Category Archives: Research

SMM 2017 Conference Presentation

I’m now safely home after attending the Society for Marine Mammalogy’s biennial conference in Halifax, Nova Scotia.  It was an amazing eight days of conference talks and workshops, interspersed with plenty of networking.  As well as meeting lots of interesting new people, it was particularly wonderful to catch up with so many old friends.  Totally worth the 35hrs of one-way travel and 12hr time difference jetlag!

I’m currently preparing a detailed conference report for the Journal of Animal Ecology’s blog, but in the meantime I wanted to make my conference presentation available online.  To download a PDF version, click here.  The full abstract is provided below.  Feedback welcome!

SMM 2017 - Sarah Marley

Acoustic habitats and behavioural responses of bottlenose dolphins in Western Australia

Marley, S.A., Salgado Kent, C.P., Erbe, C., Parnum, I.M. and Parsons, M.J.G.

As human activities continue to expand across the marine environment, anthropogenic ocean noise is also rapidly increasing.  This is of concern to acoustically-specialised species, particularly those displaying a high degree of habitat overlap with anthropogenic activities, such as bottlenose dolphins (Tursiops sp.).  There is a need to describe the soundscape of coastal dolphin habitats and examine how prominent anthropogenic noise sources may impact these animals.  The Swan River in Western Australia flows through the state capital of Perth, containing over 1.4 million people, and consequently experiences a range of anthropogenic activities.  However, the river is also extensively used by a resident community of Indo-Pacific bottlenose dolphins (T. aduncus).  Autonomous underwater acoustic recorders were used to collect data throughout the Swan River, which were analysed via weekly spectrograms, power spectrum density percentile plots, octave-band levels, broadband noise levels, and generalised estimating equations.  Land-based theodolite tracking at two sites provided information on vessel traffic and dolphin behaviour, which were assessed using generalised additive models and Markov chains.  Acoustic datasets collected from 2005 to 2015 indicated that the Swan River was comprised of multiple acoustic habitats, each with its own characteristic soundscape and temporal patterns in underwater noise.  The ‘noisiest’ site from an anthropogenic perspective and in relation to dolphin communications was the Fremantle Inner Harbour (mean broadband noise level: 106 dB re 1 µPa rms [10 Hz – 11 kHz]).  Theodolite tracking at this site found that dolphins remained present during periods of high vessel traffic.  However, behavioural observations indicated significant alterations to dolphin movement speeds and activity states at high vessel densities.  Furthermore, whistle characteristics varied in conditions of high broadband noise.  This work suggests that dolphins maintain occupancy at key foraging sites within the Swan River despite the presence of vessels, but alter their behaviour in periods of high vessel traffic.

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New Paper: A Tale of Two Soundscapes

I am a little bit behind in posting about my various PhD publications.  But a pretty cool one that came out in the August edition of Acoustics Australia focused on comparing the acoustic characteristics of urban versus pristine coastal dolphin habitats.

I’ve previously spoken about the need to define the soundscape of dolphin habitats and examine patterns of when and where noise occurs.  But whilst we can monitor dolphin acoustic habitats and describe how they are now, in many cases it is hard to say how they were in the past.  We simply don’t have enough long-term datasets that capture the expansion of human activities into the marine environments – i.e. datasets that go far enough back in time to capture when the habitat was pristine and free of human influence.  Understandably, this can also make it hard to decide how we best manage man-made noise in these habitats into the future.  It’s hard to determine what noise mitigation measures are necessary when you don’t know how quiet an area is ‘supposed’ to be.

A potential solution to this conundrum for managing ‘urban’ areas is to find comparable ‘pristine’ areas which are also used by the study species, and see what differences exist.  Of course, this is reliant upon pristine areas still existing in the first place.  However, in Western Australia we are fortunate enough to have some areas up in the remote north of the state.

The Kimberley region in north-western Australia is one of the most remote, pristine wildernesses in the world.  The largest town in the region is Broome, which has a permanent population of only 16,000 people (although the temporary population can increase to 45,000 in the tourism season).  Broome is located on the shores of Roebuck Bay, with a relatively large population of snubfin dolphins and is also regularly used by bottlenose dolphins and humpback dolphins.  This area offers a nice contrast with the busy, urban environment of the Swan River, which flows through the Western Australian state capital of Perth.  This river is also used by bottlenose dolphins.  To create successful noise mitigation strategies for coastal dolphins, there is a need to compare ‘quiet’ and ‘noisy’ acoustic habitats.  Roebuck Bay and the Swan River offer the perfect opportunity to do just this.

Prepping the Roebuck Bay acoustic gear

I chose to compare the pristine soundscape of Roebuck Bay with the Swan River’s anthropogenically-noisiest site, the Fremantle Inner Harbour.  I used autonomous underwater acoustic recorders to monitor the soundscape at these sites, and assessed these using a combination of weekly spectrograms, power spectrum density percentile plots and probability densities, octave-band levels, broadband noise levels, and generalised estimating equations – i.e. a shedload of nifty acoustic analyses.

What these essentially showed were that these two sites are very different in their acoustic characteristics.  In Roebuck Bay, biological sounds (such as crustaceans and fish) were the most prevalent sound sources, with very few instances of vessel noise.  However, in the Fremantle Inner Harbour, man-made noise dominated.  This worked out to a 20 dB difference between sites on average, and the frequencies used by dolphins for communication were more likely to be masked in Fremantle Inner Harbour based on elevated noise levels.

In this study, I was also lucky enough to get some acoustic recordings of sounds produced by snubfin and bottlenose dolphins in Roebuck, and could use these for a comparison with the sounds produced by bottlenose dolphins in Fremantle.  This helped me to discuss the potential consequences on Roebuck Bay dolphins if noise levels were to increase at that site.  Such information is going to be useful going into the future, as several coastal developments are currently planned for Roebuck Bay.

To find out more, check the paper out online or contact me!

Snubbies are happy little dolphins – hopefully they stay that way! (Photo: Sarah Marley)

 

New paper: Behavioural and acoustical responses of dolphins to vessel traffic and noise

Last night, my sixth (and final) PhD paper was published in the journal Scientific Reports!

In earlier papers, I established that the Swan River is a pretty noisy place.  One of the noisiest sites from an anthropogenic perspective is the Fremantle Inner Harbour, which experiences high levels of vessel traffic.  However, during my initial visual observations I discovered that dolphins continued using the harbour, even though it was a busy noisy environment.  So in this latest paper, I searched for evidence of dolphins responding to boats and noise at a subtler scale.

To do this, I used a combination of visual and acoustic monitoring techniques.  I found that dolphins significantly increased their movement speeds when vessel traffic occurred at high levels.  Similarly, dolphins also changed their behavioural budgets at high vessel densities, spending more time travelling and less time resting or socialising.

I monitored dolphin movement speeds and behaviours, to see how these changed as vessel traffic increased

I also looked for acoustic responses, by measuring nine characteristics to describe the shape and frequencies of dolphin whistles in different noise scenarios.  I found that all nine of these characteristics varied with increasing levels of broadband noise, and that the response was particularly strong for low-frequency noise.

I used nine characteristics to describe dolphin whistles

I’ve spoken before about the importance of scientific publishing, in terms of career brownie points for researchers.  So I’m pretty chuffed to have completed publishing my PhD!  To view the full list of papers from this and other projects, check out my Publications page.  Now to deal with all the ‘leftover’ PhD data that I collected, but didn’t get around to including!

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!

 

 

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 🙂

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!

 

Full Disclosure

Sorry, this isn’t a post divulging all my anecdotes and secrets!  It’s a quick note to point you in the direction of a new page created on this site, titled “CV“.

Here you can find links to my various online profiles listing my work / research history.  Alternatively, you can check out the slightly longer versions by viewing my full CV and Curtin University student capability statement.

Happy browsing!

Roebuck Bay - Sarah on Teena B

Filming snubfin dolphins in Roebuck Bay (Photo:  Joshua Smith)

 

First PhD Chapter Published!

After months of graft, I’m extremely chuffed to announce that my first PhD chapter has now been published online!

Chapter 1 - Marley et al 2016

To view the full article, please visit the Springer website.  If you have any issues, please contact me.

One down, one draft on supervisor’s desk, and three more to go!