120 Works

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...

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: 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...

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...

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...

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, Michael J. Travers, Euan S. Harvey, Zoe T. Richards, Joseph D. DiBattista, Stephen J. Newman & Craig L. Skepper
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...

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: 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: 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: 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...

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: 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: 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...

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)....

Residual CO2 trapping in oil-wet sandstone

Adriana Paluszny, Stefan Iglauer & Maxim Lebedev
MicroCT images of residual CO2 trapping in oil wet sandstone.

Data from: Demonstrating multiple benefits from periodically harvested fisheries closures

Jordan S. Goetze, Joachim Claudet, Fraser Januchowski-Hartley, Timothy J. Langlois, Shaun K. Wilson, Crow White, Rebecca Weeks & Stacy D. Jupiter
1.Periodically harvested closures (PHCs) are one of the most common forms of fisheries management in Melanesia, demonstrating multiple objectives, including sustaining fish stocks and increasing catch efficiency to support small-scale fisheries. No studies have comprehensively assessed their ability to provide short-term fisheries benefits across the entire harvest regime. 2.We present a novel analytical framework to guide a meta-analysis and assist future research in conceptualizing and assessing the potential of PHCs to deliver benefits for multiple...

Data from: Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey

Frederik V. Seersholm, Theresa L. Cole, Alicia Grealy, Nicolas J. Rawlence, Karen Greig, Michael Knapp, Michael Stat, Anders J. Hansen, Luke J. Easton, Lara Shepherd, Alan J. D. Tennyson, R. Paul Scofield, Richard Walter & Michael Bunce
New Zealand’s geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans (c. 1280 AD), its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and...

Data from: Precipitation drives global variation in natural selection

Adam Siepielski, Michael B. Morrissey, Mathieu Buoro, Stephanie M. Carlson, Christina M. Caruso, Sonya M. Clegg, Tim Coulson, Joseph DiBattista, Kiyoko M. Gotanda, Clinton D. Francis, Joe Hereford, Joel G. Kingsolver, Kate E. Augustine, Loeske E. B. Kruuk, Ryan A. Martin, Ben C. Sheldon, Nina Sletvold, Erik I. Svensson, Michael J. Wade & Andrew D. C. MacColl
Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation—natural selection—are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By...

Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds

Yoshan Moodley, Juan F. Masello, Gopi K. Munimanda, Theresa L. Cole, Marco R. Thali, Rachael Alderman, Richard J. Cuthbert, Manuel Marin, Melanie Massaro, Joan Navarro, Richard A. Phillips, Peter G. Ryan, Cristián G. Suazo, Yves Cherel, Henri Weimerskirch, Petra Quillfeldt & Luciano Calderon
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in...

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