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.

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.

Episode 3 - Noisemakers Series by Salty Wave Blue

Welcome to the podcast series – Noisemakers – presented by Salty Wave Blue. This episode features my interview with Dr. Sebastian Thomas (March 2017) from the University of Melbourne, who discusses why mangrove forests are considered the major players of blue carbon, amazing sounds from the noisemakers of the wild, quizzes to solve and some fascinating tales to follow from the rainforest to the reef.

Stock Media provided by Pond 5 and Monsoon Enterprises.

This podcast is dedicated to my dog, Scruffy, who loved mangrove forest walks.

Episode 3

Viral Vectors for Change

Viruses have dominated the microscopic world of the oceans for billions of years and researchers find it difficult to track and isolate their activities because they are invisible to the naked eye.

But science has finally caught up with these tiny vectors of change, says Marine researcher, Dr Karen Weynburg, a Synthetic Biology Fellow at the CSIRO and University of Queensland.

“For some people, it's just not on their radar that viruses are so central to everything in life” Weynburg says.

Stock media provided by Ryhor Bruyeu / Pond5

In the paper: Marine prasinoviruses and their tiny plankton hosts: a review, research led by Weynburg reported viruses co-evolved with their hosts and are immersed in a constant battle of survival to outwit and outplay for control.

“Recently there's been a discovery that probably what happened was that all life was RNA” Weynburg says. This research has shown viruses existed before cells and were the precursors of life. Viruses switched from RNA to DNA to avoid their genomes being attacked and removed by the host cell.

Viruses are not regarded by science as a real organism because they cannot reproduce or metabolise without a host cell. Traditionally, they are classified according to the host they infect, be it an animal, a plant or prokaryotic bacteria.

“The jury's still out on whether viruses are living or not, because they don't fulfill all the requirements of a living organism, but they have a sort of key if you like, the way they outwit hosts, they're clever players in the oceans of the world” says Weynburg.

“In terms of the marine environment, in one teaspoon of sea water you're going to have as many as ten million viruses, but those viruses will again, not just be abundant, they'll be hugely diverse, because they're affecting so many different hosts."

Sea turtle swimming in a coral reef habitat. Stock media provided by Charlie Blacker / Pond5

What Weynburg finds intriguing about viruses is they can be vectors for disease or work as part of an organisms’ immune system. A good example is when the activity of coral specific viral communities control the threat of bacterial pathogens, suggesting bacterial and viral communities have co-evolved with their coral hosts.

“I don't think it's a straight forward black and white situation where they're all good, they're all bad. It’s quite complicated and there's a lot of dynamics and interactions going on” Weynburg says.

“Viruses have to be very specific, very intimate with their host and therefore they've fine-tuned a strategy over millions of years."

Coral reef growing in Komodo National Park in the waters of Indonesia. Stock media provided by Ethan D / Pond5

Innovative technology is assisting researchers like Weynburg to understand just who and what viruses are and their interaction with the environment.

“People are beginning to realise they're playing a really crucial role and we have to start including them in future marine models and what's actually happening in the oceans in terms of biological dynamics.”

Microscopic marine cyanobacteria drove the oxygenation of Earth 2.5 billion years ago and they continue to generate 50 percent of atmospheric oxygen and primary production in the oceans. Every week viruses spearhead a massive turnover of microbes in the world’s oceans by initiating a new generation.

“If you took all the viruses out of the ocean today, there would be no life in it tomorrow” Weynburg says.

“Everything would grind to a halt because viruses keep the system ticking over. They keep the whole energetics and dynamics in the oceans going.”

Wave crashes on the ocean surface. Stock media provided by Quincy Dein / Pond5

With climate change a reality, Weynburg says, it is hard to predict how viruses will survive exposure to higher levels of UV and warmer ocean temperatures.

“We need more biological modelers to come in and really start plugging the data that we generate into models of what might happen in terms of climate change. We really don't have the answer yet” Weynburg says.

In her research paper, Weynburg refers to how a virus’ selective behaviour during infection is geared toward protecting its survival in the environment, for example, holding onto heat shock proteins to survive heat stress.

“Virus’ only keep the bits of DNA that work for them” Weynburg says. “They don't carry junk DNA like we do in our genomes. So, if they hold onto something like a heat-shock protein, it's going to be playing an important role in their infection."

Weynburg says viruses free up energy and nutrients for growing new cells by infecting and releasing the contents wrapped up in microscopic cells of marine microbes at the end of their lifetime.

These viruses also vicariously influence cloud formation by controlling blooms of cocolithophores in the sea and contribute to the recycling of iron crucial to biological processes in nutrient poor oceans.

“The blooms of the cocolithophores that you can see from space are huge and end up causing these cloud formations. The end of the blooms are actually only caused by two or three different strains of virus, which is quite fascinating” says Weynberg.

Cloud formation is stimulated by the activity of blooms of coccolithophores in the oceans, visible from space. Stock media provided by Nikolai Sorokin / Pond5

Management of climate is just one part of the viral power play. Since the mid 1970’s there has been an enormous leap in our understanding of marine virology. Weynburg’s research currently aims to mimic how viruses capture DNA segments to create whole genomes or existing genes.

“I'm sure down the line, viruses will have a myriad of roles that we can exploit if we think cleverly about it and we understand the system well enough” says Weynburg.

Scientists working in an experimental laboratory. Stock media provided by Yuralaits Edhar / Pond5

Questions about the ethics of applying these synthetic biology tools are already being considered by researchers long before “the horse has bolted” says Weynburg. The synthesised genomes can be targeted to treat disease and delivered by viral infection.

“Some people have already used virus captures to deliver proteins that will target cancer cells” she says. “If you think that you could use a virus to deliver something that would specifically attack a rogue cell, that is really exciting. We're on that brink of discovery now. It's real cutting edge technology”.

Report by Gabrielle Ahern


My interview with Dr Karen Weynburg will feature in an upcoming podcast episode of the SaltyWaveBlue NOISEMAKERS series published via Sound Cloud and iTunes, so stay tuned.

The paper - 'Marine prasinoviruses and their tiny plankton hosts: a review' is published by the journal - Viruses.

Images of marine microbes and more ecology themed boards are available on the SaltyWave Pinterest site: https://www.pinterest.com.au/saltywave/

Kissing coral in the Great Barrier Reef

Tube lip wrasses use mucus-coated lips to feed on the surface of corals. When they feed, these fishes close their mouths, push their fleshy lips against the coral, and suck off the coral’s mucus and flesh. These “kisses” are possible thanks to a protective coat of slime around their lips. Image courtesy of Victor Huertas and David Bellwood.

Small changes in any organism take millions of years and multiple generations to evolve and learning why the design and function of certain traits are successful is not as easy. Tube lip wrasses are a familiar sight in tropical coral reefs across the Indian and Pacific Oceans and recognised for their thick, fleshy, tube shaped lips. 

Intrigued by this conspicuous physical adaptation, fish biologists Victor Huertas and Professor David Bellwood from James Cook University decided to investigate further. “We wanted to see if this morphology in the lips of tube lip wrasses matched with the hypothesis they feed on coral mucus” Huertas says.

Damaged coral produces more mucus than healthy coral and observations in the field report tube lip wrasses preference for feeding in damaged coral areas. Coral mucus is not a nutritional source of food for fish and it is difficult to imagine how these wrasse species survive on it.

To the naked eye, the lips of Labropsis australis appear smooth but when magnified by scanning electron microscopy the images revealed the surface has numerous grooves similar to the underside of a mushroom with a reduced tooth. It is a remarkably different trait when contrasted to the lips of other reef fish and even those of typical non-coral feeding wrasse species, Coris gaimard, which have thin, smooth lips with a protruding tooth. “There are species of damsel fish that have larger than usual lips. But it was only in these tube lip wrasses, these fish that feed on coral, that we observed this new adaptation” says Huertas.

The mouth of a tube lip wrasse with self-lubricating lips. 

These lips enable the fish to ‘kiss’ mucus and flesh from the surface of corals. 

SEM image courtesy of Victor Huertas and David Bellwood.

It is normal for any fish to produce mucus from their skin, they’re slippery to hold onto when you catch one. So it was extraordinary when histology showed the mouth of L. australis contained a very high proportion of mucus-secreting goblet cells. “We noticed that among these groups there was a large number of mucus producing cells. Occasionally, you find goblet cells in the lips and the lip skin but it is quite rare. In this case, what we saw is a lot of them” says Huertas. “This was the eureka moment. We realised this is what enables the fishes to feed on coral”. 

In their paper “Mucus-secreting lips offer protection to suction-feeding corallivorous fishes” published in Current Biology early in 2017, the authors compared the grooved lips to tissues that usually line a fish’s gut. “The reason why we wanted to make the analogy is to highlight surfaces or tissues that specialise in either secreting or absorbing substances, generally tend to show this type of morphology” says Huertas.

How all these elements conspire together so successfully shows the devil in the design. High-speed videos recorded L. australis swim toward a coral with its closed mouth forming a tube to suck off coral mucus and flesh. The ‘kissing action’ or suction only lasts a brief 13.1 milliseconds and you can actually hear a short ‘tuk’ sound.

Tube lip wrasses use mucus-coated lips to feed on the surface of corals. When they feed, these fishes close their mouths, push their fleshy lips against the coral, and suck off the coral’s mucus and flesh. These “kisses” are possible thanks to a protective coat of slime around their lips. Gif image courtesy of Victor Huertas and David Bellwood.

It appears as though the fish suck up the coral mucus through their lips like a straw. The fish don’t appear to grab or hold any coral material and the lubricated lips enable the fish to latch onto the uneven surface and achieve a more efficient suction. “The problem with tube lip wrasses is they have to push their lips against the coral surface, so these lips become exposed all of a sudden to the coral they fancy” says Huertas.

Huertas suggests the slime produced from their lips is a protective mechanism, which shields the fish from stinging nematocyst cells that might be accidentally eaten; and from any damage posed by the sharp coral surfaces. “If they didn’t have this mucus they would probably not be able to feed on corals” says Huertas.

Traditionally, it has been assumed tube lip wrasses fed on coral polyps like butterfly fish. “They do not inspect the coral surface very carefully. They pretty much go in there and start striking. If they were feeding on specific things that grow on the coral surface, like parasitic worms, you would expect to see the fish approach and then stop and inspect the surface, but that’s not what we saw” says Huertas.   

18 species out of the 600 wrasses in Family Labridae feed on coral in the Great Barrier Reef and judging by the population numbers of wrasses distributed across reefs in the Indo-Pacific region, the success of these slimy sucking lips is evident. Determining what triggered this unusual feeding trait is the pandora box the researchers are looking forward to opening.

“Tube lip wrasses have found a very creative way to overcome the corals defenses. How this mechanism happened in evolution? We really don’t know. But we know that these are the only group of fishes that have been able to evolve it. There could be others, but so far, this is the only one that we have found” Huertas says.

Story by Gabrielle Ahern

My interview with Victor Huertas will soon feature in the SaltyWaveBlue podcast series so stay tuned!