Uses of GBIF in scientific research

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

List of publications

  • Almeida D, Gusmão L, Miller A (2017)

    A new species of Bertiella (Melanommataceae) from Brazil and a key to accepted species

    Mycosphere 8(4) 392-396.

    During an inventory of ascomycetes in the semi-arid region of Brazil, an undescribed specimen of Bertiella was found. It is described and illustrated as B. gelatinosa sp. nov., based on morphological data. The new fungus is distinguished by the size of the ascospores, which are surrounded by a gelatinous sheath. A synoptic table and a key to all known species of Bertiella are presented.

    Keywords: Ascomycota, Dothideomycetes, Pleosporales, Taxonomy

  • Brandt L, Benscoter A, Harvey R, Speroterra C, Bucklin D, Romañach S et al. (2017)

    Comparison of climate envelope models developed using expert-selected variables versus statistical selection

    Ecological Modelling 345 10-20.

    Climate envelope models are widely used to describe potential future distribution of species under different climate change scenarios. It is broadly recognized that there are both strengths and limitations to using climate envelope models and that outcomes are sensitive to initial assumptions, inputs, and modeling methods Selection of predictor variables, a central step in modeling, is one of the areas where different techniques can yield varying results. Selection of climate variables to use as predictors is often done using statistical approaches that develop correlations between occurrences and climate data. These approaches have received criticism in that they rely on the statistical properties of the data rather than directly incorporating biological information about species responses to temperature and precipitation. We evaluated and compared models and prediction maps for 15 threatened or endangered species in Florida based on two variable selection techniques: expert opinion and a statistical method. We compared model performance between these two approaches for contemporary predictions, and the spatial correlation, spatial overlap and area predicted for contemporary and future climate predictions. In general, experts identified more variables as being important than the statistical method and there was low overlap in the variable sets (<40%) between the two methods Despite these differences in variable sets (expert versus statistical), models had high performance metrics (>0.9 for area under the curve (AUC) and >0.7 for true skill statistic (TSS). Spatial overlap, which compares the spatial configuration between maps constructed using the different variable selection techniques, was only moderate overall (about 60%), with a great deal of variability across species. Difference in spatial overlap was even greater under future climate projections, indicating additional divergence of model outputs from different variable selection techniques. Our work is in agreement with other studies which have found that for broad-scale species distribution modeling, using statistical methods of variable selection is a useful first step, especially when there is a need to model a large number of species or expert knowledge of the species is limited. Expert input can then be used to refine models that seem unrealistic or for species that experts believe are particularly sensitive to change. It also emphasizes the importance of using multiple models to reduce uncertainty and improve map outputs for conservation planning. Where outputs overlap or show the same direction of change there is greater certainty in the predictions. Areas of disagreement can be used for learning by asking why the models do not agree, and may highlight areas where additional on-the-ground data collection could improve the models.

    Keywords: Climate adaptation, Conservation planning, Expert opinion, Florida, Threatened and endangered species

  • Cabİ e, soreng rj G (2017)

    Taxonomy of Poa jubata and a new section of the genus (Poaceae)


    Poa jubata A. Kern. is an ephemeral, southeastern European species of which little is known. A molecular phylogenetic analysis of Poa L. including all previously identified major lineages, shows this species to be isolated, with a genotype here designated as J (plastid) J (nrDNA). It is assigned to the monotypic P. sect. Jubatae sect. nov. The section is differentiated from other Poa sections in having 5-nerved upper glumes, very narrow palea flanges, an annual habit, and erect solitary culms. Poa jubata occurs along coastal regions of the Balkans and is rather rare. Two new collections were made in 2015 in Thrace, Turkey, in vernal pool habitats with clay soils, thus expanding its known habitat. The species is described in detail, illustrated, and its relationships are discussed.

    Keywords: Balkans region, DNA, Europe, Morphology, annual habit, genotype, phylogeny, taxonomy

  • De Pooter D, Appeltans W, Bailly N, Bristol S, Deneudt K, Eliezer M et al. (2017)

    Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

    Biodiversity Data Journal 5 e10989.

    The Ocean Biogeographic Information System (OBIS) is the world’s most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.

    Keywords: Darwin Core Archive, data standardisation, ecosystem data, environmental data, oceanographic data, sample event, species occurrence, telemetry data

  • Feldman R, Peers M, Pickles R, Thornton D, Murray D (2017)

    Climate driven range divergence among host species affects range-wide patterns of parasitism

    Global Ecology and Conservation 9 1-10.

    Species interactions like parasitism influence the outcome of climate-driven shifts in species ranges. For some host species, parasitism can only occur in that part of its range that overlaps with a second host species. Thus, predicting future parasitism may depend on how the ranges of the two hosts change in relation to each other. In this study, we tested whether the climate driven species range shift of Odocoileus virginianus (white-tailed deer) accounts for predicted changes in parasitism of two other species from the family Cervidae, Alces alces (moose) and Rangifer tarandus (caribou), in North America. We used MaxEnt models to predict the recent (2000) and future (2050) ranges (probabilities of occurrence) of the cervids and a parasite Parelaphostrongylus tenuis (brainworm) taking into account range shifts of the parasite’s intermediate gastropod hosts. Our models predicted that range overlap between A. alces/R. tarandus and P. tenuis will decrease between 2000 and 2050, an outcome that reflects decreased overlap between A. alces/R. tarandus and O. virginianus and not the parasites, themselves. Geographically, our models predicted increasing potential occurrence of P. tenuis where A. alces/R. tarandus are likely to decline, but minimal spatial overlap where A. alces/R. tarandus are likely to increase. Thus, parasitism may exacerbate climate-mediated southern contraction of A. alces and R. tarandus ranges but will have limited influence on northward range expansion. Our results suggest that the spatial dynamics of one host species may be the driving force behind future rates of parasitism for another host species.

    Keywords: Boreal, Cervidae, Climate change, Evolution, Parasitism, Synergistic effects

  • Ferreira Júnior J, Blume G, Sousa S, Carvalho C, Gardiner C, Ferreira Júnior J et al. (2017)

    Anatomo-pathological aspects of parasitism by nematodes of the superfamily Metastrongyloidea in wild crab-eating fox (Cerdocyon thous) in Midwestern Brazil

    Ciência Rural 47(2).

    Nematodes of the superfamily Metastrongyloidea affect the respiratory, cardiovascular, and nervous systems of domestic carnivores and are uncommonly detected in wild animals. This report describes the lesions associated with pulmonary parasitism by nematodes of the superfamily Metastrongyloidea in a wild crab-eating fox ( Cerdocyon thous ) in the Federal District, Brazil. Grossly, there was pulmonary hyperemia, edema, and emphysema. Microscopically, there was granulomatous arteritis associated with intravascular metastrongylid. The anatomical location, characteristic lesion, and histological features of the parasite suggested that the nematode involved in this case is Angiostrongylus vasorum . This worm is frequently reported parasitizing pulmonary arteries of domestic canids but is uncommonly described in wild canids in Midwestern Brazil.

    Keywords: Angiostrongylus, nematode, pathology, wild canids

  • Gutiérrez E, Marinho-Filho J (2017)

    The mammalian faunas endemic to the Cerrado and the Caatinga

    ZooKeys 644 105-157.

    We undertook a comprehensive, critical review of literature concerning the distribution, conservation status, and taxonomy of species of mammals endemic to the Cerrado and the Caatinga, the two largest biomes of the South American Dry-Diagonal. We present species accounts and lists of species, which we built with criteria that, in our opinion, yielded results with increased scientific rigor relative to previously published lists – e.g., excluding nominal taxa whose statuses as species have been claimed only on the basis of unpublished data, incomplete taxonomic work, or weak evidence. For various taxa, we provided arguments regarding species distributions, conservation and taxonomic statuses previously lacking in the literature. Two major findings are worth highlighting. First, we unveil the existence of a group of species endemic to both the Cerrado and the Caatinga (i.e., present in both biomes and absent in all other biomes). From the biogeographic point of view, this group, herein referred to as Caatinga-Cerrado endemics, deserves attention as a unit – just as in case of the Caatinga-only and the Cerrado-only endemics. We present preliminary hypotheses on the origin of these three endemic faunas (Cerrado-only, Caatinga-only, and Caatinga-Cerrado endemics). Secondly, we discovered that a substantial portion of the endemic mammalian faunas of the Caatinga and the Cerrado faces risks of extinction that are unrecognized in the highly influential Red List of Threatened Species published by the International Union for Conservation of Nature (IUCN). “Data deficient” is a category that misrepresents the real risks of extinction of these species considering that (a) some of these species are known only from a handful of specimens collected in a single or a few localities long ago; (b) the Cerrado and the Caatinga have been sufficiently sampled to guarantee collection of additional specimens of these species if they were abundant; (c) natural habitats of the Cerrado and the Caatinga have been substantially altered or lost in recent decades. Failures either in the design of the IUCN criteria or in their application to assign categories of extinction risks represent an additional important threat to these endemic faunas because their real risks of extinctions become hidden. It is imperative to correct this situation, particularly considering that these species are associated to habitats that are experiencing fast transformation into areas for agriculture, at an unbearable cost for biodiversity.

    Keywords: Bolivia, Brazil, Dry Diagonal, biogeography, checklist, conservation, evolution, habitat, mammals, nomenclature, savannas, taxonomy

  • Jarnevich C, Young N, Sheffels T, Carter J, Sytsma M, Talbert C (2017)

    Evaluating simplistic methods to understand current distributions and forecast distribution changes under climate change scenarios: an example with coypu (Myocastor coypus)

    NeoBiota 32 107-125.

    Invasive species provide a unique opportunity to evaluate factors controlling biogeographic distributions; we can consider introduction success as an experiment testing suitability of environmental conditions. Predicting potential distributions of spreading species is not easy, and forecasting potential distributions with changing climate is even more difficult. Using the globally invasive coypu (Myocastor coypus [Molina, 1782]), we evaluate and compare the utility of a simplistic ecophysiological based model and a correlative model to predict current and future distribution. The ecophysiological model was based on winter temperature relationships with nutria survival. We developed correlative statistical models using the Software for Assisted Habitat Modeling and biologically relevant climate data with a global extent. We applied the ecophysiological based model to several global circulation model (GCM) predictions for mid-century. We used global coypu introduction data to evaluate these models and to explore a hypothesized physiological limitation, finding general agreement with known coypu distribution locally and globally and support for an upper thermal tolerance threshold. Global circulation model based model results showed variability in coypu predicted distribution among GCMs, but had general agreement of increasing suitable area in the USA. Our methods highlighted the dynamic nature of the edges of the coypu distribution due to climate non-equilibrium, and uncertainty associated with forecasting future distributions. Areas deemed suitable habitat, especially those on the edge of the current known range, could be used for early detection of the spread of coypu populations for management purposes. Combining approaches can be beneficial to predicting potential distributions of invasive species now and in the future and in exploring hypotheses of factors controlling distributions.

    Keywords: Ecophysiological model, climate change, correlative model, coypu, nutria

  • Jorgensen S, Barrington D (2017)

    Two Beringian Origins for the Allotetraploid Fern Polystichum braunii (Dryopteridaceae)

    Systematic Botany 42(1) 6-16.

    Although some polyploids in the genus Polystichum are well studied and have well-resolved evolutionary histories, the origin of the circumboreally distributed allotetraploid Polystichum braunii remains obscure. We use the chloroplast markers rbcL, rps4-trnS, and trnL-F as well as the nuclear markers pgiC and gapCp to demonstrate that P. braunii is a single allotetraploid with a minimum of two origins. The two variants isolated from the nucleus resolve with divergent clades, one eastern Asian and one North American. However, they do not have near allies among morphologically appropriate taxa in our sample; the North American progenitor appears to be extinct. A divergence-time analysis based on the cpDNA markers yielded evidence of an older time of origin for P. braunii than for an array of well-known allotetraploids in the eupolypod ferns. Niche modeling in the light of geological and paleontological evidence leads to the conclusion that the two origins were in Beringia. Since P. braunii is genetically undifferentiated but widely distributed, we argue that it has expanded to its circumboreal range in the recent past, though it has a relatively ancient origin.

    Keywords: Allopolyploidy, Beringia, chloroplast DNA, nuclear DNA

  • Larson P (2017)

    Brooding sea anemones (Cnidaria: Anthozoa: Actiniaria): paragons of diversity in mode, morphology, and maternity

    Invertebrate Biology.

    Brooding has been reported in at least 57 species of sea anemone. More than three quarters (44/57) of the species that are known to brood have been described since the last comprehensive treatment of brooding in this lineage. Different authors focusing on different taxonomic groups within sea anemones over the last 115 years have collectively produced an imprecise and inconsistent set of terminology with respect to brooding in general and to the variety of conditions of brooding in particular. In this review, I characterize brooding as a behavior in which offspring are retained by the adult to at least the juvenile stage, in contrast with the more common release of eggs, embryos, or larvae. Brooding occurs in two primary modes, internal and external, in which offspring may be produced via sexual or asexual means. I categorize structures associated with external brooding in three types: pits, chambers, and grooves. Early inferences that external brooding has a primarily bipolar distribution continue to be supported with current data, but it is doubtful that small size and simultaneous hermaphroditism are correlated with brooding in sea anemones. Finally, I identify open questions about brooding in sea anemones and suggest future lines of research that will broaden our understanding of this phenomenon.

    Keywords: Allopolyploidy, Beringia, chloroplast DNA, nuclear DNA