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

  • 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

  • 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

  • Mendoza , Ospina O, Cárdenas-Henao H, García-R J (2015)

    A likelihood inference of historical biogeography in the world's most diverse terrestrial vertebrate genus: Diversification of direct-developing frogs (Craugastoridae: Pristimantis) across the Neotropics.

    Molecular phylogenetics and evolution 85 50-58.

    The geology of the northern Andean region has driven the evolutionary history of Neotropical fauna through the creation of barriers and connections that have resulted in speciation and dispersal events, respectively. One of the most conspicuous groups of anuran fauna in the Andes and surrounding areas is the direct-developing species of the genus Pristimantis. We investigated the molecular phylogenetic placement of 12 species from the montane Andes of Colombia in a broader geographical context with a new genus-level phylogeny in order to identify the role of Andean orogeny over the last 40 million years and the effect of elevational differences in diversification of Pristimantis. We examined the biogeographic history of the genus using ancestral range reconstruction by biogeographic regions and elevational ranges. We recognized the middle elevational band (between 1000 and 3000 m) in the Northwestern Andes region of Colombia and Ecuador as a focal point for the origin and radiation of Pristimantis species. Additionally, we found several Andean migrations toward new habitats in Central Andes and Merida Andes for some species groups. We suggest that the paleogeological changes in the Northwestern Andes were the main promoter of speciation in Pristimantis, and may have served as a corridor for the dispersion of lowland species.

    Keywords: Ancestral range reconstruction, Andes, Biogeography, Diversification, Terrarana

  • Onstein R, Carter R, Xing Y, Richardson J, Linder H (2015)

    Do Mediterranean-type ecosystems have a common history? - insights from the Buckthorn family (Rhamnaceae).

    Evolution; international journal of organic evolution.

    Mediterranean-type ecosystems (MTEs) are remarkable in their species-richness and endemism, but the processes which have led to this diversity remain enigmatic. Here, we hypothesize that continent-dependent speciation and extinction rates have led to disparity in diversity between the five MTEs of the world: the Cape, California, Mediterranean Basin, Chile and Western Australia. To test this hypothesis, we built a phylogenenetic tree for 280 Rhamnaceae species, estimated divergence times using eight fossil calibrations and use Bayesian methods and simulations to test for differences in diversification rates. Rhamnaceae lineages in MTEs generally show higher diversification rates than elsewhere, but speciation and extinction dynamics show a pattern of continent-dependence. We detected high speciation and extinction rates in California and significantly lower extinction rates in the Cape and Western Australia. The independent colonization of four out of five MTEs may have occurred conterminously in the Oligocene/Early Miocene, but colonization of the Mediterranean Basin happened later, in the Late Miocene. This suggests that the in situ radiations of these clades were initiated before the onset of winter-rainfall in these regions. These results indicate independent evolutionary histories of Rhamnaceae in MTEs, possibly related to the intensity of climate oscillations and the geological history of the regions. This article is protected by copyright. All rights reserved.

    Keywords: Californian Floristic Province, Cape, Western Australia, diversification rate, extinction, speciation

  • Poisot T, Gravel D, Leroux S, Wood S, Fortin M, Baiser B et al. (2015)

    Synthetic datasets and community tools for the rapid testing of ecological hypotheses


    The increased availability of both open ecological data, and software to interact with it, allows the fast collection and integration of information at all spatial and taxonomic scales. This offers the opportunity to address macroecological questions in a cost-effective way. In this contribution, we illustrate this approach by forecasting the structure of a stream food web at the global scale. In so doing, we highlight the most salient issues needing to be addressed before this approach can be used with a high degree of confidence.

    Keywords: Californian Floristic Province, Cape, Western Australia, diversification rate, extinction, speciation

  • Schiaparelli S, Ahyong S, Bowden D (2015)

    Evidence of niche conservatism and host fidelity in the polar shrimp Lebbeus kiae n. sp. (Decapoda: Caridea: Thoridae) from the Ross Sea, Antarctica


    We report a remarkable case of ‘bipolarism’, where two different polar species, namely Lebbeus polaris in the northern hemisphere and Lebbeus kiae n. sp., here described from the Southern Ocean, have been found to share similar ecologies. Despite the great geographical distance between the two species, both show high host fidelity in associations with two congeneric sea anemones: Bolocera tuediae and Bolocera kerguelensis, respectively. A close molecular phylogenetic relationship between the two Lebbeus species is indicated by COI data, which clearly show them as sister clades with respect to other congeners as well as a plurality of other Antarctic species. This is the first reported case of a defensive association in the Southern Ocean involving shrimps and sea anemones. The distribution of the new species, limited to seamount systems off the Ross Sea, may be the result of a specific colonisation/speciation event in the past, although more molecular data are needed to unravel the phylogenetic relationships within the genus Lebbeus. Despite this uncertainty, the persistence of ecological traits, i.e., the defensive association with sea anemones, indicates the presence of niche conservatism in this clade of shrimps

    Keywords: Antarctica, Caridea, Decapoda, Defensive association, Lebbeus, New species, Niche conservatism, Thoridae

  • Shavandi A, A. Bekhit A, Ali A, Sun Z, Ratnayake J (2015)

    Microwave-assisted synthesis of high purity β-tricalcium phosphate crystalline powder from the waste of Green mussel shells (Perna canaliculus)

    Powder Technology 273 33-39.

    Beta-tricalcium phosphate (β-TCP) was successfully synthesized using the waste of Green mussel shells, Perna canaliculus. Calcined mussel shells and phosphoric acid were mixed in 1.5 Ca/P molar ratio and subjected to microwave irradiation (1100W) for 30min and subsequently calcined at 750°C. The synthesized powder was chemically, compositionally and structurally characterized and was found to be very similar to a commercial β-TCP. Furthermore, the obtained powder was stable up to 1000°C and lost only 2% of its weight. Its toxic metallic contents (e.g. Cd, Pb and As) were lower than standard limits for biogenic calcium phosphate for medical application. The synthesized β-TCP powder shows spherical morphology having diameter in the range of 100–150nm and Ca/P molar ratio of 1.49, which is close to the stoichiometric ratio. The results obtained in this study showed that pure β-TCP can be produced from waste mussel shells in a simple and fast way using microwave irradiation.

    Keywords: Calcium phosphate, Mussel shells, β-TCP