119 Works

Data from: Changes in soil microbial communities in post mine ecological restoration: implications for monitoring using high throughput DNA sequencing

Mieke Van Der Heyde, Michael Bunce, Kingsley Dixon, Grant Wardell-Johnson, Nicole E White & Paul Nevill
The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool,...

Data from: Refining trophic dynamics through multi-factor Bayesian mixing models: a case study of subterranean beetles.

Mattia Saccò, Alison J. Blyth, William F. Humphreys, Steve Cooper, Andrew D. Austin, Josephine Hyde, Debashish Mazumder, Quan Hua, Nicole White & Kliti Grice
Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi-factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ13C and δ15N) with radiocarbon data (Δ14C), and prior information from metagenomic analyses....

Data from: Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Phillip A. Morin, Kim M. Parsons, Frederick I. Archer, María C. Ávila-Arcos, Lance G. Barrett-Lennard, Luciano Dalla Rosa, Sebastián Duchêne, John W. Durban, Graeme M. Ellis, Steven H. Ferguson, John K. Ford, Michael J. Ford, Cristina Gabrilao, M. Thomas P. Gilbert, Kristin Kaschner, Craig O. Matkin, Stephen D. Petersen, Kelly M. Robertson, Ingrid N. Visser, Paul R. Wade, Simon Y. W. Ho & Andrew D. Foote
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from...

Large-scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north-western Australia

Katrina West, Michael Travers, Michael Stat, Euan Harvey, Zoe Richards, Joseph DiBattista, Stephen Newman, Alastair Harry, Craig Skepper, Matthew Heydenrych & Michael Bunce
Aim: Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales, or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break, and evaluate its use as a regional biomonitoring tool in Australia. Location: North-western Australia (NWA) Methods: We applied metabarcoding assays targeting...

Data from: Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Michael Stat, Jeffrey John, Joseph D. DiBattista, Stephen J. Newman, Michael Bunce & Euan S. Harvey
Monitoring communities of fish is important for the management and health of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are one of the most effective non‐destructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, while BRUVs can sample visually conspicuous biota, some taxa are under‐sampled or not recorded at all. Here, we compared the diversity of fishes characterised using BRUVs with metabarcoding of environmental DNA (eDNA) extracted from...

Data from: Cool echidnas survive the fire

Julia Nowack, Christine Cooper, Fritz Geiser & Christine Elizabeth Cooper
Fires have occurred throughout history, including those associated with the meteoroid impact at the Cretaceous-Palaeogene (K-Pg) boundary that eliminated many vertebrate species. To evaluate the recent hypothesis that the survival of the K-Pg fires by ancestral mammals was dependent on their ability to use energy-conserving torpor, we studied body temperature fluctuations and activity of an egg-laying mammal, the echidna (Tachyglossus aculeatus), often considered to be a ‘living fossil’, before, during and after a prescribed burn....

Data from: Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

Joseph D. DiBattista, James D. Reimer, Michael Stat, Giovanni D. Masucci, Piera Biondi, Maarten De Brauwer & Michael Bunce
Background. Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA)...

Data from: Changes in ectomycorrhizal fungal community composition and declining diversity along a 2-million-year soil chronosequence

Felipe E. Albornoz, François P. Teste, Hans Lambers, Michael Bunce, Dáithí C. Murray, Nicole E. White & Etienne Laliberté
Ectomycorrhizal (ECM) fungal communities covary with host plant communities along soil fertility gradients, yet it is unclear whether this reflects changes in host composition, fungal edaphic specialization or priority effects during fungal community establishment. We grew two co-occurring ECM plant species (to control for host identity) in soils collected along a 2-million-year chronosequence representing a strong soil fertility gradient and used soil manipulations to disentangle the effects of edaphic properties from those due to fungal...

Data from: Local genetic patchiness but no regional differences between Indo-West Pacific populations of the dogtooth tuna Gymnosarda unicolor

Blair P. Bentley, Euan S. Harvey, Stephen J. Newman, David J. Welch, Adam K. Smith, Winn J. Kennington, DJ Welch, ES Harvey, SJ Newman, BP Bentley & WJ Kennington
Physical barriers can have profound impacts on dispersal in marine species. Here, we investigate population structure and levels of relatedness among individuals of the coral reef associated fish, the dogtooth tuna Gymnosarda unicolor, collected from 15 sites across the Indo-West Pacific region. We screened 92 individuals for genetic variation at 13 nuclear microsatellite loci and the cytochrome oxidase subunit 1 (CO1) mitochondrial DNA (mtDNA) gene. We detected no genetic differentiation between ocean basins or between...

Data from: Long-term data suggest jarrah-forest establishment at restored mine sites is resistant to climate variability

Rachel J. Standish, Matthew I. Daws, Aaron D. Gove, Raphael K. Didham, Andrew H. Grigg, John M. Koch & Richard J. Hobbs
1. Global climate change is projected to increase the frequency and intensity of drought in dry regions due to warming temperatures and declining rainfall. Severe drought can trigger tree mortality and drive persistent vegetation change. 2. To date, most empirical studies have focused on drought-induced mortality of adult trees, but this needs to be matched by similar efforts to understand drought impacts on seedling establishment if we are to understand the resilience of the world's...

Data from: Habitat-based species distribution modelling of the Hawaiian deepwater snapper-grouper complex

Zack. S. Oyafuso, Jeffrey C. Drazen, Cordelia H. Moore & Erik C. Franklin
Deepwater snappers and groupers are valuable components of many subtropical and tropical fisheries globally and understanding the habitat associations of these species is important for spatial fisheries management. Habitat-based species distribution models were developed for the deepwater snapper-grouper complex in the main Hawaiian Islands (MHI). Six eteline snappers (Pristipomoides spp., Aphareus rutilans, and Etelis spp.) and one endemic grouper (Hyporthodus quernus) comprise the species complex known as the Hawaiian Deep Seven Bottomfishes. Species occurrence was...

Data from: Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species

Sheree Walters, Todd Robinson, Margaret Byrne, Grant Wardell-Johnson & Paul Nevill
Sympatric tree species are subject to similar climatic drivers, posing a question as to whether they display comparable adaptive responses. However, no study has explicitly examined local adaptation of co-occurring parasitic and autotrophic plant species to the abiotic environment. Here we test the hypotheses that a generalist parasitic tree would display a weaker signal of selection and genomic variation would associate with fewer climatic variables (particularly precipitation) but have similar spatial patterns to a sympatric...

Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia

Katrina West, Zoe Richards, Euan Harvey, Robert Susac, Alicia Grealy & Michael Bunce
Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic ‘stygofauna’ assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23...

Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

Joseph DiBattista, James Reimer, Michael Stat, Giovanni Masucci, Piera Biondi, Maarten De Brauwer, Shaun Wilkinson, Anthony Chariton & Michael Bunce
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine...

Data from: New populations of the black-flanked rock-wallaby (Petrogale lateralis) from the Little Sandy Desert and Murchison, Western Australia

Jeff M. Turpin, Nicole E. White, Judy A. Dunlop & M. J. Bamford
During two independent fauna surveys, rock-wallaby (Petrogale) scats were recorded from caves located outside the current known Petrogale distribution. Scats collected from Desert Queen Baths (Little Sandy Desert, Western Australia, 2012), and the Barr Smith Range (Murchison, Western Australia, 2015) were genetically analysed and a follow-up motion camera survey confirmed an extant rock-wallaby population at Desert Queen Baths. The combination of sampling techniques overcame the detection difficulties associated with rare and cryptic taxa, and together...

Greece

Stylianos Papathanassopoulos , Achilleas  Karadimitriou, Christos  Kostopoulos  & Ioanna Archontaki

Diminishing potential for tropical reefs to function as coral diversity strongholds under climate change conditions

Arne Adam
Aim: Forecasting the influence of climate change on coral biodiversity and reef functioning is important for informing policy decisions. Dominance shifts, tropicalisation and local extinctions are common responses of climate change, but uncertainty surrounds the reliability of predicted coral community transformations. Here, we use species distribution models (SDMs) to assess changes in suitable coral habitat and associated patterns in biodiversity across Western Australia (WA) under present-day and future climate scenarios (RCP 2.6 and RCP 8.5)....

Climate-assisted persistence of tropical fish vagrants in temperate marine ecosystems

Joseph DiBattista, Laura Gajdzik, Thomas DeCarlo, Adam Koziol, Mahsa Mousavi-Derazmahalleh, Megan Coghlan, Matthew Power, Michael Bunce, David Fairclough, Michael Travers & Glenn Moore
Rising temperatures and extreme climatic events are propelling tropical species into temperate marine ecosystems, but not all species can persist. Here, we used the heatwave-driven expatriation of tropical black rabbitfish (Siganus fuscescens) to the temperate environments of Western Australia to assess the ecological and evolutionary mechanisms that may entail their persistence. Population genomic assays for this rabbitfish indicated little genetic differentiation between tropical residents and vagrants to temperate environments due to high migration rates, which...

Data from: Point process models for presence-only analysis

Ian W. Renner, Jane Elith, Adrian Baddeley, William Fithian, Trevor Hastie, Steven Phillips, Gordana Popovic & David I. Warton
1. Presence-only data are widely used for species distribution modelling, and point process regression models are a exible tool that has considerable potential for this problem, when data arise as point events. 2. In this paper we review point process models, some of their advantages, and some common methods of fitting them to presence-only data. 3. Advantages include (and are not limited to): clarification of what the response variable is that is modelled; a framework...

Data from: A questionnaire study of injections prescribed and dispensed for patients diagnosed with mild/moderate community-acquired pneumonia in Mongolia

Gereltuya Dorj, Bruce Sunderland, Delia Hendrie & Richard W. Parsons
Purpose. The study aimed to determine the extent of and factors influencing the prescribing of injections for the treatment of mild/moderate community acquired pneumonia (CAP) in Mongolia. Methods. Questionnaires were developed and administered to medication providers (34 Pharmacists, 27 pharmacy technicians) and prescribers (22 general doctors and 49 medical specialists) working in Mongolia. Results. Cefalosporins were prescribed for patients with mild pneumonia and doctors tended to prescribe injectable cefalosporins (cefazolin) rather than oral dosage forms....

Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Joseph D. DiBattista, Pablo Saenz-Agudelo, Marek J. Piatek, Xin Wang, Manuel Aranda & Michael L. Berumen
Data from a large-scale restriction site associated DNA (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction-site (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to...

Data from: Applying the multistate capture-recapture robust design to characterize metapopulation structure

Delphine Chabanne, Kenneth H. Pollock, Hugh Finn, Lars Bejder & Delphine B. H. Chabanne
1. Population structure must be considered when developing mark-recapture (MR) study designs as the sampling of individuals from multiple populations (or subpopulations) may increase heterogeneity in individual capture probability. Conversely, the use of an appropriate MR study design which accommodates heterogeneity associated with capture-occasion varying covariates due to animals moving between ‘states’ (i.e. geographic sites) can provide insight into how animals are distributed in a particular environment and the status and connectivity of subpopulations. 2....

Data from: Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity

Michael R. Whitehead, Renee A. Catullo, Monica Ruibal, Kingsley W. Dixon, Rod Peakall & Celeste C. Linde
The increasing availability of DNA sequence data enables exciting new opportunities for fungal ecology. However, it amplifies the challenge of how to objectively classify the diversity of fungal sequences into meaningful units, often in the absence of morphological characters. Here, we test the utility of modern multilocus Bayesian coalescent-based methods for delimiting cryptic fungal diversity in the orchid mycorrhiza morphospecies Serendipita vermifera. We obtained 147 fungal isolates from Caladenia, a speciose clade of Australian orchids...

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