Oct 31, 2019 -  A new paper from our group entitled ‘Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba)’ was just published based on research done by Léonie Suter as part of her Swiss National Science Foundation Post-doctoral fellowship. 

Antarctic krill are a critically important and hyper-abundant species in the Antarctic marine ecosystem, but many aspects of their biology remain mysterious. One observation that has left ecologists wondering is that the sex ratio in wild krill swarms is often biased towards either males or females. For example, on the K-Axis research voyage off East Antarctica, the female proportion of twelve large krill swarms ranged from 7 to 82%. One of the difficulties in studying sex-ratios in krill is that males and females can only be microscopically differentiated when they are sexually mature – juveniles all look very similar and adult krill regress in the winter, so that no external sexual characteristics are observable. In her study, Leonie developed a molecular test that for the first time allows unambiguous sex determination of krill samples lacking external sex-specific features. While no sex-specific DNA regions (e.g. sex chromosomes) were found, Leonie identified some genes in the genome that were only being turned on in females. The test works for all krill from juvenile stages onwards, including the sexually regressed krill she examined from the AAD aquarium. The paper provides insight into the process of sexual differentiation and a new tool to help us understand krill biology. The paper is open access and all the details are available here.

May 6, 2019 - An editorial comment on DNA metabarcoding was just published in the journal Molecular Ecology by a group of scientists (see it here). It outlines our concerns that the rapid growth in the application of DNA metabarcoding is occurring at a pace and in a manner that often loses sight of the challenges in producing high‐quality and reproducible data. Really, it is just reminding us all that while producing spectacular DNA sequence data sets that have seemingly endless potential is now quite easy, making sure they are accurate data sets with ecological meaning is a bit more complicated...

April 3, 2019 - A paper by PhD student Ricardo De Paoli-Iseppi  based on work he did in the AAD genetics lab was published in Molecular Ecology Resources (see paper here). Ric's PhD study focussed on finding genetic markers that could be used to determine the age of seabirds. To do this he's been working with a population of short-tailed shearwaters which have been monitored for decades and the ages of most birds are known. His latest paper is a great study that applied a method to scan the genome of animals with no existing genetic information and identify new epigenetic markers (modifications to the DNA). In his data set (using bird DNA from blood) he identified several epigenetic markers that change in a predictable way in shearwaters as they age. The age structure of wild animal populations tells us a lot about their ecology and this approach may be the way ecologists determine age of their favorite study species in the future.

Jan 2, 2019 - A couple more papers led by Laurence Clarke have been published based on samples collected during the 2016 K-Axis research voyage in the Indian sector of the Southern Ocean. Both papers use DNA markers to study marine communities made up of tiny organisms, but they characterise very different groups of taxa from very different habitats. The papers are described below - and a map of the are is provided 

(1) The first paper looked at the eukaryotic plankton in water samples taken near the ocean surface. Plankton communities were separated into size classes by sequentially filtering 10L of water before analysis: microplankton (> 20μm), nanoplankton (5–20μm) and piconanoplanton (0.45–5μm). The two larger size fractions had more spatial structuring compared to the piconanoplankton in the 284 samples taken across the study area. Days since sea-ice melt was the key driver of community composition and a number of biologically distinct regions were identified in this survey area. All the details are available in the paper published in Deep Sea Research Part II: Topical Studies in Oceanography.

(2) The second paper looked at bacterial communities associated with Antarctic krill (Euphausia superba). Host-associated bacterial communities represent distinct nutrient-rich niches compared to the surrounding environment and since Antarctic krill are a super-abundant species with a circumpolar distribution, the krill microbiome may make a substantial contribution to marine bacterial diversity in the Southern Ocean. This study produced a detailed catalogue of the types of bacteria living on and within krill and provides a baseline for more detailed studies of this specialised community. This paper was published in Frontiers in Microbiology.

Nov 9, 2018 - Research done by PhD Candidate Cathy Cavallo (Monash University) has recently been published (see paper here). Cathy collaborated with the AAD genetics group to do a DNA-based analysis of the diet of little penguins from colonies at Phillip Island. She collected data from >200 scats collected in the Austral summer 2015/16 (August–February) using a DNA marker (18S) that provides a broad picture of the prey groups present. Not surprisingly fish were the most common type of food detected, but DNA from salps (a type of gelatinous, mostly transparent plankton) also showed up as common in some months of the study. It is not completely clear if this signature came from penguins directly eating salps, or partially from salps present in stomachs of the fish they consumed. It is clear that these sea jellies are part of the marine food web and their importance is becoming increasingly recognised (see a broader discussion here).

Nov 6, 2018 - A paper led by Laurence Clarke titled 'A globally distributed Syndiniales parasite dominates the Southern Ocean micro-eukaryote community near the sea-ice edge' has been published in Journal of the International Society for Microbial Ecology. The paper shows the surprising  prevalence of a tiny plankton-killing parasite in the Southern Ocean (based DNA sequences from water samples collected during the 2016 K-Axis research voyage). This research finding illustrates how much we still have to learn about this ecosystem and the factors impacting the population dynamics of critical organisms at the bottom of the food web. The paper was highlighted on the Australian Antarctic Division website (AAD story) and in Australian media (ABC story). 

Sept 10, 2018 - A paper led by Laurence Clarke titled 'DNA-based diet analysis of mesopelagic fish from the southern Kerguelen Axis' has been published in  Deep Sea Research Part II: Topical Studies in Oceanography. In this study, mesopelagic fish (those living mostly in mid-water ~100-1000m of the open ocean) were dissected and food remains in their stomachs characterised using DNA metabarcoding. The samples were collected during the  2016 K-Axis research voyage to the Southern Indian Ocean and the paper is part of a special journal issue focussed on the findings of this broad ecosystem study. Laurence's work had a number of interesting findings: the Lanternfishes (Myctophidae) ate mostly amphipods, euphausiids and copepods, whereas the Deep-sea Smelt (Bathylagus sp.) ate many gelatinous animals, such as jellyfish; the diet of all the fish species changed with fish size (i.e. larger fish tended to have krill present in stomach). To examine a technical issue, we determined if secondary predation (i.e. prey from the stomachs of food items) would be detected by our method. This was done by removing relatively intact prey items from the fish stomach and processing them using the standard technique - any extra DNA signal not from the prey item itself is likely from their stomach contents. The signal from secondary predation was very weak in this experiment, indicating the fish directly consumed most of the species that we detected.

July 10, 2018 - The primary focus of our work at the AAD is doing scientific research that contributes to Australia’s role in international agreements governing Antarctica and the Southern Ocean. One such agreement is the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR). Two papers were recently submitted to a CCAMLR Working Group on Ecosystem Monitoring and Management based on projects we've been working on over the last year:

(i) The first CCAMLR paper (summary available here) was based on our work using DNA barcoding to identify fish caught as bycatch in the Antarctic krill fishery. These are mostly larval or juvenile fish that are caught along with Antarctic krill, some are taken out of the catch and identified (based on morphology) by fisheries observers for reporting purposes. Our samples were provided by observers on Aker BioMarine fishing vessels (through James Clark at MRAG). The research we were doing looked at the accuracy of fish identifications being submitted to CCAMLR. Based on this work additional resources have been put into development of improved guides for fish identification in order to provide a more accurate picture of potential impacts on these non-target species.

(ii) The second CCAMLR paper (summary available here) was based work we've done with colleagues from the British Antarctic Survey comparing penguin diet determined using faecal DNA versus stomach flushing. The aim of this work is to eventually incorporated DNA-based methods to record the diet of key indicator species in the CCAMLR Ecosystem Monitoring Program (detailed description in link to poster below - June 20th).

June 22, 2018 - A paper I've been working on with a group of colleagues on DNA-based diet analysis has been published in Molecular Ecology (all the details are available here). The article summarises our thoughts on how to interpret counts of DNA sequences we get from samples in animal diet studies (usually faecal samples). It is relevant to the research we do on seabirds here at the AAD, but also in a wide range of other diet studies, and anywhere DNA sequencing is used to measure biodiversity.

June 20, 2018 - Three posters from our group are being presented at a major conference for Antarctic/Polar science in Switzerland (POLAR 2018). Laurence Clarke is presenting his work on genetic detections of a parasite that he has shown is extremely common near the ice edge in the southern Indian Ocean - it is also found in oceans globally, and may have an important role in marine ecosystems. Laurence is also presenting our work on genetic monitoring of zooplankton (poster below). Claire Waluda, a colleague from the British Antarctic Survey, is presenting work we've done comparing penguin diet determined using faecal DNA versus stomach flushing (poster below).

June 18, 2018 - A nice story on the Australian Antarctic Division website covering the environmental DNA project we are working on can be found here.  It includes rare footage of me in the lab, taking credit for the work actually being done by Andrea Polanowski...

March 27, 2018 - Andrea Polanowski and I from the AAD genetics group just came back from doing marine science on a short Aurora Australis voyage (V4 Macquarie Island resupply). We were collecting environmental DNA samples from sea water as well as zooplankton specimens (using the continuous plankton recorder) - these will be used to refine DNA-based methods of measuring marine biodiversity (see link to project here). We collected several hundred DNA samples from the open ocean between Tasmania and Macquarie Island as well as from transects close to the subantarctic island. The photo below shows a view from the Island with the ship Aurora Australis just visible on the horizon.  

December 21, 2017 - A paper by PhD student Ricardo De Paoli-Iseppi  has been published in PLOS ONE: DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird (PDF).

In this study Ric set out to find genetic markers that could be used to determine the age of seabirds. To do this he's been working with a population of short-tailed shearwaters which have been monitored for decades and the ages of most individuals are known (birds are identified by leg bands put on when they are chicks). In this paper he focussed on genes that have been shown to have age-specific chemical modifications in mammals (epigenetic changes - DNA methylation - observed in humans, mice and/or whales). His data show that these genes don't have the same patterns of epigenetic changes with age in shearwaters. The level of DNA methylation observed in birds is also often quite different compare to what has been observed in mammals. This suggests that the control of genes (regulated by DNA methylation) varies between different groups of organisms and this makes finding age-related markers in birds a bit harder. Ric is now moving on to a new approach which scans the genome of the shearwater to find age-related markers directly in his study species.

December 5, 2017 - There are quite a few molecular ecologists based in Hobart and we use similar approaches in our research, but we are spread across different research institutes and study very different organisms and ecosystem, so don't often cross paths. To strengthen the links in this community and to hear some interesting science talks Laurence Clarke and I organised the Hobart Molecular Ecology Workshop. The program included 17 talks on a wide range of topics, From marine microbes and Eucalyptus adaptation genetics to shark populations and using molecular methods to trace infections in hospitals. Thanks to the ACE-CRC for providing snacks, lunch and a lovely venue on the Hobart waterfront.

November 22, 2017 - A paper we've been working on for quite a while has been accepted in Molecular Ecology Resources (ReadOnly PDF). The study looked at samples collected using the Continuous Plankton Recorder (CPR). This device has been used to characterise zooplankton biodiversity along transects covering hundreds of thousands of kilometers in the Southern Ocean CPR survey. Plankton collected in the survey is currently identified using classical taxonomy (i.e. using a microscope and morphological features). We investigated the potential to use DNA metabarcoding (species identification from DNA mixtures) as a tool for rapid collection of taxonomic data from CPR samples.

In our study, zooplankton were collected between Tasmania and Macquarie Island. Plankton were identified by microscope and by DNA sequencing (COI marker). DNA increased the number of 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 a problem. In some samples the prevalence of DNA from large plankton (e.g. krill) masked the presence of smaller species (e.g. copepods). Overall, the genetic data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging.

One of the main outcome of the work was an evaluation of how DNA methods can move from the current snapshot studies to the requirements of a long-term monitoring program. This topic has been discussed in a number of other recent paper (e.g. a nice study looking at freshwater ecosystems). The particular areas that we think need special consideration for standardised surveys include:

(1) Assigning taxonomy to DNA sequences This step that is still far from perfect. At the very least, an imperfect, but standard, method needs to be adopted. The sequence data can be re-analysed as the methods improve, which is a strength of DNA metabarcoding.  

(2) Contamination A well documented problem: minuscule amounts DNA can be recovered and used for biomonitoring, but trace DNA in laboratories or on sampling equipment will also be detected. Just need to be vigilant, hopefully should be less of an issue in long-term studies with large data sets. 

(3) Relative biomass versus presence-absence data Are the proportion of DNA sequence reads reflect of the relative abundance (biomass) of each species in a sample? Are detection sensitivities consistent across samples when we convert data to a presence-absence matrix?

(4) Estimating biomass with an internal standard To compare the relative amount of plankton DNA across samples we tried adding a standard amount of mouse DNA to each sample. This approach may have some merit, but needs further testing.

(5) Generating coherent long-term data sets. One of the great strengths of the CPR survey is that it has used essentially the same technology for the past 80 years. In contrast, high-throughput sequencing is recent technology in a state of flux making it hard to adopt a standard protocol.

November 17, 2017 - Over the last few months I have had the opportunity to attend a couple great meetings. I gave a plenary talk at a Symposium on Ecological Networks and Molecular Analysis of Trophic Interactions in Sweden. It was fantastic to meet many scientist whose work I have been reading for many years and see many interesting applications using DNA in diet studies.

Closer to home I also attended a Symposium on Kerguelen Plateau Marine Ecosystem and Fisheries this covered broad topics relevant to an amazing part of the Southern Ocean.

August 31, 2017 - Three papers have been published recently by PhD students Julie McInnes and Ricardo De Paoli-Iseppi who are both working in the AAD Ecological Genetics laboratory.

Julie's two papers are the last chapters from her thesis and use DNA to document the diet of black-browed albatross (and closely related Campbell albatross) throughout their circumpolar range. One paper is focused on the broad diet and highlights the prevalence of jellyfish. Her other paper focuses on the type of fish in the albatross diet and consumption of fisheries discards in some locations (e.g. Falkland Islands and Iles Kerguelen). More details are available here: 

McInnes JC et al. (2017) High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding. Molecular Ecology 26:4831-4845 (Abstract)

McInnes JC et al. (2017) DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatross. Frontiers in Marine Science: 4:277 (PDF)

Ricardo's paper is from the first chapter of his thesis - a review of work that has been done to use signals in the genomes of animals (DNA methylation) to determine their age. This is the topic of his PhD, a relatively new and exciting field!

De Paoli-Iseppi R et al. (2017) Measuring animal age with DNA methylation: from humans to wild animals. Frontiers in Genetics: 8:106 (PDF)

May 15, 2017 - Enjoyed being involved in the seventh DNA metabarcoding Spring School in Portugal at the beginning of the month (see metabarcoding.org)! It was a great to hear about a large number of interesting projects and thoughts from both the instructors and students. 

Feb 22, 2017 - Two papers have recently been published featuring work carried out in the Ecological Genetics group.

The first paper was led by Laurence Clarke and looks at the performance of different DNA metabarcoding markers for comparing samples of zooplankton communities. This work was done in collaboration with marine ecologists who characterised parallel samples using morphological methods. Three DNA barcode markers were examined, the standard barcode of life marker (COI) did a good job at both recovering a wide range of different species and providing high resolution taxonomy due to a large reference database. The ability to recover DNA from a range of species with this marker was surprising given the large amount of variation in primer binding sites (see post below from Sept. 2014). The paper is available here 

Jan 17, 2017 - PhD student Julie McInnes recently published a paper looking at sample collection issues for DNA diet studies of vertebrates (see paper here). The work is based on results from shy albatross scat collections she made over a two year period. DNA data were collected from the samples using high-throughput Illumina sequencing of a marker which recovers information from all major animal lineages (V7 region of the nuclear small subunit ribosomal DNA gene [18S]). I think one of the most interesting things about the paper is it clearly shows that proportions of DNA from various sources (i.e. diet and non-diet components) in animal faeces varies between samples considerably . Sometimes dietary DNA is a relatively high proportion (~20%), other times DNA from diet items is only a tiny fraction of what is present. This variation in diet information is masked when using group-specific markers (e.g. recovering DNA from only particular prey groups) since these studies don't quantify the total amount of DNA. With group specific markers, only targeted taxa are recovered, therefore you can't differentiate between samples where diet sequences represent 0.5%  of the sequences versus 50%. Julie's broader investigation of what information is in scats has important implications about the quality of data we get from samples. Fortunately, Julie's data also show that we can predict which samples provide the highest quality data in dietary studies - this has practical implications for ongoing Antarctic seabird diet studies at the AAD and for other researchers using this approach. Julie put together a nice video summarising of some of the recommendations (video here).

Oct 24, 2016 - A nice application of some of the DNA-based methods for dietary analysis developed at the AAD has been published (see abstract here). This work was carried out by Austen Thomas and the study looks at Pacific salmon species being eaten by harbour seals in coastal waters of British Columbia, Canada (Strait of Georgia). This region is of interest because salmon migrating to and from local rivers (adult and juvenile salmon respectively) support important First Nation, commercial and recreational fisheries. In the study over 1000 scats were collected over two years (4 different collection locations). The bones and fish DNA in each sample were characterised. Bones from different salmon species are hard to distinguish, and those from small fish are are often completely digested; however, the DNA methods allowed the five different species of salmon to be distinguished and also detection of juvenile salmon consumption . Herring and gadoid species were most common fish consumed by the seals, but salmon constituted a significant proportion of the diet both during fall (mostly adults salmon returning to spawn) and spring (mostly juvenile salmon). The two salmon species of highest conservation concern (coho and Chinook) were not the major salmon prey consumed in the fall, but were being consumed more than other salmon in the spring as juveniles. 

Sept 16, 2016 - A book chapter on the 'Genetics of Antarctic Krill' written by Simon Jarman and I has been published in a book on the 'Biology and Ecology of Antarctic Krill'. Other chapters include one on krill reproduction and development written by AAD scientist So Kawaguchi and one by former AAD scientist Steve Nicol and Jacqueline Foster on the krill fishery.