Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from United States.
Extracted from the Mendeley GBIF Public Library.

List of publications

  • Baltensperger, A., Huettmann, F., 2015.

    Predictive spatial niche and biodiversity hotspot models for small mammal communities in Alaska: applying machine-learning to conservation planning

    Landscape Ecology.

    Context Changing global environmental conditions, especially at northern latitudes, are threatening to shift species distributions and alter wildlife communities. Objective We aimed to establish current distributions and community arrangements of small mammals to provide important baselines for monitoring and conserving biodiversity into the future. Methods We used 4,408 archived museum and open-access records and the machine learning algorithm, RandomForests, to create high-resolution spatial niche models for 17 species of rodents and shrews in Alaska. Models were validated using independent trapping results from 20 locations stratified along statewide mega-transects, and an average species richness curve was calculated for field samples. Community cluster analyses (varclus) identified geographic patterns of sympatry among species. Species models were summed to create the first small-mammal species richness map for Alaska. Results Species richness increased logarithmically to a mean of 3.3 species per location over 1,500 trap-nights. Distribution models yielded mean accuracies of 71 % (45–90 %), and maps correctly predicted a mean of 75 % (60–95 %) of occurrences correctly in the field. Top predictors included Soil Type, Ecoregion, Landfire Land-cover, December Sea Ice, and July Temperature at the geographic scale. Cluster analysis delineated five community groups (3–4 species/group), and species richness was highest (11–13 species) over the Yukon-Tanana Uplands. Conclusions Models presented here provide spatial predictions of current small mammal biodiversity in Alaska and an initial framework for mapping and monitoring wildlife distributions across broad landscapes into the future.

    Keywords: Arctic, Boreal Forest, Ecological niche modeling, Lemmings, Machine learning, Megatransect sampling, Open-access data, RandomForests, Shrews, Voles


  • Barker, B., Rodríguez-Robles, J., Cook, J., 2015.

    Climate as a driver of tropical insular diversity: comparative phylogeography of two ecologically distinctive frogs in Puerto Rico

    Ecography n/a-n/a.

    The effects of late Quaternary climate on distributions and evolutionary dynamics of insular species are poorly understood in most tropical archipelagoes. We used ecological niche models under past and current climate to derive hypotheses regarding how stable climatic conditions shaped genetic diversity in two ecologically distinctive frogs in Puerto Rico. Whereas the mountain coquí Eleutherodactylus portoricensis is restricted to montane forest in the Cayey and Luquillo Mountains, the red-eyed coquí E. antillensis is a habitat generalist distributed across the entire Puerto Rican Bank (Puerto Rico and the Virgin Islands, excluding St Croix). To test our hypotheses, we conducted phylogeographic and population genetic analyses based on mitochondrial and nuclear loci of each species across their range in Puerto Rico. Patterns of population differentiation in E. portoricensis, but not in E. antillensis, supported our hypotheses. For E. portoricensis, these patterns include: individuals isolated by long-term unsuitable climate in the Río Grande de Loíza Basin in eastern Puerto Rico belong to different genetic clusters; past and current climate strongly predicted genetic differentiation; and Cayey and Luquillo Mountains populations split prior to the last interglacial. For E. antillensis, these patterns include: genetic clusters did not fully correspond to predicted long-term unsuitable climate; and past and current climate weakly predicted patterns of genetic differentiation. Genetic signatures in E. antillensis are consistent with a recent range expansion into western Puerto Rico, possibly resulting from climate change and anthropogenic influences. As predicted, regions with a large area of long-term suitable climate were associated with higher genetic diversity in both species, suggesting larger and more stable populations. Finally, we discussed the implications of our findings for developing evidence-based management decisions for E. portoricensis, a taxon of special concern. Our findings illustrate the role of persistent suitable climatic conditions in promoting the persistence and diversification of tropical island organisms

    Keywords: Arctic, Boreal Forest, Ecological niche modeling, Lemmings, Machine learning, Megatransect sampling, Open-access data, RandomForests, Shrews, Voles


  • Botello, F., Sarkar, S., Sánchez-Cordero, V., 2015.

    Impact of habitat loss on distributions of terrestrial vertebrates in a high-biodiversity region in Mexico

    Biological Conservation 184 59-65.

    Mexico is considered a country of biological megadiversity because of its exceptional species richness and endemism. However, much of Mexico’s biodiversity is under threat due to a variety of factors, in particular, habitat loss. The Mexican legal standard (Norma Oficial Mexicana; NOM-ECOL-059-2010) uses four criteria to analyze specieś extinction risk at a national scale. However, when prioritizing areas for biodiversity conservation it is also important to incorporate knowledge of the conservation status of species at a more localized scale (regional, state, or municipal levels) for identifying possible risks associated with population declines. This paper focuses on Guerrero, which is the fourth most biologically diverse state in Mexico. The total extent of the conservation areas in Guerrero is low, amounting to 0.09% of its total area. We analyzed data for 582 terrestrial vertebrate species in Guerrero (53 amphibians, 115 reptiles, 334 birds and 80 mammals), modeling their potential distribution using a maximum entropy algorithm, and 114,555 occurrence records, and 23 predictive environmental (19 climatic and four topographical) variables. The portion of the potential distribution for each species including only remnant natural habitat was designated as its predicted distribution. The area of the predicted distribution was used to compute the fraction of natural habitat remaining for each species overlapping within decreed protected areas at the state and national levels, that is, for Guerrero and all of Mexico. Results show significant differences in the fraction of species’ predicted distribution and species’ potential distribution at different scales (state and national) and differences between the vertebrate groups analyzed. Because quantitative conservation targets are typically set for individual species, this exercise enables an analysis of the impact of the habitat lost on each species’ distribution by assessing the fraction of its predicted distribution that coincides with protected areas. We conclude that this must be part of systematic conservation planning to prioritize areas for potential conservation in Guerrero.

    Keywords: Biodiversity, Deforestation, Distribution, Guerrero, Maximum entropy modeling, Protected areas


  • Bradley, B., Early, R., Sorte, C., 2015.

    Space to invade? Comparative range infilling and potential range of invasive and native plants

    Global Ecology and Biogeography n/a-n/a.

    Aim Our understanding of potential ranges for native and non-native species is often based on their current geographic distributions. Non-native species have had less time than co-occurring native species to expand their ranges following introduction, so non-native ranges may under-represent suitable conditions. Therefore it is often assumed that species distribution models will predict disproportionately smaller potential ranges for non-natives than natives. We compare the distributions of native, endemic, alien and invasive plants to determine how the different range attributes of these groups might influence ecological forecasting. Location Continental USA. Methods We compared the geographic ranges of 13,575 plant species (9402 native, 2397 endemic, 1201 alien and 755 invasive) using (1) US only and (2) global distribution data from herbarium records. We calculated US longitudinal and latitudinal range extents as potential indicators of range-limiting factors, modelled potential range based on climate using principal components analysis, and calculated occupancy of potential ranges (range infilling). Results Contrary to expectations, modelled potential ranges were significantly larger for non-natives than natives, even for species with few occurrences. Distributions of native species, not invasive species, appeared strongly limited longitudinally. However, invasive plants occupied substantially less area within their climatically suitable ranges than native plants (lower range infilling). Main conclusions Invasive plant distributions were consistently broader, both climatically and geographically, than comparable native species. This suggests that invasive plant distribution models at regional scales are not underpredicting potential ranges relative to models for native species. In contrast, the comparatively limited longitudinal ranges of native species suggest a high degree of non-climatic limitation, which is likely to cause distribution models to underpredict the potential ranges of native species. Invasive plants have not achieved the degree of range infilling expected relative to natives. Thus, plants introduced to the US still have plenty of space to invade.

    Keywords: Alien, bioclimatic envelope model, dispersal, ecological niche model, equilibrium, exotic, introduced, occupancy, plant invasion


  • Davis, M., 2015.

    Evolutionary Relationships of the Deep-Sea Pearleyes (Aulopiformes: Scopelarchidae) and a New Genus of Pearleye from Antarctic Waters

    Copeia 103(1) 64-71.

    This study investigates the evolutionary relationships among species in the family Scopelarchidae with molecular (eight genes) and morphological data. A new genus of pearleye is diagnosed, Lagiacrusichthys, new genus, from a previously described species (Benthalbella macropinna) distributed in Antarctic waters. The diagnosis of Lagiacrusichthys is based on molecular and anatomical information, including a highly reduced dorsal fin (5–6 rays) and a long anal fin (35–39 rays). The results represent the most taxonomically comprehensive molecular and total evidence hypotheses of the evolutionary relationships of the pearleyes to date (13 of 18 species), and these frameworks are used to comment on the historical biogeography of this widespread group. It is inferred that the pearleyes likely first evolved in central-tropical waters, with two independent invasions into Antarctic waters.

    Keywords: Alien, bioclimatic envelope model, dispersal, ecological niche model, equilibrium, exotic, introduced, occupancy, plant invasion


  • Ferretti, F., Morey Verd, G., Seret, B., Sulić Šprem, J., Micheli, F., 2015.

    Falling through the cracks: the fading history of a large iconic predator

    Fish and Fisheries n/a-n/a.

    Human impact on the oceans predates scientific observation, which for many animal populations has captured only recent changes. Such a limited knowledge can hamper finding optimal management and conservation strategies including setting appropriate recovery targets. Sawfishes are among the most endangered marine vertebrates in the ocean. Historical human impacts have resulted in sawfish extinction in many coastal areas around the world; however, in the Mediterranean Sea, their past presence and possible extinction have been debated for decades. Recently, it was concluded that the region never hosted resident populations because of unsuitable environmental conditions. Through an extensive bibliographic and archival search and an extinction analysis, we reconstructed the history of sawfishes in the Mediterranean Sea. Between 1576 and 1959, there were 48 independent accounts of the occurrence of two sawfish species (Pristis pristis, Pristidae and Pristis pectinata, Pristidae), including 24 documented catches. Sawfishes were mainly recorded in the western Mediterranean, in areas close to large rivers with light human impact. Most of the documented individuals were juveniles, suggesting local parturition. Extinction analyses yielded variable results and were affected by the sparseness of records but suggested that both species went extinct in the Mediterranean Sea in the 1960s–1970s. Our results challenge current assumptions on sawfish ecology and biogeography, offer new options for sawfish conservation in the Atlantic and highlight the importance of historical analyses for reconstructing ecosystem baselines and setting recovery targets.

    Keywords: bibliographic analysis, ecological baselines, extinction analyses, historical ecology, museum records, sawfish


  • Feuda, R., Bannikova, A., Zemlemerova, E., Di Febbraro, M., Loy, A., Hutterer, R., Aloise, G., Zykov, A., Annesi, F., Colangelo, P., 2015.

    Tracing the evolutionary history of the mole, Talpa europaea , through mitochondrial DNA phylogeography and species distribution modelling

    Biological Journal of the Linnean Society 114(3) 495-512.

    Our understanding of the effect of Pleistocene climatic changes on the biodiversity of European mammals mostly comes from phylogeographical studies of non-subterranean mammals, whereas the influence of glaciation cycles on subterranean mammals has received little attention. The lack of data raises the question of how and to what extent the current amount and distribution of genetic variation in subterranean mammals is the result of Pleistocene range contractions/expansions. The common mole (Talpa europaea) is a strictly subterranean mammal, widespread across Europe, and represents one of the best candidates for studying the influence of Quaternary climatic oscillation on subterranean mammals. Cytochrome b sequences, as obtained from a sampling covering the majority of the distribution area, were used to evaluate whether Pleistocene climate change influenced the evolution of T. europaea and left a trace in the genetic diversity comparable to that observed in non-subterranean small mammals. Subsequently, we investigated the occurrence of glacial refugia by comparing the results of phylogeographical analysis with species distribution modelling. We found three differentiated mitochondrial DNA lineages: two restricted to Spain and Italy and a third that was widespread across Europe. Phylogenetic inferences and the molecular clock suggest that the Spanish moles represent a highly divergent and ancient lineage, highlighting for the first time the paraphyly of T. europaea. Furthermore, our analyses suggest that the genetic break between the Italian and the European lineages predates the last glacial phase. Historical demography and spatial principal component analysis further suggest that the Last Glacial Maximum left a signature both in the Italian and in the European lineages. Genetic data combined with species distribution models support the presence of at least three putative glacial refugia in southern Europe (France, Balkan Peninsula and Black Sea) during thelast glacial maximum that likely contributed to post-glacial recolonization of Europe. By contrast, the Italian lineage remained trapped in the Italian peninsula and, according to the pattern observed in other subterranean mammals, did not contribute to the recolonization of northern latitudes

    Keywords: Europe, Last Glacial Maximum, SDM, cytochrome b, glacial refugia, historical demography, paraphyly, phylogenetics, sPCA


  • Forrestel, E., Donoghue, M., Smith, M., 2015.

    Functional differences between dominant grasses drive divergent responses to large herbivore loss in mesic savanna grasslands of North America and South Africa

    Journal of Ecology n/a-n/a.

    1.Grazing and fire are disturbances integral to the evolution and maintenance of savanna grasslands. Humans are altering or completely eliminating these disturbance regimes at a global scale, with important consequences for savanna ecosystem structure and function. It is unknown whether the alteration of these disturbance regimes will have similar effects on grass communities of savanna grasslands in different geographic regions that vary in their biogeographic and evolutionary histories, as well as in the diversity of extant grazers. 2.Here we examined the effects of large herbivore loss on different aspects of grass community structure – taxonomic, phylogenetic, and functional – across a range of fire frequencies in C4-dominated mesic savanna grassland sites of North America (Konza Prairie Biological Station, Kansas, USA) and South Africa (Kruger National Park). The goal of the study was to determine whether the loss of large herbivores exerted a consistent effect on the grass communities of two physiognomically similar grasslands with different biogeographic and grazing histories. 3.The removal of large herbivores resulted in divergent responses in the grass communities at Konza and Kruger that was consistent across fire treatments. At Konza, there was a rapid and significant response to grazing exclusion while the response was muted, and transient at Kruger. Functional syndromes associated with grazing resistance were generally conserved across sites, and it was the functional strategies of the dominant species at each site that drove the divergent responses. Further, our study supports the hypothesis that grazing and aridity may be selective forces that act in parallel as those species that were grazing resistant also occupied drier niches. 4.Synthesis: Our study demonstrates that savanna grassland communities with different biogeographic and grazing histories respond differently to the removal of large herbivores, and that climate, fire, and grazing are interactive forces in maintaining savanna grassland diversity and function. We show that the functional attributes of the dominant grasses, which are in part driven by the biogeographic and grazing history experienced, are the most relevant in predicting the response of savanna ecosystems to the loss of large herbivores.

    Keywords: biogeography, determinants of plant community diversity and stru, disturbance, dominant species, drought, fire, functional traits, grass community, grazing, phylogeny


  • Fuller, P., Neilson, M., 2015.

    The U.S. Geological Survey’s Nonindigen ous Aquatic Species Da tabase: over thirty years of tracking introduced aquatic species in the Unit ed States (and counting)

    Management of Biological Invasions 6.

    The U.S. Geological Survey’s Nonindigenous Aquatic Species (NAS) Databa se has tracked introductions of freshwater aquatic organ isms in the United States for the past four decades. A website provides access to occurrence reports, distribution maps, and fact sheets fo r more than 1,000 species. The site also includes an on-line reporting system and an alert system for new occurrences. We provide an historical o verview of the database, a description of its current capabilities and functionality, and a basic characterization of the data contained withi n the database.

    Keywords: United States, aquatic species, database, trends


  • Garcia, T. S., Rowe, J. C., Doyle, J., 2015.

    A tad too high: Sensitivity to UV-B radi ation may limit invasion potential of American bullfrogs ( Lithobates catesbeianus ) in the Pacific Nort hwest invasion range

    Aquatic Invasions 10.

    Biological invasion potential can be strongly influenced by abiotic factors such as temperature, water availability, and solar radiation. Invasive species that possess phenotypically plasti c traits can mediate impacts from these stressors, but may be una ble to recognize and respond to dangerous levels in a novel environment. Understanding potential constraints on appropriate trait resp onses induced by abiotic stressors can aid in the management and cont rol of important invaders. Our study explored tolerance and plas tic trait response to UV-B radi ation in an invasive anur an, the American bullfrog ( Lithobates catesbeianus Shaw, 1802). We experimentally quantified larval mortality ra tes and color change responses across two la rval size classes. In a second experim ent, we investigated the potential for a correlated color change and behavioral (refuge use) response in the small size class. We pr edicted that individuals would respond to stressfu l and potentially harmful UV-B exposure ra tes with darkening of body coloration, and when refuge was available, a co rrelated defense strategy utilizing both color change and refu ge. We found an increase in larval mortality across both size classes at UV -B exposure rates typical to both low and high elevation aquati c breeding sites (10- 12μW/cm 2 and 20-24μW/cm 2 , respectively). Only bullfrog larvae in the small size class exhibited a darkening in body color when exposed to high UV-B treatments. Although this smaller size class did exhibit color pl asticity, individuals did not correlate c hanges in body coloration with changes in refuge use. These results s uggest ontogenetic differences (estim ated by size class) in plast ic color response to UV-B stress as well as cons traints on behavioral use of refuge. These findings are important in understanding diffe rences in bullfrog occupancy of breeding habitats across an elevational gradient, particularly in Oregon’s Cascade Mountain Range, whe re bullfrog distributions are currently limited at elevations above 1000m

    Keywords: American bullfrog, invasion, ultraviolet radi ati