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

  • 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

  • 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

  • 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


    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

  • Bateman B, Pidgeon A, Radeloff V, Flather C, Van Der Wal J, Akçakaya H et al. (2016)

    Potential breeding distributions of U.S. birds predicted with both short-term variability and long-term average climate data

    Ecological Applications.

    Climate conditions, such as temperature or precipitation averaged over several decades strongly affect species distributions, as evidenced by experimental results and a plethora of models demonstrating statistical relations between species occurrences and long-term climate averages. However, long-term averages can conceal climate changes that have occurred in recent decades and may not capture actual species occurrence well because the distributions of species, especially at the edges of their range, are typically dynamic and may respond strongly to short-term climate variability. Our goal here was to test whether bird occurrence models can be predicted by either covariates based on short-term climate variability or on long-term climate averages. We parameterized species distribution models (SDMs) based on either short-term variability or long-term average climate covariates for 320 bird species in the conterminous U.S., and tested whether any life-history trait-based guilds were particularly sensitive to short-term conditions. Models including short-term climate variability performed well based on their cross-validated AUC score (0.85), as did models based on long-term climate averages (0.84). Similarly, both models performed well compared to independent presence/absence data from the North American Breeding Bird Survey (independent AUC of 0.89 and 0.90, respectively). However, models based on short-term variability covariates more accurately classified true absences for most species (73% of true absences classified within the lowest quarter of environmental suitability versus 68%). In addition, they have the advantage that they can reveal the dynamic relationship between species and their environment because they capture the spatial fluctuations of species potential breeding distributions. With this information we can identify which species and guilds are sensitive to climate variability, identify sites of high conservation value where climate variability is low, and assess how species’ potential distributions may have already shifted due recent climate change. However, long-term climate averages require less data and processing time and may be more readily available for some areas of interest. Where data on short-term climate variability are not available, long-term climate information is a sufficient predictor of species distributions in many cases. However, short-term climate variability data may provide information not captured with long-term climate data for use in SDMs.

    Keywords: Maxent, North American breeding birds, climate change, guilds, species distribution model (SDM), species range

  • Bean W, Tange D, Osborn S (2016)

    A Suitability Model for White-Footed Voles with Insights into Habitat Associations at the Southern Boundary of Their Range

    Northwestern Naturalist 97(2) 105-112.

    Abstract The White-footed Vole (Arborimus albipes) is one of the least-studied small mammals in North America. Most reported occurrence data come from incidental captures from larger trapping efforts and have demonstrated a strong affinity for Red Alder (Alnus rubra) trees. Recent research represented a range expansion in western Oregon, but little is known about the species at the southern end of its range in California. We developed a distribution model for the species to identify areas best targeted for additional White-footed Vole research. We used this model to survey by trapping in Humboldt and Del Norte Counties, California, and documented 3 new occurrences for the species. These 3 occurrences were incorporated into a final distribution model. This model suggests the possibility of White-footed Vole occurrence in southern Humboldt and northern Mendocino Counties, which would represent a southern expansion of their range. White-footed Voles were captured in areas with smaller alders than non-capture...

    Keywords: Arborimus albipes, Del Norte County, Humboldt County, Maxent, White-footed Vole, niche limits, species distribution model

  • Blaine Marchant D, Soltis D, Soltis P (2016)

    Patterns of abiotic niche shifts in allopolyploids relative to their progenitors

    New Phytologist.

    Polyploidy has extensive genetic, physiological, morphological, and ecological ramifications. While the patterns underlying the genetic and morphological consequences of polyploidy are being rapidly elucidated, the effects on ecological niche are still largely unknown. This study investigated 13 allopolyploid systems in North America (10 ferns and three angiosperms) using digitized natural history museum specimens. The abiotic niches of the allopolyploids were compared with those of their diploid progenitors using ecological niche modeling, niche analyses, and multivariate analyses. We identified four patterns of niche shifts through our analyses: niche expansion, niche contraction, niche intermediacy, and niche novelty. The classification of these shifts depended on the amount of niche overlap and breadth between the polyploid and progenitors. The most common niche shift was niche intermediacy in which the polyploid inhabited a geographic range between that of the progenitors and had a high degree of niche overlap. Each polyploid had at least partial geographic sympatry and abiotic niche overlap with one of its progenitors, suggesting that biotic and/or microclimate factors may play a larger role in polyploid establishment than previously hypothesized. This study provides a baseline for future comparisons of the diverse outcomes of genome merger and duplication on abiotic niche preference.

    Keywords: Arborimus albipes, Del Norte County, Humboldt County, Maxent, White-footed Vole, niche limits, species distribution model

  • Bocsi T, Allen J, Bellemare J, Kartesz J, Nishino M, Bradley B (2016)

    Plants' native distributions do not reflect climatic tolerance

    Diversity and Distributions.

    Aim Biogeographers have long known that plant species do not fully encompass their fundamental niche. Nonetheless, in practice, species distribution modelling assumes that plant distributions represent a reasonable approximation of their environmental tolerance. For ecological forecasting, projections of habitat loss due to climate change assume that many species will be unable to tolerate climate conditions outside of those found within their current distributional ranges. We aim to test how well occurrences in the native range approximate the climatic conditions in which plant species can survive. Location Continental USA. Methods We compared the climatic conditions between occurrences in the US native versus US non-native ranges using 144 non-invasive plant species. We quantified differences in January minimum temperature, July maximum temperature and annual precipitation as indicators of climatic tolerance. We also compared modelled potential distributions throughout the US based on native and total ranges to test how expanded climatic tolerance translates into predicted geographical range. Results Most species (86%) had non-native occurrences in climates outside those described by their native distributions. For the 80 species with lower minimum temperatures at non-native occurrences, the median expansion of minimum temperature tolerance was −2.9 °C. Similarly, for the 90 species with lower precipitation at non-native occurrences, the median expansion of minimum annual precipitation was −23 cm. Broader climatic conditions at non-native occurrences expanded the modelled potential geographical range by a median of 35%, with smaller range species showing larger expansions of potential geographical range. Main conclusions Our results show that plants' native ranges strongly underestimate climatic tolerance, leading species distribution models to underpredict potential range. The climatic tolerance of species with narrow native ranges appears most prone to underestimation. These findings suggest that many plants will be able to persist in situ with climate change for far longer than projected by species distribution models.

    Keywords: Maxent, climate tolerance, climatic suitability, dispersal, ecological niche, endemic plants, range limits, range size, species distribution modelling