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

  • 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


  • 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


  • 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


  • Liu D, Wang R, Gordon D, Sun X, Chen L, Wang Y (2017)

    Predicting Plant Invasions Following China’s Water Diversion Project

    Environmental Science & Technology 51(3) 1450-1457.

    China’s South to North Water Diversion (SNWD) project connects portions of the Yangtze River in the south to the Yellow River system in the north, overcoming biogeographic barriers to water movement. The diversion will supply potable water to over 110 million people and provide multiple other socioeconomic benefits. However, an inadvertent negative impact of this connection includes creation of conduits for species invasions. Alligator weed (Alternanthera philoxeroides), water hyacinth (Eichhornia crassipes), and water lettuce (Pistia stratiotes) are the only aquatic plant species on China’s shortlists for special control. These species are mainly invasive in the Yangtze River basin. If these species are able to invade the SNWD and further spread via the SNWD, they have the potential to alter water supply, including water quantity and quality, as well as local ecology and agriculture, threatening the goals of the diversion. Understanding the full potential for these species to invade northern China is cri...

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


  • López-Alcaide S, Nakamura M, Smith E, Martínez-Meyer E (2017)

    Would behavioral thermoregulation enables pregnant viviparous tropical lizards to cope with a warmer world?

    Integrative Zoology.

    Sceloporus lizards depend on external heat to achieve their preferred temperature (Tse1) for performing physiological processes. Evidence both in the field and laboratory indicates that pregnant females of this genus select body temperatures (Tb) lower than 34°C as higher temperatures may be lethal to embryos. Therefore, thermoregulation is crucial for successful embryo development. Given the increase in global air temperature, it is expected that the first compensatory response of species that inhabit tropical climates will be behavioral thermoregulation. We tested if viviparous Sceloporus formosus group lizards in the wild exhibited differences in thermoregulatory behavior to achieve the known Tse1 for developing embryos regardless of local thermal conditions. We quantified field active body temperature, thermoregulatory behavior mechanisms (time of sighting, microhabitat used and basking time), and available microhabitat thermal conditions (i.e., operative temperature) for ten lizard species during gestation, distributed along an altitudinal gradient. We applied both conventional and phylogenic analyses to explore if Tb or behavioral thermoregulation could be regulated in response to different thermal conditions. These species showed no significant differences in field Tb during gestation regardless of local thermal conditions. In contrast, they exhibited significant differences in their behavioral thermoregulation associated to local environmental conditions. Based on these observations, the differences in thermoregulatory behavior identified are interpreted as compensatory adjustments to local thermal conditions. We conclude that these species may deal with higher stressing environmental temperatures scenarios forecasted to the tropics by modulating their thermoregulatory behavior repertoire as first reaction.

    Keywords: Altitudinal gradient, Sceloporus formosus, behavior, global warming, thermal stress


  • MacFadden B, Guralnick R (2017)

    Horses in the Cloud: big data exploration and mining of fossil and extant Equus (Mammalia: Equidae)

    Paleobiology 43(01) 1-14.

    Extant species of the genus Equus(e.g., horses, asses, and zebras) have a widespread distribution today on all continents except Antarctica. Extinct species of Equus represented by fossils were likewise widely distributed in the Pliocene and even more so during the Pleistocene. In order to understand the efficacy of “big data” for (paleo)biogeographic analyses, location records (latitude, longitude) and fossil occurrences for the genus Equus were mined and further explored from six databases, including iDigBio, Paleobiology Database, VertNet, BISON, Neotoma, and GBIF. These were chosen from a priori knowledge of where relevant data might be aggregated. We also realized that these databases have different objectives and data sources and therefore would provide a useful comparative study of the widespread taxon Equus in space and time.

    Keywords: Altitudinal gradient, Sceloporus formosus, behavior, global warming, thermal stress


  • Pellegrini A, Anderegg W, Paine C, Hoffmann W, Kartzinel T, Rabin S et al. (2017)

    Convergence of bark investment according to fire and climate structures ecosystem vulnerability to future change

    Ecology Letters.

    Fire regimes in savannas and forests are changing over much of the world. Anticipating the impact of these changes requires understanding how plants are adapted to fire. In this study, we test whether fire imposes a broad selective force on a key fire-tolerance trait, bark thickness, across 572 tree species distributed worldwide. We show that investment in thick bark is a pervasive adaptation in frequently burned areas across savannas and forests in both temperate and tropical regions where surface fires occur. Geographic variability in bark thickness is largely explained by annual burned area and precipitation seasonality. Combining environmental and species distribution data allowed us to assess vulnerability to future climate and fire conditions: tropical rainforests are especially vulnerable, whereas seasonal forests and savannas are more robust. The strong link between fire and bark thickness provides an avenue for assessing the vulnerability of tree communities to fire and demands inclusion in global models.

    Keywords: Bark thickness, fire ecology, forest, functional traits, global change, savanna


  • Potter K, Crane B, Hargrove W (2017)

    A United States national prioritization framework for tree species vulnerability to climate change

    New Forests 1-26.

    Climate change is one of several threats that will increase the likelihood that forest tree species could experience population-level extirpation or species-level extinction. Scientists and managers from throughout the United States Forest Service have cooperated to develop a framework for conservation priority-setting assessments of forest tree species. This framework uses trait data and predictions of expected climate change pressure to categorize and prioritize 339 native tree species for conservation, monitoring, management and restoration across all forested lands in the contiguous United States and Alaska. The framework allows for the quantitative grouping of species into vulnerability classes that may require different management and conservation strategies for maintaining the adaptive genetic variation of the species within each group. This categorization is based on risk factors relating to the species’ (1) exposure to climate change, (2) sensitivity to climate change, and (3) capacity to adapt to climate change. We used K-means clustering to group species into seven classes based on these three vulnerability dimensions. The most vulnerable class encompassed 35 species with high scores for all three vulnerability dimensions. These will require the most immediate conservation intervention. A group of 43 species had high exposure and sensitivity, probably requiring conservation assistance, while a group of 69 species had high exposure and low adaptive capacity, probably needing close monitoring. This assessment tool should be valuable for scientists and managers determining which species and populations to target for monitoring efforts and for pro-active gene conservation and management activities.

    Keywords: Climate change, Forest health, Forest management, Gene conservation, Project CAPTURE, Vulnerability