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

  • Amador L, Ayala-Varela F, Nárvaez A, Cruz K, Torres-Carvajal O (2017)

    First record of the invasive Brown Anole, Anolis sagrei Duméril & Bibron, 1837 (Squamata: Iguanidae: Dactyloinae), in South America

    Check List 13(2) 2083.

    We report the first record of the invasive Brown Anole, Anolis sagrei Duméril & Bibron, 1837, in South America based on nine specimens from Samborondón, Guayas province, Ecuador. We also present some information related to the current distribution in Ecuador, and its possible impacts on native lizard species.

    Keywords: Ecuador, Guayas, distribution, introduced species, lizards, range extension, urban areas


  • Carew M, Nichols S, Batovska J, St Clair R, Murphy N, Blacket M et al. (2017)

    A DNA barcode database of Australia’s freshwater macroinvertebrate fauna

    Marine and Freshwater Research.

    Macroinvertebrates are widely used for monitoring freshwater ecosystems. In most monitoring programs, identifications take substantial time and expense. Methods that improve the speed, accuracy and cost-effectiveness of macroinvertebrate identification would benefit such programs. Increasingly, DNA barcodes are being used to provide accurate species-level identifications and have the potential to change how macroinvertebrates are routinely identified. Herein we discuss the need for DNA barcodes of freshwater macroinvertebrates with particular reference to Australia. We examine the use of DNA barcodes for species identification and compare DNA barcoding efforts of macroinvertebrates from Australia with those globally. We consider the role of high-throughput sequencing of DNA barcodes in freshwater bioassessment and its potential use in biosurveillance. Finally, we outline a strategy for developing a comprehensive national DNA barcode database for Australian freshwater macroinvertebrates and present the initial efforts in creating this database.

    Keywords: BOLD, Barcode of Life Data System, DNA sequences, biological monitoring, biosecurity, national database


  • 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.

    Keywords: BOLD, Barcode of Life Data System, DNA sequences, biological monitoring, biosecurity, national database


  • 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


  • Grossenbacher D, Brandvain Y, Auld J, Burd M, Cheptou P, Conner J et al. (2017)

    Self-compatibility is over-represented on islands

    New Phytologist.

    Because establishing a new population often depends critically on finding mates, individuals capable of uniparental reproduction may have a colonization advantage. Accordingly, there should be an over-representation of colonizing species in which individuals can reproduce without a mate, particularly in isolated locales such as oceanic islands. Despite the intuitive appeal of this colonization filter hypothesis (known as Baker's law), more than six decades of analyses have yielded mixed findings. We assembled a dataset of island and mainland plant breeding systems, focusing on the presence or absence of self-incompatibility. Because this trait enforces outcrossing and is unlikely to re-evolve on short timescales if it is lost, breeding system is especially likely to reflect the colonization filter. We found significantly more self-compatible species on islands than mainlands across a sample of > 1500 species from three widely distributed flowering plant families (Asteraceae, Brassicaceae and Solanaceae). Overall, 66% of island species were self-compatible, compared with 41% of mainland species. Our results demonstrate that the presence or absence of self-incompatibility has strong explanatory power for plant geographical patterns. Island floras around the world thus reflect the role of a key reproductive trait in filtering potential colonizing species in these three plant families.

    Keywords: Baker's law, biogeography, ecological filtering, island, mainland, self‐incompatibility


  • Haque M, Nipperess D, Gallagher R, Beaumont L (2017)

    How well documented is Australia's flora? Understanding spatial bias in vouchered plant specimens

    Austral Ecology.

    Massive digitization of natural history collections (NHC) has opened the door for researchers to conduct inferential studies on the collection of biological diversity across space and time. The widespread use of NHCs in scientific research makes it essential to characterize potential sources of spatial bias. In this study, we assessed spatial patterns in records from the Australian Virtual Herbarium (AVH), based on >3 000 000 vouchered specimens of around 21 000 native plant species. The AVH is the main database for describing Australia's flora, and identifying its limitations is of paramount interest for the validity of conservation and environmental studies. We characterized how sampling effort is distributed across each Interim Bioregion of Australia (IBRA), then asked: (i) How complete are species inventories for each bioregion? We define completeness (C) as the ratio of observed to estimated species richness, using the Chao 1 estimator, (ii) How is sampling effort related to a commonly used Human Influence Index (HII)? and (iii) What is the probability that additional collections would result in the identification of previously unrecorded species in each bioregion? Sampling effort across bioregions is unequal, which partially reflects the collecting behaviour of naturalists in relation to species richness patterns. The density of records in bioregions ranges from 0.02–8.37 km−2. At the bioregional scale, completeness is generally high with 79% of bioregions estimated to have records for at least 80% of their species. Completeness is partly explained by sampling effort (r = 0.43, p = 0.01), although some bioregions (e.g. Northern Kimberley and Burt Plain) have high completeness yet relatively low sampling effort. The inventory of Hampton, however, is substantially less complete than other bioregions (C = 0.66). Bioregions with high HII consistently have high completeness, while regions with low HII span the full range of completeness values. We calculated that an additional specimen collected from a bioregion has a 0.33% (Wet Tropics) to 11.7% (Arnhem Coast) probability of representing a new species for that region. Our assessment can assist with directing future systematic survey efforts by identifying bioregions where additional surveying may result in the greatest return, in terms of increasing knowledge of species richness and diversity.

    Keywords: Baker's law, biogeography, ecological filtering, island, mainland, self‐incompatibility


  • 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


  • Hungate B, Barbier E, Ando A, Marks S, Reich P, van Gestel N et al. (2017)

    The economic value of grassland species for carbon storage

    Science Advances 3(4).

    Carbon storage by ecosystems is valuable for climate protection. Biodiversity conservation may help increase carbon storage, but the value of this influence has been difficult to assess. We use plant, soil, and ecosystem carbon storage data from two grassland biodiversity experiments to show that greater species richness increases economic value: Increasing species richness from 1 to 10 had twice the economic value of increasing species richness from 1 to 2. The marginal value of each additional species declined as species accumulated, reflecting the nonlinear relationship between species richness and plant biomass production. Our demonstration of the economic value of biodiversity for enhancing carbon storage provides a foundation for assessing the value of biodiversity for decisions about land management. Combining carbon storage with other ecosystem services affected by biodiversity may well enhance the economic arguments for conservation even further.

    Keywords: biodiversity, carbon storage, economic value, grassland, social cost of carbon, species diversity, species richness, valuation