ORCID Profile
0000-0002-0792-9686
Current Organisations
CSIRO
,
Curtin University
,
University of Western Australia
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Ecological Impacts of Climate Change | Marine and Estuarine Ecology (incl. Marine Ichthyology) | Ecosystem Function | Ecological Applications | Applied Mathematics | Ecology | Applied Statistics | Biological Mathematics | Theoretical Physics |
ANZSRC Socio-Economic Objective (SEO)
Ecosystem Adaptation to Climate Change | Effects of Climate Change and Variability on Australia (excl. Social Impacts) | Fisheries - Wild Caught not elsewhere classified | Global Effects of Climate Change and Variability (excl. Australia, New Zealand, Antarctica and the South Pacific) (excl. Social Impacts) | Expanding Knowledge in the Biological Sciences | Marine Flora, Fauna and Biodiversity | Biological sciences | Mathematical sciences
Related Links
Publications
Author Correction: Passive eDNA collection enhances aquatic biodiversity analysis
Publisher: Springer Science and Business Media LLC
Date: 06-04-2021
DOI: 10.1038/S42003-021-01994-6
Abstract: A Correction to this paper has been published: 0.1038/s42003-021-01994-6
Diet results from Adelie penguins at Bechervaise Island and Whitney Point, 2012-2013
Publisher: Australian Antarctic Data Centre
Date: 2016
DNA metabarcoding-Need for robust experimental designs to draw sound ecological conclusions.
Publisher: Wiley
Date: 04-2019
DOI: 10.1111/MEC.15060
Comparison of materials for rapid passive collection of environmental DNA
Publisher: Cold Spring Harbor Laboratory
Date: 10-11-2021
DOI: 10.1101/2021.11.08.467842
Abstract: Passive collection is an emerging s ling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive, efficient, and requires minimal equipment, making it suited to high density s ling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3 million litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibers and 1% chitosan, cotton fibres, hemp fibres and sponge with either zeolite or active carbon) for intervals between five and 1080 minutes. We show that for most materials, with as little as five minutes submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 to 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19-32). Using scanning electron microscopy, we visualised biological matter adhered to the surface of materials, rather than entrapped, with images also revealing a ersity in size and structure of putative eDNA particles. Environmental DNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost and time-sensitive biological surveys, and where access to equipment is limited.
An epigenetic clock to estimate the age of living beluga whales
Publisher: Wiley
Date: 03-02-2021
DOI: 10.1111/EVA.13195
Abstract: DNA methylation data facilitate the development of accurate molecular estimators of chronological age or “epigenetic clocks.” We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas , developed for an endangered population in Cook Inlet, Alaska, USA. We used a custom methylation array to measure methylation levels at 37,491 cytosine–guanine sites (CpGs) from skin s les of dead whales ( n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R 2 = 0.92 for the training data and an R 2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross‐validation. We applied the epigenetic clock to an independent dataset of 38 skin s les collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. The epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.
High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding
Publisher: Wiley
Date: 16-08-2017
DOI: 10.1111/MEC.14245
Abstract: Gelatinous zooplankton are a large component of the animal biomass in all marine environments, but are considered to be uncommon in the diet of most marine top predators. However, the diets of key predator groups like seabirds have conventionally been assessed from stomach content analyses, which cannot detect most gelatinous prey. As marine top predators are used to identify changes in the overall species composition of marine ecosystems, such biases in dietary assessment may impact our detection of important ecosystem regime shifts. We investigated albatross diet using DNA metabarcoding of scats to assess the prevalence of gelatinous zooplankton consumption by two albatross species, one of which is used as an indicator species for ecosystem monitoring. Black-browed and C bell albatross scats were collected from eight breeding colonies covering the circumpolar range of these birds over two consecutive breeding seasons. Fish was the main dietary item at most sites however, cnidarian DNA, primarily from scyphozoan jellyfish, was present in 42% of s les overall and up to 80% of s les at some sites. Jellyfish was detected during all breeding stages and consumed by adults and chicks. Trawl fishery catches of jellyfish near the Falkland Islands indicate a similar frequency of jellyfish occurrence in albatross diets in years of high and low jellyfish availability, suggesting jellyfish consumption may be selective rather than opportunistic. Warmer oceans and overfishing of finfish are predicted to favour jellyfish population increases, and we demonstrate here that dietary DNA metabarcoding enables measurements of the contribution of gelatinous zooplankton to the diet of marine predators.
Quantifying prey availability using the foraging plasticity of a marine predator, the little penguin
Publisher: Wiley
Date: 06-07-2020
A three-year, Australian-wide, environmental DNA (eDNA) study reveals spatial and temporal patterns in marine biodiversity
Publisher: Wiley
Date: 26-04-2023
DOI: 10.1111/DDI.13699
Abstract: To use a long‐term collection of bulk plankton s les to test the capacity of DNA metabarcoding to characterize the spatial and seasonal patterns found within a range of zooplankton communities, and investigate links with concurrent abiotic data collected as part of Australia's Integrated Marine Observing System (IMOS) programme. S les were sourced seasonally for 3 years from nine Pan‐Australian marine sites (n = 90). Here, we apply a multi‐assay metabarcoding approach to environmental DNA extracted from bulk plankton s les. Six assays (targeting 16SrRNA and COI genes) were used to target, lify and sequence the zooplankton ersity found within each s le. The data generated from each assay were filtered and clustered into OTUs prior to analysis. Abiotic IMOS data collected contemporaneously enabled us to explore the physical and chemical drivers of community composition. From over 25 million sequences, we identified in excess of 500 distinct taxa and detected clear spatial differences. We found that site and sea surface temperature are the most consistent predictors of differences between zooplankton communities. We detected endangered and invasive species such as the bryozoan Membranipora membranacea and the mollusc Maoricolpus roseus , and seasonal occurrences of species such as humpback whales ( Megaptera novaeangliae ). We also estimated the number of s les required to detect any significant seasonal changes. For OTU richness, this was found to be assay dependent and for OTU assemblage, a minimum of nine s les per season would be required. Our results demonstrate the ability of DNA to capture and map zooplankton community changes in response to seasonal and spatial stressors and provide vital evidence to environmental stakeholders. We confirm that a metabarcoding method offers a practical opportunity for an ecosystem‐wide approach to long‐term biomonitoring and understanding marine biomes where morphological analysis is not feasible.
Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists
Publisher: Wiley
Date: 26-08-2019
A genomic predictor of lifespan in vertebrates
Publisher: Springer Science and Business Media LLC
Date: 12-12-2019
DOI: 10.1038/S41598-019-54447-W
Abstract: Biological ageing and its mechanistic underpinnings are of immense biomedical and ecological significance. Ageing involves the decline of erse biological functions and places a limit on a species’ maximum lifespan. Ageing is associated with epigenetic changes involving DNA methylation. Furthermore, an analysis of mammals showed that the density of CpG sites in gene promoters, which are targets for DNA methylation, is correlated with lifespan. Using 252 whole genomes and databases of animal age and promotor sequences, we show a pattern across vertebrates. We also derive a predictive lifespan clock based on CpG density in a selected set of promoters. The lifespan clock accurately predicts maximum lifespan in vertebrates (R 2 = 0.76) from the density of CpG sites within only 42 selected promoters. Our lifespan clock provides a wholly new method for accurately estimating lifespan using genome sequences alone and enables estimation of this challenging parameter for both poorly understood and extinct species.
Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates
Publisher: Australian Antarctic Data Centre
Date: 2016
DNA metabarcoding assays reveal a diverse prey assemblage for Mobula rays in the Bohol Sea, Philippines
Publisher: Wiley
Date: 30-01-2019
DOI: 10.1002/ECE3.4858
Environmental DNA metabarcoding studies are critically affected by substrate selection
Publisher: Wiley
Date: 21-12-2019
Abstract: Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field s ling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA s ling on the ersity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic ersity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA s les from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi-assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and <6% of families were found in all four substrates. Taxonomic composition varied significantly depending on the substrate s led implying that the suitability (and bias) of an eDNA substrate will depend on the focal taxa. These findings demonstrate that single substrate eDNA metabarcoding likely underestimates the total eukaryotic ersity. Future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.
Fish species lifespan prediction from promoter cytosine‐phosphate‐guanine density
Publisher: Wiley
Date: 19-03-2023
Abstract: Lifespan is a key attribute of a species' life cycle and varies extensively among major lineages of animals. In fish, lifespan varies by several orders of magnitude, with reported values ranging from less than 1 year to approximately 400 years. Lifespan information is particularly useful for species management, as it can be used to estimate invasion potential, extinction risk and sustainable harvest rates. Despite its utility, lifespan is unknown for most fish species. This is due to the difficulties associated with accurately identifying the oldest in idual(s) of a given species, and/or deriving lifespan estimates that are representative for an entire species. Recently it has been shown that CpG density in gene promoter regions can be used to predict lifespan in mammals and other vertebrates, with variable accuracy across taxa. To improve accuracy of lifespan prediction in a non‐mammalian vertebrate group, here we develop a fish‐specific genomic lifespan predictor. Our new model includes more than eight times the number of fish species included in the previous vertebrate model ( n = 442) and uses fish‐specific gene promoters as reference sequences. The model predicts fish lifespan from genomic CpG density alone (measured as CpG observed/expected ratio), explaining 64% of the variance between known and predicted lifespans. The predictions are highly robust to variation in genome quality and are applicable to all classes of fish a taxonomically erse and speciose group. The results demonstrate the value of promoter CpG density as a universal predictor of fish lifespan that can applied where empirical data are unavailable, or impracticable to obtain.
Age estimation in a long-lived seabird (Ardenna tenuirostris) using DNA methylation-based biomarkers
Publisher: Wiley
Date: 06-02-2019
Abstract: Age structure is a fundamental aspect of animal population biology. Age is strongly related to in idual physiological condition, reproductive potential and mortality rate. Currently, there are no robust molecular methods for age estimation in birds. Instead, in iduals must be ringed as chicks to establish known-age populations, which is a labour-intensive and expensive process. The estimation of chronological age using DNA methylation (DNAm) is emerging as a robust approach in mammals including humans, mice and some non-model species. Here, we quantified DNAm in whole blood s les from a total of 71 known-age Short-tailed shearwaters (Ardenna tenuirostris) using digital restriction enzyme analysis of methylation (DREAM). The DREAM method measures DNAm levels at thousands of CpG dinucleotides throughout the genome. We identified seven CpG sites with DNAm levels that correlated with age. A model based on these relationships estimated age with a mean difference of 2.8 years to known age, based on validation estimates from models created by repeated s ling of training and validation data subsets. Longitudinal observation of in iduals re-s led over 1 or 2 years generally showed an increase in estimated age (6/7 cases). For the first time, we have shown that epigenetic changes with age can be detected in a wild bird. This approach should be of broad interest to researchers studying age biomarkers in non-model species and will allow identification of markers that can be assessed using targeted techniques for accurate age estimation in large population studies.
How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis
Publisher: Wiley
Date: 16-07-2018
DOI: 10.1111/MEC.14779
Comparison of materials for rapid passive collection of environmental DNA
Publisher: Wiley
Date: 06-2022
Abstract: Passive collection is an emerging s ling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive and efficient, and requires minimal equipment, making it suited to high‐density s ling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3‐million‐litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibres and 1% chitosan, cotton fibres, hemp fibres, and sponge with either zeolite or active carbon) for intervals between 5 and 1080 min. We show that for most materials, with as little as 5 min of submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 and 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19–32). Using scanning electron microscopy, we visualized biological matter adhering to the surface of materials, rather than entrapped, with images also revealing a ersity in size and structure of putative eDNA particles. eDNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost‐ and time‐sensitive biological surveys, and where access to equipment is limited.
A review of applications of environmental DNA for reptile conservation and management
Publisher: Wiley
Date: 06-2022
DOI: 10.1002/ECE3.8995
Abstract: Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community ersity at erse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.
High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding
Publisher: Australian Antarctic Data Centre
Date: 2017
Maximising fish detection with eDNA metabarcoding
Publisher: Wiley
Date: 20-02-2020
DOI: 10.1002/EDN3.74
Passive eDNA collection enhances aquatic biodiversity analysis
Publisher: Springer Science and Business Media LLC
Date: 22-02-2021
DOI: 10.1038/S42003-021-01760-8
Abstract: Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and bio ersity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or distribution often require more s les than can be practically collected with current filtration methods. Here we demonstrate how eDNA can be passively collected in both tropical and temperate marine systems by directly submerging filter membranes (positively charged nylon and non-charged cellulose ester) in the water column. Using a universal fish metabarcoding assay, we show that passive eDNA collection can detect fish as effectively as active eDNA filtration methods in temperate systems and can also provide similar estimates of total fish bio ersity. Furthermore, passive eDNA collection enables greater levels of biological s ling, which increases the range of ecological questions that eDNA metabarcoding can address.
Antarctic pack ice algal distribution: Floe‐scale spatial variability and predictability from physical parameters
Publisher: American Geophysical Union (AGU)
Date: 28-07-2017
DOI: 10.1002/2017GL074346
Related Organisations
University Of Aberdeen
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
Linkage Projects - Grant ID: LP140100404
Start Date: 11-2014
End Date: 08-2019
Amount: $193,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP0877447
Start Date: 06-2008
End Date: 06-2012
Amount: $240,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP150100007
Start Date: 03-2015
End Date: 12-2017
Amount: $322,704.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP200100483
Start Date: 2021
End Date: 2024
Amount: $324,006.00
Funder: Australian Research Council
View Funded Activity