New Paper: Spatial and temporal variation in dolphin acoustic habitats

There is a growing awareness of underwater noise in our oceans and the potential impacts of such noise on marine life, an issue which was the major theme of my PhD thesis.  This is particularly relevant for “acoustically-specialised” species, such as dolphins.  However, before we can start investigating the effects of noise on these animals, we first need to define the soundscape of dolphin habitats and examine patterns of when and where noise occurs.

We get a glimpse of them at the surface – but what about their acoustic habitat beneath the surface? (Photo: Sarah Marley)

This description of noise in dolphin habitats formed my third PhD chapter, which has now been published online in the scientific journal Frontiers in Marine Science.  In this paper, I examine spatial and temporal variability in the soundscape of the Swan River using over 11,600 hours of acoustic data collected from five sites within the river system across eight years.  Multiple sound sources were recorded at these sites, but the prevalence of these sounds at each site differed, giving each location a characteristic soundscape.  Consequently, some sites were ‘noisier’ than others.

Deploying acoustic recording equipment with help from Fremantle Ports. Spot the dolphins in the background! (Photo: Jeanette Murray)

Want to know more?  The full paper is available online! I’d love to hear your thoughts 🙂

Marley et al. (2017) Spatial and temporal variation in the acoustic habitat of bottlenose dolphins (Tursiops aduncus) within a highly urbanised estuary.  Frontiers in Marine Science, 4: 197.

And watch this space, as the remaining three PhD papers should be going up online in the next few months!

 

 

Ph-inishe-D: PhD Submitted!

The sun is shining, the sky is brighter, the birds are singing…

Since I submitted my PhD for examination, the world has become a happier place.

I actually submitted just over five weeks ago, but only now am I really starting to feel human again.  Part of the reason for this was that submission took place two weeks after I finished writing the thesis, thanks to an unforeseen administrative error.  This resulted in me turning up at uni, support squad in tow, and being told that I wasn’t allowed to submit.  Hello world crashing down…  But t went in, eventually.

PhD submission day, complete with support crew and toy dolphins! (Note, this was taken prior to submission debacle - hence manic expression of relief on my face)

PhD submission day, complete with support crew and toy dolphins!  (Note, this was taken prior to submission debacle, hence manic expression of relief on my face)

The other reason for my vacant expression of the past few weeks is that completing a PhD is exhausting.

I’ve seen my fiance finish his PhD.  I’ve seen some of my best friends finish their PhDs.  I’ve seen my officemates finish their PhDs.  I thought I had a pretty good idea of what to expect.  But it’s a unique experience, individually tailored, and nothing can really prepare you for The End.  I still can’t particularly face writing about it now (why burst this happiness bubble?), but one day I’ll explain the whole thing in detail.  Probably after I’ve dealt with the eventual examiner comments.

So now for my long-awaited period of rest and relaxation!  Well, not quite…

I’ve spent the past six weeks on a Publication Scholarship, which essentially means the uni has been paying me to turn my thesis chapters into scientific publications.  One is submitted, another two should sneak in this week, and the final paper is due for submission in April.  Around this, I have also been working on grant applications, giving presentations, submitting conference abstracts, preparing for a trip to Europe, and attending a surprising number of meetings.  The last has actually been the most daunting – after several months of PhD lockdown, limited social interaction and working from home, it’s weird having to converse with dozens of people at once.  This combined with the ‘mushy brain syndrome‘ typical of recently-submitted PhD students has left me with a strong need to lie down in a dark room after meetings.  But I’m slowly improving.  And as much as I love my PhD project (no, I didn’t end up hating it!), it is actually quite nice to work on other things and bounce between different research projects.

Now I just need to keep my fingers crossed for some successful grant applications so this research can continue…

New Video: The Dolphin and the Sound

As you know, I’m fortunate enough to be sister to the amazing wildlife film-maker Lisa Marley.  I’ve written about her documentary on Scottish raptor poisonings here previously (and incidentally, this work is currently touring the film festivals – scroll to the end for details!).  But in June, we actually worked together on a short film project as part of the Aquatic Noise 2016 conference I attended in Dublin.

The conference held a public evening involving short lectures around the theme of underwater noise, and also invited submission of videos on this topic.  Lisa and I worked together to create a short film describing the effects of human noise on coastal dolphins, similar to the idea of my 3MT speech – but with much cooler visuals than just me standing on a stage!

I wonder if anyone recognises the locations involved in this production?  Suggestions on a postcard please…!

So now I have a professional video to highlight my research AND had the awesome experience of working on a creative project with my sister.  And all without a single sibling squabble to be seen!


“Red Sky on the Black Isle” lastest screenings:

  • Hebrides International Film Festival (on Lewis, Harris, Uist and Barra; UK):  14-17 September 2016
  • Aberdeen Film Festival (UK):  17 October 2016
  • Festival de Menigoute (France):  27 October 2016

Follow the film’s Facebook page for more updates!

Conference Attendance – Aquatic Noise 2016

Last month I had the privilege of flying to Dublin to attend this year’s “Effects of Noise on Aquatic Life” conference, also known as Aquatic Noise 2016.  Not only was I able to present the first two chapters of my PhD thesis, but I was able to contribute to the conference itself as part of the Media Committee.

Members of CMST attending the Aquatic Noise 2016 Conference in Dublin

Members of CMST attending the Aquatic Noise 2016 Conference in Dublin

Over 300 people from 23 countries attended the week-long conference, including representatives from universities, government research institutions, fisheries, and industry groups.  Talks were given regarding a variety of acoustic topics, including descriptions of noise sources, sound propagation analyses, and the responses of numerous animal species.  Conference attendees also included ten members of my lab, the Centre for Marine Science and Technology (CMST).  It was great to head overseas as a team, presenting our research to an international audience!

Poster PicMy talk was part of the student speed sessions – five minutes to describe our research and findings, followed by an evening poster session where we had the chance to answer questions, engage in discussions, and network.  I feel the talk went well, despite my nerves.  I’m much more used to interactive presentations involving members of the public than presenting to seasoned professional scientists.  But even without any audience participation, dramatic displays or unexpected explosions, I think I did alright!  You can view my poster by clicking here:  Marley AN2016 Poster.

Marley Dolphin Presentation AN2016

Being on the Media Committee meant I was part of a team responsible for promoting the conference, particularly our public evening.  This was attended by over 70 members of the public, who had an evening of lectures and short videos (more about this in my next post!).  I was also involved in live-tweeting the conference.  This was a way of extending the conference reach to the masses, scientists or otherwise, by posting summaries of each talk on Twitter under the conference hashtag.  I’ve now summarised each day of talks as a separate story using a combination of Tweets from myself and other conference attendees, which are available for anyone to read using the links below:

https://storify.com/sarahmarley86/aquatic-noise-2016-day-1

https://storify.com/sarahmarley86/an2016-effects-of-noise-on-behaviour-and-physiolog

https://storify.com/sarahmarley86/aquatic-noise-2016-day-3

https://storify.com/sarahmarley86/aquatic-noise-2016-day-4

https://storify.com/sarahmarley86/aquatic-noise-2016-day-5

New Paper: Fish Choruses in Darwin Harbour

ICES Journal ArticleAs well as working on my PhD, I’m also lucky enough to be involved in other projects at the Centre for Marine Science and Technology (CMST) from time-to-time.  Now the results from one of these projects have been published in the ICES Journal of Marine Science.

A couple of years ago, I was asked to review acoustic data from Darwin Harbour, in the Northern Territory of Australia.  I’ve written before about the variety of sounds produced by fish, and in the Darwin data we found oodles of different fish choruses.  Fish sounds can be species and size specific, and such en masse sound production often has behavioural associations, for example by corresponding with feeding or reproduction.

So there is a lot of information to be gained by listening in on fish!

In this paper, we recorded nine different types of fish choruses and investigate their patterns of occurrence.  Environmental conditions such as lunar patterns, time of sunset, temperature, tidal information and salinity levels all contributed to the context of when particular choruses were heard.  These results are useful not only to scientists but also to fisheries managers, as it provides improved knowledge regarding species distribution, fish habitat-use, identifies spawning seasons, and monitors behaviour.  Which, when you can’t see fish below the surface, is often difficult data to collect!

The full paper (doi: 10.1093/icesjms/fsw037) is available here.

Course Review: Spatial Analysis of Ecological Data using R

Based on my previous statistical rantings, it might not surprise many of you that my idea of a holiday involves a stats course.  But let me at least try to defend this…

Back in April, Phil and I took a “working holiday” home to Europe.  A ‘holiday’ because we got to see our families, attend a wedding, get engaged ourselves, etc etc…  But a ‘working’ one because we respectively had French work meetings to attend and a PhD to finish.  Just when we were deciding what date to fly over, we both received a glowing advertisement for a statistics course on the West Coast of Scotland.  With no hesitation whatsoever, we booked our flights a week earlier than planned and got instantly psyched up for a week of geeky fun!

The course was called “Spatial Analysis of Ecological Data using R (SPAE)“, run by PR Statistics.  If the title alone wasn’t enough to entice you, it promised to investigate analyses relevant to different types of data (transect, grid, point), examine species distributions, determine environmental drivers, and quantify uncertainty.  With your statistical appetite thoroughly whetted, you would then learn above applying the results of these methods to wildlife conservation and resource management.  Altogether, a biologist’s dream.

The Teaching

IMG_3200

Learning in action!

We hadn’t come across PR Statistics before, so were um-ing and ah-ing about how good the course would be.  But what really swung it for us was the instructor – Prof Jason Matthiopoulos.  As well as being an esteemed biostatistician, Jason was one of our professors back on the Masters course in St Andrews – so once we saw he was the primary instructor we couldn’t wait to get back in his classroom!  As it turned out, we were beyond lucky with all regards to this course.  As well as Jason, the other two instructors – Helen Wade and James Grecian – were fabulous.  Full of information and willing to help, I really enjoyed the opportunity to soak up their R knowledge and brain-storm my own data with them.

The Company

PR Statistics is a relatively new company, founded by Oliver Hooker during his PhD back in 2014.  Oliver’s aim was to draw on the experience of academic scientists with strong statistical backgrounds and assist them in providing high-quality ecology-based courses.  Since delivering the first workshop, PR Statistics now offers 12 courses, covering everything from spatial ecology to bioinformatics, genetic analysis  to Bayesian modelling, using a mix of R, Python and Linux.  A full list of the courses available are listed here.

The Experience

Can statistical knowledge improve your Jenga prowess?  Jason puts it to the test...

Can statistical knowledge improve your Jenga prowess? Jason puts it to the test…

Throughout my undergrad, I experienced a few wet and dreary field trips in Scotland, so was unsure what to expect at the Millport Field Station, located on the small island of Cumbrae.  But the accommodation was fabulous – clean, warm and brand-new twin ensuite rooms just across the courtyard from the teaching facilities.  I enjoyed most of the meals provided in the canteen (although there were some dark mutterings from those previously unacquainted with the idea of Lorne sausages and haggis for breakfast), plus there was a games room and “adults only” bar lounge to facilitate some fierce pool games and Jenga battles in the evening.  I wish we’d had this during undergrad!

The course lasted for seven days, with the first five days focused on a series of lectures and practicals, and the final two days based on discussion groups.  Jason has a remarkable ability to take the fear out of statistical modelling; he explains all concepts in an easy-to-understand manner, and his enthusiasm for the subject convinces you that this really is amazingly interesting stuff!  The lectures were short enough to be digestible, with an emphasis on getting to the practicals to put these new skills to use.  During the two discussion days, we broke into smaller groups to discuss problems specific to our particular research projects.  After six years in Australia, I’ve become used to a different research culture – everyone here seems more closed about their research, scared of sharing ideas for fear of theft, much more ‘us’ and ‘them’.  So being in a group of people keen to share ideas, help each other problem-solve, and have open discussions about their work was amazing.

The people were one of the best things about this course.  As well as Oliver and the teaching team being super friendly and helpful, the students were a lovely bunch – keen to help each other in class and socialise in the evenings.  My 30th birthday fell mid-course, and I had been a bit worried about having it with a load of strangers on a wee island…  But Phil secretly went into cahoots with Oliver to organise a great celebration – booze, cake, and a quiz night!  A very personalised, memorable birthday 🙂  My birthday also coincidentally fell on a “half day”, so a bunch of us went kayaking around the island in the afternoon.  Getting up close with the local harbour and grey seals was awesome.  We’d been watching these guys from afar, as the classroom’s sea-ward wall consisted of a series of windows, allowing us to keep an eye out for porpoises, seals and otters throughout the day.  In the evenings, groups of us would go out otter-hunting, and on the final day one was spotted from the classroom window – cue 25 biologists running from the classroom and haring across the woodland, to follow the otter as it foraged around the coast!  Definitely people with a similar mind frame!

The SPAE April 2016 Team!

The SPAE April 2016 Team!

So, all in all, I thoroughly recommend checking out the PR Statistics courses.  Not only will you come away with bounds of new knowledge and ideas for your own research, but you’ll have the chance to spend a week in a wonderful location meeting a great bunch of people.  Statistics at its best 🙂

I said “Oui”

A few weeks ago, Phil and I were back in Scotland and had a couple of days to visit the town of St Andrews, where we first met and studied together.

I thought we were there to visit some old friends, reminisce, and search for puffins.

But it turns out that Phil had another thing in mind too…

Needless to say, I said “Oui” – though now I probably do need to learn a bit more French than that!

 

Guest Blogger for University of St Andrews

A few weeks ago, I was chatting with Sonja Heinrich, the coordinator of the Masters program I undertook at the University of St Andrews.  She was really interested to hear of my science communication experiences, and invited me to write a guest blog post for the Masters website about winning the 3-Minute-Thesis (3MT) competition.

Field Trip to the Isle of Mull (April 2009)

Field Trip to the Isle of Mull (April 2009)

The guest post itself is up on the St Andrews Postgraduate blog.  But I thought this would also be a good opportunity to talk about my experience on the Masters.

I studied Marine Mammal Science at the University of St Andrews from 2008-09.  It was one of the most amazing years of my life.  I attended the oldest university (and one of the most prestigious) in Scotland, made a fabulous bunch of new friends, and met my amazing partner Phil.  We watched fascinating lectures and participated in interesting labs, both taught by leaders in this field.  We sailed the West Coast of Scotland, looking for whales and dolphins.  We scrambled down cliffs, conducting population surveys of seals (which led to a near-death experience, but that’s a whole other story).  We assisted in the necropsy of a stranded porpoise (seven years later, I can still vividly remember the smell…).

My thesis project led to it’s own collection of exciting tales (locked in a forest and rescued by gypsies; hiding in the sand dunes from a gun-man; trapped in a hut by highland cattle – to name but a few!).  But it also taught me how to organise fieldwork, developed my analysis and scientific writing skills, and gave me a real taste of independent research.  There’s no question that I wouldn’t be where I am today if it wasn’t for this course.

Saying goodbye to my Masters field site

Saying goodbye to my Masters field site

Masters Marine Mammal Science - Class of 2008-09

Masters Marine Mammal Science – Class of 2008-09

When I began, the Masters was only in it’s second year of existence.  Applications have now closed for the 10th year of the Masters in Marine Mammal Science!  Graduates have gone on to study PhDs, advance to post-doctorate research, or take up leading positions in government organisations.  They have dispersed all over the world, creating an amazing network of alumni.

Even after moving to Australia, I have still worked on projects with Masters alumni (it’s funny who you meet in the middle of the sea…).  One of them lives 5mins down the road!  Marine mammal science is a small world, but a pretty great one to be a part of.

Congratulations Dr Phil!

It is my pleasure to introduce to you – Dr Philippe Jean-Francois Bouchet!!!

Dr Phil Bouchet and his primary supervisor, Prof Jessica Meeuwig at Phil's graduation ceremony

Dr Phil Bouchet and his primary supervisor, Prof Jessica Meeuwig at Phil’s graduation ceremony

Two weeks ago, Phil graduated from the University of Western Australia.  He also had the honour of delivering the Valedictory Address to close his graduation ceremony:

You can read more about his thesis, publication, and PhD highlights on a specially-dedicated blog post on the Meeuwig Lab website.

Needless to say, I could not be more proud 🙂

Dr Phil Bouchet and his extremely proud partner!

Dr Phil Bouchet and his extremely proud partner!

 

Perth Research Bazaar

Earlier this month, I had the pleasure of being one of 75 researchers selected to attend the inaugural Perth Research Bazaar.

Unix and Coffee

Coding? Just add coffee…

This three-day event offered researchers of all levels and disciplines an intensive introduction to some commonly-used programming software.  We were taught the basics of Unix, Python, R, GitHub, LaTeX, NVivo, and D3 from every-day users of these tools, who were all-too-happy to share their secret tips.  So despite my “imposter syndrome” feelings about coding, I had a really great time and left feeling more confident about programming than I believed possible.

One of my favourite things about #PerthResBaz was how the group interacted through Twitter.  On the first day alone, I think I spoke with more attendees over social media than I did in person!  It allowed us to network with other Perth researchers and provided the opportunity to share our knowledge of different research tools, whilst also keeping up a running commentary on proceedings for those unable to attend.

Given this, I’ve created a Storify summary using tweets from across the three days, broken down to reflect the different sessions and software utilised by the conference.

These events are spreading throughout the world.  This year Research Bazaars were held in Melbourne, Brisbane, Sydney, Auckland, Wellington, Vancouver, Oklahoma and beyond!  So if you ever get the chance, I thoroughly recommend participating.  Better yet, why not bring it to your own institution?  See the main Research Bazaar website for more details.

If this sounds too big, how about hosting a regular Hacky Hour?  These casual meetings generally involve researchers meeting up at a bar or coffee shop to help trouble-shoot each others code.  So if you feel like you need help with your programming (that you could be of assistance to someone else!), look for a Hacky Hour near you!  For those of you in Perth, there is one at Curtin University – follow @CUHackyHour on Twitter for updates!