ORCID Profile
0000-0002-1060-5447
Current Organisation
James Cook University
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Publisher: Springer Science and Business Media LLC
Date: 11-05-2021
Publisher: Cold Spring Harbor Laboratory
Date: 05-12-2022
DOI: 10.1101/2022.11.29.518289
Abstract: Terrestrial invasive invertebrates can rapidly colonize new areas, causing detrimental effects on bio ersity, economy, and lifestyle. Targeted environmental DNA (eDNA) methods could constitute an early detection tool given their sensitivity to small numbers of in iduals. We hypothesized that terrestrial runoff would transport eDNA from the land into adjacent water bodies and used the invasive yellow crazy ant ( Anoplolepis gracilipes ) as a model species to test this hypothesis. We collected water s les from four waterbodies adjacent to infestations following rainfall events for eDNA analysis. We also collected soil s les from areas of known infestations and tested five eDNA extraction methods to determine their efficiency to extract eDNA from soil. Water s les resulted in positive yellow crazy ant eDNA lification (20–100% field replicates across all sites), even at one site located 300 m away from where ants had been detected visually. Soil s les resulted in a high percentage of false negatives when s led from ant transit areas than from nest entrances. Unpurified DNA extracts from soil also resulted in false negative detections, and only after applying a purification step of DNA extracts, we detected yellow crazy ant eDNA in 40–100% of field replicates across all methods and sites. This is the first study to empirically show that eDNA from a terrestrial invertebrate can be successfully isolated and lified from adjacent or downstream waterbodies. Our results indicate that eDNA has the potential to be a useful method for detecting terrestrial invertebrates from soil and water.
Publisher: Wiley
Date: 09-03-2022
DOI: 10.1002/EDN3.279
Abstract: Environmental DNA (eDNA) methods are increasingly applied in the marine environment to identify species and community structure. To establish widely applicable eDNA techniques for elasmobranchs, we used the Critically Endangered largetooth sawfish ( Pristis pristis Linnaeus, 1758) as a model species for: (1) assessing eDNA particle size distribution (2) assessing the efficiency of long‐term preservation of water s les and (3) comparing the efficiency and detection sensitivity of filtration and precipitation methods. Water s les (1 L) collected from a tank containing one largetooth sawfish specimen were sequentially filtered through five filter membranes of decreasing pore size (20, 10, 5, 1.2, and 0.45 μm). The proportion of sawfish eDNA retained within each size class was determined through quantitative real‐time PCR (qPCR) using a species‐specific TaqMan probe assay. A linear mixed‐effects model (lme) showed that the 1.2 and 20 µm filters captured most of the eDNA particles present in the s led water. Additionally, whole water s les (0.375 L) were preserved in Longmire's buffer, stored at tropical ambient temperatures (26.3°C ± 3.0 SD) and extracted at five time points: immediately, one, two, and three months after collection, as well as frozen and extracted three months later, to assess the preservation efficiency of Longmire's buffer via qPCR analysis. A linear mixed‐effects model showed that s les maintained maximal eDNA yield for at least three months after collection at ambient storage. Lastly, when comparing the filtration and precipitation methods, filtration using 0.45 µm pore size was more sensitive to capture of largetooth sawfish eDNA than filtration with 20 µm filter or water precipitation. However, water precipitation was more efficient when accounting for volume of water processed. These results provide options for best capture and preservation of elasmobranch eDNA.
Publisher: Wiley
Date: 27-06-2020
DOI: 10.1002/EDN3.114
Publisher: Wiley
Date: 22-07-2021
DOI: 10.1002/EDN3.243
Abstract: Environmental DNA (eDNA) monitoring has revolutionized the way bio ersity is surveyed and has been proposed as a reliable method to inform management decisions. Recognition of eDNA techniques as reliable tools to inform management and biosecurity require stringent standards to assess s le quality and reliability of results. Laboratories can have their workflows assessed and certified through accreditation and be involved in proficiency testing schemes provided to test the accuracy and precision of molecular methods. Currently, there is only one eDNA‐based proficiency testing scheme designed to test competency of laboratories in lifying eDNA from the Great Crested Newt, Triturus cristatus (Laurenti, 1768) in water s les. This test, however, is a closed scheme currently run by invitation only to laboratories in the United Kingdom. Given the paucity of eDNA‐based proficiency schemes to ensure high‐quality services, this commentary discusses how future proficiency testing schemes could be designed to assess eDNA s le quality and reliability on detection results for environmental management and biosecurity applications. We discuss the use of tissue‐derived and synthetic oligonucleotides as reference materials, the need for proficiency testing schemes to assess the capacity of analytical facilities to determine s le quality as well as accurately detecting trace eDNA in blind s les and discuss the context in which fit for purpose eDNA testing schemes could be designed. To complement the future development of eDNA proficiency testing schemes, we provide firsthand accounts and lessons learned while developing the current Great Crested Newt eDNA proficiency scheme. Lastly, we highlight current limitations in standardizing rapidly improving eDNA‐based techniques and discuss disadvantages to accreditation and standardization from an Australian‐centered perspective as a means to promote an active debate on the topic of future eDNA accreditation and proficiency testing.
Publisher: Wiley
Date: 07-02-2023
DOI: 10.1002/EDN3.395
Abstract: Environmental DNA (eDNA)‐based methods are increasingly used by government agencies to detect pests and threatened species, and for broader bio ersity monitoring. Given rapid technological advances and a growing number of commercial service providers, there is a need to standardize methods for quality assurance and to maintain confidence in eDNA‐based results. Here, we introduce two documents to provide best‐practice guidelines for Australian and New Zealand eDNA researchers and end‐users (available from ublications ): the Environmental DNA protocol development guide for biomonitoring provides minimum standard considerations for eDNA and environmental RNA projects across the complete workflow, from ethical considerations and experimental design to interpreting and communicating results. The Environmental DNA test validation guidelines outline key steps to be used in assay development and validation for species‐specific testing and metabarcoding. Both guidelines were developed as an initiative of the Australian Government Department of Agriculture, Fisheries and Forestry and led by the Southern eDNA Society in a collaborative process including multiple consultation rounds with eDNA experts, end‐users, and stakeholders to adapt the guidelines to Australian and New Zealand needs. The aim of these guidelines is not to be prescriptive, but to set minimum standards to support a consistent and best‐practice approach to eDNA testing. We anticipate that the guidelines will be reviewed and regularly updated as required. Our aspiration is that these best‐practice guidelines will ensure environmental managers are provided with robust scientific evidence to support decision‐making.
Publisher: PeerJ
Date: 27-09-2021
DOI: 10.7717/PEERJ.12013
Abstract: Globally, hibian species have suffered drastic population declines over the past 40 years. Hundreds of species are now listed as Critically Endangered, with many of these considered “possibly extinct”. Most of these species are stream-dwelling frogs inhabiting remote, montane areas, where remnant populations are hard to find using traditional surveys. Environmental DNA (eDNA) could revolutionize surveys for ‘missing’ and endangered hibian populations by screening water s les from downstream sections to assess presence in the upstream catchments. However, the utility of this survey technique is dependent on quantifying downstream detection probability and distances. Here we tested downstream detection distances in two endangered stream frogs ( Litoria lorica and L. nannotis ) that co-occur in a remote stream catchment in north-east Australia, and for which we know precise downstream distributional limits from traditional surveys. Importantly, the two last populations of L. lorica persist in this catchment: one small (~1,000 frogs) and one very small (~100 frogs). We conducted eDNA screening at a series of sites kilometers downstream from the populations using precipitation from two fixed water volumes (15 and 100 mL) and via water filtering (mean 1,480 L). We detected L. nannotis and the small L. lorica population (~1,000 frogs) at most s ling sites, including 22.8 km downstream. The filtration method was highly effective for far-downstream detection, as was precipitation from 100 mL water s les, which also resulted in consistent detections at the far-downstream sites (including to 22.8 km). In contrast, we had limited downstream detection success for the very small L. lorica population (~100 frogs). The ecological aspects of our study system, coupled with thorough traditional surveys, enabled us to measure downstream eDNA detection distances with accuracy. We demonstrate that eDNA from a small population of approximately 1,000 frogs can be detected as far as 22.8 km downstream from the population. Water filtration is considered best for eDNA detection of rare aquatic species—indeed it was effective in this study—but we also achieved far-downstream detections when precipitating eDNA from 100 mL water s les. Collecting small water volumes for subsequent precipitation in the lab is more practical than filtration when surveying remote areas. Our downstream detection distances ( km) suggest eDNA is a valuable tool for detecting rare stream hibians. We provide recommendations on optimal survey methods.
Publisher: Pensoft Publishers
Date: 03-04-2202
DOI: 10.3897/NEOBIOTA.83.98898
Abstract: Terrestrial invasive invertebrates can rapidly colonise new areas, causing detrimental effects on bio ersity, economy and lifestyle. Targeted environmental DNA (eDNA) methods could constitute an early detection tool given their sensitivity to small numbers of in iduals. We hypothesised that terrestrial runoff would transport eDNA from the land into adjacent waterbodies and used the invasive yellow crazy ant ( Anoplolepis gracilipes ) as a model species to test this hypothesis. We collected water s les from four waterbodies adjacent (& 10 m from the creek edge) to infestations following rainfall events for eDNA analysis. We also collected soil s les from areas of known infestations and tested five eDNA extraction methods to determine their efficiency to extract eDNA from soil. Water s les resulted in positive yellow crazy ant eDNA lification (20–100% field replicates across all sites), even at one site located 300 m away from where ants had been detected visually. Soil s les resulted in a higher percentage of false negatives when s led from ant transit areas than from nest entrances. Unpurified DNA extracts from soil also resulted in false negative detections and only after applying a purification step of DNA extracts, did we detect yellow crazy ant eDNA in 40–100% of field replicates across all methods and sites. This is the first study to empirically show that eDNA from a terrestrial invertebrate can be successfully isolated and lified from adjacent or downstream waterbodies. Our results indicate that eDNA has the potential to be a useful method for detecting terrestrial invertebrates from soil and water.
Publisher: Public Library of Science (PLoS)
Date: 04-04-2014
Publisher: Springer Science and Business Media LLC
Date: 18-07-2023
DOI: 10.1007/S00338-023-02405-4
Abstract: Population irruptions of crown-of-thorns seastar (CoTS, Acanthaster spp.) represent a perennial threat to Indo-Pacific coral reefs. Age determination of CoTS is challenging, thereby hindering understanding and management of this nuisance species. Telomeres, which are protective DNA structure found at the ends of eukaryotic chromosomes that shorten at each cell ision, have been used to estimate age in wild animals. To investigate the use of telomeres in CoTS, we optimized a quantitative PCR protocol to measure relative telomere length (rTL) in CoTS for the first time. Comparing rTL among four age groups (4, 7, 16, 24 months post-settlement), we found that adult CoTS generally exhibit shorter rTL than juveniles, which is the first evidence of age-related telomere attrition in CoTS. However, there was large within-age class variation, and no significant relationships were found between adult CoTS rTL and potential age-indicating external features. Furthermore, we found accelerated telomere attrition under sub-optimal diet, where in iduals that were fed crustose coralline algae for 16 months exhibited shorter rTL than their counterparts fed on coral. A positive correlation was found between rTL of tube feet and pyloric caeca, suggesting synchronization of telomere dynamics across somatic tissues in CoTS. Overall, our results suggest that rTL could be used to classify CoTS into broad age groups, though in idual variation constrains the ability to resolve specific cohorts. The present study contributes to the understanding of telomere dynamics in marine invertebrates, while laying the groundwork for future research into rTL as biomarker for age and potentially stress for CoTS.
Publisher: Wiley
Date: 28-03-2020
DOI: 10.1111/ACV.12583
Publisher: Wiley
Date: 09-12-2018
DOI: 10.1111/MEC.14427
Abstract: Population structure of many marine organisms is spatially patchy and varies within and between years, a phenomenon defined as chaotic genetic patchiness. This results from the combination of planktonic larval dispersal and environmental stochasticity. Additionally, in species with bi-partite life, postsettlement selection can magnify these genetic differences. The high fecundity (up to 500,000 eggs annually) and protracted larval duration (12-24 months) and dispersal of the southern rock lobster, Jasus edwardsii, make it a good test species for chaotic genetic patchiness and selection during early benthic life. Here, we used double digest restriction site-associated DNA sequencing (ddRADseq) to investigate chaotic genetic patchiness and postsettlement selection in this species. We assessed differences in genetic structure and ersity of recently settled pueruli across four settlement years and between two sites in southeast Australia separated by approximately 1,000 km. Postsettlement selection was investigated by identifying loci under putative positive selection between recently settled pueruli and postpueruli and quantifying differences in the magnitude and strength of the selection at each year and site. Genetic differences within and among sites through time in neutral SNP markers indicated chaotic genetic patchiness. Recently settled puerulus at the southernmost site exhibited lower genetic ersity during years of low puerulus catches, further supporting this hypothesis. Finally, analyses of outlier SNPs detected fluctuations in the magnitude and strength of the markers putatively under positive selection over space and time. One locus under putative positive selection was consistent at both locations during the same years, suggesting the existence of weak postsettlement selection.
Publisher: Springer Science and Business Media LLC
Date: 23-07-2019
Publisher: Wiley
Date: 11-2022
DOI: 10.1002/ECE3.9519
Abstract: Environmental conditions experienced during the larval dispersal of marine organisms can determine the size‐at‐settlement of recruits. It is, therefore, not uncommon that larvae undergoing different dispersal histories would exhibit phenotypic variability at recruitment. Here, we investigated morphological differences in recently settled southern rock lobster ( Jasus edwardsii ) recruits, known as pueruli, along a latitudinal and temporal gradient on the east coast of Tasmania, Australia. We further explored whether natural selection could be driving morphological variation. We used double digest restriction site‐associated DNA sequencing (ddRADseq) to assess differences in the genetic structure of recently settled recruits on the east coast of Tasmania over 3 months of peak settlement during 2012 (August–October). Phenotypic differences in pueruli between sites and months of settlement were observed, with significantly smaller in iduals found at the northernmost site. Also, there was a lack of overall genetic ergence however, significant differences in pairwise F ST values between settlement months were observed at the southernmost study site, located at an area of confluence of ocean currents. Specifically, in iduals settling into the southernmost earlier in the season were genetically different from those settling later. The lack of overall genetic ergence in the presence of phenotypic variation indicates that larval environmental history during the dispersal of J. edwardsii could be a possible driver of the resulting phenotype of settlers.
No related grants have been discovered for Cecilia Villacorta-Rath.