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


  • 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


  • 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


  • Bush M, McMichael C (2016)

    Holocene Variability of an Amazonian Hyperdominant

    Journal of Ecology.

    Little is known regarding the long-term stability or instability of Amazonian plant communities. We assessed whether the most abundant species, hyperdominants, may have risen to prominence at the Pleistocene-Holocene transition, following subsequent changes in moisture regimes, or as a result of human activity later in the Holocene. The fossil pollen history of the commonest western Amazonian tree, Iriartea deltoidea (hereafter Iriartea), is investigated using fossil pollen data from 13 lakes. Iriartea is a monospecific genus with diagnostic pollen. It is also considered a ‘useful’ plant, and its abundance could have been enriched by human action. Iriartea pollen was found to have increased in abundance in the last 3000 years, but did not show a consistent relationship with human activity. The suggestion that the hyperdominants in modern Amazonian forests are a legacy of pre-Columbian people is unsupported. The abundance of Iriartea pollen is related to increasing precipitation, not human activity over the last 3000 years. This member of the hyperdominant category of Amazonian trees has only recently acquired this status. Synthesis: Our findings our consistent with the observation that communities in complex systems are ephemeral. The populations of even the most abundant species can change over a few tens of generations. The relative abundance of tree species, even in relatively stable systems such as those of Amazonian floodplains, changes on ecological not evolutionary timescales.

    Keywords: Anthropocene, Climate change, Forest enrichment, Fossil charcoal, Fossil pollen, Human disturbance, Hyperdominant tree, Iriartea deltoidea, Palaeoecology, Plant–climate interactions


  • Bush M, Correa-Metrio A, McMichael C, Sully S, Shadik C, Valencia B et al. (2016)

    A 6900-year history of landscape modification by humans in lowland Amazonia

    Quaternary Science Reviews 141 52-64.

    A sedimentary record from the Peruvian Amazon provided evidence of climate and vegetation change for the last 6900 years. Piston cores collected from the center of Lake Sauce, a 20 m deep lake at 600 m elevation, were 19.7 m in length. The fossil pollen record showed a continuously forested catchment within the period of the record, although substantial changes in forest composition were apparent. Fossil charcoal, found throughout the record, was probably associated with humans setting fires. Two fires, at c. 6700 cal BP and 4270 cal BP, appear to have been stand-replacing events possibly associated with megadroughts. The fire event at 4270 cal BP followed a drought that caused lowered lake levels for several centuries. The successional trajectories of forest recovery following these large fires were prolonged by smaller fire events. Fossil pollen of Zea mays (cultivated maize) provided evidence of agricultural activity at the site since c. 6320 cal BP. About 5150 years ago, the lake deepened and started to deposit laminated sediments. Maize agriculture reached a peak of intensity between c. 3380 and 700 cal BP. Fossil diatom data provided a proxy for lake nutrient status and productivity, both of which peaked during the period of maize cultivation. A marked change in land use was evident after c. 700 cal BP when maize agriculture was apparently abandoned at this site. Iriartea, a hyperdominant of riparian settings in western Amazonia, increased in abundance within the last 1100 years, but declined markedly at c. 1070 cal BP and again between c. 80 and −10 cal BP.

    Keywords: Agriculture, Forest enrichment, Fossil charcoal, Fossil diatoms, Fossil pollen, Human disturbance, Iriartea, Maize, Mauritia, Pre-Columbian


  • Butterfield B, Copeland S, Munson S, Roybal C, Wood T (2016)

    Prestoration: using species in restoration that will persist now and into the future

    Restoration Ecology.

    Climate change presents new challenges for selecting species for restoration. If migration fails to keep pace with climate change, as models predict, the most suitable sources for restoration may not occur locally at all. To address this issue, we propose a strategy of “prestoration”: utilizing species in restoration for which a site represents suitable habitat now and into the future. Using the Colorado Plateau, United States, as a case study, we assess the ability of grass species currently used regionally in restoration to persist into the future using projections of ecological niche models (or climate envelope models) across a suite of climate change scenarios. We then present a technique for identifying new species that best compensate for future losses of suitable habitat by current target species. We found that the current suite of species, selected by a group of experts, is predicted to perform reasonably well in the short term, but that losses of prestorable habitat by mid-century would approach 40%. Using an algorithm to identify additional species, we found that fewer than 10 species could compensate for nearly all of the losses incurred by the current target species. This case study highlights the utility of integrating ecological niche modeling and future climate forecasts to predict the utility of species in restoring under climate change across a wide range of spatial and temporal scales.

    Keywords: biodiversity, climate envelope model, dispersal limitation, priority species, species distribution model


  • Cardinal-McTeague W, Sytsma K, Hall J (2016)

    Biogeography and diversification of Brassicales: A 103million year tale

    Molecular Phylogenetics and Evolution.

    Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 150 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6–62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6–40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.

    Keywords: Arabidopsis thaliana, BAMM, BEAST, BioGeoBEARS, Brassicaceae, Cleomaceae, K–Pg extinction event, Pierid butterflies, Species diversification, Whole genome duplication