Fish hearing "specialization" - a re-evaluation.

Investigators working with fish bioacoustics used to refer to fishes that have a narrow hearing bandwidth and poor sensitivity as "hearing generalists" (or "non-specialists"), while fishes that could detect a wider hearing bandwidth and had greater sensitivity were referred to as specialists. However, as more was learned about fish hearing mechanism and capacities, these terms became hard to apply since it was clear there were gradations in hearing capabilities. Popper and Fay, in a paper in Hearing Research in 2011, proposed that these terms be dropped because of the gradation. While this was widely accepted by investigators, it is now apparent that the lack of relatively concise terminology for fish hearing capabilities makes it hard to discuss fish hearing. Thus, in this paper we resurrect the terms specialist and non-specialist but use them with modifiers to express the specific structure of function that is considered a specialization. Moreover, this resurrection recognizes that hearing specializations in fishes may not only be related to increased bandwidth and/or sensitivity, but to other, perhaps more important, aspects of hearing such as sound source localization, discrimination between sounds, and detection of sounds in the presence of masking signals.

Substrate vibrations and their potential effects upon fishes and invertebrates.

This paper reviews the nature of substrate vibration within aquatic environments where seismic interface waves may travel along the surface of the substrate, generating high levels of particle motion. There are, however, few data on the ambient levels of particle motion close to the seabed and within the substrates of lakes and rivers. Nor is there information on the levels and the characteristics of the particle motion generated by anthropogenic sources in and on the substrate, which may have major effects upon fishes and invertebrates, all of which primarily detect particle motion. We therefore consider how to monitor substrate vibration and describe the information gained from modeling it. Unlike most acoustic modeling, we treat the substrate as a solid. Furthermore, we use a model where the substrate stiffness increases with depth but makes use of a wave that propagates with little or no dispersion. This shows the presence of higher levels of particle motion than those predicted from the acoustic pressures, and we consider the possible effects of substrate vibration upon fishes and invertebrates. We suggest that research is needed to examine the actual nature of substrate vibration and its effects upon aquatic animals.

Sound detection by Atlantic cod: An overview.

The Atlantic cod (Gadus morhua) is among the commercially most important fish species in the world. Since sound plays such an important role in the lives of Atlantic cod and its related species, understanding of their bioacoustics is of great importance. Moreover, since cod are amenable to studies of hearing, especially in open bodies of water, they have the potential to become a "model species" for investigations of fish hearing. To serve as the basis for future studies, and to bring together what is now known about cod hearing, this paper reviews the literature to date. While there is some discussion of other species in the paper, the focus is upon what is already known about cod hearing, and what now needs to be known. An additional focus is on what knowledge of cod hearing tells about hearing in fishes in general.

Taking the Animals' Perspective Regarding Anthropogenic Underwater Sound.

Anthropogenic (man-made) sound has the potential to harm marine biota. Increasing concerns about these effects have led to regulation and mitigation, despite there being few data on which to base environmental management, especially for fishes and invertebrates. We argue that regulation and mitigation should always be developed by looking at potential effects from the perspectives of the animals and ecosystems exposed to the sounds. We contend that there is currently a need for far more data on which to base regulation and mitigation, as well as for deciding on future research priorities. This will require a process whereby regulators and researchers come together to identify and implement a strategy that links key scientific and regulatory questions.

How to set sound exposure criteria for fishes.

Underwater sounds from human sources can have detrimental effects upon aquatic animals, including fishes. Thus, it is important to establish sound exposure criteria for fishes, setting out those levels of sound from different sources that have detrimental effects upon them, in order to support current and future protective regulations. This paper considers the gaps in information that must be resolved in order to establish reasonable sound exposure criteria for fishes. The vulnerability of fishes is affected by the characteristics of underwater sounds, which must be taken into account when evaluating effects. The effects that need to be considered include death and injuries, physiological effects, and changes in behavior. Strong emphasis in assessing the effects of sounds has been placed upon the hearing abilities of fishes. However, although hearing has to be taken into account, other actual effects also have to be considered. This paper considers the information gaps that must be filled for the development of future guidelines and criteria.

The importance of underwater sounds to gadoid fishes.

The codfish family includes more than 500 species that vary greatly in their abundance in areas like the North Sea and are widely fished. Gadoids (codfish) gather at particular locations to spawn, where they exhibit complex reproductive behavior with visual and acoustic displays. Calls have been described from seven species, including the Atlantic cod and haddock. They vocalize by means of a specialized apparatus, consisting of rapidly contracting striated muscles (the drumming muscles) attached to the gas-filled swim bladder. Several gadoids, such as the ling and the Greenland cod, possess drumming muscles and are likely to make sounds. Non-vocal gadoids, such as the poor cod, lack these muscles. It is suggested that the sonic apparatus was present in the early species of the gadoids, with some species having lost their sonic ability. Interestingly, silent gadoids are mainly small schooling fishes. Gadoid species are most sensitive to sounds from 30 to 500 Hz. Gadoid hearing can be masked by ambient sound but also by anthropogenic sounds, which may therefore adversely affect their reproduction, with potential effects upon discrete local stocks. Listening for gadoid sounds provides a reliable, non-invasive way of locating spawning sites, which can enhance the protection of reproducing fish from human impacts.

Effects of sound exposure from a seismic airgun on heart rate, acceleration and depth use in free-swimming Atlantic cod and saithe.

Airguns used for offshore seismic exploration by the oil and gas industry contribute to globally increasing anthropogenic noise levels in the marine environment. There is concern that the omnidirectional, high intensity sound pulses created by airguns may alter fish physiology and behaviour. A controlled short-term field experiment was performed to investigate the effects of sound exposure from a seismic airgun on the physiology and behaviour of two socioeconomically and ecologically important marine fishes: the Atlantic cod (Gadus morhua) and saithe (Pollachius virens). Biologgers recording heart rate and body temperature and acoustic transmitters recording locomotory activity (i.e. acceleration) and depth were used to monitor free-swimming individuals during experimental sound exposures (18-60 dB above ambient). Fish were held in a large sea cage (50 m diameter; 25 m depth) and exposed to sound exposure trials over a 3-day period. Concurrently, the behaviour of untagged cod and saithe was monitored using video recording. The cod exhibited reduced heart rate (bradycardia) in response to the particle motion component of the sound from the airgun, indicative of an initial flight response. No behavioural startle response to the airgun was observed; both cod and saithe changed both swimming depth and horizontal position more frequently during sound production. The saithe became more dispersed in response to the elevated sound levels. The fish seemed to habituate both physiologically and behaviourally with repeated exposure. In conclusion, the sound exposures induced over the time frames used in this study appear unlikely to be associated with long-term alterations in physiology or behaviour. However, additional research is needed to fully understand the ecological consequences of airgun use in marine ecosystems.

An overview of fish bioacoustics and the impacts of anthropogenic sounds on fishes.

Fishes use a variety of sensory systems to learn about their environments and to communicate. Of the various senses, hearing plays a particularly important role for fishes in providing information, often from great distances, from all around these animals. This information is in all three spatial dimensions, often overcoming the limitations of other senses such as vision, touch, taste and smell. Sound is used for communication between fishes, mating behaviour, the detection of prey and predators, orientation and migration and habitat selection. Thus, anything that interferes with the ability of a fish to detect and respond to biologically relevant sounds can decrease survival and fitness of individuals and populations. Since the onset of the Industrial Revolution, there has been a growing increase in the noise that humans put into the water. These anthropogenic sounds are from a wide range of sources that include shipping, sonars, construction activities (e.g., wind farms, harbours), trawling, dredging and exploration for oil and gas. Anthropogenic sounds may be sufficiently intense to result in death or mortal injury. However, anthropogenic sounds at lower levels may result in temporary hearing impairment, physiological changes including stress effects, changes in behaviour or the masking of biologically important sounds. The intent of this paper is to review the potential effects of anthropogenic sounds upon fishes, the potential consequences for populations and ecosystems and the need to develop sound exposure criteria and relevant regulations. However, assuming that many readers may not have a background in fish bioacoustics, the paper first provides information on underwater acoustics, with a focus on introducing the very important concept of particle motion, the primary acoustic stimulus for all fishes, including elasmobranchs. The paper then provides background material on fish hearing, sound production and acoustic behaviour. This is followed by an overview of what is known about effects of anthropogenic sounds on fishes and considers the current guidelines and criteria being used world-wide to assess potential effects on fishes. Most importantly, the paper provides the most complete summary of the effects of anthropogenic noise on fishes to date. It is also made clear that there are currently so many information gaps that it is almost impossible to reach clear conclusions on the nature and levels of anthropogenic sounds that have potential to cause changes in animal behaviour, or even result in physical harm. Further research is required on the responses of a range of fish species to different sound sources, under different conditions. There is a need both to examine the immediate effects of sound exposure and the longer-term effects, in terms of fitness and likely impacts upon populations.

Clinker: visualizing fusion genes detected in RNA-seq data.

Background: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-sequencing (RNA-seq) data, visualizing these transcripts and their supporting reads remains challenging. Findings: Clinker is a bioinformatics tool written in Python, R, and Bpipe that leverages the superTranscript method to visualize fusion genes. We demonstrate the use of Clinker to obtain interpretable visualizations of the RNA-seq data that lead to fusion calls. In addition, we use Clinker to explore multiple fusion transcripts with novel breakpoints within the P2RY8-CRLF2 fusion gene in B-cell acute lymphoblastic leukemia. Conclusions: Clinker is freely available software that allows visualization of fusion genes and the RNA-seq data used in their discovery.

The importance of particle motion to fishes and invertebrates.

This paper considers the importance of particle motion to fishes and invertebrates and the steps that need to be taken to improve knowledge of its effects. It is aimed at scientists investigating the impacts of sounds on fishes and invertebrates but it is also relevant to regulators, those preparing environmental impact assessments, and to industries creating underwater sounds. The overall aim of this paper is to ensure that proper attention is paid to particle motion as a stimulus when evaluating the effects of sound upon aquatic life. Directions are suggested for future research and planning that, if implemented, will provide a better scientific basis for dealing with the impact of underwater sounds on marine ecosystems and for regulating those human activities that generate such sounds. The paper includes background material on underwater acoustics, focusing on particle motion; the importance of particle motion to fishes and invertebrates; and sound propagation through both water and the substrate. Consideration is then given to the data gaps that must be filled in order to better understand the interactions between particle motion and aquatic animals. Finally, suggestions are provided on how to increase the understanding of particle motion and its relevance to aquatic animals.

Directional hearing and sound source localization by fishes.

Directional hearing may enable fishes to seek out prey, avoid predators, find mates, and detect important spatial cues. Early sound localization experiments gave negative results, and it was thought unlikely that fishes utilized the same direction-finding mechanisms as terrestrial vertebrates. However, fishes swim towards underwater sound sources, and some can discriminate between sounds from different directions and distances. The otolith organs of the inner ear detect the particle motion components of sound, acting as vector detectors through the presence of sensory hair cells with differing orientation. However, many questions remain on inner ear functioning. There are problems in understanding the actual mechanisms involved in determining sound direction and distance. Moreover, very little is still known about the ability of fishes to locate sound sources in three-dimensional space. Do fishes swim directly towards a source, or instead "sample" sound levels while moving towards the source? To what extent do fishes utilize other senses and especially vision in locating the source? Further behavioral studies of free-swimming fishes are required to provide better understanding of how fishes might actually locate sound sources. In addition, more experiments are required on the auditory mechanism that fishes may utilize.

Snapshot recordings provide a first description of the acoustic signatures of deeper habitats adjacent to coral reefs of Moorea.

Acoustic recording has been recognized as a valuable tool for non-intrusive monitoring of the marine environment, complementing traditional visual surveys. Acoustic surveys conducted on coral ecosystems have so far been restricted to barrier reefs and to shallow depths (10-30 m). Since they may provide refuge for coral reef organisms, the monitoring of outer reef slopes and describing of the soundscapes of deeper environment could provide insights into the characteristics of different biotopes of coral ecosystems. In this study, the acoustic features of four different habitats, with different topographies and substrates, located at different depths from 10 to 100 m, were recorded during day-time on the outer reef slope of the north Coast of Moorea Island (French Polynesia). Barrier reefs appeared to be the noisiest habitats whereas the average sound levels at other habitats decreased with their distance from the reef and with increasing depth. However, sound levels were higher than expected by propagation models, supporting that these habitats possess their own sound sources. While reef sounds are known to attract marine larvae, sounds from deeper habitats may then also have a non-negligible attractive potential, coming into play before the reef itself.

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes.

Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a single sequence. The Lace software is provided to construct superTranscripts from any set of transcripts, including de novo assemblies. We demonstrate how superTranscripts enable visualisation, variant detection and differential isoform detection in non-model organisms. We further use Lace to combine reference and assembled transcriptomes for chicken and recover hundreds of gaps in the reference genome.

Acoustic indices provide information on the status of coral reefs: an example from Moorea Island in the South Pacific.

Different marine habitats are characterised by different soundscapes. How or which differences may be representative of the habitat characteristics and/or community structure remains however to be explored. A growing project in passive acoustics is to find a way to use soundscapes to have information on the habitat and on its changes. In this study we have successfully tested the potential of two acoustic indices, i.e. the average sound pressure level and the acoustic complexity index based on the frequency spectrum. Inside and outside marine protected areas of Moorea Island (French Polynesia), sound pressure level was positively correlated with the characteristics of the substratum and acoustic complexity was positively correlated with fish diversity. It clearly shows soundscape can be used to evaluate the acoustic features of marine protected areas, which presented a significantly higher ambient sound pressure level and were more acoustically complex than non-protected areas. This study further emphasizes the importance of acoustics as a tool in the monitoring of marine environments and in the elaboration and management of future conservation plans.

Effects of Exposure to the Sound from Seismic Airguns on Pallid Sturgeon and Paddlefish.

This study examined the effects of exposure to a single acoustic pulse from a seismic airgun array on caged endangered pallid sturgeon (Scaphirhynchus albus) and on paddlefish (Polyodon spathula) in Lake Sakakawea (North Dakota, USA). The experiment was designed to detect the onset of physiological responses including minor to mortal injuries. Experimental fish were held in cages as close as 1 to 3 m from the guns where peak negative sound pressure levels (Peak- SPL) reached 231 dB re 1 µPa (205 dB re 1 µPa2·s sound exposure level [SEL]). Additional cages were placed at greater distances in an attempt to develop a dose-response relationship. Treatment and control fish were then monitored for seven days, euthanized, and necropsied to determine injuries. Necropsy results indicated that the probability of delayed mortality associated with pulse pressure following the seven day monitoring period was the same for exposed and control fish of both species. Exposure to a single pulse from a small air gun array (10,160 cm3) was not lethal for pallid sturgeon and paddlefish. However, the risks from exposure to multiple sounds and to sound exposure levels that exceed those reported here remain to be examined.

Auditory sensitivity in aquatic animals.

A critical concern with respect to marine animal acoustics is the issue of hearing "sensitivity," as it is widely used as a criterion for the onset of noise-induced effects. Important aspects of research on sensitivity to sound by marine animals include: uncertainties regarding how well these species detect and respond to different sounds; the masking effects of man-made sounds on the detection of biologically important sounds; the question how internal state, motivation, context, and previous experience affect their behavioral responses; and the long-term and cumulative effects of sound exposure. If we are to better understand the sensitivity of marine animals to sound we must concentrate research on these questions. In order to assess population level and ecological community impacts new approaches can possibly be adopted from other disciplines and applied to marine fauna.