Uses of GBIF in scientific research

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

List of publications

  • 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


  • Dunne J, Maschner H, Betts M, Huntly N, Russell R, Williams R et al. (2016)

    The roles and impacts of human hunter-gatherers in North Pacific marine food webs.

    Scientific reports 6 21179.

    There is a nearly 10,000-year history of human presence in the western Gulf of Alaska, but little understanding of how human foragers integrated into and impacted ecosystems through their roles as hunter-gatherers. We present two highly resolved intertidal and nearshore food webs for the Sanak Archipelago in the eastern Aleutian Islands and use them to compare trophic roles of prehistoric humans to other species. We find that the native Aleut people played distinctive roles as super-generalist and highly-omnivorous consumers closely connected to other species. Although the human population was positioned to have strong effects, arrival and presence of Aleut people in the Sanak Archipelago does not appear associated with long-term extinctions. We simulated food web dynamics to explore to what degree introducing a species with trophic roles like those of an Aleut forager, and allowing for variable strong feeding to reflect use of hunting technology, is likely to trigger extinctions. Potential extinctions decreased when an invading omnivorous super-generalist consumer focused strong feeding on decreasing fractions of its possible resources. This study presents the first assessment of the structural roles of humans as consumers within complex ecological networks, and potential impacts of those roles and feeding behavior on associated extinctions.

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


  • Hattab T, Leprieur F, Lasram F, Gravel D, Loc'h F, Albouy C (2016)

    Forecasting fine-scale changes in the food-web structure of coastal marine communities under climate change

    Ecography.

    Climate change is inducing deep modifications in local communities worldwide as a consequence of individualistic species range shifts. Understanding how complex interaction networks will be reorganized under climate change represents a major challenge in the fields of ecology and biogeography. However, forecasting the potential effects of climate change on local communities, and more particularly on food-web structure, requires the consideration of highly structuring processes, such as trophic interactions. A major breakthrough is therefore expected by combining predictive models integrating habitat selection processes, the physiological limits of marine species and their trophic interactions. In this study, we forecasted the potential impacts of climate change on the local food-web structure of the highly threatened Gulf of Gabes ecosystem located in the south of the Mediterranean Sea. We coupled the climatic envelope and habitat models to an allometric niche food web model, hence taking into account the different processes acting at regional (climate) and local scales (habitat selection and trophic interactions). Our projections under the A2 climate change scenario showed that future food webs would be composed of smaller species with fewer links, resulting in a decrease of connectance, generality, vulnerability and mean trophic level of communities and an increase of the average path length, which may have large consequences on ecosystem functioning. The unified framework presented here, by connecting food-web ecology, biogeography and seascape ecology, allows the exploration of spatial aspects of interspecific interactions under climate change and improves our current understanding of climate change impacts on local marine food webs.

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


  • Lee-Yaw J, Kharouba H, Bontrager M, Mahony C, Csergő A, Noreen A et al. (2016)

    A synthesis of transplant experiments and ecological niche models suggests that range limits are often niche limits

    Ecology Letters.

    Global change has made it important to understand the factors that shape species' distributions. Central to this area of research is the question of whether species' range limits primarily reflect the distribution of suitable habitat (i.e. niche limits) or arise as a result of dispersal limitation. Over-the-edge transplant experiments and ecological niche models are commonly used to address this question, yet few studies have taken advantage of a combined approach for inferring the causes of range limits. Here, we synthesise results from existing transplant experiments with new information on the predicted suitability of sites based on niche models. We found that individual performance and habitat suitability independently decline beyond range limits across multiple species. Furthermore, inferences from transplant experiments and niche models were generally concordant within species, with 31 out of 40 cases fully supporting the hypothesis that range limits are niche limits. These results suggest that range limits are often niche limits and that the factors constraining species' ranges operate at scales detectable by both transplant experiments and niche models. In light of these findings, we outline an integrative framework for addressing the causes of range limits in individual species.

    Keywords: Abiotic constraints, climate, dispersal limitation, fitness, geographical distribution, over the edge transplant, species distribution modelling


  • Moyes C, Shearer F, Huang Z, Wiebe A, Gibson H, Nijman V et al. (2016)

    Predicting the geographical distributions of the macaque hosts and mosquito vectors of Plasmodium knowlesi malaria in forested and non-forested areas.

    Parasites & vectors 9(1) 242.

    BACKGROUND: Plasmodium knowlesi is a zoonotic pathogen, transmitted among macaques and to humans by anopheline mosquitoes. Information on P. knowlesi malaria is lacking in most regions so the first step to understand the geographical distribution of disease risk is to define the distributions of the reservoir and vector species. METHODS: We used macaque and mosquito species presence data, background data that captured sampling bias in the presence data, a boosted regression tree model and environmental datasets, including annual data for land classes, to predict the distributions of each vector and host species. We then compared the predicted distribution of each species with cover of each land class. RESULTS: Fine-scale distribution maps were generated for three macaque host species (Macaca fascicularis, M. nemestrina and M. leonina) and two mosquito vector complexes (the Dirus Complex and the Leucosphyrus Complex). The Leucosphyrus Complex was predicted to occur in areas with disturbed, but not intact, forest cover (> 60 % tree cover) whereas the Dirus Complex was predicted to occur in areas with 10-100 % tree cover as well as vegetation mosaics and cropland. Of the macaque species, M. nemestrina was mainly predicted to occur in forested areas whereas M. fascicularis was predicted to occur in vegetation mosaics, cropland, wetland and urban areas in addition to forested areas. CONCLUSIONS: The predicted M. fascicularis distribution encompassed a wide range of habitats where humans are found. This is of most significance in the northern part of its range where members of the Dirus Complex are the main P. knowlesi vectors because these mosquitoes were also predicted to occur in a wider range of habitats. Our results support the hypothesis that conversion of intact forest into disturbed forest (for example plantations or timber concessions), or the creation of vegetation mosaics, will increase the probability that members of the Leucosphyrus Complex occur at these locations, as well as bringing humans into these areas. An explicit analysis of disease risk itself using infection data is required to explore this further. The species distributions generated here can now be included in future analyses of P. knowlesi infection risk.

    Keywords: Entomology, Infectious Diseases, Parasitology, Tropical Medicine


  • Rivkin L, Case A, Caruso C (2016)

    Why is gynodioecy a rare but widely distributed sexual system? Lessons from the Lamiaceae.

    The New phytologist.

    Gynodioecy, a sexual system where females and hermaphrodites co-occur, is found in < 1% of angiosperm species. To understand why gynodioecy is rare, we need to understand why females are maintained in some lineages, but not in others. We modelled the evolution of gynodioecy in the Lamiaceae, and investigated whether transition rates between gynodioecious and nongynodioecious states varied across the family. We also investigated whether the evolution of gynodioecy was correlated with the evolution of a herbaceous growth form and temperate distribution. Transition rates differed between Lamiaceae subfamilies. In the Nepetoideae, there were many transitions towards gynodioecy (n = 11), but also many reversions to nongynodioecy (n = 29). In addition, a herbaceous growth form, but not a temperate distribution, affected the rate of transitions both towards and away from gynodioecy; transitions towards gynodioecy occurred ˜16 times more frequently and transitions away from gynodioecy occurred ˜11 times more frequently in herbaceous lineages than in woody lineages. Within the Lamiaceae, lineages in which gynodioecy has frequently evolved also have a high rate of reversions to the nongynodioecious state. Consequently, to understand why gynodioecy is rare, we need to understand why sexual systems are more evolutionarily labile in some lineages than in others.

    Keywords: angiosperm, herbaceous, phylogeny, temperate zone, transition rate


  • Rodrigues A, Stefanović S (2016)

    Present-Day Genetic Structure of the Holoparasite Conopholis americana (Orobanchaceae) in Eastern North America and the Location of Its Refugia during the Last Glacial Cycle

    International Journal of Plant Sciences 177(2) 132-144.

    Premise of research. Understanding how various organisms respond to previous changes in climate could provide insight into how they may respond or adapt to the current changes. Conopholis americana has a broad distribution across eastern North America, covering both previously glaciated and unglaciated regions. In this study, we investigated the postglacial history and phylogeographic structure of this parasitic plant species to characterize its genetic variation and structure and to identify the number and locations of refugia.Methodology. Molecular data from 10 microsatellite markers and DNA sequences from the plastid gene/introns (clpP) were obtained for 281 individuals sampled from 75 populations spanning the current range of the species in eastern North America and analyzed using a variety of phylogeographic methods. Distribution modeling was carried out to determine regions with relatively suitable climate niches for populations at the Last Glacial Maximum (LGM) and present.Pivotal results. We infer...

    Keywords: Last Glacial Maximum, eastern North America, microsatellites, parasitic plant, phylogeography, plastid DNA


  • Zhang L, Liu S, Sun P, Wang T, Wang G, Wang L et al. (2016)

    Using DEM to predict Abies faxoniana and Quercus aquifolioides distributions in the upstream catchment basin of the Min River in southwest China

    Ecological Indicators 69 91-99.

    The species distribution model (SDM), which is used to spatially predict species distributions, can also identify the probable causes of the location of certain species (i.e. the mathematical description of habitat requirements). Therefore, SDM has the potential to guide resource management and biodiversity conservation. In the topographically complex terrain, SDMs are often complicated by the lack of environmental data; however, the first information that is typically obtained for these analyses is a topographic map. Here, the possibility of using 16 predictor variables derived from the digital elevation model (DEM) to model the distributions of Abies faxoniana and Quercus aquifolioides in the mountainous upstream catchment basin of the Min River (UCBM) in southwest China was investigated. In particular, with the ensemble modeling approach based on eight niche models and nine model-training and -testing datasets, changes in model performance and shifts in the explanatory power of the predictor variable over five different levels of spatial resolution (30m, 90m, 120m, 240m, 900m) were assessed. Almost all models succeed in predicting the distributions of both species, although predictive accuracies differed significantly among spatial scales and model classes. On average, model accuracies increased to the highest level at the meso-scale (120m and 240m for A. faxoniana and Q. aquifolioides, respectively) and then decreased as resolution became coarser, indicating that high spatial resolution does not imply a better model. The relative importance rankings for each topographical variable were consistent across all spatial scales, but their explanatory powers did differ significantly among spatial scales. Elevation and terrain-distributed solar radiation for growing season (SRG) drive the distributions of A. faxoniana and Q. aquifolioides with a much higher level of confidence than other predictors across all spatial scales; the former tended to decrease, and the latter tended to increase when spatial resolution became coarse. Our findings confirm that DEM can be used exclusively and effectively to predict species distribution. Multi-scale analysis is needed to detect highly subtle variations in species habitat requirements, and to select the spatial scale that corresponds to known spatial characteristics of the species habitat. This has broad implications for distribution modeling of species in rugged terrain.

    Keywords: Digital elevation model, Forestation, Spatial resolution, Species distribution model, Topographical variable


  • Barbosa N, Fernandes G, Sanchez-Azofeifa A (2015)

    A relict species restricted to a quartzitic mountain in tropical America: an example of microrefugium?

    Acta Botanica Brasilica 29(3) 299-309.

    We examined the distribution of Coccoloba cereifera, a tropical endemic species that occurs in a small area in the Espinhaço mountain range, southeastern Brazil. It is hypothesized that its narrow distribution is strongly related to the spatially scattered distribution of sandfields. However, this soil type extends far beyond the small region where C. cereifera is currently found, indicating that other factors might be involved in the distribution of this species. Coccoloba cereifera also displays all traits of a relict population in a microrefugium. As a result, we were encouraged to explore other factors potentially related to the distribution of the species. In an attempt to aid in the understanding of the processes and mechanisms that lead C. cereiferato present the narrow actual distribution, we applied two distribution modelling approaches to investigate the potential distribution of the species beyond the small known distribution area. The distribution seems to be strongly associated with sandy patches/grasslands formed among rocky outcrops and is limited by some topoclimatic and/or topographic features. Some of them related to the existence of a microrefugium, a fact also suggested by the pattern of distribution of the species in the past. From the management point of view, the existence of a microrefugium in this area calls for changes in conservation efforts and priorities.

    Keywords: Coccoloba cereifera, Espinhaço Mountains, Serra do Cipó, maximum entropy, rupestrian grasslands


  • Breusing C, Johnson S, Tunnicliffe V, Vrijenhoek R (2015)

    Population structure and connectivity in Indo-Pacific deep-sea mussels of the Bathymodiolus septemdierum complex

    Conservation Genetics 750.

    Current pressures to mine polymetallic sulfide deposits pose threats to the animal communities found at deep-sea hydrothermal vents. Management plans aimed at preserving these unusual communities require knowledge of historical and contemporary forces that shaped the distri- butions and connectivity of associated species. As most vent research has focused on the eastern Pacific and mid-Atlantic ridge systems less is known about Indo-Pacific vents, where mineral extraction activities are imminent. Deep-sea mus- sels (Bivalvia: Mytilidae) of the genus Bathymodiolus include the morphotypic species B. septemdierum , B. brev- ior , B. marisindicus , and B. elongatus which are among the dominant vent taxa in western Pacific back-arc basins and the Central Indian Ridge. To assess their interpopulational relationships, we examined multilocus genotypes based on DNA sequences from four nuclear and four mitochondrial genes, and allozyme variation encoded by eleven genes. Bayesian assignment methods grouped mussels from seven widespread western Pacific localities into a single cluster, whereas the Indian Ocean mussels were clearly divergent. Thus, we designate two regional metapopulations. Notably, contemporary migration rates among all sites appeared to be low despite limited population differentiation, which high- lights the necessity of obtaining realistic data on recovery times and fine-scale population structure to develop and manage conservation units effectively. Future studies using population genomic methods to address these issues in a range of species will help to inform management plans aimed at mitigating potential impacts of deep-sea mining in the Indo-Pacific region

    Keywords: Allozymes, Bathymodiolus, Gene flow, Nuclear markers, mtDNA