18 Works

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...

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...

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....

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...

The evolution of autotomy in leaf-footed bugs

Zachary Emberts, Colette M St. Mary, Cody Coyotee Howard, Michael Forthman, Philip W. Bateman, Ummat Somjee, Wei Song Hwang, Daiqin Li, Rebecca T Kimball & Christine W Miller
Sacrificing body parts is one of many behaviors that animals use to escape predation. This trait, termed autotomy, is classically associated with lizards. However, several other taxa also autotomize, and this trait has independently evolved multiple times throughout Animalia. Despite having multiple origins and being an iconic anti-predatory trait, much remains unknown about the evolution of autotomy. Here, we combine morphological, behavioral, and genomic data to investigate the evolution of autotomy within leaf-footed bugs and...

The construction of small-scale, quasi-mechanistic spatial models of insect energetics in habitat restoration: a case study of beetles in Western Australia

Sean Tomlinson
Aim: The management and restoration of ecological processes mediated by biotic interactions is now broadly advocated, and may be achieved by the targeting restoration towards key agents. Although theoretically examined, a practical approach to incorporating the physiology and energetics of insects into restoration planning is poorly articulated. I aimed to provide a case study using the thermal biology and energetics of beetles to identify the distribution of habitat suitability in a large restoration landscape. Location:...

The applicability of eDNA metabarcoding approaches for sessile benthic surveying in the Kimberley region, north-western Australia

Katrina West, Arne Adam, Nicole White, Will Robbins, Daniel Barrow, Adrian Lane & Zoe Richards
The application of environmental DNA technologies is a promising new approach to rapidly audit biodiversity across large-scale, remote regions. Here, we examine the efficacy of a dual-assay eDNA metabarcoding approach for sessile benthic bioassessments in the turbid waters of the Lalang-garram Marine Parks, in the inshore Kimberley region, north-western Australia. We ask three principal questions: 1. Is the eDNA released by sessile benthic taxa (i.e. hard and soft corals, sponges and tunicates) locally detectable? 2....

Fatal and non-fatal events within 14 days after early, intensive mobilization post stroke

Julie Bernhardt, Karen Borschmann, Janice Collier, Amanda Thrift, Peter Langhorne, Sandy Middleton, Richard Lindley, Helen Dewey, Philip Bath, Catherine Said, Leonid Churilov, Fiona Ellery, Christopher Bladin, Christopher Reid, Judith Frayne, Velandai Srikanth, Stephen Read & Geoffrey Donnan
Objective: We examined fatal and non-fatal Serious Adverse Events (SAEs) at 14 days within AVERT. Method: A prospective, parallel group, assessor blinded, randomized international clinical trial comparing very early intensive mobilization training (VEM) with usual care (UC); with follow up to 3 months. Included: Patients with ischaemic and haemorrhagic stroke within 24 hours of onset and physiological parameters within set limits. Treatment with thrombolytics allowed. Excluded: Patients with severe premorbid disability and/or comorbidities. Interventions continued...

Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean

Patricia Wepfer, Patricia H. Wepfer, Yuichi Nakajima, Makamas Sutthacheep, Veronica Z. Radice, Zoe Richards, Put Ang, Tullia Terraneo, Mareike Sudek, Atsushi Fujimura, Robert J. Toonen, Alexander S. Mikheyev, Evan P. Economo & Satoshi Mitarai
Stony corals (Scleractinia) form the basis for some of the most diverse ecosytems on Earth, but we have much to learn about their evolutionary history and systematic relationships. In order to improve our understanding of species in corals we here investigated phylogenetic relationships between morphologically defined species and genetic lineages in the genus Galaxea (Euphyllidae) using a combined phylogenomic and phylogeographic ap- proach. Previous studies revealed the nominal species G. fascicularis included three genetically well-differ-...

Cold call: the acoustic repertoire of Ross Sea killer whales (Orcinus orca, Type C) in McMurdo Sound, Antarctica

Rebecca Wellard, Robert Pitman, John Durban & Christine Erbe
Killer whales (Orcinus orca) are top marine predators occurring globally. In Antarctic waters, five ecotypes have been described, with Type C being the smallest form of killer whale known. Acoustic recordings of nine encounters of Type C killer whales were collected in 2012 and 2013 in McMurdo Sound, Ross Sea. In a combined 3.5 hours of recordings, 6386 killer whale vocalisations were detected and graded based on their signal-to-noise ratio. Spectrograms of the highest-quality calls...

Data from: Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA (eDNA) metabarcoding

Mieke E Van Der Heyde, Michael Bunce, Grant Wardell-Johnson, Kristen Fernandes, Nicole White & Paul Nevill
Biological surveys based on visual identification of the biota are challenging, expensive, and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample...

Predicting hydrologic responses to climate changes in highly glacierized and mountainous region Upper Indus Basin

Muhammad Izhar Shah, Asif Khan, Tahir Ali Akbar, Quazi K Hassan, Asim Jahangir Khan & Ashraf Dewan
The Upper Indus Basin (UIB) is a major source of supplying water to different areas because of snow and glaciers melt and is also enduring the regional impacts of global climate change. The expected changes in temperature, precipitation, and snowmelt could be reasons for further escalation of the problem. Therefore, estimation of hydrological processes is critical for UIB. The objectives of this paper were to estimate the impacts of climate change on water resources and...

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

Joseph DiBattista, Pablo Saenz-Agudelo, Marek Piatek, Fernando Cagua, Brian Bowen, John Choat, Luiz Rocha, Michelle Gaither, Jean-Paul Hobbs, Tane Sinclair-Taylor, Jennifer McIlwain, Mark Priest, Camrin Braun, Nigel Hussey, Steven Kessel & Michael Berumen
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and...

eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem

Katrina West, Michael Stat, Euan Harvey, Craig Skepper, Joseph DiBattista, Zoe Richards, Michael Travers, Stephen Newman & Michael Bunce
Environmental DNA (eDNA) metabarcoding, a technique for retrieving multi-species DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for efficient whole-ecosystem surveying approaches to baseline biodiversity, study assemblage...

Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback

Christina Andronis
This spectral data is in support for the manuscript 'Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback'. This data was used to detect errors in the draft genome and curate previously undescribed genes in the Phytophthora cinnamomi genome.

Registration Year

  • 2020

Resource Types

  • Dataset


  • Curtin University
  • University of Newcastle Australia
  • University of Queensland
  • Australian Museum
  • Department of Primary Industries and Regional Development
  • King Abdullah University of Science and Technology
  • University of Guam
  • Victoria University of Wellington
  • University of Washington
  • COMSATS University Islamabad