New production by Salty Wave

Salty Wave has been busy producing a series of Video Explainers for the Institute of Molecular Bioscience at the University of Queensland, Australia. 

Take a look at The Science of Acute Pain to understand how pain is felt and experienced by many people.

The sounds cavefish make

Scientists have discovered one of the ways cavefish have adapted to subterranean living is by using sound differently to surface fish morphs.

“Astyanax mexicanus is the only vertebrate where extant cave-dwelling and surface-dwelling morphotypes still exist within the same species” says Dr Sylvie Retaux, a neuroscientist from the Paris-Saclay Institute of Neuroscience, France, who is fascinated by sonic cavefish. 

A cavefish recorded in the Pachon cave, located in the North of the Sierra de El Abra, North-East Mexico.
(Photo © Sylvie Rétaux)

25,000 years ago, the ancestors of A. mexicanus were swept away from their river habitat into the caves of North-Eastern Mexico by flood waters. Trapped in the caves and isolated from the surface, the cavefish gradually lost their eyes and pigment as a consequence, but kept their hearing, a finding reported by Arthur Popper in the 1970’s.

Retaux led the research study “Evolution of acoustic communication in blind cavefish” published by Nature Communications to determine whether this loss of sight was compensated by other senses. “We wanted to test whether acoustic communication would exist and would have evolved with their adaptation to darkness” said Retaux. 

The research team ventured to six of the thirty caves that host Astyanax mexicanus troglomorphic cavefish populations in San Luis Potosi and Tamaulipas, North-Eastern Mexico (Molino, Pachón, Los Sabinos, Tinaja, Chica, and Subterráneo); and a well in the village of Praxedis Guerrero, inhabited by the surface morphs. 

Reaching the cavefish proved to be no ordinary task, and an adventure in the making. The team traversed through mud, contended with the dark, and wore masks to protect against histoplasmosis, a disease of the lungs caused by fungus, all while carrying heavy backpacks full of electronic equipment. The researchers also had to contend with a sheer 68-metre vertical rock face to reach the Molino study site. But once inside the caves, the acoustic environment was very calm says Retaux. “It is a kind of dream for bio-acousticians. Almost no sonic pollution down there.”

Pool number 1 in the Los Sabinos cave, located in the middle of the Sierra de El Abra.
(Photo © Jean-Louis Lacaille-Muzquiz)

Both Astyanax morphs are known to produce the same repertoire of 6 sounds: clicks, serial clicks, sharp clicks, clocs, serial clocs and rumblings; and the anatomical structures used to make these noises are conserved between the morphs. “They scrape their teeth, use a series of small bones (the Weber apparatus), drum on the swim bladder or they can produce hydrodynamic waves with their fins” Retaux says.

The team discovered a sound made by wild cavefish when compared to surface morphs represented a different behaviour. The sharp click by surface morphs is visually triggered in the presence of rivals and is used to establish and maintain hierarchy. However, when cavefish produced the same sound it was in response to detecting food odours while foraging. 

Unlike the surface morphs, cavefish don’t display schooling behaviour and are non-aggressive. “It is unclear whether they ‘call’ other individuals to come and share food when they find some, but it is a possibility. In any case, communication about finding food is crucial for cavefish, much more beneficial than spending energy in aggressive behaviours” Retaux explains. “Drastic environmental changes can induce significant evolution or shifts in behaviours and probably, in the brain, the neural circuits that govern these behaviours” she says.

Even though morphological, physiological and behavioural changes occurred in cavefish, studies report Astyanax morphs breed with one another when flood waters wash surface morphs into the cave system. “A really interesting hypothesis is that one of the sounds of their repertoire, which again, is shared by the two forms, is used during courtship. In this case, a prediction is that the use and meaning of this particular sound has not changed, contrary to the sharp click that has evolved from an aggressive signal to a feeding signal” says Retaux.   

Both Astyanax morphs are the perfect model for researchers to reconstruct the evolutionary paths each morphotype has taken since their common ancestors were separated. The lateral line in cavefish is enhanced, an adaptation which has increased their sensitivity and response to living in confined zones with no light. “It is a sense that we humans do not have but that fishes and amphibians do have, which allows them to detect differences in the water pressure around them.”  

The only audible sounds in the caves, are water dripping or bats chirping and Retaux plans a return trip to record the acoustic environment. She wants to answer the ironic question Arthur Popper asked when he first discovered cavefish have exceptional hearing: what are cavefish listening to?

Thank you to Dr. Sylvie Retaux for permission to publish her field trip photos.

Adventures with Blue Whales and Blue Waters

My book review - Adventures with Blue Whales and Blue Waters - featuring The Secret Life of Whales by marine biologist, Micheline Jenner; and The Oceans, A Deep History by paleoceanographer, Eelco Rohling - was published by Cosmos Magazine Winter 79 Edition.

I recommend both books, which are very different stories, but written by scientists who share a great respect and love of the ocean and its wildlife. Fantastic stories.

Eye for Adventure

The ocean is there to be discovered and Steve Brady is an intrepid diver who has explored many underwater locations with a salty tale to tell.

“We’ve got it all and there’s just so much diversity of marine life in and around Australia. It’s amazing” Brady says. “This is probably a funny thing to say but if I had gills I’d be a very happy boy.”

With a litany of dive experiences under his belt, Brady wanted others to learn what the ocean has to offer. Informed by research from marine biologists and feedback from pro divers, he developed a calendar featuring marine wildlife events throughout the year, and uses the calendar to schedule dive trips at all levels of experience from beginner to advanced around Australia and beyond.

“Finding where you can go to see certain marine life is a very big thing for people and I’m the same. I want to see mola molas, I want to see mantas, so I want to go to a place that has the best chance at the best time to see them” says Brady.

Brady has an eye for adventure and despite the unpredictable nature of the sea, he is not deterred from making new discoveries. He recalls an incredible rendezvous with a manta ray after travelling out to an open ocean destination via spotter plane in West Australia.

“In West Australia we went to the township of Coral Bay. We specifically went out on a trip where they have spotter planes, and you aren’t on a reef. You’re in open water. Sandy bottoms, maybe twenty metres of water and you’re snorkeling with them. They’re just down there, just swimming around, very acrobatic, very inquisitive. Just to have one of them come gliding over the top of you, that’s very special” says Brady.

Australian dive sites are world renowned for their pristine waters, thanks to clean up projects led by conservation organisations and social media groups. Despite awareness campaigns and changes to the community’s attitude toward disposing rubbish, microplastics are severely impacting the health of marine life globally.

When marine organisms filter seawater for their food and to absorb oxygen, they vicariously take in these tiny microplastic pieces. This plastic can become lodged in digestive and respiratory tracts, causing animals to suffer health problems or worse, mortality. In the ocean, it's not just small filter feeding species like corals and clams that are being negatively affected, the larger pelagic animals, whales and sharks, are also being hit hard by this invisible threat. 

“Plastic is everywhere, even in places we can’t see” says Ian Kiernan, founder of Clean Up Australia, an organisation that coordinates community clean up events of the environment every year in Australia and worldwide.

“Even if you aren’t really concerned about the health of marine creatures, you might pause when you know that you cannot escape that easily because they are in our drinking water” Kiernan says.

To decrease the problem of microplastics in our water, Kiernan recommends consumers buy clothes made with natural fabrics instead of synthetic material and avoid purchasing products like cosmetics, soaps, shampoos and detergents that do not clearly state they are free of microplastics.

Another way of overcoming obstacles to the continued health of the marine world is through ecotourism, which is offering coastal communities the benefit of financial return, by showing visitors how beautiful preserved natural environments are.

The Great Barrier Reef along Queensland’s coast and Ningaloo Reef off Exmouth in West Australia, both World Heritage listed areas, are prime examples of ecotourism’s success.

Divers share their once in a lifetime experiences when they dive with whales, sharks and dolphins through social media, attracting a lot of attention which ultimately turns marine species into major tourism draw cards overnight. “People’s expectations are all different and everyone enjoys diving around the coral. But when people are fortunate enough to see species like mantas that would be their trip for the rest of their lives” says Brady.

Spectacular Coral Sea locations lying beyond the Great Barrier Reef are a prize ready for the taking. “You’re talking thousands of metres of water, massive drop offs, just awesome visibility and you will get large pelagic marine life out there. If you like sharks, that’s the place to go” says Brady.

Another exciting dive destination is the S.S. Yongala shipwreck, which sunk in 1911 off Alva Beach, Ayr, in North Queensland. “It’s a feeding station for mantas, bull rays, groupers and sharks. It’s safe to go learning to dive because you don’t have strong currents. You’ve got pristine visibility. You’ve got nice corals. I would promote it as one of the best places to learn to dive” says Brady.

The Ribbon Reefs are part of the Great Barrier Reef, which extend from Port Douglas all the way up passed Lizard Island. 

“In June, July each year, you get the migration of the Minke whale coming through and that’s very special. That’s really a highlight for me in terms of marine species” says Brady.

And for the nouveau diver who stumbles upon a manta ray or a whale shark for the first time? 

“You just let them be in their natural environment, you let them be the inquisitive one and you’re in for a great experience” says Brady.

Report by Gabrielle Ahern

Steve Brady manages ‘Dive In Australia’ located in Cairns (https://diveinaustralia.com.au) a travel agency matching dive companies to divers looking for their ideal wildlife encounter.

All images © Steve Brady - Dive In Australia - www.diveinaustralia.com.au

My interview with Steve Brady will feature in a future podcast episode of the Noisemaker series. So stay tuned.

Ecologists Wild on Sound

Have you ever thought of using sound to navigate through the landscape? A team of scientists convert sound into a spectrum of coded colour bands to decipher hidden clues about the environment. Their work is making waves in ecology circles, with the identification of species so cryptic, even trained specialists can’t spot them in the field. 

False colour spectrogram. Image courtesy of QUT Ecoacoustics.

In the paper “Long duration false colour spectrograms detecting species in large audio data sets” (Journal of Ecoacoustics) led by Dr Michael Towsey at the Queensland University of Technology, long duration sound recordings are visually represented in a false colour spectrogram (LDFC). By applying a set of mathematical formulae, sound waves are converted into their visual counterpart called spectral indices. Several spectral indices (symbolised by a three letter code) are calculated and represent different concentrations of acoustic energy recorded in the study area. 

Long duration spectrograms prepared from 3 different acoustic indices representing 4 hours. The H(t) Index refers to temporal entropy. CVR is short for cover. Each index reveals different components or events in the acoustic sound-space. Image courtesy of QUT Ecoacoustics.

Depending on the aims of the research, the spectrogram produced reflects different combinations of these spectral indices that are assigned to the red, blue or green channels of colour (RGB) – a process inspired by false colour satellite imagery techniques used to produce pictures captured of the Earth from space. “The eyes have got the capacity to absorb huge amounts of information very quickly, so it can scan an image much faster than the ear can scan a recording” says Towsey.

Image representing the same four hour recording (16:00 to 20:00) from above. Red, green and blue colours are assigned to the three different spectrograms and produce the long-duration, false-colour spectrogram (RHS). CITATION: Towsey M., Znidersic E., Broken-Brow J., Indraswari K., Watson D., Phillips Y., et al. (2018). Long-duration, false-colour spectrograms for detecting species in large audio data-sets. Journal of Ecoacoustics. 2: #IUSWUI, https://doi.org/10.22261/JEA.IUSWUI

The final spectrogram is a colourful account of the soundscape or environment. The calls of wild organisms, for example, frogs, insects and birds, are a distinctive contrast to the background environmental sound and referred to as soundmarks or acoustic signatures. They are used like landmarks by the research team to ‘navigate’ through the study environment to find answers to specific ecological questions.

Different combinations of indices give different views of the soundscape. Here are two LDFC spectrograms of the same recordings using different combinations of indices. Image courtesy of  QUT Ecoacoustics.

Ecologists can identify the calls of different wildlife species in the spectrogram according to the filter applied. Image courtesy of QUT Ecoacoustics.

The LDFC technique was vital to assisting the researchers scope out clues for the whereabouts of the Lewin’s Rail in Tasman Island, Tasmania, a shy bird species normally hidden from ‘view’ in its wetland habitat and usually only identifiable by its vocalisations. The spectrogram reduced the need for the manual analysis of hundreds of hours of sound and enabled quick identification of the bird species. It also saved the research team the alternative cost of hiring extra crew to visually monitor the site on the ground. 

Ecologist, Elizabeth Znidersic, in the field, collecting data from a passive audio recorder. Image courtesy of Elizabeth Znidersic.

Elizabeth Znidersic, an ecologist at Charles Sturt University, uses the less invasive method of passive sound recording to study wildlife in Tasmania and recognises the value of the LDFC technique. Armed with a spectrogram, Znidersic can not only capture cryptic species but she can visualise bird species that make no noise at all, only because they share a mutual relationship with a wildlife species recorded nearby. “Not all species will be primarily detected by their vocalisations, some will be silent, so we can look outside the box and see if there is a surrogate species for that species that doesn’t vocalise, so we can have that relationship and we can start to look for that species on a visual level” says Znidersic. 

The “grunt” and “wheeze” vocalisations of the Lewins Rail can be identified in the eight seconds of greyscale spectrogram (Figure B) and as green vertical lines in the range 100 – 3,500 Hz (in the white rectangles) in the six hour sample represented by the LDFC spectrogram (Figure A). The bird chorus at dawn is represented by the green and pink hues that commence at 05:00 in the 1,500 – 5000 Hz frequency range (Figure A). CITATION: Towsey M., Znidersic E., Broken-Brow J., Indraswari K., Watson D., Phillips Y., et al. (2018). Long-duration, false-colour spectrograms for detecting species in large audio data-sets. Journal of Ecoacoustics. 2: #IUSWUI, https://doi.org/10.22261/JEA.IUSWUI 

The soundscapes being produced by the team at QUT Ecoacoustics with the LDFC technique are starting to blur the line between ecoaccoustics and bioacoustics – research areas normally considered to be two distinct disciplines. Ecoaccoustics studies the total sound generated by an environment, while the latter only records and monitors specific wildlife species calls. “The more experience we get with interpreting images of soundscapes, the more we’re seeing they reflect what bioaccousticians have already published” says Towsey.  

Image shows two LDFC spectrograms of a 24 hour recording taken with a hydrophone in a pond of the Einasleigh River, northern Queensland, dry season. It highlights the change in sound during the day compared to the night. All the acoustic activity in this recording are due to aquatic insects. Recording courtesy of Simon Link and Toby Gifford, Griffith University, Brisbane.

Ecoaccoustics recorded at a location can be separated into three categories: geophony (surf, wind and rain), biophony (wildlife calls) and anthropophony (manmade noise). 

Soundscape ecologists broadly categorise three or four sound sources, which they label biophony, geophony, anthropophony and sometimes a fourth is added, technophony. A spectrogram like this can direct an ecologist to those parts of the recording in which birds are singing, thereby saving a lot of time. Image courtesy of QUT Ecoacoustics.

Insects chorusing at the start and end of the day and birdcalls in the morning are being used as soundmarks by Towsey to determine the acoustic structure of sites, especially beneficial to observing slight differences in ecosystems located close together.

Two consecutive days of recording were made at six sites for another research study, giving 12 days of recording in total. The contents of the 27 clusters were identified by selecting the false-colour spectrum of each minute in each cluster (top image). Cluster Y contained very quiet night-time recording segments, while cluster V included the morning chorus and other segments with much bird activity. The use of acoustic indices enables the calculation of acoustic signatures that characterise the soundscapes at different locations. CITATION: Sankupellay, M., Towsey, M., Truskinger, A., & Roe, P. (2015). Visual Fingerprints of the Acoustic Environment: The Use of Acoustic Indices to Characterise Natural Habitats, IEEE International Symposium on Big Data Visual Analytics, Tasmania, Australia, 22 – 25 Sep 2015. Image courtesy of QUT Ecoacoustics.

Once the wildlife call is identified, Towsey can use the combination of spectral indices to construct and apply an automated recogniser to the data via computer and locate the acoustic signature or soundmark of that wildlife species at a much faster rate. “We are using machine learning technology or artificial intelligence to recognise all the different categories of sound and we can break the day up into that” says Towsey. The team can even pinpoint the geographic location of a study, just by looking at an LDFC spectrogram.“I actually can look at a spectrogram and have a bit of an idea where that spectrogram was taken from and that can be two locations in America or multiple in Tasmania. I look for certain species, I look for frog chorus, I look for insects and for the intensity of dawn chorus and evening chorus, and what kind of night time activity there is” says Znidersic.

This image compares three 24-hour, false-colour spectrograms of three soundscapes from different latitudes. All these recordings were obtained in the first week of July (winter) 2015. The top recording in Papua New Guinea is dominated by insects (Eddie Game, The Nature Conservancy). The middle recording in Brisbane is dominated by birds (Yvonne Phillips, QUT Ecoacoustics Research Group) and the bottom desert recording is dominated by wind (David Watson, Charles Sturt University).

Towsey says the applications for the LDFC technique is limitless and it has already been applied to visually monitor the progress of environmental restoration projects and provide corroborating evidence for the conservation of natural environments. “People think about this field as being relatively new but I like to think it is beginning to mature. The ecological applications are only just being scratched” says Towsey.

LDFC spectrogram was obtained from the Adelbert Ranges, Papua New Guinea, by The Nature Conservancy (TNC). TNC is a global conservation organisation who are attempting to preserve some of the natural forests of PNG. The local terrain for this recording is mountainous jungle. The entire sound-space is filled with acoustic activity, most of it due to insects, while birds are, for the most part, restricted to the lower frequency band. Image courtesy of QUT Ecoacoustics.

Dr Anthony Truskinger is the research software engineer responsible for building the computer infrastructure vital to the research teams work at QUT Ecoacoustics and compares their library of sounds with an astronomical observatory. “We actually use a service provided by a collaboration of universities to store research data. We store 90 Terabytes of data. That’s only possible because there’s a national infrastructure for technological investment and prices keep dropping in storage” says Truskinger.  

Four LDFC spectrograms, each 3 hours duration. White rectangles identify frog choruses and calls of interest. The vertical Hertz scale is the same for all spectrograms. (a) Intermittent chorusing of the ornate burrowing frog. (b) Chorusing of the Northern dwarf tree frog. (c) Chorusing of the flood plain toadlet. (d) The evening soundscape. CITATION: Towsey M., Znidersic E., Broken-Brow J., Indraswari K., Watson D., Phillips Y., et al. (2018). Long-duration, false-colour spectrograms for detecting species in large audio data-sets. Journal of Ecoacoustics. 2: #IUSWUI, https://doi.org/10.22261/JEA.IUSWUI

In the past the team applied the LFDC technique to process other scientists recordings but have recently released the Ecoacoustics Analysis Programs software packagevia GitHub as an open source for researchers to run their own analyses. “Open source sciences is what the future is” explains Truskinger. 

Long term the team will investigate how subtle temporal changes in soundscapes across land and water, for example, biodiversity, ecosystem health and behaviour of migratory wildlife populations, will be influenced by climate change. 

Written by Gabrielle Ahern

Thank you to Dr Michael Towsey, Dr Anthony Truskinger and Elizabeth Znidersic for permission to use their images. Follow the link to QUT Ecoacoustics environmental sound recordings available via Ecosounds.

My interview with the research team will feature in an episode of the podcast series NOISEMAKERS, so stay tuned.