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


  • 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


  • Aguirre-Santoro J, Michelangeli F, Stevenson D (2016)

    Molecular Phylogenetics of the Ronnbergia Alliance (Bromeliaceae, Bromelioideae) and insights into their morphological evolution.

    Molecular phylogenetics and evolution 100 1-20.

    The tank-epiphytic clade of berry-fruited bromeliads, also known as the Core Bromelioideae, represents a remarkable event of adaptive radiation within the Bromeliaceae; however, the details of this radiation have been difficult to study because this lineage is plagued with generic delimitation problems. In this study, we used a phylogenetic approach to investigate a well supported, albeit poorly understood, lineage nested within the Core Bromelioideae, here called the "Ronnbergia Alliance." In order to assess the monophyly and phylogenetic relationships of this group, we used three plastid and three nuclear DNA sequence markers combined with a broad sampling across three taxonomic groups and allied species of Aechmea expected to comprise the Ronnbergia Alliance. We combined the datasets to produce a well-supported and resolved phylogenetic hypothesis. Our main results indicated that the Ronnbergia Alliance was a well-supported monophyletic group, sister to the remaining Core Bromelioideae, and it was composed by species of the polyphyletic genera Aechmea, Hohenbergia and Ronnbergia. We identified two major internal lineages with high geographic structure within the Ronnbergia Alliance. The first of these lineages, called the Pacific Clade, contained species of Aechmea and Ronnbergia that occur exclusively from southern Central America to northwestern South America. The second clade, called the Atlantic Clade, contained species of Aechmea, Hohenbergia and Ronnbergia mostly limited to the Atlantic Forest and the Caribbean. We also explored the diagnostic and evolutionary importance of 13 selected characters using ancestral character reconstructions on the phylogenetic hypothesis. We found that the combination of tubular corollas apically spreading and unappendaged ovules had diagnostic value for the Ronnbergia Alliance, whereas flower size, length of the corolla tube, and petal pigmentation and apex were important characters to differentiate the Pacific and Atlantic clades. This study opens new perspectives for future taxonomic reorganizations and provides a framework for evolutionary and biogeographic studies.

    Keywords: Atlantic Forest, Bromeliaceae, Bromelioideae, Caribbean, Chocó-Tumbes-Magdalena region, Ronnbergia Alliance


  • Albuquerque F, Beier P (2016)

    Predicted rarity-weighted richness, a new tool to prioritize sites for species representation

    Ecology and Evolution.

    Lack of biodiversity data is a major impediment to prioritizing sites for species representation. Because comprehensive species data are not available in any planning area, planners often use surrogates (such as vegetation communities, or mapped occurrences of a well-inventoried taxon) to prioritize sites. We propose and demonstrate the effectiveness of predicted rarity-weighted richness (PRWR) as a surrogate in situations where species inventories may be available for a portion of the planning area. Use of PRWR as a surrogate involves several steps. First, rarity-weighted richness (RWR) is calculated from species inventories for a q% subset of sites. Then random forest models are used to model RWR as a function of freely available environmental variables for that q% subset. This function is then used to calculate PRWR for all sites (including those for which no species inventories are available), and PRWR is used to prioritize all sites. We tested PRWR on plant and bird datasets, using the species accumulation index to measure efficiency of PRWR. Sites with the highest PRWR represented species with median efficiency of 56% (range 32%–77% across six datasets) when q = 20%, and with median efficiency of 39% (range 20%–63%) when q = 10%. An efficiency of 56% means that selecting sites in order of PRWR rank was 56% as effective as having full knowledge of species distributions in PRWR's ability to improve on the number of species represented in the same number of randomly selected sites. Our results suggest that PRWR may be able to help prioritize sites to represent species if a planner has species inventories for 10%–20% of the sites in the planning area.

    Keywords: conservation planning, prioritization, random forest, species representation, surrogacy


  • Alimi T, Fuller D, Herrera S, Arevalo-Herrera M, Quinones M, Stoler J et al. (2016)

    A multi-criteria decision analysis approach to assessing malaria risk in northern South America.

    BMC public health 16(1) 221.

    BACKGROUND: Malaria control in South America has vastly improved in the past decade, leading to a decrease in the malaria burden. Despite the progress, large parts of the continent continue to be at risk of malaria transmission, especially in northern South America. The objectives of this study were to assess the risk of malaria transmission and vector exposure in northern South America using multi-criteria decision analysis. METHODS: The risk of malaria transmission and vector exposure in northern South America was assessed using multi-criteria decision analysis, in which expert opinions were taken on the key environmental and population risk factors. RESULTS: Results from our risk maps indicated areas of moderate-to-high risk along rivers in the Amazon basin, along the coasts of the Guianas, the Pacific coast of Colombia and northern Colombia, in parts of Peru and Bolivia and within the Brazilian Amazon. When validated with occurrence records for malaria, An. darlingi, An. albimanus and An. nuneztovari s.l., t-test results indicated that risk scores at occurrence locations were significantly higher (p < 0.0001) than a control group of geographically random points. CONCLUSION: In this study, we produced risk maps based on expert opinion on the spatial representation of risk of potential vector exposure and malaria transmission. The findings provide information to the public health decision maker/policy makers to give additional attention to the spatial planning of effective vector control measures. Therefore, as the region tackles the challenge of malaria elimination, prioritizing areas for interventions by using spatially accurate, high-resolution (1 km or less) risk maps may guide targeted control and help reduce the disease burden in the region.

    Keywords: Biostatistics, Environmental Health, Epidemiology, Medicine/Public Health, Public Health, Vaccine, general


  • Allen J, Bradley B (2016)

    Out of the weeds? Reduced plant invasion risk with climate change in the continental United States

    Biological Conservation 203 306-312.

    Identifying invasion risk is critical for regional prioritization of management and monitoring, however, we currently lack a comprehensive assessment of the invasion risk posed by plants for the United States. We aim to quantify geographic invasion risk for currently established terrestrial invasive plants in the continental U.S. under current and future climate. We assembled a comprehensive occurrence database for 896 terrestrial invasive plant species from 33 regional collections of field and museum data and projected species ranges using MaxEnt species distribution models based on current (1950–2000 average) and future (2040–2060 average) climate. We quantified geographic invasion risk as differences in species richness, invasion debt, range infilling, and identification of hotspots. Potential invasive plant richness was higher than observed richness, particularly in eastern temperate forests, where as many as 83% of species with suitable climate have not yet established. A small percentage (median=0.22%) of species' potential ranges are currently occupied by them. With climate change, potential invasive plant richness declined by a median of 7.3% by 2050. About 80% of invasive plant hotspots were geographically stable with climate change, with the remaining 20% shifting northward. Invasion hotspots and current invasion debt reveal extensive, ongoing risk from existing invasive plants across the U.S., particularly in the Southeast. Climate change alters the spatial distributions of focal species for monitoring and is likely to reduce overall invasion risk in many areas. Early detection and rapid response programs could be most effective in stemming the spread of invasive plant species in areas with increased risk under climate change, while areas with persistent high risk are candidates for containment and control. The areas with reduced risk are prime locations for invasion of new imports from tropical and subtropical climates, highlighting the simultaneous need for prevention strategies.

    Keywords: Biodiversity, Conservation biology, Invasion debt, Invasive plant management, Invasive species, Species richness


  • André T, Salzman S, Wendt T, Specht C (2016)

    Speciation dynamics and biogeography of Neotropical spiral gingers (Costaceae)

    Molecular Phylogenetics and Evolution 103 55-63.

    Species can arise via the divisive effects of allopatry as well as due to ecological and/or reproductive character displacement within sympatric populations. Two separate lineages of Costaceae are native to the Neotropics; an early-diverging clade endemic to South America (consisting of ca. 16 species in the genera Monocostus, Dimerocostus and Chamaecostus); and the Neotropical Costus clade (ca. 50 species), a diverse assemblage of understory herbs comprising nearly half of total familial species richness. We use a robust dated molecular phylogeny containing most of currently known species to inform macroevolutionary reconstructions, enabling us to examine the context of speciation in Neotropical lineages. Analyses of speciation rate revealed a significant variation among clades, with a rate shift at the most recent common ancestor of the Neotropical Costus clade. There is an overall predominance of allopatric speciation in the South American clade, as most species display little range overlap. In contrast, sympatry is much higher within the Neotropical Costus clade, independent of node age. Our results show that speciation dynamics during the history of Costaceae is strongly heterogeneous, and we suggest that the Costus radiation in the Neotropics arose at varied geographic contexts.

    Keywords: Diversification, Macroevolution, Phylogenetics, Zingiberales


  • Asase A, Peterson A (2016)

    Completeness of Digital Accessible Knowledge of the Plants of Ghana

    Biodiversity Informatics 11.

    Biodiversity Informatics Open Journal Systems Journal Help Current Issue Atom logo RSS2 logo RSS1 logo User Username Password Remember me Journal Content Search Search Scope Browse By Issue By Author By Title Other Journals Information For Readers For Authors For Librarians Article Tools Print this article Indexing metadata How to cite item Email this article (Login required) Email the author (Login required) Home About Login Register Search Current Archives Home > 2016 > Asase Cover Image Completeness of Digital Accessible Knowledge of the Plants of Ghana Alex Asase, A. Townsend Peterson Abstract Providing comprehensive, informative, primary, research-grade biodiversity information represents an important focus of biodiversity informatics initiatives. Recent efforts within Ghana have digitized >90% of primary biodiversity data records associated with specimen sheets in Ghanaian herbaria; additional herbarium data are available from other institutions via biodiversity informatics initiatives such as the Global Biodiversity Information Facility. However, data on the plants of Ghana have not as yet been integrated and assessed to establish how complete site inventories are, so that appropriate levels of confidence can be applied. In this study, we assessed inventory completeness and identified gaps in current Digital Accessible Knowledge (DAK) of the plants of Ghana, to prioritize areas for future surveys and inventories. We evaluated the completeness of inventories at ½° spatial resolution using statistics that summarize inventory completeness, and characterized gaps in coverage in terms of geographic distance and climatic difference from well-documented sites across the country. The southwestern and southeastern parts of the country held many well-known grid cells; the largest spatial gaps were found in central and northern parts of the country. Climatic difference showed contrasting patterns, with a dramatic gap in coverage in central-northern Ghana. This study provides a detailed case study of how to prioritize for new botanical surveys and inventories based on existing DAK.

    Keywords: Ghana, biodiversity informatics, botanical surveys, data gaps, flora, inventory completeness, primary data


  • Ballesteros-Mejia L, Kitching I, Jetz W, Beck J (2016)

    Putting insects on the map: Near-global variation in sphingid moth richness along spatial and environmental gradients

    Ecography.

    Despite their vast diversity and vital ecological role, insects are notoriously underrepresented in biogeography and conservation, and key broad-scale ecological hypotheses about them remain untested – largely due to generally incomplete and very coarse spatial distribution knowledge. Integrating records from publications, field work and natural history collections, we used a mixture of species distribution models and expert estimates to provide geographic distributions and emergent richness patterns for all ca. 1,000 sphingid moth species found outside the Americas in high spatial detail. Total sphingid moth richness, the first for a higher insect group to be documented at this scale, shows distinct maxima in the wet tropics of Africa and the Oriental with notable decay toward Australasia. Using multivariate models controlling for spatial autocorrelation, we found that primary productivity is the dominant environmental variable associated with moth richness, while temperature, contrary to our predictions, is an unexpectedly weak predictor. This is in stark contrast to the importance we identify for temperature as a niche variable of individual species. Despite divergent life histories, both main sub-groups of moths exhibit these relationships. Tribal-level deconstruction of richness and climatic niche patterns indicate idiosyncratic effects of biogeographic history for some of the less species-rich tribes, which in some cases exhibit distinct richness peaks away from the tropics. The study confirms, for a diverse insect group, overall richness associations of remarkable similarity to those documented for vertebrates and highlights the significant within-taxon structure that underpins emergent macroecological patterns. Results do not, however, meet predictions from vertebrate-derived hypotheses on how thermoregulation affects the strength of temperature-richness effects. Our study thus broadens the taxonomic focus in this data-deficient discourse. Our procedures of processing incomplete, scattered distribution data are a template for application to other taxa and regions.

    Keywords: Distribution modelling, Lepidoptera, Productivity, Spatial scale, Sphingidae, Tropics


  • Barve V, Otegui J (2016)

    bdvis: visualizing biodiversity data in R

    Bioinformatics btw333.

    Biodiversity studies are relying increasingly on primary biodiversity records (PBRs) for modelling and analysis. Because biodiversity data are frequently ‘harvested’—i.e. not collected by the researcher for that particular study, but obtained from data aggregators such as the Global Biodiversity Information Facility—researchers need to be aware of strengths and weaknesses of their data before they venture into further analysis. R is becoming a lingua franca of data exploration and analysis. Here, we describe an R package, bdvis, which facilitates efforts to understand the gaps and strengths of PBR data with quick and useful visualization functions.

    Keywords: Distribution modelling, Lepidoptera, Productivity, Spatial scale, Sphingidae, Tropics