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


  • 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


  • 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


  • Brown K, Parks K, Bethell C, Johnson S, Mulligan M (2015)

    Predicting plant diversity patterns in Madagascar: understanding the effects of climate and land cover change in a biodiversity hotspot.

    PloS one 10(4) e0122721.

    Climate and land cover change are driving a major reorganization of terrestrial biotic communities in tropical ecosystems. In an effort to understand how biodiversity patterns in the tropics will respond to individual and combined effects of these two drivers of environmental change, we use species distribution models (SDMs) calibrated for recent climate and land cover variables and projected to future scenarios to predict changes in diversity patterns in Madagascar. We collected occurrence records for 828 plant genera and 2186 plant species. We developed three scenarios, (i.e., climate only, land cover only and combined climate-land cover) based on recent and future climate and land cover variables. We used this modelling framework to investigate how the impacts of changes to climate and land cover influenced biodiversity across ecoregions and elevation bands. There were large-scale climate- and land cover-driven changes in plant biodiversity across Madagascar, including both losses and gains in diversity. The sharpest declines in biodiversity were projected for the eastern escarpment and high elevation ecosystems. Sharp declines in diversity were driven by the combined climate-land cover scenarios; however, there were subtle, region-specific differences in model outputs for each scenario, where certain regions experienced relatively higher species loss under climate or land cover only models. We strongly caution that predicted future gains in plant diversity will depend on the development and maintenance of dispersal pathways that connect current and future suitable habitats. The forecast for Madagascar's plant diversity in the face of future environmental change is worrying: regional diversity will continue to decrease in response to the combined effects of climate and land cover change, with habitats such as ericoid thickets and eastern lowland and sub-humid forests particularly vulnerable into the future.

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


  • Costea, M., García, M. A., Stefanovic S (2015)

    A Phylogenetically Based Infrageneric Classification of the Parasitic Plant Genus Cuscuta (Dodders, Convolvulaceae)

    Systematic Botany 40(1) 269-285.

    Cuscuta (dodders, Convolvulaceae) is one of the largest and most economically important lineages of parasitic plants. The genus has a sub-cosmopolitan distribution with more than 75% of the species diversifying in the New World. The last monograph, published by Truman George Yuncker in 1932, provided a solid species-level taxonomic foundation. However, as revealed by recent phylogenetic studies, its infrageneric classification has been in great need of a taxonomic reappraisal, mainly because the morphological characters used in the previous classifications have been greatly affected by convergent evolution. Several recent phylogenetic and character evolution studies with broad sampling, as well as species-level revisions, have illustrated the deficiencies of previous classifications and provided an explicit and robust phylogenetic framework. Here we propose a new phylogenetic classification that places all 194 currently accepted species of Cuscuta into four subgenera and 18 sections. Sections have a strong morphological and biogeographical predictive value and include from one to 31 species. Thirteen section names are new or applied for the first time at the sectional rank: Babylonicae (Yunck.) M. A. Garcı ́ a, Subulatae (Engelm.) Costea & Stefanovic ́ , Obtusilobae (Engelm.) Costea & Stefanovic ́ , Prismaticae (Yunck.) Costea & Stefanovic ́ , Ceratophorae (Yunck.) Costea & Stefanovic ́ , Umbellatae (Yunck.) Costea & Stefanovic ́ , Gracillimae Costea & Stefanovic ́ , Californicae (Yunck.) Costea & Stefanovic ́ , Indecorae (Yunck.) Costea & Stefanovic ́ , Oxycarpae (Engelm. ex Yunck.) Costea & Stefanovic ́ , Racemosae (Yunck.) Costea & Stefanovic ́ , Partitae Costea & Stefanovic ́ ,and Denticulatae (Yunck.) Costea & Stefanovic ́ . An identification key to sections is included together with an overview of morphology, geographical distribution, taxonomic notes, and lists of included species.

    Keywords: Molecular phylogeny, morphology, systematics, taxo


  • Deck J, Guralnick R, Walls R, Blum S, Haendel M, Matsunaga A et al. (2015)

    Meeting report: Identifying practical applications of ontologies for biodiversity informatics

    Standards in Genomic Sciences 10(1) 25.

    This report describes the outcomes of a recent workshop, building on a series of workshops from the last three years with the goal if integrating genomics and biodiversity research, with a more specific goal here to express terms in Darwin Core and Audubon Core, where class constructs have been historically underspecified, into a Biological Collections Ontology (BCO) framework. For the purposes of this workshop, the BCO provided the context for fully defining classes as well as object and data properties, including domain and range information, for both the Darwin Core and Audubon Core. In addition, the workshop participants reviewed technical specifications and approaches for annotating instance data with BCO terms. Finally, we laid out proposed activities for the next 3 to 18 months to continue this work.

    Keywords: Biodiversity, Community, Darwin core, Microbial ecology, OWL, Ontology, Population, RDF, Sequencing