Uses of GBIF in scientific research

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

List of publications

  • Cabrelli, A., Hughes, L., 2015.

    Assessing the vulnerability of Australian skinks to climate change

    Climatic Change.

    A framework for assessing species vulnerability to climate change was developed and applied to the largest family of reptiles in Australia, the scincid lizards (skinks). This framework integrated the projections of environmental niche models (ENMs) with an index of vulnerability based on the species’ ecological traits. We found vulnerability to be highly variable among species, suggesting that responses to climate change will be idiosyncratic, and identified a number of species that by virtue of their ecological traits and model projections may be at risk of significant range contractions in the near future. Importantly, we also found that extrinsic vulnerability (as measured by the degree of range change) and intrinsic vulnerability (based on species traits) were not correlated, highlighting the importance of considering both types of information. This framework provides a transparent and objective tool for assessing climate change vulnerability and can provide a basis upon which to develop conservation strategies.

  • Harvey, K., Nipperess, D., Britton, D., Hughes, L., 2015.

    Comparison of invertebrate herbivores on native and non-native S enecio species: Implications for the enemy release hypothesis

    Austral Ecology n/a-n/a.

    The enemy release hypothesis posits that non-native plant species may gain a competitive advantage over their native counterparts because they are liberated from co-evolved natural enemies from their native area. The phylogenetic relationship between a non-native plant and the native community may be important for understanding the success of some non-native plants, because host switching by insect herbivores is more likely to occur between closely related species. We tested the enemy release hypothesis by comparing leaf damage and herbivorous insect assemblages on the invasive species Senecio madagascariensis Poir. to that on nine congeneric species, of which five are native to the study area, and four are non-native but considered non-invasive. Non-native species had less leaf damage than natives overall, but we found no significant differences in the abundance, richness and Shannon diversity of herbivores between native and non-native Senecio L. species. The herbivore assemblage and percentage abundance of herbivore guilds differed among all Senecio species, but patterns were not related to whether the species was native or not. Species-level differences indicate that S. madagascariensis may have a greater proportion of generalist insect damage (represented by phytophagous leaf chewers) than the other Senecio species. Within a plant genus, escape from natural enemies may not be a sufficient explanation for why some non-native species become more invasive than others.

    Keywords: enemy release hypothesis, invasive plants, naturalization hypothesis, non-invasive plant, plant–insect interaction

  • Lin, Y., Deng, D., Lin, W., Lemmens, R., Crossman, N., Henle, K., Schmeller, D., 2015.

    Uncertainty analysis of crowd-sourced and professionally collected field data used in species distribution models of Taiwanese moths

    Biological Conservation 181 102-110.

    The purposes of this study are to extract the names of species and places for a citizen-science monitoring program, to obtain crowd-sourced data of acceptable quality, and to assess the quality and the uncertainty of predictions based on crowd-sourced data and professional data. We used Natural Language Processing to extract names of species and places from text messages in a citizen science project. Bootstrap and Maximum Entropy methods were used to assess the uncertainty in the model predictions based on crowd-sourced data from the EnjoyMoths project in Taiwan. We compared uncertainty in the predictions obtained from the project and from the Global Biodiversity Information Facility (GBIF) field data for seven focal species of moth. The proximity to locations of easy access and the Ripley K method were used to test the level of spatial bias and randomness of the crowd-sourced data against GBIF data. Our results show that extracting information to identify the names of species and their locations from crowd-sourced data performed well. The results of the spatial bias and randomness tests revealed that the crowd-sourced data and GBIF data did not differ significantly in respect to both spatial bias and clustering. The prediction models developed using the crowd-sourced dataset were the most effective, followed by those that were developed using the combined dataset. Those that performed least well were based on the small sample size GBIF dataset. Our method demonstrates the potential for using data collected by citizen scientists and the extraction of information from vast social networks. Our analysis also shows the value of citizen science data to improve biodiversity information in combination with data collected by professionals.

    Keywords: Citizen science, Large-scale monitoring program, Natural language, Prediction of species distribution, Social media, Uncertainty, Volunteer survey

  • Vårhammar, A., Wallin, G., McLean, C., Dusenge, M., Medlyn, B., Hasper, T., Nsabimana, D., Uddling, J., 2015.

    Photosynthetic temperature responses of tree species in Rwanda: evidence of pronounced negative effects of high temperature in montane rainforest climax species.

    The New phytologist.

    The sensitivity of photosynthetic metabolism to temperature has been identified as a key uncertainty for projecting the magnitude of the terrestrial feedback on future climate change. While temperature responses of photosynthetic capacities have been comparatively well investigated in temperate species, the responses of tropical tree species remain unexplored. We compared the responses of seedlings of native cold-adapted tropical montane rainforest tree species with those of exotic warm-adapted plantation species, all growing in an intermediate temperature common garden in Rwanda. Leaf gas exchange responses to carbon dioxide (CO2 ) at different temperatures (20-40°C) were used to assess the temperature responses of biochemical photosynthetic capacities. Analyses revealed a lower optimum temperature for photosynthetic electron transport rates than for Rubisco carboxylation rates, along with lower electron transport optima in the native cold-adapted than in the exotic warm-adapted species. The photosynthetic optimum temperatures were generally exceeded by daytime peak leaf temperatures, in particular in the native montane rainforest climax species. This study thus provides evidence of pronounced negative effects of high temperature in tropical trees and indicates high susceptibility of montane rainforest climax species to future global warming.

    Keywords: Africa, leaf energy balance, maximum rate of electron transport (Jmax), optimum temperature (Topt), stomatal conductance (gs), the maximum carboxylation rate of oxygenase (Vcmax, tropical montane rainforest

  • van Kleunen, M., Dawson, W., Essl, F., Pergl, J., Winter, M., Weber, E., Kreft, H., Weigelt, P., Kartesz, J., Nishino, M., Antonova, L., Barcelona, J., Cabezas, F., Cárdenas, D., Cárdenas-Toro, J., Castaño, N., Chacón, E., Chatelain, C., Ebel, A., Figueiredo, E., Fuentes, N., Groom, Q., Henderson, L., Kupriyanov, A., Masciadri, S., Meerman, J., Morozova, O., Moser, D., Nickrent, D., Patzelt, A., Pelser, P., Baptiste, M., Poopath, M., Schulze, M., Seebens, H., Shu, W., Thomas, J., Velayos, M., Wieringa, J., Pyšek, P., 2015.

    Global exchange and accumulation of non-native plants

    Nature advance on.

    Keywords: Africa, leaf energy balance, maximum rate of electron transport (Jmax), optimum temperature (Topt), stomatal conductance (gs), the maximum carboxylation rate of oxygenase (Vcmax, tropical montane rainforest

  • Barnes, M., Jerde, C., Wittmann, M., Chadderton, W., Ding, J., Zhang, J., Purcell, M., Budhathoki, M., Lodge, D., 2014.

    Geographic selection bias of occurrence data influences transferability of invasive Hydrilla verticillata distribution models

    Ecology and Evolution.

    Due to socioeconomic differences, the accuracy and extent of reporting on the occurrence of native species differs among countries, which can impact the per- formance of species distribution models. We assessed the importance of geo- graphical biases in occurrence data on model performance using Hydrilla verticillata as a case study. We used Maxent to predict potential North Ameri- can distribution of the aquatic invasive macrophyte based upon training data from its native range. We produced a model using all available native range occurrence data, then explored the change in model performance produced by omitting subsets of training data based on political boundaries. We also com- pared those results with models trained on data from which a random sample of occurrence data was omitted from across the native range. Although most models accurately predicted the occurrence of H. verticillata in North America (AUC > 0.7600), data omissions influenced model predictions. Omitting data based on political boundaries resulted in larger shifts in model accuracy than omitting randomly selected occurrence data. For well-documented species like H. verticillata, missing records from single countries or ecoregions may mini- mally influence model predictions, but for species with fewer documented occurrences or poorly understood ranges, geographic biases could misguide pre- dictions. Regardless of focal species, we recommend that future species distribu- tion modeling efforts begin with a reflection on potential spatial biases of available occurrence data. Improved biodiversity surveillance and reporting will provide benefit not only in invaded ranges but also within under-reported and unexplored native ranges.

    Keywords: aquatic macrophyte, biological invasion, habitat model, maximum entropy, model, niche, prediction, spatial bias

  • Beaumont, L., Gallagher, R., Leishman, M., Hughes, L., Downey, P., 2014.

    How can knowledge of the climate niche inform the weed risk assessment process? A case study of Chrysanthemoides monilifera in Australia

    Diversity and Distributions 20(6) 613-625.

    Aim Climate change and the ability of alien populations to realize different climatic niches compared to native populations pose challenges for pre-empting invasion risk. These issues are not addressed in Weed Risk Assessments (WRAs), which have been developed to identify potentially invasive species and prevent their importation. Chrysanthemoides monilifera, native to Southern Africa, has two subspecies invasive in Australia, which has led to an importation ban on all six subspecies. We assess whether the two invasive subspecies occupy different realized climatic niches, compared with native populations, and the climatic suitability of Australia for all subspecies under current and future climate scenarios. Location Southern Africa and Australia Methods Realized climatic niches of native and alien populations of two invasive subspecies (Bitou Bush and Boneseed) were compared using niche identity tests. The distribution of climatically suitable habitat within Australia for all subspecies was modelled using MaxEnt, under current and future climate scenarios. For invasive subspecies, models were calibrated using (1) native or (2) alien range data. Results Realized climatic niches of native and alien populations are not identical, with some alien populations of Boneseed occupying climatic niches absent from Southern Africa. As such, MaxEnt models for Boneseed based on native range data failed to classify one-third of Australian populations as inhabiting suitable climate. Main Conclusions We validate the Australian decision to ban all subspecies by showing that climatically suitable habitat in Australia for non-introduced subspecies exceeds that of introduced subspecies, under current and future climates. Niche shifts and climate change alter estimates of invasion risks, and this may reduce efficacy of current WRAs. We call for greater dialogue to identify and standardize a comprehensive system for incorporating these challenging issues into WRA systems to ensure that they remain effective in reducing the weed risk into the future.

    Keywords: chrysanthemoides monilifera, climate change, climatic niche, invasive species, maxent, sons ltd, species distribution models, weed risk assessment

  • Bell, K., Heard, T., Manion, G., Ferrier, S., van Klinken, R., 2014.

    Characterising the phytophagous arthropod fauna of a single host plant species: assessing survey completeness at continental and local scales

    Biodiversity and Conservation 23(12) 2985-3003.

    Quantifying survey completeness is a key step in designing and interpreting biodiversity assessments. To date this has only been examined either at a local scale through repetitive sampling, or across broader geographic areas through multiple survey sites. In this paper, we determine the completeness of sampling at both local and continental scales, of the phytophagous arthropod assemblage on the Neotropical shrub Parkinsonia aculeata (Leguminosae). We used survey gap analysis (SGA) to determine whether existing surveys adequately sampled the diversity of environments and geographic space covered by the plant. Within defined geographic regions, we determined survey completeness at a local scale with species accumulation curves. SGA identified the highest priority sites for future sampling in the Sonoran Desert and the Pacific Coast of South America. The arthropods sampled on P. aculeata differed significantly between seasons, highlighting the importance of including surveys throughout the year. At the local scale, surveys in most regions were estimated to have sampled <50 % of all species. Only the Mexican Gulf, following 84 samples including 902 individuals, had a reasonably complete sample of all species (more than 50 %). As in other studies, rare species will continue to be detected even after extensive surveying, and it is likely that close to 100 samples or 1,000 individuals will be needed to attain 50 % survey completeness in a region. However, if the objective is to document close “host-associations” then effort may be better directed at surveying ecologically distinct new areas rather than exhaustive sampling in existing ones. Methods such as SGA can direct such surveys, and in conjunction with species-richness estimates, can be used to assess the adequacy of existing surveys.

    Keywords: chrysanthemoides monilifera, climate change, climatic niche, invasive species, maxent, sons ltd, species distribution models, weed risk assessment

  • Booth, T., 2014.

    Using biodiversity databases to verify and improve descriptions of tree species climatic requirements

    Forest Ecology and Management 315 95-102.

    Understanding tree species climatic adaptability, as well as climatic conditions within their natural distributions, is crucial for managing forests for both commercial and conservation objectives under climate change. Multi-million dollar investments in biodiversity databases are providing forestry professionals with freely accessible tools to carry out these kinds of analyses for many tree species. The climatic requirements of hundreds of tree species have been described in the commercially available Forestry Compendium developed by CAB International, but these descriptions have often relied on expert opinion where information is lacking. It is desirable that descriptions of tree species climatic requirements should, as far as possible, be explicit, quantitative and based on specific observations. This paper describes how the Atlas of Living Australia (ALA) and the Global Biodiversity Information Facility (GBIF) can provide specific observations to assist verifying and, where necessary, improving descriptions of tree species climatic requirements. It focuses mainly on Australian species as the ALA is one of the most sophisticated biodiversity databases currently available for a single country. However, the ALA also has international relevance as Australian eucalypts and acacias are important plantation species in many countries. Data in the GBIF complement the ALA data by providing very useful information on where Australian tree species are growing outside Australia. Analyses of a commercially important species (Eucalyptus nitens) and a lesser-known species (E. botryoides) demonstrate how descriptions of climatic requirements can be verified and, if necessary, improved. However, the general methods described have the potential to be applied to many tree species. Some of the advantages and disadvantages of these systems are discussed and possible improvements are suggested.

    Keyword: bioclimatic analysis

  • Cabrelli, A., Stow, A., Hughes, L., 2014.

    A framework for assessing the vulnerability of species to climate change: a case study of the Australian elapid snakes

    Biodiversity and Conservation 23(12) 3019-3034.

    Frameworks that provide a system for assessing species according to their vulnerability to climate change can offer considerable guidance to conservation managers who need to allocate limited resources among a large number of taxa. To date, climate change vulnerability assessments have largely been based on projected changes in range size derived from the output of species distribution models (SDMs). A criticism of risk assessments based solely on these models is that information on species ecological and life history traits is lacking. Accordingly, we developed a points-based framework for assessing species vulnerability to climate change that considered species traits together with the projections of SDMs. Applying this method to the Australian elapid snakes (family Elapidae), we determined which species may be particularly susceptible in the future and assessed broad-scale biogeographic patterns in species vulnerability. By offering a more comprehensive and rigorous method for assessing vulnerability than those based solely on SDMs, this framework provides greater justification for resource allocation, and can help guide decisions regarding the most appropriate adaptation strategies.

    Keywords: climate change, conservation priorities, elapidae, species distribution modelling, species traits, vulnerability assessment