Author Archives: Sarah Marley

New paper: Effects of ship noise on marine mammals

I’m excited to announce the publication of my co-authored paper on “The Effects of Ship Noise on Marine Mammals—A Review” in Frontiers in Marine Science.

The number of vessels utilising the marine environment is on the rise, with a corresponding increase in noise pollution from this activity. But what are the effects of ship noise on marine mammals? We reviewed 154 scientific articles to document the species, areas, and effects studied. From this, we were able to identify common themes and important research gaps.

This was a hugely satisfying project and a delight to work on. One of the best parts of research is finding great people to work with, which was certainly the case here!

The paper is already receiving good reviews and the Altmetric score is soaring! I’m looking forward to seeing how this paper can help shape future research.

 

 

 

 

Machine Learning and Acoustics

As computer systems continue to improve, there is an increased ability to complete tasks using artificial intelligence. A computer system can be trained to perceive its environment, make decisions, and take actions. One of the methods for achieving this is machine learning (ML), where machines ‘learn’ tasks from without the need for explicit programming. Given sufficient training, ML can process large, complex datasets to reveal patterns.

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Photo by Pixabay on Pexels.com

Acoustics is one of the fields generating large amounts of data. For example, every time I deploy a hydrophone in the English Channel, it can record for 3 weeks and return approximately 250 GB of data! It doesn’t take long for the data to quickly add up to an overwhelming amount. Never mind the added challenge of searching through it for sounds of interest, such as fish and vessels. ML could provide the answer, if I could train the computer system to recognise these sounds and search the data for the presence. Similarly, ML could also greatly contribute to other types of acoustic research, like speech processing, sound localisation, noise mitigation, health monitoring, and so on.

But how do young acousticians (yes, I am still counting myself in this category!) learn how to develop and use ML tools? That is where the UK Acoustic Network (UKAN) comes in! The network contains several special interest groups, including one specially devoted to Early Career Researchers that holds an annual Summer School. This year, their aim was to provide training for early career acousticians to get to grips with ML tools. So I joined over 30 scientists at Gregynog Hall in Wales this week for the UKAN Summer School 2019 (#UKANSS19).

The week started with an introduction to Python. This was led by Dr Prasun Ray, a Strategic Teaching Fellow in Applied Mathematics at Imperial College London. Prasun took us through the fundamentals of programming and data analysis in Python, alternating between a mixture of seminars and interactive examples to put us through the paces. Although I haven’t used Python much since 2016, it was good to re-familiarise and get updated on what the software can do!

The ML classes were delivered by Dr Ramon Fuentes (Research Scientist at Callsign Ltd and Visiting Researcher at the University of Sheffield), who has previously applied ML for signal processing and the development of autonomous inspection systems. Although the mathematics of this went whooshing over my biological head, it was still interesting to learn some of the fundamental ideas that ML is built upon. Although anywhere Ramon speaks in the future might want to invest in some additional whiteboards…

Finally, we had a series of lectures on audio and speech applications of ML delivered by Professor Nilesh Madhu from Ghent University. In my opinion, these were the highlight of the week! Nilesh was an excellent speaker, expertly leading us from one topic to another with a strong storyline, a balanced level of detail, plenty of examples, and good humour. His own research focus is on signal detection, analysis and enhancement with application to mobile devices. Despite this seeming fairly different from my own work on the surface, it had a lot of deeper similarities. For example, the problem of recognising and classifying signals in challenging contexts will be particularly relevant to my “Decoding the Deep” project.

As well as generating ideas, the other great thing about this event was meeting people. All too often it is easy to get ‘stuck’ in your own research bubble, only speaking with or working alongside people in the same field. Whilst this can be a good thing, it is still good to step back every so often and look around – because that’s how ideas are born! UKAN exists to support and facilitate networking – and that was a strong highlight of this week. Living with 30+ acousticians for five days means that you never know when an interesting conversation will arise: over the breakfast table; during a lunch break; whilst trying out some casual archery; building a cardboard tower in a competitive team-building exercise; on a hike through the grounds; in a subterranean prison surrounded by the ghosts of past inmates… (not even joking). There were lots of opportunities for networking, bonding, and discussions throughout the week. I think everyone went home with some new contacts and friends, several of which I will be following up with over coming months.

Overall, a successful week for the UKAN Summer School 2019! The ECR Special Interest Group are planning to run another next year, along with some smaller events. Be sure to get in touch to register your interest, propose other events, or join the network!

 

PhD Available: Vessel collisions with large whales

One week left to apply for a PhD on “Vessel Collisions with Large Whales: Behavioural responses and areas of risk”, supervised by myself, Professor Alex Ford, and Ms Lucy Babey!

800px-FinhvalThis PhD aims to quantify vessel collision risks for fin whales in the Bay of Biscay. Organisation Cetacea (ORCA), a cetacean conservation charity, has been utilising platforms-of-opportunity to collect cetacean sightings around the world since 2001. On-board observers collect data relating to effort, ship location / speed / heading, and whale sightings. The current project will both utilise ORCA’s long-term dataset and conduct fieldwork to collect additional data. Behavioural analyses will assess fine-scale behaviour of whales during vessel encounters, whilst density surface models will be used to identify high-risk areas.

A full project description and application form is available on FindAPhD: https://www.findaphd.com/phds/project/vessel-collisions-with-large-whales-behavioural-responses-and-areas-of-risk/?p105039

This competition-funded PhD is open to UK / European students only. A BSc (minimum second-class) or a Masters degree in a relevant subject is required, along with English language proficiency at a minimum of IELTS band 6.5 (with no component score below 6.0). The ideal candidate would also have previous field experience (e.g. vessel-based surveys, marine mammal observations, behavioural observations), proficiency in R and GIS software, and a strong background in statistical techniques.

The deadline for applications is 17th February 2019.

Living in the Acoustic Environment

Last month, I attended the Acoustical Society of America (ASA) conference in Minnesota. I prepared a conference report for the Journal of Animal Ecology Blog, which I have reposted below.

Animal Ecology In Focus

Our Blog Editor, Dr Sarah Marley, reports back on last month’s Spring Meeting of the Acoustical Society of America (ASA) in Minnesota, USA. Find out what made it such a successful conference, and why she did not end up being the loner she expected to be…

Last month, several hundred acousticians descended on Minneapolis, Minnesota for the 175th Meeting of the Acoustical Society of America (ASA). I was among them, attending this conference for the first time. Although I have been conducting research in acoustics for over five years, I still feel very new to this field and was nervous about presenting to ‘hardcore’ acousticians rather than my normal audience of biologists. And, although I was an invited speaker, I did not actually know many people attending this primarily American conference beyond my PhD supervisor and a few Twitter acquaintances. So the 27hr plane ride over from Western Australia…

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New Job!

I am excited to announce that I have a new job! Starting in August, I will be a Lecturer in Marine Biology at the University of Portsmouth. This means a big change in more ways than one, as – after 8yrs down under – we will be moving back to the UK.

I think our friends and families on both sides of the world are still in shock, with one side having given up hope of us returning and the other thinking they’d managed to claim us for keeps. I’m still feeling pretty shocked myself, alternating between being Extremely Excited  and Totally Terrified. The positives are obviously the idea of going home and being closer to family, all to do a job that sounds perfect for me. I love teaching, and this position will allow me to broaden that by developing new materials and supervising students, as well as continuing my research activities. However, moving means saying goodbye to some amazing people, a big lifestyle change, and an overwhelming amount of logistics. As I wander around our house, mentally categorising items as ‘sell’ or ‘ship’, I can’t help but think how much simpler it was when we first came out here with just a backpack each. If it wasn’t for the fact we’re going to need so many layers whilst our internal thermostats adjust, that might still be an option.

close up photo of three sweatshirts

Photo by Daria Shevtsova on Pexels.com

What makes the logistics particularly challenging is that neither of us have ever actually been to Portsmouth before. The whole hiring process (including an interview, a mock lecture, and a presentation about my research) was all conducted over skype. So whilst all these virtual meetings have gone well and my new colleagues seem lovely, it is still a bit disconcerting to be moving to the otherside of the world to a place you’ve never been. Although saying that, I did the same thing in 2010 by coming to Australia… Maybe I’m just getting old.

However, this issue will soon be rectified! Phil and I are both presenting at the International Statistical Ecology Conference next month, which conveniently enough is being held in St Andrews. This not only allows us both to tie in a trip to see our parents, but means we’ll also have the chance to visit our new home.

It does mean my life at the moment has been pretty FIFO (Australianism: fly-in, fly-out). Last month I was over in the US to present my research at the Acoustical Society of America conference in Minnesota. After a 27hr flight and 13hr time difference, I had an amazing trip despite being wrecked by jetlag. The fact that I was only there for a week meant that by the time my body clock got its act together it was time to go home and spend another week temporally confused! Now, after a month back home, we’ll be heading to Europe for a month, followed by a month back in Oz before the Big Move over to Portsmouth. Crikey.

It is a lot to take in, but there is no doubt in my mind that this going to be a great experience! So stay tuned for posts about moving dramas, culture shock, and academic adventures!

 

Laborastory Talk – My Science Heroes

A couple of months ago, I was invited to participate in the Perth Laborastory event. The Laborastory is a science storytelling event usually held in Melbourne that comes to tell the stories of science – “the heroes, the egos, the breakthroughs and the mistakes of genius”. This was the second time it had been held over West, and I was delighted to be involved!

Laborastory quote

My science story revolved around two of my heroes – David Attenborough and Gerald Durrell. Whilst you are no doubt well aware of the first, you might not be so familiar with the second. In my story, I describe my failed close encounter with Attenborough, my captivation with Durrell, and how both men contributed to my zoological career.

Hear the full story below. Unfortunately the acoustics are a little on the quiet side, so you’ll need to turn it up! And yes, I swear the audience is laughing in those quiet pauses…!

Sound Science in the Swan

On Monday, I gave a presentation about dolphin acoustics in the Swan River at a free public seminar called “Sound Science in the Swan“, supported by Acoustics2017, the annual conference of the Australian Acoustical Society.  Over 60 people attended the two-hour seminar, with the audience containing both scientists and members of the public.

The evening kicked off with an introduction by the organiser, Dr Miles Parsons from Centre for Marine Science and Technology (CMST) at Curtin University, who explained what sound is and how animals use it underwater.  I then demonstrated this through my interactive Soundscape Game, where the audience members are each allocated the role of a different underwater sound source and produce them together to create a ‘soundscape’.

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Me yelling at some audience members to “make snapping shrimp noises” (Photo: Sylvia Parsons)

Miles then explained more about some of the anthropogenic (man-made) sound sources in the Swan River system, including things like vessels, pile-driving, airplanes, drones, and even human swimmers!

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Miles presenting experiments examining sounds produced by swimmers (Photo: Sylvia Parsons)

This was followed by Dr Iain Parnum (also of CMST) who explained his work using underwater acoustics for the purposes of habitat mapping within the Swan.

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Iain using acoustics to ‘see’ underwater (Photo: Sylvia Parsons)

After the break, I was up to present about dolphins!  I started with examples of the different sounds dolphins make and why underwater sound is vital for their survival.  I then applied this to the Swan River, by showing it as a busy, noisy environment – and therefore rather challenging for dolphins!  However, as I explained, my research shows that the dolphins don’t necessarily leave noisy areas, although they might have strategies for dealing with them.

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Me showing some theodolite tracks of dolphins and vessels within the Swan River (Photo: Sylvia Parsons)

I was then able to present some research on dolphins and pile-driving, on behalf of my PhD supervisor Dr Chandra Salgado Kent, who was unable to attend that evening.

The evening finished back with Miles, who spoke about mulloway and some of the research surrounding the calls made by these fish.

A thoroughly enjoyable way to spend an evening!

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.

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!