Fish bioacoustics

The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history

The pinfish (Lagodon rhomboides) is an ecologically, economically, and culturally relevant member of the family Sparidae, playing crucial roles in the marine food webs of the western Atlantic Ocean and Gulf of Mexico. Despite their high abundance and ecological importance, there is a scarcity of genomic resources for this species. We assembled and annotated a chromosome-scale genome for the pinfish, resulting in a highly contiguous 785 Mb assembly of 24 scaffolded chromosomes. The high-quality assembly contains 98.9% complete BUSCOs and shows strong synteny to other chromosome-scale genomes of fish in the family Sparidae, with a limited number of large-scale genomic rearrangements. Leveraging this new genomic resource, we found evidence of significant expansions of dietary gene families over the evolutionary history of the pinfish, which may be associated with an ontogenetic shift from carnivory to herbivory seen in this species. Estimates of historical patterns of population demography using this new reference genome identified several periods of population growth and contraction which were associated with ancient climatic shifts and sea level changes. This genome serves as a valuable reference for future studies of population genomics and differentiation and provides a much-needed genomic resource for this western Atlantic sparid.

Acoustic signatures in Mexican cavefish populations inhabiting different caves

Complex patterns of acoustic communication exist throughout the animal kingdom, including underwater. The river-dwelling and the Pachón cave-adapted morphotypes of the fish Astyanax mexicanus are soniferous and share a repertoire of sounds. Their function and significance is mostly unknown. Here, we explored whether and how sounds produced by blind cavefishes inhabiting different Mexican caves may vary. We compared "Clicks" and "Serial Clicks" produced by cavefish in six different caves distributed in three mountain ranges in Mexico. We also sampled laboratory-bred cavefish lines originating from four of these caves. Sounds were extracted and analyzed using both a manual method and a machine learning-based automation tool developed in-house. Multi-parametric analyses suggest wild cave-specific acoustic signatures, or "accents". An acoustic code also existed in laboratory cavefish lines, suggesting a genetic basis for the evolution of this trait. The variations in acoustic parameters between caves of origin did not seem related to fish phenotypes, phylogeography or ecological conditions. We propose that the evolution of such acoustic signatures would progressively lead to the differentiation of local accents that may prevent interbreeding and thus contribute to speciation.

Invited review - the effects of anthropogenic abiotic stressors on the sensory systems of fishes

Climate change is a growing global issue with many countries and institutions declaring a climate state of emergency. Excess CO₂ from anthropogenic sources and changes in land use practices are contributing to many detrimental changes, including increased global temperatures, ocean acidification and hypoxic zones along coastal habitats. All senses are important for aquatic animals, as it is how they can perceive and respond to their environment. Some of these environmental challenges have been shown to impair their sensory systems, including the olfactory, visual, and auditory systems. While most of the research is focused on how ocean acidification affects olfaction, there is also evidence that it negatively affects vision and hearing. The effects that temperature and hypoxia have on the senses have also been investigated, but to a much lesser extent in comparison to ocean acidification. This review assembles the known information on how these anthropogenic challenges affect the sensory systems of fishes, but also highlights what gaps in knowledge remain with suggestions for immediate action. Olfaction, vision, otolith, pH, freshwater, seawater, marine, central nervous system, electrophysiology, mechanism.

Vocal repertoire and sound characteristics in the variegated cardinalfish, Fowleria variegata (Pisces: Apogonidae)

The variegated cardinalfish Fowleria variegata produces grunt and hoot calls during agonistic and courtship interactions. Both sounds are tonal and occur as single and multiunit calls. Grunts are of short duration with variable frequency spectra. Hoots are longer, have a higher fundamental frequency, and a more developed harmonic structure. Agonistic grunt calls and short hoot calls (1-2 hoots) are produced during chases and when striking an individual or a mirror. Grunts are produced primarily in male-female and mirror-image encounters, and short hoot calls are produced primarily in male-male interactions. During the reproductive period, long hoot calls (three and four hoots) are the main sound type in a mix-sexed tank and at Dongsha Atoll. These are likely produced by males because isolated females are silent, and isolated males emit long hoot calls. Courtship interactions are mostly silent, and males are silent after capturing eggs for oral brooding. Tank sounds peak at dusk to early evening with a smaller peak at noon, although there are dusk and dawn peaks at Dongsha Atoll. Tank sounds exhibit a semilunar rhythm with peaks at the new and full moon. Other cardinalfish species from the atoll produce grunts but not hoot calls.

Temperature (but not acclimation) affects hearing in fishes adapted to different temperature regimes

Temperature affects various metabolic and physiological processes in ectothermic animals, including auditory systems. The current study investigates the effect of temperature and thermal acclimation time on hearing sensitivities in a eurythermal and a stenothermal fish possessing accessory hearing structures. Using the auditory evoked potential (AEP) recording technique, we determined thresholds from 0.1 to 4 kHz and peak latencies of AEP-waveforms in response to a click stimulus. The goldfish Carassius auratus was chosen as a model for eurythermal and the Amazonian catfish Megalodoras uranoscopus as a model for stenothermal species. Both species were tested at two different temperatures (C. auratus: 15 °C and 25 °C, M. uranoscopus: 22 °C and 30 °C) and acclimation periods, within 22 h (unacclimated) or three to four weeks (acclimated) after reaching the target temperature. A frequency-dependent increase in auditory sensitivity and a decrease of peak latencies was recorded in both species at higher temperatures, independent of acclimation time. The change in hearing thresholds per degree Celsius was more pronounced in the stenothermal catfish. The data indicate that higher temperatures improved hearing (lower thresholds, shorter latencies), whereas acclimation had no effect on hearing in either species. The latter data contradict previous findings in the eurythermal channel catfish Ictalurus punctatus in which acclimation slightly improved hearing when raising the temperatures. A comparison of changes in hearing sensitivity per degree Celsius of all seven species tested so far revealed no differences between eurythermal and stenothermal species.

Coordinated gas release among the physostomous fish sprat (Sprattus sprattus)

Previous experimental studies suggest that the production of sound associated with expelling gas from an open swimbladder may play a role in communication. This would suggest non-random gas release. We used deployed echosounders to study patterns of gas release among a fjord population of sprat (Sprattus sprattus). The echosounder records concurrently revealed individual fish and their release of gas. The gas release primarily occurred at night, partly following recurrent temporal patterns, but also varying between nights. In testing for non-randomness, we formulated a data-driven simulation approach. Non-random gas release scaled with the length of the analyzed time intervals from 1 min to 6 h, and above 30 min the release events in more than 50% of the intervals were significantly connected.

Ocean acidification effects on fish hearing

Humans are rapidly changing the marine environment through a multitude of effects, including increased greenhouse gas emissions resulting in warmer and acidified oceans. Elevated CO₂ conditions can cause sensory deficits and altered behaviours in marine organisms, either directly by affecting end organ sensitivity or due to likely alterations in brain chemistry. Previous studies show that auditory-associated behaviours of larval and juvenile fishes can be affected by elevated CO₂ (1000 µatm). Here, using auditory evoked potentials (AEP) and micro-computer tomography (microCT) we show that raising juvenile snapper, Chrysophyrs auratus, under predicted future CO₂ conditions resulted in significant changes to their hearing ability. Specifically, snapper raised under elevated CO₂ conditions had a significant decrease in low frequency (less than 200 Hz) hearing sensitivity. MicroCT demonstrated that these elevated CO₂ snapper had sacculus otolith's that were significantly larger and had fluctuating asymmetry, which likely explains the difference in hearing sensitivity. We suggest that elevated CO₂ conditions have a dual effect on hearing, directly effecting the sensitivity of the hearing end organs and altering previously described hearing induced behaviours. This is the first time that predicted future CO₂ conditions have been empirically linked through modification of auditory anatomy to changes in fish hearing ability. Given the widespread and well-documented impact of elevated CO₂ on fish auditory anatomy, predictions of how fish life-history functions dependent on hearing may respond to climate change may need to be reassessed.

A Review on Fish Sensory Systems and Amazon Water Types With Implications to Biodiversity

The Amazon has the highest richness of freshwater organisms in the world, which has led to a multitude of hypotheses on the mechanisms that generated this biodiversity. However, most of these hypotheses focus on the spatial distance of populations, a framework that fails to provide an explicit mechanism of speciation. Ecological conditions in Amazon freshwaters can be strikingly distinct, as it has been recognized since Alfred Russel Wallace’s categorization into black, white, and blue (= clear) waters. Water types reflect differences in turbidity, dissolved organic matter, electrical conductivity, pH, amount of nutrients and lighting environment, characteristics that directly affect the sensory abilities of aquatic organisms. Since natural selection drives evolution of sensory systems to function optimally according to environmental conditions, the sensory systems of Amazon freshwater organisms are expected to vary according to their environment. When differences in sensory systems affect chances of interbreeding between populations, local adaptations may result in speciation. Here, we briefly present the limnologic characteristics of Amazonian water types and how they are expected to influence photo-, chemical-, mechano-, and electro-reception of aquatic organisms, focusing on fish. We put forward that the effect of different water types on the adaptation of sensory systems is an important mechanism that contributed to the evolution of fish diversity. We point toward underexplored research perspectives on how divergent selection may act on sensory systems and thus contribute to the origin and maintenance of the biodiversity of Amazon aquatic environments.

Temperature affects sound production in fish with two sets of sonic organs: The Pictus cat

Sound communication is affected by ambient temperature in ectothermic animals including fishes. The present study examines the effects of temperature on acoustic signaling in a fish species possessing two different sound-generating mechanisms. The Amazonian Pictus catfish Pimelodus pictus produces low-frequency harmonic sounds (swimbladder drumming muscles) and high-frequency stridulation sounds (rubbing pectoral fin spines in the pectoral girdle). Sounds of 15 juveniles were recorded when hand-held after three weeks of acclimation at 30 °C, 22 °C and again 30 °C. The following sound characteristics were investigated: calling activity, sound duration, fundamental frequency of drumming sounds and dominant frequency of stridulation sounds. The number of both sound types produced within the first minute of experiments did not change with temperature. In contrast, sound duration was significantly shorter at 30 °C than at 22 °C (drumming: 78-560 ms; stridulation: 23-96 ms). The fundamental frequency of drumming sounds and thus the drumming muscle contraction rate varied from 127 Hz to 242 Hz and increased with temperature. The dominant frequency of broadband stridulation sounds ranged from 1.67 kHz to 3.39 kHz and was unaffected by temperature changes. Our data demonstrate that temperature affects acoustic signaling in P. pictus, although the changes differed between sound characteristics and sound type. The effects vary from no change in calling activity and dominant frequency, to an increase in fundamental frequency and shortened duration of both sound types. Together with the known effects of temperature on hearing in the Pictus cat, the present results indicate that global warming may affect acoustic communication in fishes.

Evolution of acoustic communication in blind cavefish

Acoustic communication allows the exchange of information within specific contexts and during specific behaviors. The blind, cave-adapted and the sighted, river-dwelling morphs of the species Astyanax mexicanus have evolved in markedly different environments. During their evolution in darkness, cavefish underwent a series of morphological, physiological and behavioral changes, allowing the study of adaptation to drastic environmental change. Here we discover that Astyanax is a sonic species, in the laboratory and in the wild, with sound production depending on the social contexts and the type of morph. We characterize one sound, the "Sharp Click", as a visually-triggered sound produced by dominant surface fish during agonistic behaviors and as a chemosensory-, food odor-triggered sound produced by cavefish during foraging. Sharp Clicks also elicit different reactions in the two morphs in play-back experiments. Our results demonstrate that acoustic communication does exist and has evolved in cavefish, accompanying the evolution of its behaviors.

Disturbance calls of five migratory Characiformes species and advertisement choruses in Amazon spawning sites

Species-specific disturbance calls of five commercially-important characiform species are described, the Curimatidae commonly called branquinhas: Potamorhina latior, Potamorhina altamazonica and Psectrogaster amazonica; Prochilodontidae: jaraquí Semaprochilodus insignis and curimatã Prochilodus nigricans. All species have a two-chambered swimbladder and the sonic mechanism, present exclusively in males, utilises hypertrophied red muscles between ribs that adhere to the anterior chamber. The number of muscles is unusually plastic across species and varies from 1 to 4 pairs suggesting considerable evolution in an otherwise conservative system. Advertisement calls are produced in river confluences in the Madeira Basin during the high-water mating season (January-February). Disturbance calls and sampling allowed recognition of underwater advertisement choruses from P. latior, S. insignis and P. nigricans. The advertisement calls of the first two species have largely similar characteristics and they mate in partially overlapping areas in the Guaporé River. However, P. latior sounds have a lower dominant frequency and it prefers to call from river confluences whereas S. insignis shoals occur mostly in the main river channel adjacent to the confluence. These results help identify and differentiate underwater sounds and evaluate breeding areas during the courtship of commercially important characids likely to be affected by two hydroelectric dams.

The effect of underwater sounds on shark behaviour

The effect of sound on the behaviour of sharks has not been investigated since the 1970s. Sound is, however, an important sensory stimulus underwater, as it can spread in all directions quickly and propagate further than any other sensory cue. We used a baited underwater camera rig to record the behavioural responses of eight species of sharks (seven reef and coastal shark species and the white shark, Carcharodon carcharias) to the playback of two distinct sound stimuli in the wild: an orca call sequence and an artificially generated sound. When sounds were playing, reef and coastal sharks were less numerous in the area, were responsible for fewer interactions with the baited test rigs, and displayed less ‘inquisitive’ behaviour, compared to during silent control trials. White sharks spent less time around the baited camera rig when the artificial sound was presented, but showed no significant difference in behaviour in response to orca calls. The use of the presented acoustic stimuli alone is not an effective deterrent for C. carcharias. The behavioural response of reef sharks to sound raises concern about the effects of anthropogenic noise on these taxa.

Ecology of sound communication in fishes

Fishes communicate acoustically under ecological constraints which may modify or hinder signal transmission and detection and may also be risky. This makes it important to know if and to what degree fishes can modify acoustic signalling when key ecological factors-predation pressure, noise and ambient temperature-vary. This paper reviews short-time effects of the first two factors; the third has been reviewed recently (Ladich, 2018). Numerous studies have investigated the effects of predators on fish behaviour, but only a few report changes in calling activity when hearing predator calls as demonstrated when fish responded to played-back dolphin sounds. Furthermore, swimming sounds of schooling fish may affect predators. Our knowledge on adaptations to natural changes in ambient noise, for example caused by wind or migration between quiet and noisier habitats, is limited. Hearing abilities decrease when ambient noise levels increase (termed masking), in particular in taxa possessing enhanced hearing abilities. High natural and anthropogenic noise regimes, for example vessel noise, alter calling activity in the field and laboratory. Increases in sound pressure levels (Lombard effect) and altered temporal call patterns were also observed, but no switches to higher sound frequencies. In summary, effects of predator calls and noise on sound communication are described in fishes, yet sparsely in contrast to songbirds or whales. Major gaps in our knowledge on potential negative effects of noise on acoustic communication call for more detailed investigation because fishes are keystone species in many aquatic habitats and constitute a major source of protein for humans.

Hearing capacities and morphology of the auditory system in Serrasalmidae (Teleostei: Otophysi)

Like all otophysan fishes, serrasalmids (piranhas and relatives) possess a Weberian apparatus that improves their hearing capacities. We compared the hearing abilities among eight species of serrasalmids having different life-history traits: herbivorous vs. carnivorous and vocal vs. mute species. We also made 3D reconstructions of the auditory system to detect potential morphological variations associated with hearing ability. The hearing structures were similar in overall shape and position. All the species hear in the same frequency range and only slight differences were found in hearing thresholds. The eight species have their range of best hearing in the lower frequencies (50–900 Hz). In vocal serrasalmids, the range of best hearing covers the frequency spectrum of their sounds. However, the broad overlap in hearing thresholds among species having different life-history traits (herbivorous vs. carnivorous and vocal vs. non-vocal species) suggests that hearing ability is likely not related to the capacity to emit acoustic signals or to the diet, i.e. the ability to detect sounds is not associated with a given kind of food. The inner ear appears to be highly conservative in this group suggesting that it is shaped by phylogenetic history or by other kinds of constraints such as predator avoidance.

Sound production in Japanese medaka (Oryzias latipes) and its alteration by exposure to aldicarb and copper sulfate

This study is the first to report sound production in Japanese medaka (Oryzias latipes). Sound production was affected by exposure to the carbamate insecticide (aldicarb) and heavy-metal compound (copper sulfate). Medaka were exposed at four concentrations (aldicarb: 0, 0.25, 0.5, and 1 mg L^-1; copper sulfate: 0, 0.5, 1, and 2 mg L^-1), and sound characteristics were monitored for 5 h after exposure. We observed constant average interpulse intervals (approx 0.2 s) in all test groups before exposure, and in the control groups throughout the experiment. The average interpulse interval became significantly longer during the recording periods after 50 min of exposure to aldicarb, and reached a length of more than 0.3 s during the recording periods after 120 min exposure. Most medaka fish stopped to produce sound after 50 min of exposure to copper sulfate at 1 and 2 mg L^-1, resulting in significantly declined number of sound pulses and pulse groups. Relative shortened interpulse intervals of sound were occasionally observed in medaka fish exposed to 0.5 mg L^-1 copper sulfate. These alternations in sound characteristics due to toxicants exposure suggested that they might impair acoustic communication of medaka fish, which may be important for their reproduction and survival. Our results suggested that using acoustic changes of medaka has potential to monitor precipitate water pollutions, such as intentional poisoning or accidental leakage of industrial waste.

Acoustic communication in terrestrial and aquatic vertebrates

Sound propagates much faster and over larger distances in water than in air, mainly because of differences in the density of these media. This raises the question of whether terrestrial (land mammals, birds) and (semi-)aquatic animals (frogs, fishes, cetaceans) differ fundamentally in the way they communicate acoustically. Terrestrial vertebrates primarily produce sounds by vibrating vocal tissue (folds) directly in an airflow. This mechanism has been modified in frogs and cetaceans, whereas fishes generate sounds in quite different ways mainly by utilizing the swimbladder or pectoral fins. On land, vertebrates pick up sounds with light tympana, whereas other mechanisms have had to evolve underwater. Furthermore, fishes differ from all other vertebrates by not having an inner ear end organ devoted exclusively to hearing. Comparing acoustic communication within and between aquatic and terrestrial vertebrates reveals that there is no ‘aquatic way’ of sound communication, as compared with a more uniform terrestrial one. Birds and mammals display rich acoustic communication behaviour, which reflects their highly developed cognitive and social capabilities. In contrast, acoustic signaling seems to be the exception in fishes, and is obviously limited to short distances and to substrate-breeding species, whereas all cetaceans communicate acoustically and, because of their predominantly pelagic lifestyle, exploit the benefits of sound propagation in a dense, obstacle-free medium that provides fast and almost lossless signal transmission.

Animated images in the analysis of zebrafish behavior

This invited review is based upon a recent oral paper I presented at the Virtual Reality Symposium of the 34th International Ethological Conference (2015, Cairns, Australia), and as such it describes studies conducted mainly in my own laboratory. It reviews how we utilized visual stimuli for inducing behavioral responses in the zebrafish with a focus on shoaling, group forming behavior. The zebrafish is gaining increasing popularity in neuroscience. With this interest, its behavior is also more frequently studied. One of the many advantages of the zebrafish over traditional laboratory rodents is that this species is diurnal, and it relies heavily upon its visual system. Thus, similarly to our own species, zebrafish respond to visual stimuli in a robust and easily quantifiable manner. For the past decade, we have been exploring how to use such visual stimuli, and have developed numerous paradigms with which we can induce and quantify a variety of behavioral responses, including shoaling. This review summarizes some of these studies, and discusses questions including whether one should use live fish as stimulus, whether and how one could present animated (moving images) of fish, and how one could optimize a range of stimulus presentation parameters to elicit the most robust responses in zebrafish. Although the zebrafish is a relative newcomer in ethology and behavioral neuroscience, and although many of our findings only represent the first steps in this research, our results suggest that the behavioral analysis of the zebrafish will have an important place in biomedical research.

Son et lumière: Sound and light effects on spatial distribution and swimming behavior in captive zebrafish

Aquatic and terrestrial habitats are heterogeneous by nature with respect to sound and light conditions. Fish may extract signals and exploit cues from both ambient modalities and they may also select their sound and light level of preference in free-ranging conditions. In recent decades, human activities in or near water have altered natural soundscapes and caused nocturnal light pollution to become more widespread. Artificial sound and light may cause anxiety, deterrence, disturbance or masking, but few studies have addressed in any detail how fishes respond to spatial variation in these two modalities. Here we investigated whether sound and light affected spatial distribution and swimming behavior of individual zebrafish that had a choice between two fish tanks: a treatment tank and a quiet and light escape tank. The treatments concerned a 2 × 2 design with noisy or quiet conditions and dim or bright light. Sound and light treatments did not induce spatial preferences for the treatment or escape tank, but caused various behavioral changes in both spatial distribution and swimming behavior within the treatment tank. Sound exposure led to more freezing and less time spent near the active speaker. Dim light conditions led to a lower number of crossings, more time spent in the upper layer and less time spent close to the tube for crossing. No interactions were found between sound and light conditions. This study highlights the potential relevance for studying multiple modalities when investigating fish behavior and further studies are needed to investigate whether similar patterns can be found for fish behavior in free-ranging conditions.

Methods to study the development, anatomy, and function of the zebrafish inner ear across the life course

The inner ear is a remarkably intricate structure able to detect sound, motion, and gravity. During development of the zebrafish embryo, the ear undergoes dynamic morphogenesis from a simple epithelial vesicle into a complex labyrinth, consisting of three semicircular canals and three otolithic sensory organs, each with an array of differentiated cell types. This microcosm of biology has led to advances in understanding molecular and cellular changes in epithelial patterning and morphogenesis, through to mechanisms of mechanosensory transduction and the origins of reflexive behavior. In this chapter, we describe different methods to study the zebrafish ear, including high-speed imaging of otic cilia, confocal microscopy, and light-sheet fluorescent microscopy. Many dyes, antibodies, and transgenic lines for labeling the ear are available, and we provide a comprehensive review of these resources. The developing ear is amenable to genetic, chemical, and physical manipulations, including injection and transplantation. Chemical modulation of developmental signaling pathways has paved the way for zebrafish to be widely used in drug discovery. We describe two chemical screens with relevance to the ear: a fluorescent-based screen for compounds that protect against ototoxicity, and an in situ-based screen for modulators of a signaling pathway involved in semicircular canal development. We also describe methods for dissection and imaging of the adult otic epithelia. We review both manual and automated methods to test the function of the inner ear and lateral line, defects in which can lead to altered locomotor behavior. Finally, we review a collection of zebrafish models that are generating new insights into human deafness and vestibular disorders.

Evidence for contact calls in fish: conspecific vocalisations and ambient soundscape influence group cohesion in a nocturnal species

Soundscapes provide a new tool for the study of fish communities. Bigeyes (Pempheris adspersa) are nocturnal planktivorous reef fish, feed in loose shoals and are soniferous. These vocalisations have been suggested to be contact calls to maintain group cohesion, however direct evidence for this is absent, despite the fact that contact calls are well documented for many other vertebrates, including marine mammals. For fish, direct evidence for group cohesion signals is restricted to the use of visual and hydrodynamic cues. In support of adding vocalisation as a contributing cue, our laboratory experiments show that bigeyes significantly increased group cohesion when exposed to recordings of ambient reef sound at higher sound levels while also decreasing vocalisations. These patterns of behaviour are consistent with acoustic masking. When exposed to playback of conspecific vocalisations, the group cohesion and vocalisation rates of bigeyes both significantly increased. These results provide the first direct experimental support for the hypotheses that vocalisations are used as contact calls to maintain group cohesion in fishes, making fish the evolutionarily oldest vertebrate group in which this phenomenon has been observed, and adding a new dimension to the interpretation of nocturnal reef soundscapes.