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

  • Allan, J., McIntyre, P., Smith, S., Halpern, B., Boyer, G., Buchsbaum, A., Burton, G., Campbell, L., Chadderton, W., Ciborowski, J., Doran, P., Eder, T., Infante, D., Johnson, L., Joseph, C., Marino, A., Prusevich, A., Read, J., Rose, J., Rutherford, E., Sowa, S., Steinman, A.

    Joint analysis of stressors and ecosystem services to enhance restoration effectiveness.

    (Journal name unavailable from Mendeley API. To be updated soon...)

    With increasing pressure placed on natural systems by growing human populations, both scientists and resource managers need a better understanding of the relationships between cumulative stress from human activities and valued ecosystem services. Societies often seek to mitigate threats to these services through large-scale, costly restoration projects, such as the over one billion dollar Great Lakes Restoration Initiative currently underway. To help inform these efforts, we merged high-resolution spatial analyses of environmental stressors with mapping of ecosystem services for all five Great Lakes. Cumulative ecosystem stress is highest in near-shore habitats, but also extends offshore in Lakes Erie, Ontario, and Michigan. Variation in cumulative stress is driven largely by spatial concordance among multiple stressors, indicating the importance of considering all stressors when planning restoration activities. In addition, highly stressed areas reflect numerous different combinations of stressors rather than a single suite of problems, suggesting that a detailed understanding of the stressors needing alleviation could improve restoration planning. We also find that many important areas for fisheries and recreation are subject to high stress, indicating that ecosystem degradation could be threatening key services. Current restoration efforts have targeted high-stress sites almost exclusively, but generally without knowledge of the full range of stressors affecting these locations or differences among sites in service provisioning. Our results demonstrate that joint spatial analysis of stressors and ecosystem services can provide a critical foundation for maximizing social and ecological benefits from restoration investments.

    Keywords: Ecosystem, Environmental Monitoring, Environmental Monitoring: methods, Environmental Monitoring: statistics & numerical d, Environmental Remediation, Environmental Remediation: methods, Environmental Remediation: standards, Geographic Mapping, Geography, Great Lakes Region, Human Activities, Humans, Lakes, Models, Physiological, Physiological: physiology, Stress, Theoretical


  • Caners, R.

    Disjunct Occurrence of Harpanthus drummondii (Taylor) Grolle (Geocalycaceae, Jungermanniopsida) in the Boreal Forest of West-Central Canada

    (Journal name unavailable from Mendeley API. To be updated soon...)

    The liverwort Harpanthus drummondii (Taylor) Grolle (Geocalycaceae, Jungermanniopsida) is known mostly from temperate regions of eastern North America where it is restricted to dead wood in forests. Recently, the species was discovered in the boreal forest of west-central Canada, demonstrating a substantial disjunction from the next closest known occurrence. A distribution map is provided along with features that distinguish it from the closely related H. scutatus (F.Weber & D.Mohr) Spruce.

    Keywords: Boreal forest, dead wood, epixylic, Harpanthus scutatus, liverwort, phytogeography


  • Cárdenas, P., Rapp, H., Klitgaard, A., Best, M., Thollesson, M., Tendal, O.

    Taxonomy, biogeography and DNA barcodes of Geodia species (Porifera, Demospongiae, Tetractinellida) in the Atlantic boreo-arctic region

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Geodia species north of 60°N in the Atlantic appeared in the literature for the first time when Bowerbank described Geodia barretti and G. macandrewii in 1858 from western Norway. Since then, a number of species have been based on material from various parts of the region: G. simplex, Isops phlegraei, I. pallida, I. sphaeroides, Synops pyriformis, G. parva, G. normani, G. atlantica, Sidonops mesotriaena (now called G. hentscheli), and G. simplicissima. In addition to these 12 nominal species, four species described from elsewhere are claimed to have been identified in material from the northeast Atlantic, namely G. nodastrella and G. cydonium (and its synonyms Cydonium muelleri and Geodia gigas). In this paper, we revise the boreo-arctic Geodia species using morphological, molecular, and biogeographical data. We notably compare northwest and northeast Atlantic specimens. Biological data (reproduction, biochemistry, microbiology, epibionts) for each species are also reviewed. Our results show that there are six valid species of boreo-arctic Atlantic Geodia while other names are synonyms or mis-identifications. Geodia barretti, G. atlantica, G. macandrewii, and G. hentscheli are well established and widely distributed. The same goes for Geodia phlegraei, but this species shows a striking geographical and bathymetric variation, which led us to recognize two species, G. phlegraei and G. parva (here resurrected). Some Geodia are arctic species (G. hentscheli, G. parva), while others are typically boreal (G. atlantica, G. barretti, G. phlegraei, G. macandrewii). No morphological differences were found between specimens from the northeast and northwest Atlantic, except for G. parva. The Folmer cytochrome oxidase subunit I (COI) fragment is unique for every species and invariable over their whole distribution range, except for G. barretti which had two haplotypes. 18S is unique for four species but cannot discriminate G. phlegraei and G. parva. Two keys to the boreo-arctic Geodia are included, one based on external morphology, the other based on spicule morphology.

    Keywords: amphi-Atlantic, atlantica, barretti, Geodiidae, hentscheli, macandrewii, parva, phlegraei, sponge ground


  • He, K., Jiang, X.

    Mitochondrial phylogeny reveals cryptic genetic diversity in the genus Niviventer (Rodentia, Muroidea).

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Abstract Niviventer is a muroid genus with 17 species widely distributed in East and Southeast Asia. These animals are important components of both extant and fossil small mammal communities, and they are among the most common infectious agents in humans. In this study, we employed partitioned Bayesian and relaxed clock divergence dating analyses and included the Niviventer mitochondrial cytochrome b genes of from GenBank (n = 223). Although the intra-generic relationships were not fully resolved, we recognized four major clades/subclades that could support further division of the genus. Paraphyletic and polyphyletic species were discovered, and 21 putative species were recognized through species delimitation analysis, which indicated an imperfect taxonomy and the existent of cryptic species. Molecular dating supported Niviventer origination in the late Miocene, and relatively higher diversification rates were observed in the late Pliocene and the Pleistocene, which might correlate with climate fluctuations.

    Keywords: cryptic species, delimitation, niviventer, species, species-level paraphyly


  • Jones, M., Dye, S., Pinnegar, J., Warren, R., Cheung, W.

    Applying distribution model projections for an uncertain future: the case of the Pacific oyster in UK waters

    Aquatic Conservation: Marine and Freshwater Ecosystems.

    1. The inherent complexity of the environment is such that attempts to model it must operate under simplifications and assumptions. Considering predictions from alternative models, with a range of assumptions and data requirements, therefore provides a more robust approach. 2. The intractability and uncertainty resulting from a suite of predictions may hinder the application of science in policy, where a single prediction with little ambiguity or uncertainty would bemost desirable. Few studies modelling species’ distributions attempt to present multi-model outputs in a format most useful to the non-modelling community, and none of these have done so for the marine environment. 3. The problem of uncertainty is particularly prevalent in predicting the distribution of invasive alien species under climate change. As invasive alien species are one of the main drivers of biodiversity loss and may incur significant economic costs, the benefit of applying predictions to highlight areas of possible establishment and inform policy and management may be large. 4. An ensemble prediction is used to assess the distribution of suitable habitat for the Pacific oyster, Crassostrea gigas, in UK waters both currently and in the future. The ensemble incorporates predictions from three species distribution models, using data from two global climate models. A method is developed highlighting the agreement of the ensemble, further applying threshold values to retain information from constituent predictions in the final map of agreement. 5. Ensemble predictions made here suggest that Pacific oyster will experience an opening of suitable habitat in northern UK waters, reaching the Faroe Islands and the eastern Norwegian Sea by 2050. Habitat suitability will increase with warming temperatures in the English Channel and Central North Sea for this species. The approaches applied here can be incorporated into risk assessment frameworks for invasive species, as stipulated in the Convention on Biological Diversity

    Keywords: alien species, climate change, distribution, habitat mapping, invertebrates, ocean


  • Jones, M., Dye, S., Fernandes, J., Frölicher, T., Pinnegar, J., Warren, R., Cheung, W.

    Predicting the Impact of Climate Change on Threatened Species in UK Waters.

    PloS one 8(1) e54216.

    Global climate change is affecting the distribution of marine species and is thought to represent a threat to biodiversity. Previous studies project expansion of species range for some species and local extinction elsewhere under climate change. Such range shifts raise concern for species whose long-term persistence is already threatened by other human disturbances such as fishing. However, few studies have attempted to assess the effects of future climate change on threatened vertebrate marine species using a multi-model approach. There has also been a recent surge of interest in climate change impacts on protected areas. This study applies three species distribution models and two sets of climate model projections to explore the potential impacts of climate change on marine species by 2050. A set of species in the North Sea, including seven threatened and ten major commercial species were used as a case study. Changes in habitat suitability in selected candidate protected areas around the UK under future climatic scenarios were assessed for these species. Moreover, change in the degree of overlap between commercial and threatened species ranges was calculated as a proxy of the potential threat posed by overfishing through bycatch. The ensemble projections suggest northward shifts in species at an average rate of 27 km per decade, resulting in small average changes in range overlap between threatened and commercially exploited species. Furthermore, the adverse consequences of climate change on the habitat suitability of protected areas were projected to be small. Although the models show large variation in the predicted consequences of climate change, the multi-model approach helps identify the potential risk of increased exposure to human stressors of critically endangered species such as common skate (Dipturus batis) and angelshark (Squatina squatina).

    Keywords: alien species, climate change, distribution, habitat mapping, invertebrates, ocean


  • Lait, L., Burg, T.

    When east meets west: population structure of a high-latitude resident species, the boreal chickadee (Poecile hudsonicus).

    (Journal name unavailable from Mendeley API. To be updated soon...)

    The population genetic structure of northern boreal species has been strongly influenced both by the Quaternary glaciations and the presence of contemporary barriers, such as mountain ranges and rivers. We used a combination of mitochondrial DNA (mtDNA), nuclear microsatellites and spatial distribution modelling to study the population genetic structure of the boreal chickadee (Poecile hudsonicus), a resident passerine, and to investigate whether historical or contemporary barriers have influenced this northern species. MtDNA data showed evidence of eastern and western groups, with secondary admixture occurring in central Canada. This suggests that the boreal chickadee probably persisted in multiple glacial refugia, one in Beringia and at least one in the east. Palaeo-distribution modelling identified suitable habitat in Beringia (Alaska), Atlantic Canada and the southern United States, and correspond to divergence dates of 60-96 kya. Pairwise FST values for both mtDNA and microsatellites were significant for all comparisons involving Newfoundland, though mtDNA data suggest a more recent separation. Furthermore, unlike mtDNA data, nuclear data support population connectivity among the continental populations, possibly due to male-biased dispersal. Although both are significant, the isolation-by-distance signal is much stronger for mtDNA (r(2)=0.51) than for microsatellites (r(2)=0.05), supporting the hypothesis of male-biased dispersal. The population structure of the boreal chickadee was influenced by isolation in multiple refugia and contemporary barriers. In addition to geographical distance, physical barriers such as the Strait of Belle Isle and northern mountains in Alaska are restricting gene flow, whereas the Rocky Mountains in the west are a porous barrier.Heredity advance online publication, 12 June 2013; doi:10.1038/hdy.2013.54.

    Keywords: boreal, ecological niche modelling, glacial refugia, microsatellites, mitochondrial dna, population genetic structure


  • Leroux, S., Larrivée, M., Boucher-Lalonde, V., Hurford, A., Zuloaga, J., Kerr, J., Lutscher, F.

    Mechanistic models for the spatial spread of species under climate change

    (Journal name unavailable from Mendeley API. To be updated soon...)

    Global climate change is a major threat to biodiversity. The most common methods for predicting the response of biodiversity to changing climate do not explicitly incorporate fundamental evolutionary and ecological processes that determine species' responses to changing climate such as reproduction, dispersal, and adaptation. We provide an overview of an emerging mechanistic spatial theory of species' range shifts under climate change. This theoretical framework explicitly defines the ecological processes that contribute to species range shifts via biologically meaningful dispersal, reproductive, and climate envelope parameters. We present methods for estimating the parameters of the model with widely available species occurrence and abundance data and apply these methods to empirical data for 12 North American butterfly species to illustrate the potential use of the theory for global change biology. The model predicts species persistence in light of current climate change and habitat loss. On average, we estimate the climate envelopes of our study species are shifting north at a rate of 3.25 km/yr (± 1.36 km/yr) and that our study species produce 3.46 viable offspring per individual per year (± 1.39). Based on our parameter estimates, we are able to predict the relative risk of our 12 study species lagging behind changing climate. This theoretical framework improves predictions of global change outcomes by facilitating the development and testing of hypotheses, providing mechanistic predictions of current and future range dynamics and encouraging the adaptive integration of theory and data. The theory is ripe for future developments such as the incorporation of biotic interactions and evolution of adaptations to novel climatic conditions and has the potential to be a catalyst for the development of more effective conservation strategies to mitigate losses of biodiversity from global climate change. Read More: http://www.esajournals.org/doi/abs/10.1890/12-1407.1

    Keywords: boreal, ecological niche modelling, glacial refugia, microsatellites, mitochondrial dna, population genetic structure


  • Lindgren, C., Castro, K., Coiner, H., Nurse, R., Darbyshire, S.

    The Biology of Invasive Alien Plants in Canada. 12. Pueraria montana var. lobata (Willd.) Sanjappa & Predeep

    Canadian Journal of Plant Science 93(1) 71-95.

    Kudzu, Pueraria montana var. lobata, is a perennial climbing vine known for its rapid and competitive growth. Introduced to North America and promoted at various times as a crop, an ornamental, and an erosion prevention tool, its negative impacts have been varied and severe in the United States. Dense populations overtop and smother crops and native vegetation, alter nitrogen cycles, and have the potential to affect air quality. Kudzu is winter-deciduous in North America with stems re-growing each season. In Canada, growth occurs from May until September, long enough for production of viable seed. Although widely believed to be intolerant of winter temperatures typical in eastern Canada, underground structures may be able to withstand temperatures as low as 308C, and northward range expansion is predicted by climate change models. Dispersal in North America is primarily through intentional planting by humans, with clonal propagation and limited seed production and germination contributing to local population expansion. Only one population is known in Canada, near Leamington, Ontario. Once established, kudzu is difficult to eliminate or control without repeated actions. Efforts to prevent the movement and sale of kudzu in Canada, along with early detection and rapid response, monitoring, and education, offer potential strategies for control. Depending on the age, size and location of the population, herbicides, burning, mowing and grazing can be effective control measures.

    Keywords: invasive plant, kudzu, PUELO, Pueraria lobata, Pueraria montana var. lobata, weed biology


  • Major, K., Nosko, P., Kuehne, C., Campbell, D., Bauhus, J.

    Regeneration dynamics of non-native northern red oak (Quercus rubra L.) populations as influenced by environmental factors: A case study in managed hardwood forests of southwestern Germany

    Forest Ecology and Management 291 144-153.

    Quercus rubra L. (northern red oak), a tree species having moderate shade tolerance, is failing to regenerate across its native range in North America, largely due to its inability to compete with shade-tolerant species. Throughout central Europe, where it was introduced in the 18th and 19th centuries, Q. rubra exhibits prolific regeneration even when growing with shade-tolerant trees under closed canopy conditions. A better understanding of factors that allow the proliferation of Q. rubra in its adventive range may provide insights into the conditions necessary to promote Q. rubra in North America. Our study investigated the regeneration dynamics of Q. rubra in six hardwood stands near Freiburg, Germany in relation to site conditions and the relative abundance and growth of indigenous tree species in forest understoreys. Despite high (94–98%) canopy closure at all stands, the density of Q. rubra regeneration (<2 m in height) was greater than that of all other tree species combined, averaging 24 stems m−1. Density of Q. rubra seedlings reached 125 stems m−2 directly below seed trees; however, the lack of seedlings beyond 15 m from a seed tree suggested limited seed dispersal. Seedlings were less abundant at relatively fertile sites with lowest densities corresponding most closely to elevated soil calcium. The abundance of Q. rubra was most highly variable in the midstorey (trees and shrubs >2.0 m in height and <10 cm diameter at breast height) with densities ranging from 200 to 1500 stems ha−1. Periodic selective harvesting at all stands, appears to maintain a disturbed state of mid-succession that allows Q. rubra seedlings to persist and recruit into the midstorey as canopy gaps become available. Clearly, stands of this non-indigenous species are successfully regenerating and the dominance of Q. rubra appears to be sustainable. Despite its benign performance in North America, Q. rubra can be an effective competitor under suitable conditions. Our findings deemphasize the importance of canopy closure on Q. rubra regeneration and suggest that in North America, preliminary cuts performed prior to shelterwood harvests should focus on midstorey removal of competitor species especially following oak mast years.

    Keywords: Gap ecology, Introduced species, Invasive species, Quercus rubra, Regeneration ecology, Seedling growth