ORCID Profile
0000-0001-7651-3687
Current Organisation
CSIRO
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Publisher: Frontiers Media SA
Date: 15-01-2019
Publisher: Springer Science and Business Media LLC
Date: 11-2005
Publisher: Frontiers Media SA
Date: 31-08-2017
Publisher: Wiley
Date: 04-2019
DOI: 10.1111/MEC.15060
Publisher: Public Library of Science (PLoS)
Date: 10-02-2017
Publisher: Wiley
Date: 09-2020
DOI: 10.1111/MEC.15587
Abstract: Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan bio ersity. Zooplankton bio ersity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship‐based bulk plankton s ling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton bio ersity as conventional CPR bulk s ling (~1,500 L filtered seawater per CPR s le). We directly compared eDNA metabarcoding with (a) conventional morphological CPR s ling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired s les, respectively). A metazoan‐targeted cytochrome c oxidase I (COI) marker was used to characterize species‐level ersity. In the 2 L seawater eDNA s les, this marker lified large amounts of non‐metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR s les. COI metabarcoding of bulk DNA s les mostly avoided nonmetazoan lifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote‐targeted 18S ribosomal RNA marker detected a higher proportion, but lower ersity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean bio ersity.
Publisher: Wiley
Date: 18-05-2021
DOI: 10.1111/CSP2.439
Abstract: Species inventories and bio ersity assessments are critical to conservation. Yet cryptic species or recolonizing species can be challenging to detect. DNA metabarcoding provides an alternative tool to identify species that can be difficult to observe during field surveys. We test the efficacy of DNA analysis to identify burrowing petrel species in a rapidly changing landscape, on a remote sub‐Antarctic island following pest eradication. Discarded feathers and scats provided high quality DNA for species identification, assisting in detection of new species arrivals and new breeding sites across Macquarie Island. We highlight how DNA metabarcoding informs species inventories and is a valuable tool to complement seabird field surveys.
Publisher: Springer Science and Business Media LLC
Date: 10-2010
Publisher: The Royal Society
Date: 05-10-2011
Abstract: Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological ergences of parapatric stream–lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F ST between watersheds = 0.244 and within = 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream–lake outlier regions match those previously identified in marine–freshwater and benthic–limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream–lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.
Publisher: Inter-Research Science Center
Date: 05-05-2008
DOI: 10.3354/MEPS07307
Publisher: Wiley
Date: 17-06-2019
DOI: 10.1111/MEC.14734
Publisher: Wiley
Date: 15-12-2012
Publisher: Frontiers Media SA
Date: 17-08-2017
Publisher: Springer International Publishing
Date: 2016
Publisher: Elsevier BV
Date: 04-2020
Publisher: Wiley
Date: 12-04-2005
Publisher: Wiley
Date: 17-04-2009
Publisher: Cold Spring Harbor Laboratory
Date: 18-04-2018
DOI: 10.1101/303461
Abstract: Advances in DNA sequencing technology have revolutionised the field of molecular analysis of trophic interactions and it is now possible to recover counts of food DNA barcode sequences from a wide range of dietary s les. But what do these counts mean? To obtain an accurate estimate of a consumer’s diet should we work strictly with datasets summarising the frequency of occurrence of different food taxa, or is it possible to use the relative number of sequences? Both approaches are applied in the dietary metabarcoding literature, but occurrence data is often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. Here, we point out that diet summaries based on occurrence data overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that even with recovery biases incorporated, using relative read abundance (RRA) information can provide a more accurate view of population-level diet in many scenarios. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue to addressing methodological challenges, and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.
Publisher: Wiley
Date: 18-01-2011
DOI: 10.1111/J.1755-0998.2010.02974.X
Abstract: Reconstructing the diets of pinnipeds by visually identifying prey remains recovered in faecal s les is challenging because of differences in digestion and passage rates of hard parts. Analysing the soft-matrix of faecal material using DNA-based techniques is an alternative means to identify prey species consumed, but published techniques are largely nonquantitative, which limits their usefulness for some applications. We further developed and validated a real-time PCR technique using species-specific mitochondrial DNA primers to quantify the proportion of prey in the diets of Steller sea lions (Eumetopias jubatus), a pinniped species thought to be facing significant diet related challenges in the North Pacific. We first demonstrated that the proportions of prey tissue DNA in mixtures of DNA isolated from four prey species could be estimated within a margin of ∼ 12% of the percent in the mix. These prey species included herring Clupea palasii, eulachon Thaleichthyes pacificus, squid Loligo opalescens and rosethorn rockfish Sebastes helvomaculatus. We then applied real-time PCR to DNA extracted from faecal s les obtained from Steller sea lions in captivity that were fed 11 different combinations of herring, eulachon, squid and Pacific ocean perch rockfish (Sebastes alutus), ranging from 7% to 75% contributions per meal (by wet weight). The difference between the average percentage estimated by real-time PCR and the percentage of prey consumed was generally <12% for all diets fed. Our findings indicate that real-time PCR of faecal DNA can detect the approximate relative quantity of prey consumed for complex diets and prey species, including cephalopods and fish.
Publisher: Elsevier BV
Date: 04-2020
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.
Publisher: The Royal Society
Date: 09-2014
Abstract: DNA metabarcoding enables efficient characterization of species composition in environmental DNA or bulk bio ersity s les, and this approach is making significant and unique contributions in the field of ecology. In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding datasets is dependent on recovery of the targeted taxa using conserved lification primers. We argue that COI does not contain suitably conserved regions for most licon-based metabarcoding applications. Marker selection deserves increased scrutiny and available marker choices should be broadened in order to maximize potential in this exciting field of research.
Publisher: Wiley
Date: 15-01-2021
DOI: 10.1111/MEC.15771
Publisher: Public Library of Science (PLoS)
Date: 05-09-2007
Publisher: Wiley
Date: 06-07-2020
Publisher: Oxford University Press (OUP)
Date: 02-03-2005
Abstract: Giant squids (Architeuthis sp.) remain mysterious they have evaded observation and are rarely taken from their deep sea habitat. Information on the diet of Architeuthis is scarce due to the limited number of specimens with morphologically recognizable remains in their digestive tracts. We explored the use of polymerase chain reaction (PCR)-based methods for detection of DNA in the prey remains and amorphous slurry from an Architeuthis gut s le. The DNA region lified varied in size, allowing separation of fish and squid components. Sequence comparisons identified fish prey as Macruronus novaezelandiae. Isolation of Architeuthis DNA from an ingested tentacle and the presence of chitin fragments indicate cannibalism occurs in giant squid. Denaturing gradient gel electrophoresis was used to screen for less common DNA types, revealing a high frequency of PCR-generated false alleles, but no additional prey species.
Publisher: Wiley
Date: 12-01-2021
DOI: 10.1111/DDI.13216
Abstract: Management of competition with predators is an important consideration for fisheries, particularly within marine protected areas (MPAs) where conservation is a primary objective. We aimed to test whether static no‐take zones within a large, sustainable‐use MPA prevented overlap between gentoo penguins and a krill fishery during two winters with contrasting prey fields. South Georgia, Southwest Atlantic Ocean. We used satellite tracking ( N = 16, June–September 2018) to describe gentoo penguin movements and distribution and quantified their overlap with the MPA’s no‐take zone (NTZ) and the krill fishing grounds. DNA metabarcoding of scats ( N = 220, April–September 2018) was used to quantify diet. When krill were at moderate densities and evenly distributed in 2001, gentoo penguins would have spent all of their time within the 12 NM NTZ, but when availability was low in 2018, they spent 46.3% of their time outside the NTZ and 9.6% within the krill fishing grounds. The extension of the NTZ to 30 km in response to this finding would have produced a 14.9% increase in protection for penguins and displaced 4% of fishery hauls. Gentoo penguin diet comprised 25.8% krill, which is lower than in the late 1980s but more than in 2009. Gentoo penguins extend their foraging range when krill is scarce, which increases the potential for spatial overlap with the krill fishery during periods of nutritional stress. Current regulations allow for expansion of both extent and catches by the krill fishery and, should this occur, gentoo penguins may face heightened risks from competition. A dynamic ocean management framework, that extends closed areas in response to near real‐time data on penguin movements and krill density estimates, may reduce the potential for competition in this sustainable‐use MPA while allowing a profitable krill fishery.
Publisher: Public Library of Science (PLoS)
Date: 07-12-2017
Publisher: Wiley
Date: 28-09-2015
DOI: 10.1111/MEC.13357
Abstract: The chronological age of an in idual animal predicts many of its biological characteristics, and these in turn influence population-level ecological processes. Animal age information can therefore be valuable in ecological research, but many species have no external features that allow age to be reliably determined. Molecular age biomarkers provide a potential solution to this problem. Research in this area of molecular ecology has so far focused on a limited range of age biomarkers. The most commonly tested molecular age biomarker is change in average telomere length, which predicts age well in a small number of species and tissues, but performs poorly in many other situations. Epigenetic regulation of gene expression has recently been shown to cause age-related modifications to DNA and to cause changes in abundance of several RNA types throughout animal lifespans. Age biomarkers based on these epigenetic changes, and other new DNA-based assays, have already been applied to model organisms, humans and a limited number of wild animals. There is clear potential to apply these marker types more widely in ecological studies. For many species, these new approaches will produce age estimates where this was previously impractical. They will also enable age information to be gathered in cross-sectional studies and expand the range of demographic characteristics that can be quantified with molecular methods. We describe the range of molecular age biomarkers that have been investigated to date and suggest approaches for developing the newer marker types as age assays in nonmodel animal species.
Publisher: Springer Science and Business Media LLC
Date: 11-10-2019
DOI: 10.1007/S00300-019-02592-3
Abstract: Antarctic krill ( Euphausia superba ) is a highly abundant keystone species of the Southern Ocean ecosystem, directly connecting primary producers to high-trophic level predators. Sex ratios of krill vary remarkably between swarms and this phenomenon is poorly understood, as identification of krill sex relies on external morphological differences that appear late during development. Sex determination mechanisms in krill are unknown, but could include genetic, environmental or parasitic mechanisms. Similarly, virtually nothing is known about molecular sex differentiation. The krill genome has to date not been sequenced, and due to its enormous size and large amount of repetitive elements, it is currently not feasible to develop sex-specific DNA markers. To produce a reliable molecular marker for sex in krill and to investigate molecular sex differentiation we therefore focused on identifying sex-specific transcriptomic differences. Through transcriptomic analysis, we found large gene expression differences between testes and ovaries and identified three genes exclusively expressed in female whole krill from early juvenile stages onwards. The sex-specific expression of these three genes persisted through sexual regression, although our regressed s les originated from a krill aquarium and may differ from wild-regressed krill. Two slightly male-biased genes did not display sufficient expression differences to clearly differentiate sexes. Based on the expression of the three female-specific genes we developed a molecular test that for the first time allows the unambiguous sex determination of krill s les lacking external sex-specific features from juvenile stages onwards, including the sexually regressed krill we examined.
Publisher: Elsevier BV
Date: 2012
Publisher: Pensoft Publishers
Date: 16-12-2021
DOI: 10.3897/MBMG.5.67862
Abstract: The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8 th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (& %) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.
Publisher: Canadian Science Publishing
Date: 06-2017
Abstract: Knowing the species and life stages of prey that predators consume is important for understanding the impacts that predation may have on prey populations, but traditional methods for determining diets often cannot provide sufficient detail. We combined data from two methods of scat analysis (DNA metabarcoding and morphological prey ID) to quantify the species and life stages of salmon (Oncorhynchus spp.) consumed by harbour seals (Phoca vitulina) in the Strait of Georgia, Canada, where juvenile Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon survival is poor. Harbour seals primarily consumed adult salmon of lesser conservation concern in the fall (August–November): chum (Oncorhynchus keta: 18.4%), pink (Oncorhynchus gorbuscha: 12.6%), sockeye (Oncorhynchus nerka: 7.4%), Chinook (7.1%), and coho (1.8%). However, the opposite species trend occurred during the spring when seals preferred juvenile salmon of greater conservation concern (April–July): coho (2.9%), Chinook (2.9%), sockeye (2.5%), pink (1.4%), and chum (0.8%) — percentages that can equate to many in iduals consumed. Our data suggest that harbour seals select juveniles of salmon species that out-migrate at ages year and provide evidence of a potential causal relationship between harbour seal predation and juvenile salmon survival trends.
Publisher: Frontiers Media SA
Date: 26-10-2018
Publisher: Springer Science and Business Media LLC
Date: 20-01-2023
DOI: 10.1007/S11160-023-09756-9
Abstract: Antarctic Toothfish are a circumpolar species which are targeted in multiple fisheries around Antarctica covering nine statistical areas within the Convention for the Conservation of Antarctic Marine Living Resources. Despite this, it is still unclear whether the species forms a single stock across its circumpolar distribution, shows a pattern of isolation by distance, or exhibits discrete stock structure between different regions. Recent genetics studies of Antarctic toothfish have shown connectivity between two areas (Ross Sea and Antarctic Peninsula), but earlier studies with smaller number of markers produced inconsistent results with regards to genetic connectivity between other geographic locations. Here we present a range-wide population genetic study of Antarctic toothfish using 11,000 nuclear single nucleotide polymorphisms from 715 fish collected. Our results indicate that genetic ersity of the Antarctic toothfish is very low, with only 0.1% of genetic variability associated with geographic location. Multiple clustering methods, both supervised and unsupervised, indicated no distinct breeding populations. These results are consistent with current theories of egg and larval dispersal by the predominant Antarctic currents.
Publisher: Elsevier BV
Date: 08-2007
Publisher: Wiley
Date: 12-01-2017
DOI: 10.1002/ECE3.2667
Publisher: Wiley
Date: 17-04-2013
Abstract: A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA lified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was lified from scat DNA and licons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat s les in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify in idual s les also influenced species proportions. In addition, there were complex interactions between factors for ex le, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of s les revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.
Publisher: Wiley
Date: 18-12-2018
Abstract: DNA metabarcoding is an efficient method for measuring bio ersity, but the process of initiating long-term DNA-based monitoring programmes, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterized bio ersity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. S les (n = 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker. DNA increased the number of metazoan species identified and provided high-resolution taxonomy of groups problematic in conventional surveys (e.g., larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during s ling a problem. In some s les, the prevalence of DNA from large plankton such as krill masked the presence of smaller species. We investigated adding a fixed amount of exogenous DNA to s les as an internal control to allow determination of relative plankton biomass. Overall, the metabarcoding data represent a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing DNA metabarcoding from the current snapshot studies to the requirements of a long-term monitoring programme. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring.
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.
Publisher: Springer Science and Business Media LLC
Date: 28-09-2007
Publisher: Wiley
Date: 04-03-2013
DOI: 10.1111/MEC.12215
Publisher: Alaska Sea Grant, University of Alaska Fairbanks
Date: 05-2006
DOI: 10.4027/SLW.2006.21
Publisher: Wiley
Date: 12-03-2004
Publisher: Springer Science and Business Media LLC
Date: 02-03-2022
DOI: 10.1038/S41597-022-01152-5
Abstract: Marine trophic ecology data are in high demand as natural resource agencies increasingly adopt ecosystem-based management strategies that account for complex species interactions. Harbour seal ( Phoca vitulina ) diet data are of particular interest because the species is an abundant predator in the northeast Pacific Ocean and Salish Sea ecosystem that consumes Pacific salmon ( Oncorhynchus spp .). A multi-agency effort was therefore undertaken to produce harbour seal diet data on an ecosystem scale using, 1) a standardized set of scat collection and analysis methods, and 2) a newly developed DNA metabarcoding diet analysis technique designed to identify prey species and quantify their relative proportions in seal diets. The DNA-based dataset described herein contains records from 4,625 harbour seal scats representing 52 haulout sites, 7 years, 12 calendar months, and a total of 11,641 prey identifications. Prey morphological hard parts analyses were conducted alongside, resulting in corresponding hard parts data for 92% of the scat DNA s les. A custom-built prey DNA sequence database containing 201 species (192 fishes, 9 cephalopods) is also provided.
Publisher: Springer Science and Business Media LLC
Date: 26-10-2019
Publisher: Wiley
Date: 26-09-2015
DOI: 10.1111/MEC.13370
Abstract: Antarctic krill (Euphausia superba hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted in iduals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist.
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/MF03031
Abstract: The northern Pacific seastar, Asterias amurensis, spread to Tasmania in the 1980s from its native range in the North Pacific. The seastar has subsequently established in Port Phillip Bay on mainland Australia. Transportation of larvae in ballast water is one vector for these introductions and is likely to contribute to additional range expansion of this species. Larval identification methods are critical to assess risks of further transport to uninvaded ecosystems however, morphological identification of larval asteroids is impractical and unreliable. Therefore, we have developed a sensitive PCR-based method that specifically detects Asterias DNA. The method works on isolated seastar larva, mixed plankton and ballast water s les. Trials using uninfected ballast water s les spiked with known numbers of A. amurensis larvae indicate that the technique can detect single larva in 200 mg of plankton. The test also detects other Asterias species therefore, discrimination between seastars within the genus Asterias was accomplished using denaturing gradient gel electrophoresis (DGGE). Currently, this method is being used to facilitate research on ballast water transport, distribution and the ecology of A. amurensis larvae. The general approach can be expanded to provide a rapid and cost-effective approach for detecting a suite of marine species in ballast water and environmental s les.
Publisher: Public Library of Science (PLoS)
Date: 16-12-2013
Publisher: Wiley
Date: 12-03-2015
DOI: 10.1111/MAEC.12145
Publisher: Elsevier BV
Date: 03-2023
Publisher: Springer Science and Business Media LLC
Date: 16-08-2006
Publisher: Wiley
Date: 18-12-2016
Abstract: DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput licon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co-occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these corrections to field-collected seal scats affected species percentages from in idual s les (Δ 6.7 ± 6.6%) more than population-level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives.
Publisher: PeerJ
Date: 15-11-2021
DOI: 10.7717/PEERJ.12458
Abstract: Antarctic benthic ecosystems support high bio ersity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and s ling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based bio ersity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA s les. However, significantly different communities were detected in the two s le types at sites where both were collected ( i.e. , where paired s les were available). For ex le, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA s les, respectively. eDNA from water and sediment core s les are complementary s le types, with epifauna more likely to be detected in water column s les and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive bio ersity survey. However, our study demonstrates the choice of s le type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
Publisher: Wiley
Date: 22-01-2023
DOI: 10.1002/EDN3.394
Abstract: Antarctic krill ( Euphausia superba ) is a keystone species in the Southern Ocean ecosystem, and monitoring its distribution and abundance is crucial for the sustainable management of expanding fisheries targeting the species. Environmental DNA (eDNA)‐based monitoring could complement conventional krill surveys, but its applicability is limited by a lack of knowledge on eDNA persistence and decay in the Southern Ocean. We aimed to develop a method that can not only quantify Antarctic krill eDNA, but also estimate a relative time since this eDNA was shed (“recent” vs “older”). Three species‐specific qPCR markers targeting the mitochondrial 16S region were developed, and the eDNA decay characteristics of these markers were determined through tank experiments. Krill eDNA was partially degraded in all s les, even when krill were present. Marker concentrations decreased exponentially at similar rates after krill removal, with initial relative abundances maintained across the three markers. Over time, the concentration of the longest marker decreased faster, changing the relative abundances of the markers, and allowing discrimination of more recent s les from more degraded older s les. We employed this new method to quantify Antarctic krill eDNA collected across a 4800 km Southern Ocean transect, and estimated the age of the eDNA in these s les based on the relative abundance of markers, adding a temporal aspect to a quantitative eDNA survey. We also compared a Euphausiid‐specific metabarcoding marker to the qPCR method to assess sensitivity in detecting Antarctic krill eDNA. While these new eDNA methods should be evaluated against existing non‐molecular survey methods, they could add an important novel, dynamic layer of information to future krill surveys. Our method could not only determine where Antarctic krill eDNA is present but shed light on how they may be using certain habitats, expanding our understanding of this important species’ life cycle and contributing to more accurate abundance and distribution estimates.
Publisher: Springer Science and Business Media LLC
Date: 02-2005
DOI: 10.1007/S10126-004-0034-Z
Abstract: Management of sustainable Pacific oyster fisheries would be assisted by an early, rapid, and accurate means of detecting their planktonic larvae. Reported here is an approach, based on polymerase chain reaction (PCR), for the detection of Pacific oyster larvae in plankton s les. Species-specific primers were designed by comparing partial mitochondrial cytochrome oxidase subunit I (COI) sequences from Crassostrea gigas, with other members of the family Ostreidae including those of Crassostrea angulata. Assay specificity was empirically validated through screening DNA s les obtained from several species of oysters. The assay was specific as only C. gigas s les returned PCR-positive results. A nested PCR approach could consistently detect 5 or more D-hinge-stage larvae spiked into a background of about 146 mg of plankton. The assay does not require prior sorting of larvae. We conclude that the assay could be used to screen environmental and ballast water s les, although further specificity testing against local bivalve species is recommended in new locations.
Publisher: Wiley
Date: 07-11-2023
Publisher: Wiley
Date: 16-02-2022
Abstract: We investigated the Southern Ocean (SO) prokaryote community structure via zero‐radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. S les reveal the prokaryote ersity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn‐winter) sectors of the SO. At higher taxonomic levels (phylum‐family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus‐zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi‐ and bathy‐abyssopelagic water masses. Common surface bacteria were abundant in several deep‐water masses and vice‐versa suggesting connectivity between surface and deep‐water microbial assemblages. Bacteria from same‐sector Antarctic Bottom Water s les showed patchy, high beta‐ ersity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep‐water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide‐scale SO ecosystem microbial modelling.
Publisher: Wiley
Date: 24-10-2014
DOI: 10.1111/MEC.12523
Abstract: Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary s les and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet s les are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary s les in order to correct for technical biases introduced during licon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM(©) , we sequenced prey DNA lified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals' diet to generate tissue correction factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected) to 14 ± 9% (TCF-corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate digestion correction factors (DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.
No related grants have been discovered for Bruce Deagle.