ORCID Profile
0000-0002-0071-464X
Current Organisations
Ascension Island Government
,
Curtin University
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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
Publisher: Elsevier BV
Date: 09-2017
Publisher: Cambridge University Press (CUP)
Date: 2023
DOI: 10.1017/S0025315422001060
Abstract: The first record of the parasite Alebion carchariae in the waters of Ascension Island collected from Galapagos sharks, Carcharhinus galapagensis (Carcharhinidae), is described. No previous record of this parasite exists for Ascension Island, nor have Galapagos sharks previously been listed as a host. Specimens of A. carchariae were identified using morphological techniques and DNA barcoding of the cytochrome c oxidase I subunit (COI) gene. This study provides the first COI barcodes for this species and a brief review of known hosts. We recommend further research to understand the life cycle of this parasite, its plasticity in terms of host/habitat selection, and to determine the implications of its presence on the hosts it inhabits.
Publisher: Springer Science and Business Media LLC
Date: 13-11-2020
Publisher: Elsevier BV
Date: 04-2023
Publisher: Public Library of Science (PLoS)
Date: 04-05-2016
Publisher: Wiley
Date: 16-07-2022
Abstract: Population genetic data can provide valuable information on the demography of a species. For rare and elusive marine megafauna, s les for generating the data are traditionally obtained from tissue biopsies, which can be logistically difficult and expensive to collect and require invasive s ling techniques. Analysis of environmental DNA (eDNA) offers an alternative, minimally invasive approach to provide important genetic information. Although eDNA approaches have been studied extensively for species detection and bio ersity monitoring in metabarcoding studies, the potential for the technique to address population-level questions remains largely unexplored. Here, we applied "eDNA haplotyping" to obtain estimates of the intraspecific genetic ersity of a whale shark (Rhincodon typus) aggregation at Ningaloo reef, Australia. Over 2 weeks, we collected seawater s les directly behind in idual sharks prior to taking a tissue biopsy s le from the same animal. Our data showed a 100% match between mtDNA sequences recovered in the eDNA and tissue s le for all 28 in iduals s led. In the seawater s les, >97% of all reads were assigned to six dominant haplotypes, and a clear dominant signal (~99% of s le reads) was recovered in each s le. Our study demonstrates accurate in idual-level haplotyping from seawater eDNA. When DNA from one in idual clearly dominates each eDNA s le, it provides many of the same opportunities for population genetic analyses as a tissue s le, potentially removing the need for tissue s ling. Our results show that eDNA approaches for population-level analyses have the potential to supply critical demographic data for the conservation and management of marine megafauna.
Publisher: Wiley
Date: 29-08-2017
Abstract: Prevention and early detection are well recognized as the best strategies for minimizing the risks posed by nonindigenous species (NIS) that have the potential to become marine pests. Central to this is the ability to rapidly and accurately identify the presence of NIS, often from complex environmental s les like biofouling and ballast water. Molecular tools have been increasingly applied to assist with the identification of NIS and can prove particularly useful for taxonomically difficult groups like ascidians. In this study, we have developed real-time PCR assays suited to the specific identification of the ascidians Didemnum perlucidum and Didemnum vexillum. Despite being recognized as important global pests, this is the first time specific molecular detection methods have been developed that can support the early identification and detection of these species from a broad range of environmental s le types. These fast, robust and high-throughput assays represent powerful tools for routine marine biosecurity surveillance, as detection and confirmation of the early presence of species could assist in the timely establishment of emergency responses and control strategies. This study applied the developed assays to confirm the ability to detect Didemnid eDNA in water s les. While previous work has focused on detection of marine larvae from water s les, the development of real-time PCR assays specifically aimed at detecting eDNA of sessile invertebrate species in the marine environment represents a world first and a significant step forwards in applied marine biosecurity surveillance. Demonstrated success in the detection of D. perlucidum eDNA from water s les at sites where it could not be visually identified suggests value in incorporating such assays into biosecurity survey designs targeting Didemnid species.
Publisher: Elsevier BV
Date: 05-2009
DOI: 10.1016/J.MARENVRES.2009.03.001
Abstract: Population outbreaks of crown-of-thorns sea star (Acanthaster planci L.) remain one of the most significant biological disturbances on tropical coral reefs although the increasing attention given to other threats has greatly limited recent progress in understanding the cause and consequences of this phenomenon. In September 2005 dramatic increases in the abundance of A. planci were observed on reefs within Bootless Bay, Central Province, Papua New Guinea, where few crown-of-thorns have previously been reported. Densities of A. planci peaked at 162 sea stars per hectare and caused extensive coral mortality. This outbreak killed upwards of 55% of live corals, reducing overall coral cover from 42.4% in 2005 down to just 19.1% in March 2006. Declines in coral cover were largely driven by widespread mortality of Acropora spp. which dominated reef assemblages prior to the outbreak. The extensive depletion of Acropora spp. greatly altered the coral composition as well as the physical structure of reef habitats. In the absence of any other major disturbances these coral communities are likely to quickly recover, but this outbreak highlights the ongoing contribution of A. planci to degradation of coral reef environments.
Publisher: PeerJ
Date: 12-06-2023
DOI: 10.7717/PEERJ.15522
Abstract: Crabs can be transported beyond their native range via anthropogenic-mediated means such as aquarium trade, live seafood trade and shipping. Once introduced into new locations, they can establish persisting populations and become invasive, often leading to negative impacts on the recipient environment and native species. Molecular techniques are increasingly being used as complementary tools in biosecurity surveillance and monitoring plans for invasive species. Molecular tools can be particularly useful for early detection, rapid identification and discrimination of closely related species, including when diagnostic morphological characters are absent or challenging, such as early life stages, or when only part of the animal is available. In this study, we developed a species-specific qPCR assay, which targets the cytochrome c oxidase subunit 1 (CO1) region of the Asian paddle crab Charybdis japonica . In Australia, as well as many parts of the world, this species is considered invasive and routine biosecurity surveillance is conducted to reduce the risk of establishment. Through rigorous testing of tissue from target and non-target species we demonstrate that this assay is sensitive enough to detect as little as two copies per reaction and does not cross lify with other closely related species. Field s les and environmental s les spiked with C. japonica DNA in high and low concentrations indicate that this assay is also a promising tool for detecting trace amounts of C. japonica eDNA in complex substrates, making it a useful complementary tool in marine biosecurity assessments.
Publisher: Regional Euro-Asian Biological Invasions Centre Oy (REABIC)
Date: 2021
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.
Publisher: Wiley
Date: 09-03-2021
Abstract: Metabarcoding of environmental DNA (eDNA) when coupled with high throughput sequencing is revolutionising the way bio ersity can be monitored across a wide range of applications. However, the large number of tools deployed in downstream bioinformatic analyses often places a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility. Furthermore, scalability needs to be considered to handle the growing amount of data due to increase in sequence output and the scale of project. Here, we describe eDNAFlow, a fully automated workflow that employs a number of state‐of‐the‐art applications to process eDNA data from raw sequences (single‐end or paired‐end) to generation of curated and noncurated zero‐radius operational taxonomic units (ZOTUs) and their abundance tables. This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high‐performance computing (HPC) clusters. Finally, we present an in‐house Python script to assign taxonomy to ZOTUs based on user specified thresholds for assigning lowest common ancestor (LCA). We demonstrate the utility and efficiency of the pipeline using an ex le of a published coral ersity biomonitoring study. Our results were congruent with the aforementioned study. The scalability of the pipeline is also demonstrated through analysis of a large data set containing 154 s les. To our knowledge, this is the first automated bioinformatic pipeline for eDNA analysis using two powerful tools: Nextflow and Singularity. This pipeline addresses two major challenges in the analysis of eDNA data scalability and reproducibility.
Publisher: Wiley
Date: 31-08-2022
Abstract: Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological s les. Research institutions worldwide increasingly employ HTS methods for bio ersity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical s les and primer sets using varying laboratory procedures. Homogenized biofouling s les collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories ( lification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the s les grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality s les gave the best improvement in s le classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, s le defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future bio ersity studies using metabarcoding.
Publisher: Regional Euro-Asian Biological Invasions Centre Oy (REABIC)
Date: 2016
Publisher: Elsevier BV
Date: 10-2023
Publisher: Springer Science and Business Media LLC
Date: 16-09-2023
DOI: 10.1007/S00338-022-02301-3
Abstract: Coral reefs are bio ersity hotspots, places of high endemicity and provide essential services to billions of people globally. With increasing threats to these reefs worldwide, there is a need to implement faster, more efficient ways to monitor spatial and temporal patterns of bio ersity. Environmental DNA (eDNA) metabarcoding offers a promising tool to address this issue, as it has revolutionized our ability to monitor bio ersity from complex environmental s les such as seawater. However, the capacity for eDNA to resolve fine scale shifts in community composition across habitats in seascapes is yet to be fully explored. Here, we applied eDNA metabarcoding using the rRNA 18S Universal eukaryote assay to explore differences in community profiles between s les collected from the lagoon and reef slope habitats across more than 170 km of the Ningaloo Coast World Heritage Area in Western Australia. We recovered 2061 licon sequence variants that comprised of 401 taxa spanning 14 different metazoan phyla such as cnidarians, poriferans, molluscs, algae, worms, and echinoderms. Our results revealed strong clustering of s les by habitat type across the length of the reef. Community dissimilarity (beta ersity) between s les collected from the reef slope and lagoon habitats was high and was driven largely by a strong rate of spatial turnover, indicating a distinct set of taxa representing each reef zone community. We also detected a strong pattern of isolation by distance within our slope s les, suggesting that communities are spatially stratified across the length of the reef. Despite high connectivity due to regular flushing of the lagoon environment, our results demonstrate that metabarcoding of seawater eDNA from different habitats can resolve fine scale community structure. By generating multi-trophic bio ersity data, our study also provided baseline data for Ningaloo from which future changes can be assessed.
Publisher: Wiley
Date: 20-02-2020
DOI: 10.1002/EDN3.74
Location: Saint Helena, Ascension and Tristan da Cunha
No related grants have been discovered for Tiffany Simpson.