic niche, disjunct distribution, distant populations, niche conservatism, niche optimum, niche overlap, niche width, species distribution modelling

  • Brito J, Godinho R, Martínez-Freiría F, Pleguezuelos J, Rebelo H, Santos X et al. (2014)

    Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel

    Biological Reviews of the Cambridge Philosophical Society 89(1) 215-31.

    Deserts and arid regions are generally perceived as bare and rather homogeneous areas of low diversity. The Sahara is the largest warm desert in the world and together with the arid Sahel displays high topographical and climatic heterogeneity, and has experienced recent and strong climatic oscillations that have greatly shifted biodiversity distribution and community composition. The large size, remoteness and long-term political instability of the Sahara-Sahel, have limited knowledge on its biodiversity. However, over the last decade, there have been an increasing number of published scientific studies based on modern geomatic and molecular tools, and broad sampling of taxa of these regions. This review tracks trends in knowledge about biodiversity patterns, processes and threats across the Sahara-Sahel, and anticipates needs for biodiversity research and conservation. Recent studies are changing completely the perception of regional biodiversity patterns. Instead of relatively low species diversity with distribution covering most of the region, studies now suggest a high rate of endemism and larger number of species, with much narrower and fragmented ranges, frequently limited to micro-hotspots of biodiversity. Molecular-based studies are also unravelling cryptic diversity associated with mountains, which together with recent distribution atlases, allows identifying integrative biogeographic patterns in biodiversity distribution. Mapping of multivariate environmental variation (at 1 km × 1 km resolution) of the region illustrates main biogeographical features of the Sahara-Sahel and supports recently hypothesised dispersal corridors and refugia. Micro-scale water-features present mostly in mountains have been associated with local biodiversity hotspots. However, the distribution of available data on vertebrates highlights current knowledge gaps that still apply to a large proportion of the Sahara-Sahel. Current research is providing insights into key evolutionary and ecological processes, including causes and timing of radiation and divergence for multiple taxa, and associating the onset of the Sahara with diversification processes for low-mobility vertebrates. Examples of phylogeographic patterns are showing the importance of allopatric speciation in the Sahara-Sahel, and this review presents a synthetic overview of the most commonly hypothesised diversification mechanisms. Studies are also stressing that biodiversity is threatened by increasing human activities in the region, including overhunting and natural resources prospection, and in the future by predicted global warming. A representation of areas of conflict, landmines, and natural resources extraction illustrates how human activities and regional insecurity are hampering biodiversity research and conservation. Although there are still numerous knowledge gaps for the optimised conservation of biodiversity in the region, a set of research priorities is provided to identify the framework data needed to support regional conservation planning.

    Keywords: Africa, Sahara, Sahel, biodiversity, climate change, conservation, deserts, distribution, diversification, phylogeography

  • Mathew C, Güntsch A, Obst M, Vicario S, Haines R, Williams A et al. (2014)

    A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control

    Biodiversity Data Journal 2(2) e4221.

    The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.

    Keywords: biodiversity informatics, data cleaning, e-Science, service oriented architecture, web services, workflows

  • Meller L, Cabeza M, Pironon S, Barbet-Massin M, Maiorano L, Georges D et al. (2014)

    Ensemble distribution models in conservation prioritization: from consensus predictions to consensus reserve networks.

    Diversity & distributions 20(3) 309-321.

    AIM: Conservation planning exercises increasingly rely on species distributions predicted either from one particular statistical model or, more recently, from an ensemble of models (i.e. ensemble forecasting). However, it has not yet been explored how different ways of summarizing ensemble predictions affect conservation planning outcomes. We evaluate these effects and compare commonplace consensus methods, applied before the conservation prioritization phase, to a novel method that applies consensus after reserve selection. LOCATION: Europe. METHODS: We used an ensemble of predicted distributions of 146 Western Palaearctic bird species in alternative ways: four different consensus methods, as well as distributions discounted with variability, were used to produce inputs for spatial conservation prioritization. In addition, we developed and tested a novel method, in which we built 100 datasets by sampling the ensemble of predicted distributions, ran a conservation prioritization analysis on each of them and averaged the resulting priority ranks. We evaluated the conservation outcome against three controls: (i) a null control, based on random ranking of cells; (2) the reference solution, based on an expert-refined dataset; and (3) the independent solution, based on an independent dataset. RESULTS: Networks based on predicted distributions were more representative of rare species than randomly selected networks. Alternative methods to summarize ensemble predictions differed in representativeness of resulting reserve networks. Our novel method resulted in better representation of rare species than pre-selection consensus methods. MAIN CONCLUSIONS: Retaining information about the variation in the predicted distributions throughout the conservation prioritization seems to provide better results than summarizing the predictions before conservation prioritization. Our results highlight the need to understand and consider model-based uncertainty when using predicted distribution data in conservation prioritization.

    Keywords: consensus predictions, conservation planning, efficiency, optimization, rare species, systematic, uncertainty

  • Nuutinen V, Butt K, Jauhiainen L, Shipitalo M, Sirén T (2014)

    Dew-worms in white nights: High-latitude light constrains earthworm (Lumbricus terrestris) behaviour at the soil surface

    Soil Biology and Biochemistry 72 66-74.

    Soil is an effective barrier to light penetration that limits the direct influence of light on belowground organisms. Variation in aboveground light conditions, however, is important to soil-dwelling animals that are periodically active on the soil surface. A prime example is the earthworm Lumbricus terrestris L. (the dew-worm), an ecosystem engineer that emerges nocturnally on the soil surface. In the summer, the northernmost populations of L. terrestris are exposed to a time interval with no daily dark period. During a two-week period preceding the summer solstice, we studied the constraints that boreal night illumination imposes on L. terrestris surface activity by comparing their behaviour under ambient light with artificially-induced darkness. Looking for evidence of geographical divergence in light response, we compared the behaviour of native L. terrestris (Jokioinen, S–W Finland; 60°48′N) with two markedly more southern populations, from Preston (Lancashire, UK; 53°47′N) and Coshocton (Ohio, USA; 40°22′N) where the nights have a period of darkness throughout the year (total latitudinal range ca. 2300 km). Under ambient light conditions, L. terrestris emergence on the soil surface was diminished by half compared with the darkened treatment and it peaked at the darkest period of the night. Also mating rate decreased considerably under ambient light. The native dew-worms were generally the most active under ambient light. They emerged earlier in the evening and ceased their activity later in the morning than dew-worms from the two more southerly populations. The differences in behaviour were, however, significant mainly between native and UK dew-worms. In the darkened treatment, the behaviour of the three earthworm origins did not differ. Under the experimental conditions light condition was the dominant environmental factor controlling surface activity, but elevated night-time air temperature and humidity also encouraged dew-worm emergence without discernible differences among geographical origins. Our results show, that in boreal summer, the high level of night illumination strongly limits soil-surface activity of dew-worms. Considering the important regulatory role of L. terrestris in many ecosystem processes, this can have significant corollaries in dew-worm impacts on the environment. Although evidence for geographical differentiation in behaviour was obtained, the results point to phenotypic flexibility in L. terrestris light response.

    Keywords: consensus predictions, conservation planning, efficiency, optimization, rare species, systematic, uncertainty

  • Virtanen R (2014)

    Diaspore and shoot size as drivers of local, regional and global bryophyte distributions

    Global Ecology and Biogeography 23(6) 610-619.

    Aim: Ecological theory provides divergent views about how patterns of bryophyte occurrence are related from local to global scales. Here, I test the hypotheses that, based on the high dispersal capacity of bryophytes, patterns of occurrence are similar fromlocal to global scales and independent of variation in diaspore and size traits, or alternatively that the patterns are dissimilar and depend on traits that are important for dispersal and competition. Location: Global. Methods: The occurrence patterns of 28 bryophyte species and their relationship to diaspore and shoot size were analysed for three study systems: (1) a local metacommunity on erratic calcareous boulders; (2) a regional study system in the biogeographical provinces of the Nordic countries; and (3) based on data available from the Global Biodiversity Information Facility (GBIF). Results: Contrary to expectations, bryophyte occurrence was not similar among local or global study systems, but regional occurrences matched both local and global occurrences. Contrary to neutral theoretical assumptions, the occurrences depended on traits. In the local metacommunity, there was a tendency towards a negative relationship between occurrence and diaspore size: small and large species tended to be rare, whereas species of intermediate size tended to be widespread. In the regional study system, species with large diaspores tended to be widespread, with frequency of occurrence positively correlated with shoot length. Main conclusions: In contrast to patterns detected for micro-organisms, local and global frequencies of occurrence for bryophytes are not necessarily similar. However, occurrences at the regional scale may be useful for predicting both local and global occurrences. Links between species traits important for dispersal and competition on the one hand, and occurrences on the other, supports the utility of these traits for the analysis of distributions and questions the adequacy of assump- tions of functional equivalence.

    Keywords: Dispersal, GBIF, occupancy, rarity, size, spore

  • Schigel D (2012)

    Fungivory and host associations of Coleoptera: a bibliography and review of research approaches

    Mycology: An International Journal on Fungal Biology 3(4) 258-272.

    Fungi and Coleoptera are among the most evolutionarily successful and diverse heterotrophic organisms in the world. Due to their unique adaptive capacities, fungi and beetles co-occur and interact in various terrestrial habitats. In addition to commensal and mutualistic fungus–beetle relations, combative interactions involve aggressors from both sides such as entomopathogenic fungi and fungivorous beetles. Fungivory, most commonly in combination with saprophagy and xylophagy, is characteristic of many families of Coleoptera. The resource-exploiting fungal mycelia are most frequently consumed by beetles together with the woody substrata. The focus of the present review is on Coleoptera with larvae or adults feeding on a primarily fungal diet: fruit bodies and spores.

    Keywords: Dispersal, GBIF, occupancy, rarity, size, spore

  • Todisco V, Gratton P, Zakharov E, Wheat C, Sbordoni V, Sperling F (2012)

    Mitochondrial phylogeography of the Holarctic Parnassius phoebus complex supports a recent refugial model for alpine butterflies

    Journal of Biogeography 39(6) 1058-1072.

    the Holarctic distribution of the P. phoebus complex. A global species distribution model (SDM) was calculated by the maximum entropy (Maxent) approach, allowing assignment of samples into geographically consistent ‘operational’ units. Phylogenetic and coalescent methods were applied to describe the global mitogenetic structure and estimate population genetics parameters. Geological and palaeoecological evidence was used for internal calibration and validation of a COI substitution rate. Results Eurasian (including Alaskan) and North American populations form two distinct mitochondrial clades. The mitochondrial time to most recent common ancestor (TMRCA) of the North American clade was estimated at less than 125 ka, and the TMRCA of the Eurasian–Alaskan clade at less than 80 ka, except for a single divergent sequence from Mongolia. Pairwise divergence times between all geographical units within each continent date well within the last 100 ka, and most likely, the last 50–10 ka. Main conclusions In contrast with its currently scattered distribution within each of Eurasia and North America, the mitogenetic structure of the P. phoebus complex in both continents is shallow and weak, and shows no evidence of geographical structure dating back earlier than the last glacial cycle. We argue that mtDNA data are consistent with recent range expansion across each of the two continents and with persistent glacial long-range gene flow which ceased during the Holocene. We propose that P. phoebus may represent a model for Holarctic alpine invertebrates with moderate dispersal abilities in that its genetic structure at a continental scale reflects extensive connectivity during the most recent glacial phases.

    Keywords: Alpine butterflies, Parnassius, coalescent, correspondence, glacial cycles, holarctic, mtDNA, phylogeography, substitution rates, valentina todisco

  • Huettmann F, Artukhin Y, Gilg O, Humphries G (2011)

    Predictions of 27 Arctic pelagic seabird distributions using public environmental variables, assessed with colony data: a first digital IPY and GBIF open access synthesis platform

    Marine Biodiversity 41(1) 141-179.

    We present a first compilation, quantification and summary of 27 seabird species presence data for north of the Arctic circle (>66 degrees latitude North) and the ice-free period (summer). For species names, we use several taxonomically valid online databases [Integrated Taxonomic Information System (ITIS), AviBase, 4 letter species codes of the American Ornithological Union (AOU), The British List 2000, taxonomic serial numbers TSNs, World Register of Marine Species (WORMS) and APHIA ID] allowing for a compatible taxonomic species cross-walk, and subsequent applications, e.g., phylogenies. Based on the data mining and machine learning RandomForest algorithm, and 26 environmental publicly available Geographic Information Systems (GIS) layers, we built 27 predictive seabird models based on public open access data archives such as the Global Biodiversity Information Facility (GBIF), North Pacific Pelagic Seabird Database (NPPSD) and PIROP database (in OBIS-Seamap). Model-prediction scenarios using pseudo-absence and expert-derived absence were run; aspatial and spatial model assessment metrics were applied. Further, we used an additional species model performance metric based on the best publicly available Arctic seabird colony location datasets compiled by the authors using digital and literature sources. The obtained models perform reasonably: from poor (only a few coastal species with low samples) to very high (many pelagic species). In compliance with data policies of the International Polar Year (IPY) and similar initiatives, data and models are documented with FGDC NBII metadata and publicly available online for further improvement, sustainability applications, synergy, and intellectual explorations in times of a global biodiversity, ocean and Arctic crisis.

    Keywords: Arctic biodiversity, Circumpolar seabird colonies, Data mining synthesis, GIS (Geographic Information System), Global Biodiversity Information Facility (GBIF), International Polar Year (IPY), Open access online databases, Pelagic circumpolar seabird distribution