Uses of GBIF in scientific research

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

List of publications

  • De Pooter D, Appeltans W, Bailly N, Bristol S, Deneudt K, Eliezer M et al. (2017)

    Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

    Biodiversity Data Journal 5 e10989.

    The Ocean Biogeographic Information System (OBIS) is the world’s most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.

    Keywords: Darwin Core Archive, data standardisation, ecosystem data, environmental data, oceanographic data, sample event, species occurrence, telemetry data

  • Ouyang X, Lee S, Connolly R (2017)

    The role of root decomposition in global mangrove and saltmarsh carbon budgets

    Earth-Science Reviews 166 53-63.

    This study aims to determine the drivers of root decomposition and its role in carbon (C) budgets in mangroves and saltmarsh. We review the patterns of root decomposition, and its contribution to C budgets, in mangroves and saltmarsh: the impact of climatic (temperature and precipitation), geographic (latitude), temporal (decay period) and biotic (ecosystem type) drivers using multiple regression models. Best-fit models explain 50% and 48% of the variance in mangrove and saltmarsh root decay rates, respectively. A combination of biotic, climatic, geographic and temporal drivers influences root decay rates. Rainfall and latitude have the strongest influence on root decomposition rates in saltmarsh. For mangroves, forest type is the most important; decomposition is faster in riverine mangroves than other types. Mangrove species Avicennia marina and saltmarsh species Spartina maritima and Phragmites australis have the highest root decomposition rates. Root decomposition rates of mangroves were slightly higher in the Indo-west Pacific region (average 0.16%day−1) than in the Atlantic-east Pacific region (0.13%day−1). Mangrove root decomposition rates also show a negative exponential relationship with porewater salinity. In mangroves, global root decomposition rates are 0.15%day−1 based on the median value of rates in individual studies (and 0.14%day−1 after adjusting for area of mangroves at different latitudes). In saltmarsh, global root decomposition rates average 0.12%day−1 (no adjustment for area with latitude necessary). Our global estimate of the amount of root decomposing is 10TgCyr−1 in mangroves (8TgCyr−1 adjusted for area by latitude) and 31TgCyr−1 in saltmarsh. Local root C burial rates reported herein are 51–54gCm−2yr−1 for mangroves (58–61TgCyr−1 adjusted for area by latitude) and 191gCm−2yr−1 for saltmarsh. These values account for 24.1–29.1% (mangroves) and 77.9% (saltmarsh) of the reported sediment C accumulation rates in these habitats. Globally, dead root C production is the significant source of stored sediment C in mangroves and saltmarsh.

    Keywords: Carbon accumulation rate, Climate, Mangroves, Root decomposition rate, Root production, Saltmarsh

  • Pertierra L, Aragón P, Shaw J, Bergstrom D, Terauds A, Olalla-Tárraga M (2017)

    Global thermal niche models of two European grasses show high invasion risks in Antarctica

    Global Change Biology.

    The two non-native grasses that have established long-term populations in Antarctica (Poa pratensis and Poa annua) were studied from a global multidimensional thermal niche perspective to address the biological invasion risk to Antarctica. These two species exhibit contrasting introduction histories and reproductive strategies and represent two referential case studies of biological invasion processes. We used a multistep process with a range of species distribution modelling techniques (ecological niche factor analysis, multidimensional envelopes, distance/entropy algorithms) together with a suite of thermoclimatic variables, to characterize the potential ranges of these species. Their native bioclimatic thermal envelopes in Eurasia, together with the different naturalized populations across continents, were compared next. The potential niche of P. pratensis was wider at the cold extremes; however, P. annua life history attributes enable it to be a more successful colonizer. We observe that particularly cold summers are a key aspect of the unique Antarctic environment. In consequence, ruderals such as P. annua can quickly expand under such harsh conditions, whereas the more stress-tolerant P. pratensis endures and persist through steady growth. Compiled data on human pressure at the Antarctic Peninsula allowed us to provide site-specific biosecurity risk indicators. We conclude that several areas across the region are vulnerable to invasions from these and other similar species. This can only be visualized in species distribution models (SDMs) when accounting for founder populations that reveal nonanalogous conditions. Results reinforce the need for strict management practices to minimize introductions. Furthermore, our novel set of temperature-based bioclimatic GIS layers for ice-free terrestrial Antarctica provide a mechanism for regional and global species distribution models to be built for other potentially invasive species.

    Keywords: Poaceae, biosecurity protocols, non-native species management, nonanalogous climate, species distribution models

  • Shaik R, Burrows G, Urwin N, Gopurenko D, Lepschi B, Weston L (2017)

    The biology and management of prickly paddy melon (Cucumis myriocarpus L.), an important summer annual weed in Australia

    Crop Protection 92 29-40.

    Cucumis myriocarpus is an annual cucurbitaceous summer weed infesting fallow fields and pastures. Infestation results in reduced moisture availability for winter cereal crops as well as reduced crop yields and pasture quality. The need to manage this weed is of paramount importance given its adverse effects on farming systems, biodiversity and grazing livestock and its ranking as the number one weed of importance in Australian summer fallows of grain crops. Land management practices, including movement of grazing animals and over-stocking, are potentially assisting the spread of Cucumis myriocarpus fruits and viable seed. The plant is characterized by the presence of small, ellipsoid to spherical melon fruits with spiny appendages. Each plant can produce up to 50 or more melons per plant, with each fruit containing up to 200 viable seeds. Seed is often dormant upon fruit maturity and our results under controlled environmental conditions suggest both physiological and physical factors influence dormancy. Under field conditions, seedlings can form large vines growing upto 3 m in length. Field pollination experiments suggest that this melon is mainly self-pollinated by insects, including bees, flies and wasps. Cucumis myriocarpus is generally managed by the use of various broadleaf phenoxy herbicides and systemic post-emergent products. It is found in this study that this weed established through multiple flushes of germination, hence multiple herbicidal applications coinciding with rainfall events one suggested for more efficacious management. However, rotation of infested pastures with cereal crops such as canola and wheat also results in improved control. Additional studies into the impact of soil with and physical properties, disturbance and grazing, are recommended for development of more efficacious control measures. This review discusses taxonomy, genetic variation, biology and ecology and management of this important summer annual weed.

    Keywords: Agricultural weed, Biology, Field emergence and Seed biology, Self-pollination

  • Skeels A, Cardillo M (2017)

    Environmental niche conservatism explains the accumulation of species richness in Mediterranean-hotspot plant genera


    The causes of exceptionally high plant diversity in Mediterranean-climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus. For three genera, there were strong positive relationships between the diversity of clades within a region and their inferred length of occupation of that region. Within genera, there was evidence for strong evolutionary constraint on niche axes associated with climatic seasonality and aridity, with different niche optima for hotspot and nonhotspot clades. Evolutionary transitions away from hotspots were associated with increases in niche breadth and elevated rates of niche evolution. Our results point to a process of “hotspot niche conservatism” whereby the accumulation of plant diversity in Mediterranean-type ecosystems results from longer time for speciation, with dispersal away from hotspots limited by narrow and phylogenetically conserved environmental niches.

    Keywords: Evolutionary model comparison, Mediterranean-type ecosystems, Ornstein–Uhlenbeck model, Proteaceae, niche conservatism

  • Aljaryian R, Kumar L (2016)

    Changing global risk of invading greenbug Schizaphis graminum under climate change

    Crop Protection 88 137-148.

    The geographical range, abundance, growth rate, survival and mortality of insects are largely influenced by abiotic factors such as temperature and humidity. When suitable, these factors can positively influence the abundance of insect pests. It is in this light that the influence of climate change, particularly global warming, has direct bearing to crop protection. In this study, we simulated the potential distribution of the greenbug or wheat aphid Schizaphis graminum (Rondani) (Aphididae), a major global pest of wheat, using the climate matching tool CLIMEX (CLIMatic indEX) in global warming scenarios. To predict the potential distribution of the insect on CLIMEX at time periods 2030, 2070 and 2100, we utilize two global climate models (GCMs) at two emission scenarios. The result of CLIMEX modelling shows that the favourable climatic areas for S. graminum are subtropical to temperate at the current time. With global warming, under different scenarios current suitable and highly suitable areas in the northern hemisphere are expected to expand to higher latitudes by 2030 towards 2100; while areas in the southern hemisphere, where the pest’s living areas already have high temperature ranges, the occurrence of the pest will contract by 2030 since temperatures will exceed its heat limits. This study assists in predicting the potential risk areas that may be threatened by this pest in the future, providing supportive information for agricultural management practices and aid in the preparation of strategic plans to avoid possible economic damage posed by future expansion of the pest population due to climate change.

    Keywords: CLIMEX, Climate change, Greenbug, Wheat aphid

  • Araújo R, Assis J, Aguillar R, Airoldi L, Bárbara I, Bartsch I et al. (2016)

    Status, trends and drivers of kelp forests in Europe: an expert assessment

    Biodiversity and Conservation 25(7) 1319-1348.

    A comprehensive expert consultation was conducted in order to assess the status, trends and the most important drivers of change in the abundance and geographical distribution of kelp forests in European waters. This consultation included an on-line questionnaire, results from a workshop and data provided by a selected group of experts working on kelp forest mapping and eco-evolutionary research. Differences in status and trends according to geographical areas, species identity and small-scale variations within the same habitat where shown by assembling and mapping kelp distribution and trend data. Significant data gaps for some geographical regions, like the Mediterranean and the southern Iberian Peninsula, were also identified. The data used for this study confirmed a general trend with decreasing abundance of some native kelp species at their southern distributional range limits and increasing abundance in other parts of their distribution (Saccharina latissima and Saccorhiza polyschides). The expansion of the introduced species Undaria pinnatifida was also registered. Drivers of observed changes in kelp forests distribution and abundance were assessed using experts’ opinions. Multiple possible drivers were identified, including global warming, sea urchin grazing, harvesting, pollution and fishing pressure, and their impact varied between geographical areas. Overall, the results highlight major threats for these ecosystems but also opportunities for conservation. Major requirements to ensure adequate protection of coastal kelp ecosystems along European coastlines are discussed, based on the local to regional gaps detected in the study.

    Keyword: Kelp forests Expert consultation Status and tempor

  • Bateman B, Pidgeon A, Radeloff V, Flather C, Van Der Wal J, Akçakaya H et al. (2016)

    Potential breeding distributions of U.S. birds predicted with both short-term variability and long-term average climate data

    Ecological Applications.

    Climate conditions, such as temperature or precipitation averaged over several decades strongly affect species distributions, as evidenced by experimental results and a plethora of models demonstrating statistical relations between species occurrences and long-term climate averages. However, long-term averages can conceal climate changes that have occurred in recent decades and may not capture actual species occurrence well because the distributions of species, especially at the edges of their range, are typically dynamic and may respond strongly to short-term climate variability. Our goal here was to test whether bird occurrence models can be predicted by either covariates based on short-term climate variability or on long-term climate averages. We parameterized species distribution models (SDMs) based on either short-term variability or long-term average climate covariates for 320 bird species in the conterminous U.S., and tested whether any life-history trait-based guilds were particularly sensitive to short-term conditions. Models including short-term climate variability performed well based on their cross-validated AUC score (0.85), as did models based on long-term climate averages (0.84). Similarly, both models performed well compared to independent presence/absence data from the North American Breeding Bird Survey (independent AUC of 0.89 and 0.90, respectively). However, models based on short-term variability covariates more accurately classified true absences for most species (73% of true absences classified within the lowest quarter of environmental suitability versus 68%). In addition, they have the advantage that they can reveal the dynamic relationship between species and their environment because they capture the spatial fluctuations of species potential breeding distributions. With this information we can identify which species and guilds are sensitive to climate variability, identify sites of high conservation value where climate variability is low, and assess how species’ potential distributions may have already shifted due recent climate change. However, long-term climate averages require less data and processing time and may be more readily available for some areas of interest. Where data on short-term climate variability are not available, long-term climate information is a sufficient predictor of species distributions in many cases. However, short-term climate variability data may provide information not captured with long-term climate data for use in SDMs.

    Keywords: Maxent, North American breeding birds, climate change, guilds, species distribution model (SDM), species range

  • Brischoux F, Cotté C, Lillywhite H, Bailleul F, Lalire M, Gaspar P et al. (2016)

    Oceanic circulation models help to predict global biogeography of pelagic yellow-bellied sea snake.

    Biology letters 12(8) R861-R870.

    It is well recognized that most marine vertebrates, and especially tetrapods, precisely orient and actively move in apparently homogeneous oceanic environments. Here, we investigate the presumptive role of oceanic currents in biogeographic patterns observed in a secondarily marine tetrapod, the yellow-bellied sea snake (Hydrophis [Pelamis] platurus). State-of-the-art world ocean circulation models show how H. platurus, the only pelagic species of sea snake, can potentially exploit oceanic currents to disperse and maintain population mixing between localities that spread over two-thirds of the Earth's circumference. The very close association of these snakes with surface currents seems to provide a highly efficient dispersal mechanism that allowed this species to range extensively and relatively quickly well beyond the central Indo-Pacific area, the centre of origin, abundance and diversity of sea snakes. Our results further suggest that the pan-oceanic population of this species must be extraordinarily large.

    Keywords: Indo-Pacific oceans, biogeography, drifting, oceanic currents, sea snake

  • Byrne M, Gall M, Wolfe K, Agüera A (2016)

    From pole to pole: the potential for the Arctic seastar Asterias amurensis to invade a warming Southern Ocean

    Global Change Biology.

    Due to climatic warming, Asterias amurensis, a keystone boreal predatory seastar that has established extensive invasive populations in southern Australia, is a potential high-risk invader of the sub-Antarctic and Antarctic. To assess the potential range expansion of A. amurensis to the Southern Ocean as it warms, we investigated the bioclimatic envelope of the adult and larval life stages. We analysed the distribution of adult A. amurensis with respect to present day and future climate scenarios using habitat temperature data to construct species distribution models (SDM). To integrate the physiological response of the dispersive phase we determined the thermal envelope of larval development to assess their performance in present day and future thermal regimes and the potential for success of A. amurensis in poleward latitudes. The SDM indicated that the thermal 'niche' of the adult stage correlates with a 0-17 °C and 1-22.5 °C range, in winter and summer, respectively. As the ocean warms the range of A. amurensis in Australia will contract, while more southern latitudes will have conditions favorable for range expansion. Successful fertilisation occurred from 3-23.8 °C. By day 12, development to the early larval stage was successful from 5.5-18 °C. Although embryos were able to reach the blastula stage at 2 °C, they had arrested development and high mortality. The optimal thermal range for survival of pelagic stages was 3.5-19.2 °C with a lower and upper critical limit of 2.6 °C and 20.3 °C, respectively. Our data predict that A. amurensis faces demise in its current invasive range while more favourable conditions at higher latitudes would facilitate invasion of both larval and adult stages to the Southern Ocean. Our results show that vigilance is needed to reduce the risk that this ecologically important Arctic carnivore may invade the Southern Ocean and Antarctica. This article is protected by copyright. All rights reserved.

    Keywords: Antarctica, asteroid, climate change, introduced species, larva, ocean warming, southern migration, thermal tolerance