Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from Canada.
For all researches, please visit our "Peer-reviewed publications" page.

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


  • Cheek M, Semple J (2016)

    First official record of naturalised populations of Solidago altissima L. var. pluricephala M.C. Johnst. (Asteraceae: Astereae) in Africa

    South African Journal of Botany 105 333-336.

    Solidago altissima var. pluricephala is recorded for the first time as naturalised in Africa, with two populations detected in South Africa. One 0.5ha population has been found near Harding and another of 403 shoots near Hilton, both in KwaZulu-Natal. A projected species distribution model for South Africa indicates that the grassland biome is the most at risk from invasion by this species. These plants are most likely garden escapees although we are uncertain how widely they are cultivated in South Africa.

    Keywords: Distribution model, Golden rods, Grasslands, Invasive species, Ornamental plants


  • 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: Distribution model, Golden rods, Grasslands, Invasive species, Ornamental plants


  • 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: Distribution model, Golden rods, Grasslands, Invasive species, Ornamental plants


  • 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


  • Posso-Terranova A, Andrés J (2016)

    Complex niche divergence underlies lineage diversification in Oophaga poison frogs

    Journal of Biogeography.

    Aim Despite the incredible diversity of lowland tropical rain forests, we still have limited understanding of the drivers of speciation in these ecoregions. Here, we investigated the relative contribution of geographical and environmental factors to the diversification of a Neotropical genus of poison frogs (Oophaga). Location Central and South America, including regions from southern Nicaragua to northern Ecuador. Methods We generated gene genealogies (12S, 16S, COI, CytB and tRNA-val, SIAH1, H3 and Rag1) and used species phylogenetic methods (MDC and *beast) to generate a robust phylogeny of Oophaga frogs. Then, we combined the resulting phylogenetic hypothesis with detailed geographical data and environmental niche modelling (ENM) to test the role of geographical isolation, climatic niche divergence and altitudinal gradients. Results Gene genealogies were discordant and did not show exclusive genealogical patterns; however, species tree resolved the phylogenetic relationship among Oophaga species with strong node support (> 0.9 ML/BPP). Geographical ranges showed little overlap between distantly related species. However, within the South American and Central American clades, sister taxa showed substantially overlapping ranges. Analyses of ecological disparity (DTT) indicated a departure from a neutral (Brownian) model of evolution, and age-range correlations, predicted niche occupancy profiles, and Seeva analyses showed that different species tend to evolve under different potential climatic niches. Main conclusions Oophaga frogs originated in Central America and reached South America after the closure of the Panama Isthmus. The South- and Central-American clades of this genus have convergently evolved to similar patterns of geographical distribution and niche occupancy. Within clades, sister taxa showed parapatric distributions replacing each other along elevational gradients as predicted by the models of divergence along continuous ecological gradients. Accordingly, we found strong shifts in climatic niches throughout the history of these two clades. However, the largest niche shifts seem to post-date the final elevation of the Talamanca and northern Andes. Overall, our data suggest that speciation along climatic gradients on a structured landscape has been a major evolutionary force behind the diversification of Oophaga poison frogs.

    Keywords: dendrobatids, ecological speciation, neotropics, niche divergence, niche modelling, phylogenetics


  • 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


  • Spalink D, Drew B, Pace M, Zaborsky J, Starr J, Cameron K et al. (2016)

    Biogeography of the cosmopolitan sedges (Cyperaceae) and the area-richness correlation in plants

    Journal of Biogeography.

    Aim Across angiosperm families, the area occupied by a family is strongly correlated with its richness. We explore the causes of this area-richness correlation using the cosmopolitan family, Cyperaceae Juss., as a model. We test the hypothesis that, despite a proposed tropical origin, temperate lineages in the family diversified at elevated rates. We test the hypothesis that the area-richness correlation is maintained within intrafamilial clades, and that this relationship could be described as a function of niche space. We also test the hypothesis that the partitioning of geographical and ecological space, not the extent of this space, is the factor most closely associated with clade richness. Location Cosmopolitan. Methods We use molecular data from four genes sequenced in 384 taxa to develop a chronogram of Cyperaceae. We then develop a model of ancestral ranges and measure rates of diversification throughout the history of the family. Integrating data from over 4,800,000 digitized herbarium records, we characterize the range and niche of more than 4500 species and test for correlations of the species richness maintained within clades with range size, range partitioning, range overlap, niche, clade age and rate of diversification. Results Cyperaceae originated in South America in the late Cretaceous and subsequently dispersed throughout the globe. Of three increases in diversification rate, two occurred in the temperate Northern Hemisphere. The variable most closely associated with clade richness is the partitioning of geographical space by species within each clade. Main conclusions We show that species-rich clades in Cyperaceae are not only more widespread, occupy more niche space, and diversify more quickly, but also exhibit patterns that are consistent with the partitioning of geographical and ecological space as a major correlate to diversification.

    Keywords: BAMM, BioGeoBEARS, Cyperaceae, Poales, area-richness correlation, beast, herbarium specimens, historical biogeography