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.

Coral reef fish – Butterflies of the oceans

Butterfly fish (Family Chaetodontidae) are one of the most conspicuous of the fish species inhabiting coral reefs worldwide, due to their beautiful colour, distinctive markings, morphology and interesting social behaviour. Butterfly fish species remain close to coral reefs all their lives as research shows these fish depend on coral species and other reef organisms for food, habitat and protection from predators. Generalist feeders (that rely on a variety of food sources in addition to coral species) are less common than butterfly fish that consume only corals and experience slower growth rates than their corallivorous counterparts.

Butterfly fish swimming in its coral reef habitat. Photo © Anje Ranneberg

Interestingly, some butterfly fish species have a preference for a particular species of coral so their habitats location might be linked to the type and amount of coral substrate present at various locations along the reef. The reefs exposure to the currents and the protection it provides against egg predators might also be reason’s influencing fish preference for a location over other sites. Studies have revealed some butterfly fish species have a home range they explore to forage for food.

As juveniles, butterfly fish have been observed to find a monogamous mate. This type of pairing early in development decreases the stress levels experienced by these fish, for example, they expend less energy defending their home range or competing with other butterfly fish to reproduce. The constraints that solitary fish or fish living in a harem experience, may play to their favour. Female territories have been observed close to the male, which allows the male to protect and maintain his territory, resulting in less energy being used, much like the monogamous pairs but with multiple chances for fertilising opportunities.

Coral reef habitat. Photo © Vincenzo Piazza 

Butterfly fish use complex forms of social and mating behaviour to exploit the ecological advantages available on the coral reef. Their courtship patterns are an interesting window to their survival. Some butterfly fish mate before sunset. This timing reflects their natural behavior but also increases the chances of egg survival from predation by other fish. Some rogue male butterfly fish are opportunistic and intrude on a spawning monogamous pair by attempting to fertilise the female’s eggs with their own gametes.

Once the eggs of butterfly fish hatch, larvae usually settle close to their native spawning grounds, but this can be a temporary strategy to avoid predators or to find food quickly while migrating to another site. Many view habitat destruction from storms and cyclones negatively, but in the marine environment they have a positive affect, because the amount of coral reef refuge for butterfly fish larvae to settle in increases.

Colour might also be a reason for the success of butterfly fish in coral reef environments. Butterfly fish species are well known for their beautiful markings, which might protect individuals from attack by their counterparts or assist mate recognition. Other cues butterfly fish use to identify their mates from other fish are the sounds they make, for example, some make grunting noises while others slap their tails. So a combination of colour and sound cues improves the success of mating, territorial protection and defence against predators. 

Butterfly fish are linked to coral reefs through their colour, morphology, social behavior, courtship, mating patterns and the sounds they make. Their dependence on coral species for food, protection and recruitment, highlights their potential as a coral reef health indicator species. Coral species are experiencing declines from the effects of warmer oceans, smothering from sediment, disturbance from infrastructure development and fishing pressures.

Green sea turtle swimming off the Hawaii Islands. Photo © Chris LaCroix

A combination of all these factors and pressures from the natural environment are creating extreme conditions coral species cannot withstand for long periods of time. Although present studies are working to identify tolerant species of coral that cope with more hostile environments, alternative methods can also be pursued, by protecting coral reefs through expanding marine parks and reducing the activities that are causing their decline both in the marine and terrestrial environments.

Research studies provide evidence of how coral reefs, other marine habitats and associated plants and animals are being affected. These studies have not just been completed in the last few years but over centuries. Considering the weight of evidence that is available to read; and the benefit provided by the natural environment, you have to wonder why the facts presented by scientific research to reduce negative activities are continually being ignored.

Butterfly fish are more than just a fish species swimming around coral reefs, they have developed different ways to communicate with one another, using colour, movement and sound, creating an unforgettable panorama of beauty on many levels.

Written by Gabrielle Ahern

Salty Wave Blue – Into all things ecology.

http://www.saltywave.blue

Follow @SaltyWaveBlue on @Instagram and @Twitter

If you would like to see images of  animals in their environment, especially butterfly fishes and coral species,  please take a look at my Pinterest site: 

https://www.pinterest.com/saltywave

COLOUR OF CLAMS

Clams and their beautiful coloured mantles are just one of the many amazing marine animals that attract millions of visitors each year to the Great Barrier Reef. I studied clam populations on reefs around Heron Island as an undergraduate Marine Studies student at the University of Queensland. It was a great opportunity to observe the variation in mantle colour across reef locations.

Clams belong to Class Bivalvia, Family Tridacnae, and range in size from 15 cm long in Tridacna crocea to more than one metre long in Tridacna gigas. Similar to corals, zooxanthellae (Symbiodinium microadriactum) live inside a clam’s tissues. These symbionts can also be found in gorgonians, sea anenomes and jellyfish. These zooxanthellae are the reason why clam behaviour is often compared to plants.

Just like plants, clams need sunlight. In the mantle, clams possess what are known as, eyespots or iridophores. These pigment cells can sense light conditions and trigger a response in the clam. For instance, if light is poor, the clam improves conditions for the zooxanthellae to photosynthesise by extending its mantle out or using its shell to reflect sunlight back onto the mantle, by holding its valves wide apart. If sunlight is too intense, the iridophores also protect the clam’s zooxanthellae from harmful ultraviolet radiation by reflecting light away.

Mantle colour of clam species is a poorly researched topic. The notion that mantle pigmentation in clams differs in clams across a coral reef has not been researched widely. Interestingly, studies have shown clams are sensitive to the blue (450nm), blue-green (490nm) and ultraviolet (360nm) colours in the spectrum. Light quality on the reef may affect mantle colour, with clams expressing different pigments, or perhaps a clam’s genetic adaptation to a particular reef habitat influences the type of zooxanthellae inhabiting its mantle tissues. I noted a trend in colour for different reef zones during my fieldwork and related this data to previous reports, which have suggested clams might share symbionts with other invertebrate species in a particular zone.

Further investigation into the mantle colour of clams by applying molecular biology might reveal why particular colour patterns occur. Research could also concentrate on how clams can adapt to changing light or temperature conditions by genetic variability.

Clams are quite a stable organism and can adapt to changes in their habitat over time. However, fishing pressure has dramatically reduced populations of clams in the pacific region, leading to the extinction of several species. Conservation methods that use aquaculture assist the remediation of wild clam populations on the reef and supply aquariums with different species.

Clams are interesting to observe in their natural environment. During my research, I noted variations in colour mantle between clam populations across the reef zones and between the two sites on Heron Island. While your exploring the reef, it is definitely a feature worth looking out for.

For more information, check out the world-wide-web.

Written by Gabrielle Ahern

Salty Wave Blue – Into all things ecology.

http://www.saltywave.blue

Follow @SaltyWaveBlue on @Instagram and @Twitter

If you would like to see beautiful images of clams in their coral reef habitat, please take a look at my Pinterest site: https://www.pinterest.com/saltywave