CIE Spotlight: Long-term epidemiological survey of Kudoa thyrsites in Atlantic salmon from commercial aquaculture farms

Luis A.
Luis A.

Authors: Marshall, W. L.; Sitja-Bobadilla, A.; Brown, H. M.; MacWilliam, T.; Richmond, Z.; Lamson, H.; Morrison, D. B.; Afonso, L. O. B.

Source: JOURNAL OF FISH DISEASES, 39 (8):929-946, AUG 2016

Brief summary of the paper: Kudoa thyrsites (Myxozoa) encysts within myocytes of a variety of fishes. While infected fish appear unharmed, parasite-derived enzymes degrade the flesh post-mortem. In regions of British Columbia (BC), Canada, up to 4-7% of fillets can be affected, thus having economic consequences and impacting the competitiveness of BC’s farms.

K. thyrsites was monitored in two farms having high (HP) or low (LP) historical infection prevalence. At each farm, 30 fish were sampled monthly for blood and muscle during the first year followed by nine samplings during year two. Prevalence and intensity were measured by PCR and histology of muscle samples.

In parallel, fillet tests were used to quantify myoliquefaction. Infections were detected by PCR after 355 and 509 degree days at LP and HP farms, respectively. Prevalence reached 100% at the HP farm by 2265 degree days and declined during the second year, whereas it plateaued near 50% at the LP farm. Infection intensities decreased after 1 year at both farms. Blood was PCR-positive at both farms between 778 and 1113 degree days and again after 2000 degree days.

This is the first monitoring project in a production environment and compares data between farms with different prevalence.

CIE-HDR Conference – Photo competition deadline extended

Photo CompetitionThe deadline for the CIE-HDR conference photo competition has officially been extended to September 20th. After this date, you will have to print your photos yourself in order to enter. See the rules HERE!

Due to the change in the e-mail address provided to send photos, it would be appreciated if all entrants could re-forward their photos to this e-mail address at

Once again, the three categories are: (1) animals interacting, (2) nature’s colors and patterns, and (3) researchers at work. Each participant may submit one photo per category.

How ‪‎citizen science is helping our native ‪‎wildlife?

Fox on Camera TrapAustralia is renowned for its iconic wildlife. A bilby digging for food in the desert on a moonlit night, a dinosaur-like cassowary disappearing into the shadows of the rainforest, or a platypus diving for yabbies in a farm dam. But such images, though evocative, are rarely seen by most Australians.

For some species, our time to see them is rapidly running out. We know that unfortunately many native animals face considerable threats from habitat loss, introduced cats and foxes, and climate change, among others.

More than ever before, we need accurate and up-to-date information about where our wildlife persists and in what numbers, to help ensure their survival. But how do we achieve this in a place the sheer size of Australia, and with its often cryptic inhabitants?

Euan Ritchie and Sarah Maclagan call for all Australian wildlife lovers to get involved with some important conservation-based science via the Wildlife Spotter project.

Read all about it on The Conversation: The rise of citizen science is great news for our native wildlife.

CIE Spotlight: What does the future hold for shorebirds in the East Asian-Australasian Flyway?

Kate B.Title: What does the future hold for shorebirds in the East Asian-Australasian Flyway?

Authors: Szabo, Judit K.; Battley, Phil F.; Buchanan, Katherine L.; Rogers, Danny I.

Source: EMU, 116 (2):95-99, 2016

Brief summary of the paper: Long-distance migratory shorebirds around the world are in trouble (International Wader Study Group 2003) and, although alarming rates of decline have been reported from the American (Morrison et al. 2004) and European Flyways (van der Vlietet al. 2015), some of the steepest and most widespread declines are seen in the East Asian–Australasian Flyway (EAAF) (Amano et al. 2010).

The EAAF encompasses 22 countries from the high Arctic to Australia and New Zealand. Some shorebirds cover the entire length of the Flyway, completing a 30 000-km round-trip migration every year. Management of the EAAF is hugely challenging, with vast human pressure on habitats and resources in individual countries combining to degrade the migratory landscape for birds on the move. This is especially true around the Yellow Sea region of East Asia (MacKinnon et al. 2012).

2016 Undergraduate Award for Science Communication – Royal Society of Victoria

Anyone is up to the challenge? Please forward onto your final year undergraduate students, as they may be interested in the below. We look forward to reading some excellent entries from Deakin University!

Royal Society VictoriaThe Royal Society of Victoria is delighted to announce its inaugural Undergraduate Award for Science Communication, open to all students enrolled at a Victorian university in their final year of an undergraduate degree.

While the award is open to students of all disciplines, it is envisaged of being of most interest to those enrolled in science or humanities degrees with subjects in communication, media studies, journalism, or professional writing and editing.

Essays submitted for judging should be 2,000 words in length, reflecting the journalistic style of science journalism in the contemporary, mainstream news media. A key criterion for assessment is clear articulation and a genuine ‘grappling’ with the complexities of science communication, making complex matters relating to science and technology engaging and accessible to a lay readership.

Shortlisted finalists will each receive certificates from the Royal Society of Victoria at an award ceremony on the evening of Thursday, 10 November 2016. The winning entry will receive a prize of $500 and will have their piece published in Lateral Magazine, a platform for some of Australia’s finest, emerging science writers to explore issues in science and society.

The deadline for submissions is 5pm on 31 July, 2016. Full details and an application portal are available online from HERE.

“Statistics using R” – A new CIE website

R LogoWe are very happy to announce the launch of a new CIE website “Statistics using R“. This site is designed to help YOU use R as efficiently as possible, and also give you a platform to help others out whenever you can. It provides a lot of resources, for first time users as well as for regular users, and most importantly a discussion forum, where you can ask and answer questions.

R is an amazing tool, and let´s face it, an absolute must in your skill set. But the learning curve is notoriously steep at the start, and using R can indeed be frustrating (at any stage). We want to make this learning curve as shallow as possible for you, and to encourage you to solve problems together when you hit them.

If you´re new to R, the time you invest at the start will definitely pay-off later! There is a good reason why R has become so popular. We hope this site is useful to CIE staff and students at any level of competencies with R and statistics, because there is always something new to learn in this fast evolving area.

“Statistic using R” was set up by Marcel Klaassen and a few CIE members. The site’s administrator is Mylene Mariette, please feel free to get in touch with her if you have any suggestions on how to improve the site, and if you would like to be part of the “R and stat wiz” team (in the broad sense of the term; you definitely don´t need to know it all!). Mylene would very much appreciate your help and input. This can only work (and be fun) if people get involved. Instructions on how to register to the website are posted below, so…. stop what you’re doing right now and check it out 🙂

STEP 1: Go to CloudDeakin and log in (left hand side of the screen). Once in CloudDeakin click on the Self Registration link under More.

STEP 2: Click on Statistics Using R site link

STEP 3: Click on Register

STEP 4: Click on Submit

51st Wildlife Photographer of the Year exhibition @ the National Wool Museum

wildlife-photographerLooking for something to do this weekend in Geelong?

The 51st Wildlife Photographer of the Year exhibition, which is currently on at the National Wool Museum, 26 Moorabool St Geelong, is closing THIS SUNDAY!

The exhibition is run by the Natural History Museum, London and tours the globe with examples of the winners in the different categories. It is a stunning exhibition for anyone with an interest in the natural world. The standard is quite breathtaking.

The exhibition has been on since February and closes this Sunday. It’s only $8.25 entry and the museum is open Mon – Fri 9.30am-5pm and Sat/Sun 10am–5pm.

An introduction to Linear Mixed Effects Models and Generalised Linear Mixed Models – Registration now open

Alain F. Z. and Elena I.
Alain F. Z. and Elena I.

Between the 4th and 8th of July in 2016, we will be hosting a statistics workshop at the Burwood Corporate Centre run by renowned world-class ecological statisticians Alain Zuur and Elena Ieno. These are the two primary authors of the infamous “Modelling Book with the penguins on the cover”: ‘Mixed Effects Models and Extensions in Ecology with R.

The aim of the workshop is to provide an introduction to Linear Mixed Effects Models, and Generalised Linear Mixed Models. Only basic knowledge in R is required (e.g. how to import data), and a short revision on linear modelling is provided.  The course involves a series of lectures, and engaging examples to work through (and all R scripts and course material are provided!!!!).

They will teach:

  • When it is appropriate to run a mixed effects model
  • How to run it
  • How to check assumptions
  • How to interpret the results

You can find out more information in the flyer attached, or you can register via the Highstat website (make sure that you select the Deakin University course). However, don’t delay too long as the course is also open to participants from outside of Deakin and is limited to only 30 places.

If you require more information, please email either Travis Knox or Matt Symonds.

Why we decided to invite them to Deakin in 2016? “While there is some cost to the workshop, I attended their GLM & GAM workshop last year, and can personally say that it is well worth it. I have never attended a statistics course that was able to engage a room full of people for the entirety of a week. The content was pitched at a level that everyone could understand, and they made every effort to ‘leave no man behind’. Furthermore, I was able to walk away from the course with the ability to directly apply what I had just learnt to my own data – Travis Knox”

Could GPS technology help monitor Melbourne’s elusive powerful owls?

Powerful OwlThe researchers, from the Centre for Integrative Ecology within Deakin’s School of Life and Environmental Sciences, are hoping the GPS monitors will help reveal how to conserve Australia’s largest owl (Ninox strenua), which come out to play when the lights go out around town.

The study is part of student Nick Bradsworth’s honours project (supervised by Associate Professor Raylene Cooke) and preliminary data shows the owls are covering large areas of around four square kilometres across 12 nights.

The question is how much time do they spend using suburban backyards and other urban areas? Answering this question is critical to developing better urban planning guidelines for the conservation and enhancement of urban Powerful Owl populations

More information on this project can be found via Deakin 2016 Media releases or in an article published at The Age.