Uses of GBIF in scientific research

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

List of publications

  • Hens H, Jäkäläniemi A, Tali K, Efimov P, Kravchenko A, Kvist L (2017)

    Genetic structure of a regionally endangered orchid, the dark red helleborine (Epipactis atrorubens) at the edge of its distribution

    Genetica 1-13.

    The genetic structure and diversity of species is determined by both current population dynamics and historical processes. Population genetic structure at the edge of the distribution is often expected to differ substantially from populations at the centre, as these edge populations are often small and fragmented. In addition, populations located in regions that have experienced repeated glaciations throughout the Pleistocene, may still carry imprints from the genetic consequences of frequent distribution shifts. Using chloroplast DNA sequences and nuclear microsatellite markers we studied the genetic structure of Epipactis atrorubens at the northern edge of its distribution. Contrary to populations in the centre of the distribution, populations at the northern range are regionally endangered as they are small and disjunct. Sequence data of 2 chloroplast loci and allelic data from 6 nuclear microsatellite markers were obtained from 297 samples from Finland, Estonia and Russia. We sought for genetic indicators of past population processes, such as post-glacial colonisation history of E. atrorubens. As expected, we observed low genetic variation, in terms of numbers of substitutions, haplotypes and alleles, and significant levels of differentiation, especially pronounced in the chloroplast DNA. These features suggest that the edge populations could be prone to extinction.

    Keywords: Genetic diversity, Microsatellites, Population differentiation, intergenic spacer, rbcL-accD, trnK

  • Hoekman D, LeVan K, Ball G, Browne R, Davidson R, Erwin T et al. (2017)

    Design for ground beetle abundance and diversity sampling within the National Ecological Observatory Network

    Ecosphere 8(4) e01744.

    The National Ecological Observatory Network (NEON) will monitor ground beetle populations across a network of broadly distributed sites because beetles are prevalent in food webs, are sensitive to abiotic factors, and have an established role as indicator species of habitat and climatic shifts. We describe the design of ground beetle population sampling in the context of NEON's long-term, continental-scale monitoring program, emphasizing the sampling design, priorities, and collection methods. Freely available NEON ground beetle data and associated field and laboratory samples will increase scientific understanding of how biological communities are responding to land-use and climate change.

    Keywords: Carabidae, SpecialFeature: NEON Design, abundance, climate, diversity, global change, ground beetles, long-term monitoring

  • Quijada L, Huhtinen S, Negrín R, Beltrán-Tejera E (2017)

    Studies in Hyaloscyphaceae associated with major vegetation types in the Canary Islands II: a revision of Hyaloscypha

    Willdenowia 47(1) 31-42.

    Four species of the genus Hyaloscypha are presented for the Canary Islands. The study is based on recent collections and 12 previous records. The earlier reports of the genus (Hyaloscypha fuckelii, H. hyalina and H. leuconica) are corrected. All of the reported species are new to the Canarian archipelago (H. aureliella, H. intacta, H. spiralis and H. strobicola), and only one has been reported before from the Macaronesian region (H. aureliella). A key, descriptions, illustrations and notes about ecology are provided.

    Keywords: Ascomycota, Canary Islands, Helotiales, Hyaloscypha, Hyaloscyphaceae, Macaronesia, diversity, new records, taxonomy

  • Zuquim G, Tuomisto H, Prado J (2017)

    A free-access online key to identify Amazonian ferns

    PhytoKeys 78 1-15.

    There is urgent need for more data on species distributions in order to improve conservation planning. A crucial but challenging aspect of producing high-quality data is the correct identification of organisms. Traditional printed floras and dichotomous keys are difficult to use for someone not familiar with the technical jargon. In poorly known areas, such as Amazonia, they also become quickly outdated as new species are described or ranges extended. Recently, online tools have allowed developing dynamic, interactive, and accessible keys that make species identification possible for a broader public. In order to facilitate identifying plants collected in field inventories, we developed an internet-based free-access tool to identify Amazonian fern species. We focused on ferns, because they are easy to collect and their edaphic affinities are relatively well known, so they can be used as an indicator group for habitat mapping. Our key includes 302 terrestrial and aquatic entities mainly from lowland Amazonian forests. It is a free-access key, so the user can freely choose which morphological features to use and in which order to assess them. All taxa are richly illustrated, so specimens can be identified by a combination of character choices, visual comparison, and written descriptions. The identification tool was developed in Lucid 3.5 software and it is available at

    Keywords: Amazonia, Ferns, Free-access key, Identification key, Indicator species, Lucid3, Online identification tools, Pteridophyte, Tropical forests

  • Hällfors M, Aikio S, Fronzek S, Hellmann J, Ryttäri T, Heikkinen R (2016)

    Assessing the need and potential of assisted migration using species distribution models

    Biological Conservation 196 60-68.

    Assisted migration (AM) has been suggested as a management strategy for aiding species in reaching newly suitable locations as climate changes. Species distribution models (SDMs) can provide important insights for decisions on whether to assist a species in its migration; however, their application includes uncertainties. In this study, we use consensus SDMs to model the future suitable areas for 13 vascular plant species with poor dispersal capacity. Based on the outputs of SDMs under different climate change scenarios and future times, we quantify the predicted changes in suitable area by calculating metrics that describe the need and potential for migration. We find that, by the end of the 21st century, one of the species would benefit from AM under mild climate change, seven under moderate change, and for 12 out of 13 species studied AM appears to be a relevant conservation method under strong climate change. We also test the effect of different modeling attributes on the metrics and find little variation between SDMs constructed using different combinations of modeling methods and variable sets. However, the choice of climate variables had a larger influence on the level of the metrics than did the modeling method. We therefore suggest that the choice of climate variables should receive ample attention when measuring climate change threat using SDMs and that experiments aiming to uncover critical environmental factors for individual species should be extensively conducted. This study illustrates that dispersal assistance may be needed for many species under a wide range of possible future climates.

    Keywords: Assisted colonization, Conservation planning, Managed relocation, Model uncertainty, Translocation

  • Multimäki S, Hall A, Ahonen-Rainio P (2016)

    Comparison of Temporally Classified and Unclassified Map Animations

    Cartographic Perspectives(82).

    While animation is a natural and, under certain circumstances, effective way to present spatio-temporal information, it has its limitations. Studying animations of large point datasets can be cognitively very demanding. Aiming to help users to comprehend such data, this study presents a new concept of temporal classification. A phenomenon is classified into periods of increasing, decreasing, and steady intensity, and each is assigned different colours in an animation. This concept was tested with a group of experts in the field of the phenomenon. The results suggest that this kind of classified animation, together with a traditional animation presenting the same dataset, supports users in their analysis process and adds to the impression they get of the phenomenon. It also seems that the viewing order of the animations matters: the full potential of the tested method is reached by viewing the traditional version first and temporally classified version after that.

    Keywords: Classification, Colours, Map Animation, Temporal Behaviour, Visualisation

  • Hällfors M, Liao J, Dzurisin J, Grundel R, Hyvärinen M, Towle K et al. (2015)

    Addressing potential local adaptation in species distribution models: implications for conservation under climate change

    Ecological Applications 15-0926.1.

    Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate M...

    Keywords: Lycaeides melissa samuelis, Primula nutans var. finmarchica, biodiversity management, conservation effectiveness, environmental niche models, intraspecific variation, model uncertainty, translocation

  • 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