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

  • Carew M, Metzeling L, St Clair R, Hoffmann A (2017)

    Detecting invertebrate species in archived collections using next-generation sequencing

    Molecular Ecology Resources.

    Invertebrate biodiversity measured at mostly family level is widely used in biological monitoring programmes to assess anthropogenic impacts on ecosystems. However, next-generation sequencing (NGS) could allow development of new more sensitive biomonitoring tools by allowing rapid species identification. This could be accelerated if archived invertebrate collections and environmental information from past programmes are used to understand species distributions and their environmental responses. In this study, we take archived macroinvertebrate samples from two sites collected on multiple occasions and test whether NGS can successfully detect species. Samples had been stored in 70% ethanol at room temperature for up to 12 years. Three amplicons ranging from 197 to 274 bps within the DNA barcode region were amplified from samples and compared to DNA barcoding libraries to identify species. We were able to amplify partial DNA barcodes from most samples, and species were often detected with multiple amplicons. However, some singletons and taxa poorly covered by DNA barcoding were missed. This suggests additional DNA barcodes will be required to fill ‘gaps’ in current DNA barcode libraries for aquatic macroinvertebrates and/or that it may not be possible to detect all taxa in a sample. Furthermore, older samples often detected fewer taxa and were less reliable for amplification, suggesting NGS is best used on samples within 8 years of collection. Nevertheless, many common taxa with existing DNA barcodes were reliably identified with NGS and were often present at sites across multiple years, showing the potential of NGS for detecting common and abundant species in archived material.

  • 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

  • Deb J, Phinn S, Butt N, McAlpine C (2017)

    The impact of climate change on the distribution of two threatened Dipterocarp trees

    Ecology and Evolution.

    Two ecologically and economically important, and threatened Dipterocarp trees Sal (Shorea robusta) and Garjan (Dipterocarpus turbinatus) form mono-specific canopies in dry deciduous, moist deciduous, evergreen, and semievergreen forests across South Asia and continental parts of Southeast Asia. They provide valuable timber and play an important role in the economy of many Asian countries. However, both Dipterocarp trees are threatened by continuing forest clearing, habitat alteration, and global climate change. While climatic regimes in the Asian tropics are changing, research on climate change-driven shifts in the distribution of tropical Asian trees is limited. We applied a bioclimatic modeling approach to these two Dipterocarp trees Sal and Garjan. We used presence-only records for the tree species, five bioclimatic variables, and selected two climatic scenarios (RCP4.5: an optimistic scenario and RCP8.5: a pessimistic scenario) and three global climate models (GCMs) to encompass the full range of variation in the models. We modeled climate space suitability for both species, projected to 2070, using a climate envelope modeling tool “MaxEnt” (the maximum entropy algorithm). Annual precipitation was the key bioclimatic variable in all GCMs for explaining the current and future distributions of Sal and Garjan (Sal: 49.97 ± 1.33; Garjan: 37.63 ± 1.19). Our models predict that suitable climate space for Sal will decline by 24% and 34% (the mean of the three GCMs) by 2070 under RCP4.5 and RCP8.5, respectively. In contrast, the consequences of imminent climate change appear less severe for Garjan, with a decline of 17% and 27% under RCP4.5 and RCP8.5, respectively. The findings of this study can be used to set conservation guidelines for Sal and Garjan by identifying vulnerable habitats in the region. In addition, the natural habitats of Sal and Garjan can be categorized as low to high risk under changing climates where artificial regeneration should be undertaken for forest restoration.

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

  • ElQadi M, Dorin A, Dyer A, Burd M, Bukovac Z (2017)

    Mapping species distributions with social media geo-tagged images: Case studies of bees and flowering plants in Australia

    Ecological Informatics.

    Data sources on species distribution and range are typically expensive and time consuming to build, and traditional survey techniques often have spatial, temporal, or scale-related gaps. Social network sites, on the other hand, can provide massive amounts of cost effective data that may potentially yield information of direct benefit to supplement and understand ecological phenomena. Previous research explored using social network site content to enhance information collected by experts or professional surveys in domains including species distribution and land cover. However, the data quality and general suitability of social network sites data for answering questions related to species distribution and range is highly variable and this aspect of its value to science remains underexplored. In this research we investigate some causes of social network site data unreliability and explore how to mitigate it. We filter data points based on our estimates of reliability and relevance. We then use the filtered data to infer species ranges and distributions in concert with Global Biodiversity Information Facility (GBIF) data. Our proposed methodology was applied to four Australian case studies including two insect pollinators, and two flowering plants. The case studies were chosen from Australia because of its unique geographical features, large landmass, sparse population, and the many tourists and residents who travel across it taking photos and sharing them through social media. We show that, despite some barriers, there are instances where the social network site data clearly complements the existing source, making our technique a valuable means of making repeatable, efficient additions to traditional species distribution data.

    Keywords: Bio-diversity data, Geo-tagged images, Social network sites, Species distribution mapping

  • Hill L (2017)

    Migration of green mirid, Creontiades dilutus (Stål) and residence of potato bug, Closterotomus norwegicus (Gmelin) in Tasmania (Hemiptera: Miridae: Mirinae: Mirini)

    Crop Protection 96 211-220.

    Adults but not nymphs of green mirid, Creontiades dilutus (Stål) (Hemiptera: Miridae) are sometimes detected in Tasmania. The species has been recorded, as adults at least, from a wide range of habitats, localities and plants in mainland Australia and suitable host plants occur in Tasmania. Most Tasmanian detections of C. dilutus have been in a long-term light trap and coincide with movements of known long-distance migratory insects and airflows favourable for migration across Bass Strait. In contrast adults and juveniles of the potato bug Closterotomus norwegicus (Gmelin) (Hemiptera: Miridae) are collected regularly in crops for which details are given. A published degree-day development model for C. dilutus was used to identify several impediments to fecundity, egg and juvenile survival and adult maturation such that even ephemeral seasonal establishment is highly unlikely. The absence of juveniles, coincidence of adults with migratory insects and northerly airflows and modelled obstacles to breeding in combination indicate that C. dilutus migrates to Tasmania. The results provide another example of a pest that fails to establish, even ephemerally, in Tasmania despite repeated migration from mainland Australia. Publications stating that the distribution of C. dilutus includes Tasmania are based only on captures of migratory adults. Climate matching models are prone to error if they assume C. dilutus is resident in Tasmania.

    Keywords: Hysplit aerial trajectory model, Migration, Misleading distribution, Pest records, Presence, Thermal model

  • 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

  • da Silva R, Kumar L, Shabani F, Picanço M (2017)

    An analysis of sensitivity of CLIMEX parameters in mapping species potential distribution and the broad-scale changes observed with minor variations in parameters values: an investigation using open-field Solanum lycopersicum and Neoleucinodes elegantalis

    Theoretical and Applied Climatology 1-10.

    A sensitivity analysis can categorize levels of parameter influence on a model's output. Identifying parameters having the most influence facilitates establishing the best values for parameters of models, providing useful implications in species modelling of crops and associated insect pests. The aim of this study was to quantify the response of species models through a CLIMEX sensitivity analysis. Using open-field Solanum lycopersicum and Neoleucinodes elegantalis distribution records, and 17 fitting parameters, including growth and stress parameters, comparisons were made in model performance by altering one parameter value at a time, in comparison to the best-fit parameter values. Parameters that were found to have a greater effect on the model results are termed ``sensitive''. Through the use of two species, we show that even when the Ecoclimatic Index has a major change through upward or downward parameter value alterations, the effect on the species is dependent on the selection of suitability categories and regions of modelling. Two parameters were shown to have the greatest sensitivity, dependent on the suitability categories of each species in the study. Results enhance user understanding of which climatic factors had a greater impact on both species distributions in our model, in terms of suitability categories and areas, when parameter values were perturbed by higher or lower values, compared to the best-fit parameter values. Thus, the sensitivity analyses have the potential to provide additional information for end users, in terms of improving management, by identifying the climatic variables that are most sensitive.

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