Uses of GBIF in scientific research

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

List of publications

  • 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


  • Gaiji, S., Chavan, V., Ariño, A., Otegui, J., Hobern, D., Sood, R., Robles, E.

    Content assessment of the primary biodiversity data Published through gbif network: status, challenges and potentials

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

    With the establishment of the Global Biodiversity Information Facility (GBIF) in 2001 as an inter-governmental coordinating body, concerted efforts have been made during the past decade to establish a global research infrastructure to facilitate the publishing, discovery, and access to primary biodiversity data. The participants in GBIF have enabled the access to over 377 million records of such data as of August 2012. This is a remarkable achievement involving efforts at national, regional and global levels in multiple areas such as data digitization, standardization and exchange protocols. However concerns about the quality and ‘fitness for use’ of the data mobilized in particular for the scientific communities have grown over the years and must now be carefully considered in future developments. This paper is the first comprehensive assessment of the content mobilised so far through GBIF, as well as a reflexion on possible strategies to improve its ‘fitness for use’. The methodology builds on complementary approaches adopted by the GBIF Secretariat and the University of Navarra for the development of comprehensive content assessment methodologies. The outcome of this collaborative research demonstrates the immense value of the GBIF mobilized data and its potential for the scientific communities. Recommendations are provided to the GBIF community to improve the quality of the data published as well as priorities for future data mobilization.

    Keywords: content assessment, gap analysis, primary biodiversity data


  • Guo, W., Lambertini, C., Li, X., Meyerson, L., Brix, H.

    Invasion of Old World Phragmites australis in the New World: precipitation and temperature patterns combined with human influences redesign the invasive niche.

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

    After its introduction into North America, Euro-Asian Phragmites australis became an aggressive invasive wetland grass along the Atlantic coast of North America. Its distribution range has since expanded to the middle, south and southwest of North America, where invasive P. australis has replaced millions of hectares of native plants in inland and tidal wetlands. Another P. australis invasion from the Mediterranean region is simultaneously occurring in the Gulf region of the USA and some countries in South America. Here, we analysed the occurrence records of the two Old World invasive lineages of P. australis (Haplotype M and Med) in both their native and introduced ranges using environmental niche models (ENMs) to assess (i) whether a niche shift accompanied the invasions in the New World; (ii) the role of biologically relevant climatic variables and human influence in the process of invasion; and (iii) the current potential distribution of these two lineages. We detected local niche shifts along the East Coast of North America and the Gulf Coast of the USA for Haplotype M and around the Mississippi Delta and Florida of the USA for Med. The new niche of introduced Haplotype M accounts for temperature fluctuations and increased precipitation. The introduced Med lineage has enlarged its original subtropical niche to the tropics-subtropics, invading regions with a high annual mean temperature (> c. 10 °C) and high precipitation in the driest period. Human influence is an important factor for both niches. We suggest that an increase in precipitation in the 20(th) century, global warming and human-made habitats have shaped the invasive niches of the two lineages in the New World. However, as the invasions are on-going and human and natural disturbances occur concomitantly, the future distribution ranges of the two lineages may diverge from the potential distribution ranges detected in this study. This article is protected by copyright. All rights reserved.

    Keywords: content assessment, gap analysis, primary biodiversity data


  • Kindt, R., Lillesø, J., van Breugel, P., Bingham, M., Demissew, S., Dudley, C., Friis, I., Gachathi, F., Kalema, J., Mbago, F., Moshi, H., Mulumba, J., Namaganda, M., Ndangalasi, H., Ruffo, C., Minani, V., Jamnadass, R., Graudal, L.

    Correspondence in forest species composition between the Vegetation Map of Africa and higher resolution maps for seven African countries

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

    Abstract Question How well does the forest classification system of the 1:5,000,000 vegetation map of Africa developed by Frank White correspond with classification systems and more extensive information on species assemblages of higher resolution maps developed for Ethiopia, Kenya, Malawi, Rwanda, Tanzania, Uganda and Zambia? Methods We reviewed various national and sub-national vegetation maps for their potential in increasing the resolution of the African map. Associated documentation was consulted to compile species assemblages, and to identify indicator species, for national forest vegetation types. Indicator species were identified for each regional forest type by selecting those species that, among all the species listed for the same phytochorion (regional centre of endemism), were listed only for that forest type. For each of the national forest types, we counted the number of indicator species of the anticipated regional type. Floristic relationships (expressed by four different ecological distance measures) among national forest types were investigated based on distance-based redundancy analysis, permutational multivariate analysis of variance (PERMANOVA) using distance matrices and hierarchical clustering. Results For most of the national forests, the analysis of indicator species and floristic relationships confirmed the regional classification system for the majority of national forest types, including the allocation to different phytochoria. Permutation tests confirmed allocation of national forest types to regional typologies, although the number of possible permutations limited inferences for the Zambezian and Lake Victoria phytochoria. Two forest types from Ethiopia and Kenya did not correspond to regional forest types. Conclusions Our analysis provides support that as the classification systems are compatible, the resolution and information content of the vegetation map of Africa can be directly improved by adding information from national maps, probably leading to improved liability of its application domains. We found statistical evidence for a distinct Afromontane phytochorion. We suggest expanding the regional forest classification system with ‘Afromontane moist transitional forest’. Among the various application domains of the higher resolution maps, these maps allow for an enhanced phytochoristic analysis of eastern Africa.

    Keywords: beta-sim distance, Ethiopia, Frank White, indicator species, Kenya, Kulczynski distance, Malawi, phytochorion, Rwanda, Tanzania, Uganda, Zambia


  • Normand, S., Randin, C., Ohlemüller, R., Bay, C., Høye, T., Kjær, E., Körner, C., Lischke, H., Maiorano, L., Paulsen, J., Pearman, P., Psomas, A., Treier, U., Zimmermann, N., Svenning, J.

    A greener Greenland? Climatic potential and long-term constraints on future expansions of trees and shrubs.

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 368(1624) 20120479.

    Warming-induced expansion of trees and shrubs into tundra vegetation will strongly impact Arctic ecosystems. Today, a small subset of the boreal woody flora found during certain Plio-Pleistocene warm periods inhabits Greenland. Whether the twenty-first century warming will induce a re-colonization of a rich woody flora depends on the roles of climate and migration limitations in shaping species ranges. Using potential treeline and climatic niche modelling, we project shifts in areas climatically suitable for tree growth and 56 Greenlandic, North American and European tree and shrub species from the Last Glacial Maximum through the present and into the future. In combination with observed tree plantings, our modelling highlights that a majority of the non-native species find climatically suitable conditions in certain parts of Greenland today, even in areas harbouring no native trees. Analyses of analogous climates indicate that these conditions are widespread outside Greenland, thus increasing the likelihood of woody invasions. Nonetheless, we find a substantial migration lag for Greenland's current and future woody flora. In conclusion, the projected climatic scope for future expansions is strongly limited by dispersal, soil development and other disequilibrium dynamics, with plantings and unintentional seed dispersal by humans having potentially large impacts on spread rates.

    Keywords: beta-sim distance, Ethiopia, Frank White, indicator species, Kenya, Kulczynski distance, Malawi, phytochorion, Rwanda, Tanzania, Uganda, Zambia


  • Otegui, J., Ariño, A., Chavan, V., Gaiji, S.

    On The Dates Of The GBIF Mobilised Primary Biodiversity Data Records

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

    There are more than 390 million primary biodiversity data records published by hundreds of data publishers through the GBIF network. Thus, the GBIF network is the single most comprehensive index for this kind of data. Ensuring or, at least assessing data quality is of capital importance for the reliability and usability of this data. While conducting a time data gap analysis on this mass of data, we have detected some issues with the way date information is processed and shared. Dates can be obscured or altered under certain circumstances, when a specific combination of publisher’s error or date handling features, and faulty or inadequate date parsing and processing routines gets chained together. The extent of the date unreliability (either at the source or through GBIF portal) is relatively low, and problems are concentrated in a few data publishers. The types of errors and misprocessing in dates through the sources and the published records are analysed, impact on the overall data quality of the published index was assessed, and corrective measures are suggested. Keywords

    Keywords: data quality, dates, fitness for use, GBIF, Primary biodiversity data


  • Pedersen, M., Ginolhac, A., Orlando, L., Olsen, J., Andersen, K., Holm, J., Funder, S., Willerslev, E., Kjær, K.

    A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    Quaternary Science Reviews 75 161-168.

    We use 2nd generation sequencing technology on sedimentary ancient DNA (sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty-eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g–h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (Scrophulariaceae and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650 cal yr BP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less detailed than pollen and macrofossil analyses can be a complementary tool for establishing the composition of both terrestrial and aquatic local plant communities and a method for identifying additional taxa.

    Keywords: data quality, dates, fitness for use, GBIF, Primary biodiversity data


  • Cadena, C., Kozak, K., Gómez, J., Parra, J., McCain, C., Bowie, R., Carnaval, A., Moritz, C., Rahbek, C., Roberts, T., Sanders, N., Schneider, C., VanDerWal, J., Zamudio, K., Graham, C.

    Latitude, elevational climatic zonation and speciation in New World vertebrates.

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

    Many biodiversity hotspots are located in montane regions, especially in the tropics. A possible explanation for this pattern is that the narrow thermal tolerances of tropical species and greater climatic stratification of tropical mountains create more opportunities for climate-associated parapatric or allopatric speciation in the tropics relative to the temperate zone. However, it is unclear whether a general relationship exists among latitude, climatic zonation and the ecology of speciation. Recent taxon-specific studies obtained different results regarding the role of climate in speciation in tropical versus temperate areas. Here, we quantify overlap in the climatic distributions of 93 pairs of sister species of mammals, birds, amphibians and reptiles restricted to either the New World tropics or to the Northern temperate zone. We show that elevational ranges of tropical- and temperate-zone species do not differ from one another, yet the temperature range experienced by species in the temperate zone is greater than for those in the tropics. Moreover, tropical sister species tend to exhibit greater similarity in their climatic distributions than temperate sister species. This pattern suggests that evolutionary conservatism in the thermal niches of tropical taxa, coupled with the greater thermal zonation of tropical mountains, may result in increased opportunities for allopatric isolation, speciation and the accumulation of species in tropical montane regions. Our study exemplifies the power of combining phylogenetic and spatial datasets of global climatic variation to explore evolutionary (rather than purely ecological) explanations for the high biodiversity of tropical montane regions.

    Keywords: Altitude, Animals, Biodiversity, Biological Evolution, Climate, Genetic Speciation, Geography, Latin America, North America, Phylogeny, Vertebrates, Vertebrates: classification, Vertebrates: genetics


  • Domisch, S., Araújo, M., Bonada, N., Pauls, S., Jähnig, S., Haase, P.

    Modelling distribution in European stream macroinvertebrates under future climates

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

    Climate change is predicted to have profound effects on freshwater organisms due to rising temperatures and altered precipitation regimes. Using an ensemble of bioclimatic envelope models (BEMs), we modelled the climatic suitability of 191 stream macroinvertebrate species from 12 orders across Europe under two climate change scenarios for 2080 on a spatial resolution of 5 arc minutes. Analyses included assessments of relative changes in species’ climatically suitable areas as well as their potential shifts in latitude and longitude with respect to species’ thermal preferences. Climate-change effects were also analysed regarding species’ ecological and biological groupings, namely 1) endemicity and 2) rarity within European ecoregions, 3) life cycle, 4) stream zonation preference and 5) current preference. The BEMs projected that suitable climate conditions would persist in Europe in the year 2080 for nearly 99% of the modelled species regardless of the climate scenario. Nevertheless, a decrease in the amount of climatically suitable areas was projected for 57-59% of the species. Depending on the scenario, losses could be of 38-44% on average. The suitable areas for species were projected to shift, on average, 4.7-6.6° north and 3.9-5.4° east. Cold-adapted species were projected to lose climatically suitable areas, while gains were expected for warm-adapted species. When projections were analysed for different species groupings, only endemics stood out as a particular group. That is, endemics were projected to lose significantly larger amounts of suitable climatic areas than non-endemic species. Despite the uncertainties involved in modelling exercises such as this, the extent of projected distributional changes reveals further the vulnerability of freshwater organisms to climate change and implies a need to understand the consequences for ecological function and biodiversity conservation.

    Keywords: Bioclimatic envelope model, BIOMOD, climatically suitable area, endemic species, invertebrates, range shift, river