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The research that I have been involved in focuses on the application of advances in the field of genetics to better understand ecology, evolution and biodiversity of animal populations. I am a Research Scientist at the CSIRO Australian National Fish Collection. I previously worked at the Australian Antarctic Division.
Updates:
June 6, 2025 - A critical part of scientific research is the sharing of data, this allows results to be verified and valuable information to reused with new data to make further discoveries. But sharing data is not as simple as it seems, because the way data is collected, formatted and stored tends to be unique to each experiment.
A new paper which will help to standardise eDNA datasets has been published by Miwa Takahashi. Miwa has been working with Olly Berry in CSIRO's Environomics group to develop guidelines on how to format eDNA data. This has been done in consultation with a diverse group of eDNA researchers, data custodians, and publishers. More information on this ongoing, community-led initative can be found on the FAIR eDNA project github page.
May 12, 2025 - It was nice to get out in the field for a few days to help document the distribution of the endangered Swan galaxias in eastern Tasmania by collecting water samples containing eDNA. This work is part of a project with the Tasmanian Inland Fisheries Service and NRM South. CSIRO's role in this phase of the project was to use eDNA signatures in streams to help map the species' distribution. A few small creeks are known to have healthy populations of these fish. There are other locations where they've previously been found, but no fish have been seen in electrofishing surveys for many years. We wanted to use eDNA to survey as many locations as possible and included several sites along some streams to look at the upstream distribution limits.
The highlight of the overall project has been the translocations carried out to establish new populations of this very unique and rare fish (work led by Rob Freeman at Inland Fisheries). This year a new Swan galaxias population was established in a beautiful spring creek near Ben Lomond National Park.
May 7, 2025 - The CSIRO fish collection (ANFC) team has received funding support for several fish genome sequencing projects through the Australian Fish Genomics Initiative. This includes sequencing of the (1) Australian Longnose Skate (Dentiraja confusa), (2) the Sparsely-spotted Stingaree (Urolophus paucimaculatus) and (3) several marine bony fish. The project leads for the three projects are are myself, Floriaan Devloo-Delva and Will White, respectively. The genome sequences will be used in population genomics projects as well as phylogenomic research with Dahiana Arcila and her team at Scripps Institution of Oceanography.
April 25, 2025 - We have submitted the draft final report for our NESP project examining environmental DNA collected as part of a large offshore marine biodiversity survey in South-eastern Australia (samples collected on the first two SEA-MES voyages). This was a short project, just 12 months, but we managed to collect and analyse hundreds of samples across two voyages and provide a DNA-based view of marine life in the region, from single-celled protists to a diverse range of fishes. The draft report will be reviewed and a final version published on the NESP website in the coming months.
Figure: The diversity of fish detected in the eDNA samples shown as a tree based on genetic distance of recovered sequences (mtDNA Fish16S marker). Photos show representative taxa (Images: Australian National Fish Collection, CSIRO).
Feb 28, 2025 - Last week I was at the 2025 Australia & New Zealand Environmental DNA Conference in Wellington, New Zealand. It was an inspiring week of talks and ideas in this dynamic field of research. Katrina West and I from the CSIRO fish collection team both were invited to give plenary talks. Kat's talk was titled 'Maximising eDNA’s Informativeness for Marine Monitoring' and focussed on several cutting edge topics including her work on long-read sequencing of eDNA. My talk focussed on using eDNA methods to study animal diet and was titled 'Identifying food species in pieces of faeces: relevance of dietary DNA metabarcoding to broader eDNA research'.
Jan 28, 2025 - An important resource produced by the CSIRO Australian National fish collection (ANFC) are COI DNA barcode reference sequences. These diagnostic gene sequences obtained from fish voucher specimens are used by researchers to help identify newly collected specimens (by either confirming IDs or suggesting the fish is something new). The reference sequences are also used for matching environmental DNA sequences with the fish species they came from. Fish DNA barcoding work was initiated at CSIRO over twenty years ago by Bob Ward and the dataset has expanded over the last ten years under the leadership of Sharon Appleyard. This work also involves contributions from other fish collections from around Australia. A summary of the data from this work has been published in a new paper (available here). This paper outlines sequences from 9767 voucher specimens (representing 2220 Australian fish species).
The number of COI sequences continues to grow and the tissue samples in the ANFC are being sequenced further to recover a larger range of genetic markers as part of the National Biodiversity DNA Library project.
Oct 18, 2024 - Excited to share a new publication from CSIRO Research Scientist Katrina West which examines the detectability of eDNA from fish and mobile invertebrates on Tasmanian reefs over a 24 hour period. This work was done in collaboration with researchers from the University of Tasmania who looked at visual detectability of these species at the same sites using Reef Life Survey methods. The take home message is that on these temperate reefs the eDNA signal did not vary much between day and night. This contrasts with the large variation in the species that were spotted in the day versus night in the parallel dive surveys.
More details are available in the paper (available here). The research was done while Katrina was a postdoctoral fellow in the CSIRO fish collection team.
Aug 28, 2024 - Research carried out by Georgia Nester during her PhD at Curtin University was published this week in the journal 'Science of The Total Environment' (paper available here). The study was based on species identified in environmental DNA (eDNA) samples collected along a 3000 nautical mile transect from Hobart (Australia) to Davis Station (Antarctica) from the RSV Aurora Australis. The work builds on previous direct comparisons we've done between ship-based plankton biodiversity data collected using eDNA versus the conventional plankton monitoring technique used by the Australian Antarctic Program (CPR). In the current study Georgia also optimised eDNA techniques, showing that for open ocean zooplankton monitoring eDNA collections with larger volumes and pore sizes are better.
One of the surprises from the study was the prevalence of several species invasive in Tasmania which could pose a risk if introduced into Antarctic waters. These detections occurred not only in samples collected near Tasmania, several species of concern also had spikes in eDNA detection much further south near Antarctica. These detections outside of species range were attributed to biofouling of the ship's hull. The spikes coincided with the onset of sea ice, so it appears eDNA was released from these biofouling species as they were scraped off the hull into the water column. Abrasion by sea-ice is considered a significant factor reducing the risk of marine biofouling species introduction into the Antarctic region. However, these eDNA detections highlight the need to ensure biosecurity protocols are appropriate to prevent establishment of introduced marine pests in the pristine Antarctic environment.
June 6, 2024 - Congratulations to PhD student Charlotte Jense for a recent publication from her thesis. The study looks at genetic variation in two species of galaxiid fish (Galaxias brevipinnis and G. maculatus) that are widely distributed in the southern hemisphere. Both species spend most of their life in freshwater lakes and/or streams, but larvae/juveniles from many populations migrate into the marine environment for several months. G. brevipinnis was shown to have a divergent lineage (cryptic species) in the northern part of its Australian range. Both species have a strong genetic break between New Zealand and Australia. In fact, G. brevipinnis in Australia are more closely related to other Australian galaxias species than they are to New Zealand G. brevipinnis - and the reverse is also true - so some taxonomic revisions need to be done to expand the number of distinct species beyond the two that are currently recognised.
Galaxias maculatus
May 31, 2024 - We've had a few media stories covering our NESP environmental DNA Project which is part of the South-East Australian Marine Ecosystem Survey (SEA-MES). Over the last 30 days Sahan Jayasinghe and Cindy Bessey were onboard the Investigator collecting eDNA. There were 31 other scientists carrying out fisheries and ecosystem research projects as part of the voyage.
May 7, 2024 - A paper has been published by Madi Green on developing environmental DNA methods to reconstruct fisheries catch - this is based on research done during her CSIRO postdoctoral project. In the published work, Madi sampled brine water from fisheries vessels in the Australian Eastern Tuna Billfish Fishery to see how well DNA matched the catch recorded in log books. In this experiment it was possible to validate eDNA results with reliable catch data (consisting of seven target and bycatch species). Madi trialled a simple eDNA sampling approach (no water filtering involved) and showed DNA detections could provide information on species identification. This basic information on catch composition is lacking in many fisheries globally, indicating eDNA has the potential to become a useful fisheries monitoring tool. Madi is continuing to develop the approach in her new research poition at the University of Tasmania's Institute for Marine and Antarctic Studies (IMAS). More information is available in an IMAS website story and you can download the open access paper here.
Figure 1: Process for using eDNA in brine tank of commercial longline vessels to identify catch (taken from paper).
Feb 25, 2024 - We've received funding through the National Environmental Science Program (NESP) to further develop environmental DNA (eDNA) research being carried out as part of the South-East Australian Marine Ecosystem Survey (SEA-MES). The project involves the collection/analysis of eDNA samples from the RV Investigator on two voyages (July 2023 and May 2024) and will allow us to compare the eDNA biodiversity datasets we collect with data from more traditional survey methods (trawl net, deep-tow camera, acoustics). The overall aims are to examine how much data can be extracted from eDNA and to optimise eDNA sampling methods for ship-based surveys in offshore marine areas.
A summary of the project is provided on the NESP website (Project 4.23 Environmental DNA for measuring offshore marine biodiversity: what can DNA in water collected from the RV Investigator tell us?).
An eDNA sample from filtered water. This sample contains pigments from phytoplankton and invisible DNA from hundreds of other species. By characterising this DNA we can obtain a list of species found in the water near the collection site.
Dec 15, 2023 - A new book titled 'Applied Environmental Genomics' from CSIRO publishing was released recently. I contributed to Chapter 4 on 'Revealing animal diet and food-webs though DNA metabarcoding' with co-authors Johan Pansu, Julie McInnes and Michael Traugott. Two post-doctoral researchers from our team in the the CSIRO fish collection, Katrina West and Floriaan Delvoo-Delva, also contributed to chapters on eDNA (Chapter 5) and molecular sex identification (Chapter 8) respectively.
Click on the image below to get a preview of the book - or order your copy here (link to CSIRO publishing website).
"A detailed introduction to a fast-moving field that is transforming environmental management."
"A detailed introduction to a fast-moving field that is transforming environmental management."
"Applied Environmental Genomics synthesises the latest and most exciting uses of genomic technologies for environmental science and management. With an emphasis on diversity of applications and real-world demonstrations, leading researchers have contributed detailed chapters on innovative approaches to obtaining critical management-relevant information about the natural world. These chapters are complemented by perspective sections written by environmental managers who describe their experiences using genomics to support evidence-based decisions."
Dec 10, 2023 - Katrina, Floriaan and I from the CSIRO fish collection team recently attended the annual science meeting of CSIRO's Environomics Future Science Platform in Sydney. The Environomics FSP is a CSIRO initiative facilitating collaboration in environmental genomic research within CSIRO and with researchers in the university sector. The meeting consisted of many interesting and inspiring talks over three days covering advances in a range of topics, from eDNA methods to epigenetics and genomics. Katrina presented work comparing day/night eDNA signals at coastal Tasmanian sites and contrasted findings with data from diver visual surveys carried out at the same time. Florian presented work on methylation of DNA in Antarctic toothfish populations, this work is part of an FSP funded project investigating if methylation patterns obtained in tissues from this commercially harvested fish can be used to trace which part of the Southern Ocean the fish was caught in. Thanks very much to Olly Berry, Mark Wallace and others who helped organise the great meeting.
Nov 15, 2023 - Today a publication led by CSIRO post-doc Maarten De Brauwer was released, the document is a roadmap for integration of environmental DNA (eDNA) science into Australian marine park monitoring. It outlines applications of eDNA technology for measuring biodiversity in marine parks; primary uses include monitoring changes in biological community structure at an ecosystem-wide level and early detection of potentially invasive species.
Using Maarten's words:
"The roadmap aims to facilitate and streamline the integration of eDNA methods in marine parks and is the result of three years of consulting with marine park managers, monitoring teams, ecologists, policy makers, and molecular scientists. As such, the roadmap is based on both the needs and priorities of marine parks managers and a realistic assessment of current and future eDNA capacity in Australia"
You can find the detailed document in link below, but for a shorter read, a factsheet is here, and here's a conversation article.
July 25, 2023 - Last week I was in Melbourne at the International Congress of Genetics for many fantastic presentations on a huge range of genetic research topics. I presented an overview work I've been involved in on DNA diet analysis as part of a session on Environmental Genomics (organised by Elise Furlan & Toshifumi Minamoto). I was joined at the conference by Floriaan Devloo-Delva (post-doc in the CSIRO fish collection) who presented work from his PhD on genetic sex-determination in sharks and rays. It was also a great opportunity to catch-up with many other CSIRO genetic researchers from other sites around Australia.
June 3, 2023 - Last week I was in the field with CSIRO post-doctoral researcher Katrina West collecting eDNA from seawater at sites around Lord Howe Island. This island is a crossroads of marine biodiversity with a mixture of temperate, subtropical, and tropical species. Marine species have colonised the area from both cool southern ocean currents and the warm East Australian Current. Katrina's project is taking advantage of one of the strengths of eDNA analysis - the ability to characterise ecosystem-wide biodiversity - to study tropical-temperate transition sites off both the east and west coasts of Australia.
Katrina West recovering a Niskin bottle to collect water for eDNA analysis near Ball's Pyramid.
A Doubleheader wrasse, Coris bulbifrons, on a shallow reef that contains both coral and sea grass habitat.
March 23, 2023 - Translocations of the endangered Swan galaxias (Galaxias fontanus) were carried out this week as part of a project we are involved in. The species currently has healthy populations in only small parts of a few streams in eastern Tasmania. It was very exciting to have this fish moved to two new locations where it will hopefully flourish and provide a more promising long-term outlook for the species. Charlotte Jense and I collected some eDNA from the sites to see how much population genetic data can be extracted from a water sample. If the approach works, future genetic surveys could be done without disturbance to fish.
Rob Freeman (Inland Fisheries Service) and Zak Wheaton (NRM South) collecting Swan galaxias for translocation to new sites
Several size classes of Swan galaxias ready for transfer to their new home
March 3, 2023 - A huge amount of effort has gone into sequencing the Antarctic Krill genome and a paper summarising this project has just been been published . The work was led by Changwei Shao and a team of researchers from China with contributions from scientists based in Australia, Germany, Italy and Denmark. This genome sequencing project was technically challenging since the genome is comprised of 48 billion base pairs (it's the largest animal genome ever to be sequenced) and the gene coding regions are buried in vast regions of repetitive sequences (short repeats and transposable elements). Thanks to an extremely large amount of data from new DNA sequencing technology, advanced bioinformatics and a skilled team this valuable resource is now available for the scientific community. See paper here. A general summary of the paper is also available (BGI website article).
Feb 20, 2023 - There was a great environmental DNA (eDNA) conference in Hobart last week - many interesting talks and so many people using eDNA in their research. Also impressed by the involvement of commercial eDNA companies (and conference sponsors) providing not only eDNA services, but also involved in innovative research and pushing the field forward. A big thanks to Olly Berry and CSIRO for making this happen. Katrina West from our team who was involved in organisation of the event with the organising committee.
Jan 22, 2023 - A paper led by Leonie Suter looking at environmental DNA (eDNA) detection of Antarctic krill was published today. One of the challenges with using eDNA in surveys of common organisms is that it isn't possible to distinguish if a signal comes from recent presence of the species, or if it is remnant DNA shed from organisms in the past. In order to distinguish between these two signals Leonie looked at DNA fragment sizes in the water, with old eDNA expected to be more fragmented. First, to test if old DNA could be identified, an experiment was set up in the Australian Antarctic Division krill aquarium. Krill were allowed to live in the aquarium for a few days before being removed, then the eDNA signal monitored for several weeks. As expected, old DNA was found to be more fragmented. This model of how DNA degrades was used to classify eDNA signals from Southern Ocean samples as being recent or old. The paper is available here and a link to an article summarising the work is below.
Jan 16, 2023 - We are involved in more conservation genetic research on the Swan galaxias (Galaxias fontanus). This Tasmanian endangered freshwater fish was identified as a Priority species in Australian governments Threatened Species Action Plan 2022-2032. Previously we documented the genetic diversity in the few remaining disjunct populations of the species (see update below from May last year) to identify priority populations for conservation. In the current project the CSIRO team and University of Tasmania PhD student Charlotte Jense are developing environmental DNA (eDNA) markers for use in mapping/monitoring the species distribution. A goal of the broader project is to undertake translocations (i.e. move some fish to new streams) to establish new populations. For this part of the project we will also be using eDNA testing as one tool to help confirm that streams being considered for translocations are free of brown trout (Salmo trutta) - introduced brown trout are the primary cause of Swan galaxias decline.
Swan galaxias (Galaxias fontanus) from a population estabilshed through a translocation carried out 30 years ago.
Water samples for eDNA analysis - screening for fish eDNA is one of the survey methods being used to find trout-free translocation sites
Dec 9, 2022 - I was on a marine science voyage in October (IN2022_V08) collecting environmental DNA samples to study biodiversity. There were a large number other projects and interesting discoveries - including amazing fine-scale mapping of seamounts and a surprise trawl which contained hundreds of sharks teeth! Now other members of the CSIRO fish collection are on board the RV Investigator in another biodiversity survey (IN2022_V09) - this voyage is in Gascoyne Marine Park off the coast of Western Australia. Will White, John Pogonoski and Helen O'Neill from our team are involved in collecting/identifying fish during this extensive survey. A news story covering findings from both voyages is in the link below.
Oct 4, 2022 - I am taking part in an expedition (IN2022_V08) onboard CSIRO’s Marine National Facility (RV Investigator) to Australia’s Indian Ocean Territories (IOT). We'll be exploring deep ocean and seamounts around the remote Cocos (Keeling) Islands, which is home to a large new Australian marine park. A voyage last year (IN2021_V04) surveyed a neighbouring marine park surrounding Christmas Island. These parks were announced last year, and will help protect an massive area of 740,000 square kilometres. The voyage will map seamounts and provide some of the first samples of biodiversity from the depths of the marine park. I will be collecting eDNA samples that will be used as a small part of the biodiversity assessment - these samples will form part of Katrina West postdoctoral project. Katrina collected eDNA samples on the other leg of the voyage in July 2021. The CSIRO fish collection taxonomic/curatorial staff play a critical part in the identification and curation of fish specimens. John Pogonoski and Al Graham went on the first voyage, and are integral support for the fish collections on this voyage being led by taxonomists from Museums Victoria and Australian Museum
Museums Victoria Research Institute (MVRI) is leading a voyage and has some great information on the voyage and science objectives in the link below.
The RV Investigator will travel 13,000 kilometres on its 35-day journey to scour underwater mountains and trenches.(Supplied: Museums Victoria)
Sept 7, 2022 - A study on the rare Maugean skate led by researchers at the Institute for Marine and Antarctic Studies (IMAS) is summarised in a new report. The study set out to detect the presence of Maugean skate by looking for DNA from the species in Bathurst Harbour on the west coast of Tasmania (where the skate was originally found in the 1980's). Unfortunately the survey did not reveal a significant skate DNA signal meaning the only known population is in Macquarie Harbour on the west coast of Tasmania. Click picture below for the press release, or see the report for more information.
”Conservation of the Macquarie Harbour skates is our only option to ensure the survival of this unique species”
July 22, 2022 - We just received a large amount of data from a few environmental DNA (eDNA) projects I have been working on with Katrina West and others. Samples include eDNA Katrina collected on an Investigator voyage and other eDNA from Tasmania. We extracted DNA and PCR amplified two DNA barcode markers at the CSIRO genetics laboratory - then sent the library for NovaSeq sequencing at AGRF.
This data includes over 30 million sequences from a year of water collections at Tinderbox Marine Reserve - hopefully some will match the fish observed while snorkelling at the site!
Water sampling for eDNA at Tinderbox Marine Reserve
Gallery of fish observed Tinderbox Marine Reserve during study
June 15, 2022 - Some excitement today as a devilray was found on a beach in Eastern Tasmania. Will White and Helen O'Neill from our team drove to Coles Bay to pick it up and it was unloaded with a forklift outside the CSIRO fish collection to get as much information as possible from the specimen. The species is Mobula mobular (Japanese Devilray). It is not often seen this far south and unfortunately for this one the cool Tasmanian waters probably don't have suitable concentrations of food at this time of year . This fish is rarely found in museum collections and we could not keep the whole specimen since it was too large to fit into any of our storage tanks. Will and Helen did take detailed photographs, measurements, taxonomically informative skeletal samples and tissues for genetic analysis.
June , 2022 - A news story covering the CSIRO fish collection is in the link below. It includes a photos of potentially the ugliest fish in the collection and outlines covers some research activities our group is currently involved (shark egg cases and eDNA).
Is ugliness a subjective human aesthetic? Well, I'm sure potential prey wouldn't find this fish beautiful...
May, 2022 - I produced a summary of recent work we've done on conservation genetics of the swan galaxias (Galaxias fontanus). This project is being carried out with biologists from Inland Fisheries Service Tasmania and collaborators from the University of Tasmania. The genetic work was funded thorough the Bioplatforms Australia Threatened Species Initiative .
The Swan galaxias is an endangered freshwater fish with a severely fragmented distribution in headwater streams of two Tasmanian watersheds. Population connectivity is restricted by the downstream presence of introduced fish species. We provide the first assessment of genetic diversity in natural populations and evaluate how well diversity is preserved in translocated populations. We also carried out genome sequencing (PacBio® HiFi sequencing) and transcriptome sequencing on a single fish. All sequence data are available from the Bioplatforms Australia Threatened Species initiative data portal.
Galaxias fontanus Genetic Fact Sheet TSI CSIRO .pdfMarch 2, 2022 - A paper by Austen Thomas and collaborators presents a large dataset from a study on harbour seal diet that was initiated during Austen's PhD. The project used DNA-based and morphological methods to identify prey remains in scats collected in the Salish Sea ecosystem (a marginal sea of the Pacific Ocean located in the Canadian province of British Columbia and the U.S. state of Washington). Austen visited Tasmania duing his PhD to develop some of the genetic methods in 2011 and the project has grown from there.
The DNA-based dataset contains records from >4000 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 samples. A custom-built prey DNA sequence database containing 201 species (192 fishes, 9 cephalopods) is also provided.
Harbour seal (Phoca vitulina) hauled out near Comox BC, Canada
December, 2021 - I've been slow in providing updates since I started at CSIRO's Australian National fish collection, but here are a few pictures of activities. I'll provide some project updates in 2022!
Collection of a tissue sample from a Hoodwinker Sunfish (Mola tecta) that was washed ashore near Hobart, Tasmania.
CSIRO Post-doc Kartrina West with a green sawfish (Pristis zijsron) collected briefly for measurements before release near Bidyadanga in Western Australia. This was a field trip coordinated with Western Australia Fisheries working with the Karajarri Rangers and other Bidyadanga community members.
Electrofishing being carried out by Christopher Bassano (Inland Fisheries Service Tasmania) on a field trip in eastern Tasmania to collect a swan galaxias (Galaxias fontanus) specimen for full genome sequencing. This work is part of our Bioplatforms Australia Threatened Species Initiative project .
Safia Maher preparing some butterflyfish specimens (family Chaetodontidae) for photography. These fish are from northern Australia (Gulf of Carpentaria) and are being added to the CSIRO collection.
May 30, 2021 - A paper by Julie McInnes et al. was recently published on a survey of burrowing seabirds using genetic species identification from discarded feathers and scats. As the name suggests these birds spend most of their life at sea but return to land and nest in burrows. While breeding they incubate eggs underground or forage at sea during the day, only moving in and out of burrows under the cover of darkness. Surveys of breeding numbers are possible through burrow cameras, spotlight surveys, capturing birds or by recording their distinctive calls - but it is still difficult to monitor the species of birds nesting in an particular area. This is where genetic approaches may be able to help.
This study was done on sub-Antarctic Macquarie Island where numbers and possibly diversity of burrowing seabirds are expected to increase following vertebrate pest eradication (see details on broader project here). Using feathers and scats collected near burrows Julie obtained high quality DNA for seabird identification, assisting in detection of new species arrivals and new breeding sites. More information can be found in the Paper Link.
April 7, 2021 - DNA sequences are now commonly used to identify species in studies of biodiversity. This is only possible when we have access to reference databases containing records with reliable taxonomy and matched high-quality DNA sequences. Barcode of Life Data Systems (BOLD) is a large and trusted database linking taxonomy with DNA sequences. With over 9 million barcoded specimens the curation of data is challenging.
I played a small role in curation of marine barcode data deposited in BOLD initiated during a workshop at the 8th International Barcode of Life Conference(workshop organised by Filipe Costa and Adriana Radulovici). Data from some of the major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were examined to find potential data quality issues - i.e. incongruence between Linnaean names and Barcode Index Numbers (BINs).
Almost 40% of sequences (over 80,000) were flagged as needing curation, and these were manually reviewed. After review, we found a small proportion of these were due to specimens that were misidentified, mislabelled, or contaminated (3% of specimens). The remaining records were flagged due to other issues (multiple species that shared the same BIN, one species with multiple BINs, or the incongruence was ambiguous). The results highlight that data curation (preferably automated!) is crucial for ongoing DNA barcode applications. The findings been summarised in a new paper available here.
Jan 21, 2021 - Data on penguin diet collected by Andrea Polanowski and myself was published as part of a paper on Gentoo penguins from the sub-Antarctic island of South Georgia (paper link here). The project was led by Norman Ratcliffe, a penguin ecologist at British Antarctic Survey (BAS). The BAS team put out satellite trackers on birds to look at their foraging range and potential for overlap with the winter krill fishery in the area. They also collected poo samples for us to determine what the penguins were eating. One of the results of this research is that Gentoo penguins are now benefiting from a newly enlarged no-fishing zone around this sub-Antarctic island.
This paper has coverage on a number of websites, so you can read more at these links:
British Antarctic Survey - news story
The Pew Charitable Trusts - news story
Australian Antarctic Division - news story
Also the penguin foraging routes recorded during the study can be seen here.
Figure Gentoo penguins on South Georgia (Image from the British Antarctic Survey)
Jan 5, 2021 - A paper on geographic structuring of the bacterial communities that live on Antarctic krill has been published in the journal Molecular Ecology (paper link). This research (led by Laurence Clarke) found that krill‐associated bacterial communities are geographically structured, in direct contrast with the lack of structure observed in traditional population genetic studies of Antarctic krill. So, even though a species appears to be completely mixed based on their own genetics (i.e. a panmictic population) their associated bacterial communities can provide a distinctive signature in different parts of the species distribution. The current study showed that the differences between bacterial communities were best explained by distance (i.e. due to lack of ongoing bacterial dispersal) rather than environmental conditions. The research also showed that when krill from a single swarm are split between aquarium tanks in controlled conditions their krill‐associated bacterial communities diverge, presumably due to small random changes over time (i.e. drift). This field of research is relatively new, but could potentially be used to provide information on the stock structure of species for fisheries management and could provide novel insight into animal movement and population interactions.
Figure Plots showing data from individual krill (each point) from two sites off the coast of East Antarctica (different colours). The first plot shows that krill from the two different sites do not have a distinct signature based on their own genetics. The second plot shows that the microbe communities that live on the krill at each site are distinct.
Nov 30, 2020 - I gave a virtual talk as part of a International Virtual Conference on the use of Environmental DNA (eDNA) in Marine Environments that was run by the Partnership for Observation of the Global Ocean (POGO). A link to the video of the presentation is available here: recorded plenary talk (26 min)
POGO Deagle Final2.mp4
Aug 7, 2020 - Further work from an Australian Antarctic Science project that is focused on genetics approaches to monitor Southern Ocean plankton diversity was recently published in the journal Molecular Ecology (paper link). A nice public summary is here. This paper was led by Leonie Suter and is based on samples collected while the Antarctic icebreaker Aurora Australis was underway on a resupply voyage to Macquarie Island (see story on sampling trip). In this paper we compared the zooplankton identified by sequencing environmental DNA (recovered from 2 litre water samples) with whole organisms collected by the Continuous Plankton Recorder that was being towed behind the ship. The take-home message from this paper is that even small water volumes taken from a moving ship can provide a rich view of plankton communities along the voyage track. Standardised sampling of environmental DNA on Southern Ocean resupply voyages would complement traditional approaches to monitor biodiversity and increase our understanding of zooplankton communities in this remote region. The Aurora Australis recently completed her last voyage with the Australian Antarctic program (story here) hopefully the new ship will collect environmental DNA as standard part of underway monitoring in the new era of Australian Antarctic Science.
Dr Leonie Suter in the Australian Antarctic Division genetics lab (Photo: Simon Payne)
July 6, 2020 - A paper from recent PhD graduate Cathy Cavallo (Monash University) was just published (see paper here) - Cathy discussed the main results from her paper in an interview here. She worked with the AAD genetics group to collect DNA-based diet data from little penguins in breeding colonies at Phillip Island. This paper combined the diet data collected over two seasons with parallel data on trip duration and the weight of food the penguins collected for their chicks on each trip. Taken together this information provides a measure of how much effort is required by the penguins to capture different prey in a given season.
Figure Details of the data generation and calculations of catch per unit effort (CPUE) and prey specific CPUE (e.g. sardine). The method has three important data inputs: foraging success, which is recorded as mass change over a foraging trip, and foraging effort, which represents the duration of each foraging trip as obtained from the automated penguin monitoring system (APMS). The third input is diet composition, summarized as relative read abundance (RRA%) of DNA in faecal samples. All inputs are averaged by breeding stage: incubation (i), guard (g) and post‐guard (p)
April, 2020 - I have started a new position as a CSIRO Science Leader and team leader at the Australian National Fish Collection. This is a shift from my focus over the last 9 years in the Australian Antarctic Program - an exciting opportunity to do research on Australian fishes in a large national science organisation. I'll still be based in Tasmania - photos I've taken of local fish diversity below:
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