Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from New Zealand.
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

  • Brewer M, O'Hara R, Anderson B, Ohlemüller R (2016)

    Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling

    Methods in Ecology and Evolution.

    cologists often wish to describe mathematical relationships between response variables and climate covariates in spatial models of species distribution; these relationships are commonly termed climate envelopes. There are many situations when the functional form of the envelopes should be either unimodal or monotonic, but current practice tends towards the use of either low-degree single-variable spline curves fitted as part of a Generalised Additive Model (GAM) or piecewise linear forms in software such as maxent. We argue that such curves are often inappropriate, as they: (i) can easily produce relationships which are ecologically implausible and (ii) frequently ignore interactions between multiple climate variables in a general regression context. We propose an novel alternative parametric form for climate envelopes that appeals to ecological plausibility and can encompass realistic features of species' presence/climate relationships on several variables simultaneously. The proposed plateau climate envelope function is applied via a spatial Bayesian species distribution model to data on two European tree species to demonstrate the approach. For Fagus sylvatica, a complete climate envelope is estimable, but for Quercus coccifera, only a partial climate envelope can be estimated as the geographical extent of the data set does not cover the full environmental niche for the species. We show that such an approach is practical, produces climate envelopes with an ecologically meaningful form and furthermore allows the inclusion of information external to the data set being analysed. We discuss the use of this new plateau climate envelope function in the context of ecological niche modelling and argue that in some instances ecological realism should be regarded as more important than the use of formal model comparison statistics

    Keywords: Bayesian spatialmodels, nichemodelling, species–climate interactions

  • Brock J, Perry G, Lee W, Burns B (2016)

    Tree fern ecology in New Zealand: A model for southern temperate rainforests

    Forest Ecology and Management 375 112-126.

    Tree ferns are a ubiquitous and often locally dominant element of wet southern temperate rainforests across Australasia, southern Africa and in regions adjacent to the tropics in South America. Published data on the ecology of tree ferns throughout these forest ecosystems is piecemeal, with the most comprehensive literature describing the ecology of tree ferns coming from New Zealand. Therefore using New Zealand forests as a model system, we review the ecology and importance of tree ferns for forest structure and composition. Most studies of the ecology and function of forest species in New Zealand have focussed on spermatophytes. Even though tree ferns (Cyatheaceae, Dicksoniaceae) can represent more than 50% of basal area and more than 20% of forest biomass they have been largely overlooked and quantitative information on their contribution to forest structure and function is relatively scarce. Here for the first time we synthesise information on NZ’s indigenous tree ferns published over the last 100years and present new data on their ecology and potential ecosystem influences. Irradiance and nutrient (N, P) levels constrain development of tree fern gametophytes, with P limitation potentially influencing sporophyte production. Tree ferns establish during temporary removal of forest canopies across various spatio-temporal scales including after local disturbances, wind-throw openings of the canopy, and landslides. Members of the Cyatheaceae exhibit spatial differentiation along temperature and solar radiation gradients; the Dicksoniaceae species differentiate most strongly on their frost tolerance. Frequency/abundance of all nine understory tree fern species indigenous to New Zealand increases with total soil phosphorus, with some niche differentiation among species along a broader nutrient gradient. Tree ferns are prominent in early and mid-successional forest communities where they may persist for more than 250years. Individually, and as a group, tree-ferns impact nutrient cycling, organic matter accumulation and ground-level irradiance, often shading out tree seedlings. Tree ferns also have long-term physical impacts on the regeneration niche of associated species, with epiphytism on tree fern trunks providing alternative establishment surfaces for many species. Domination of nutrient resources by tree ferns early in succession is likely a key factor influencing community establishment. We conclude with key recommendations for future research on fundamental unknown elements of the ecology and synecology of tree ferns including greater determination of their ecophysiology and influence on forest community assemblages.

    Keywords: Community dynamics, Cyatheaceae, Dicksoniaceae, Forest regeneration, Selective effect, Tree fern

  • Saeedi H, Dennis T, Costello M (2016)

    Bimodal latitudinal species richness and high endemicity of razor clams (Mollusca)

    Journal of Biogeography.

    Aim To examine the global distribution, endemicity, and latitudinal gradients of species richness of razor clams, family Solenidae. Location Global. Methods A total of 3105 distribution records for 77 Solen and Solena species were used. Species richness was plotted in 5° latitude–longitude cells and related to environmental variables. Results The north-west Pacific and the Indo-West Pacific have the highest species richness (about 85% of all species)–mostly in the Sea of Japan, China Sea, the Gulf of Thailand and the Andaman Sea. Cluster analysis of similarity patterns of species composition (i.e., presence of Solenidae species) for 5° latitudinal–longitudinal grid cells showed 16 significant biogeographical regions that concur with existing marine biogeographical hypotheses. More than half of the species were endemic to specific biogeographical regions. The geographical distribution of species in 5° latitudinal bands showed a significant bimodal pattern. Global patterns of species richness increased from the poles to intermediate latitudes and dipped near the equator. A non-linear relationship between species richness and mean sea-surface temperature (SST) values was compatible with this bimodal pattern. Two inflection points of species richness with correlation of SST at 12 °C (low species richness) and 28 °C (high species richness) were coincident with the bimodal latitudinal species richness pattern. Species richness was highly positively correlated with mean SST over all latitudes, and within the Northern and Southern Hemispheres. Species richness decreased with SST range over all latitudes and in the Northern Hemisphere. Species richness also decreased with chlorophyll-a concentration and primary productivity, but increased with ocean area in the Northern Hemisphere (only). Main conclusions The latitudinal distribution in species richness of Solenidae peaked at 10° N and 25° S rather than at the equator, exhibiting a strongly bimodal pattern that is likely to be temperature driven.

    Keywords: Solenidae, biogeographical region, continental-shelf area, endemicity, latitudinal diversity gradient, razor clams, sea surface temperature, tropical

  • Saeedi H B (2016)

    Modelling present and future global distributions of razor clams (Bivalvia: Solenidae)

    Helgoland Marine Research 70 23.

    Razor clams (Pharidae and Solenidae) are deep-burrowing bivalves that inhabit shallow waters of the tropical, subtropical, and temperate seas. Using ‘maximum entropy’, a species distribution modelling software, we predicted the most suitable environments for the entire family and 14 Solen species to indicate their present and future geographic distributions. Distance to land, depth, and sea surface temperature (SST) were the most important environmental variables in training and creating the present and future distribution models both at the family and species level. In the present distribution models at the family level, the most suitable environment was where distance to land was between 0 and 100 km, a depth of 0–150 m, wave height of 5–7 m, a mean chlorophyll-a concentration about 0.7 mg m−3, and mean SST between 12 and 28 °C. Comparison with the future distribution models at the species level, found that most species were predicted to shift their distribution ranges poleward under the future environmental scenarios; i.e. species in the northern hemisphere would shift northward and southern species southward. Models also predicted that half of the species would expand their distribution ranges, 29% of species would not change their distribution, and 21% of species would shrink their distribution ranges under future climate change. Expanding geographic ranges would result in overlap in species ranges and thus greater species richness at regional scales. Model results predict that the mid-latitude peaks of species richness will move further apart, increasing the dip in richness near the equator, due to global climate change.

    Keywords: Background, Climate change, Global Biodiversity Information Facility, MaxEnt, Mollusca, Ocean Biogeographic Information System, Range shifts, Species distribution modelling

  • Schleuning M, Fründ J, Schweiger O, Welk E, Albrecht J, Albrecht M et al. (2016)

    Ecological networks are more sensitive to plant than to animal extinction under climate change

    Nature Communications 7 13965.

    Impacts of climate change on individual species are increasingly well documented, but we lack understanding of how these effects propagate through ecological communities. Here we combine species distribution models with ecological network analyses to test potential impacts of climate change on >700 plant and animal species in pollination and seed-dispersal networks from central Europe. We discover that animal species that interact with a low diversity of plant species have narrow climatic niches and are most vulnerable to climate change. In contrast, biotic specialization of plants is not related to climatic niche breadth and vulnerability. A simulation model incorporating different scenarios of species coextinction and capacities for partner switches shows that projected plant extinctions under climate change are more likely to trigger animal coextinctions than vice versa. This result demonstrates that impacts of climate change on biodiversity can be amplified via extinction cascades from plants to animals in ecological networks.

    Keywords: Background, Climate change, Global Biodiversity Information Facility, MaxEnt, Mollusca, Ocean Biogeographic Information System, Range shifts, Species distribution modelling

  • Vall-llosera M, Woolnough A, Anderson D, Cassey P (2016)

    Improved surveillance for early detection of a potential invasive species: the alien Rose-ringed parakeet Psittacula krameri in Australia

    Biological Invasions 1-12.

    The Rose-ringed parakeet Psittacula krameri is the most widely introduced parrot in the world, and is an important agricultural pest and competitor with native wildlife. In Australia, it is classified as an ‘extreme threat’, yet captive individuals frequently escape into the wild. The distribution and frequency of incursions are currently unknown, as are the potential impacts of the species in Australia. This lack of critical ecological information greatly limits effective biosecurity surveillance and decision-making efforts. We compiled a unique dataset, which combined passive surveillance sources from government and online resources, for all available information on parakeet detections at-large in Australia. We investigated whether geographic variables successfully predicted parakeet incursions, and used species distribution models to assess the potential distribution and economic impacts on agricultural assets. We recorded 864 incursions for the period 1999–2013; mostly escaped birds reported to missing animal websites. Escapes were reported most frequently within, or around, large cities. Incursions were best predicted by factors related to human presence and activity, such as global human footprint and intensive land uses. We recommend surveillance of high (predicted) establishment areas adjacent to cities where a feral parakeet population could most affect horticultural production. Novel passive surveillance datasets combined with species distribution models can be used to identify the regions where potential invasive species are most likely to establish. Subsequently, active surveillance can be targeted to the areas of highest predicted potential risk. We recommend an integrated approach that includes outreach programs involving local communities, as well as traditional biosecurity surveillance, for detecting new incursions.

    Keywords: Biosecurity, Economic impact, Online resources, Pet trade, Propagule pressure, Species distribution modelling

  • Aguilar G, Blanchon D, Foote H P (2015)

    Queensland Fruit Fly Invasion of New Zealand: Predicting Area Suitability Under Future Climate Change Scenarios ‹ ePress

    Unitec ePress Perspectives in Biosecurity Research Series 2.

    The Queensland fruit fly Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) is consistently described as the most damaging pest to Australia’s horticulture industries with an annual economic cost averaging around $25.7 million from 2003 to 2008 . In this paper, and corresponding online map, the authors discuss the significant risk to New Zealand of invasion by this species; the potential effects of climate change on the distribution and impacts of invasive species are well known. This paper and eMedia employs species distribution modelling using Maxent to predict the suitability of New Zealand to the Queensland fruit fly based on known occurrences worldwide and Bioclim climatic layers

    Keywords: Invasive species, climate change, species distribu

  • Byers J, Smith R, Pringle J, Clark G, Gribben P, Hewitt C et al. (2015)

    Invasion Expansion: Time since introduction best predicts global ranges of marine invaders.

    Scientific reports 5 12436.

    Strategies for managing biological invasions are often based on the premise that characteristics of invading species and the invaded environment are key predictors of the invader's distribution. Yet, for either biological traits or environmental characteristics to explain distribution, adequate time must have elapsed for species to spread to all potential habitats. We compiled and analyzed a database of natural history and ecological traits of 138 coastal marine invertebrate species, the environmental conditions at sites to which they have been introduced, and their date of first introduction. We found that time since introduction explained the largest fraction (20%) of the variability in non-native range size, while traits of the species and environmental variables had significant, but minimal, influence on non-native range size. The positive relationship between time since introduction and range size indicates that non-native marine invertebrate species are not at equilibrium and are still spreading, posing a major challenge for management of coastal ecosystems.

    Keywords: Invasive species, climate change, species distribu

  • Fraser D, Aguilar G, Nagle W, Galbraith M, Ryall C (2015)

    The House Crow (Corvus splendens): A Threat to New Zealand?

    ISPRS International Journal of Geo-Information 4(2) 725-740.

    The house crow (Corvus splendens), a native of the Indian subcontinent, has shown a rapid expansion of habitat range across Eastern Africa, the Arabian Peninsula, Europe and Asia. It is an adaptable, gregarious commensal bird which is regarded globally as an important pest species due to its impacts on livestock, agricultural and horticultural crops and indigenous fauna and as a fecal contaminator of human environments and water resources. Two Maxent (v3.3.3k) models (A) with presence data in Australia and (B) with simulated entry data locations in New Zealand) and a third ArcGIS model (C) with environmental and social layers) are used to determine an overall suitability index and establish a niche-based model of the potential spatial distribution for C. splendens within New Zealand. The results show that New Zealand, particularly the northern regions of North Island, has suitable environments for the establishment of the house crow. In order of suitability Model B showed highest potential land area suitability (31.84%) followed by Model A (13.79%) and Model C (10.89%). The potential for further expansion of this bird’s invasive range is high and, if New Zealand is invaded, impacts are likely to be significant.

    Keywords: New Zealand, house crow, modeling, spread