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.
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.
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.
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.
Much of the current regulation and mitigation of the effects of anthropogenic sound is based on a very limited dataset.Future regulation and mitigation must be approached from the perspective of the animals. Which sounds affect the animals adversely, and what is the nature of these effects?Considerable data (and funding to get that data) is needed, particularly for fishes and invertebrates, before regulation and mitigation can be properly applied.Regulators and investigators should work together to develop a plan of action that focuses on the most important questions, to inform ways to protect animals and develop appropriate mitigation and regulation, and to inform the most effective way(s) to answer those questions.Future work should focus on a limited number of species, key research questions, and experimental approaches that allow easy comparison of data across studies, species, and sound sources.
The behavior of wild, pelagic fish in response to sound playback was observed with a sonar/echo sounder. Schools of sprat Sprattus sprattus and mackerel Scomber scombrus were examined at a quiet ...coastal location. The fish were exposed to a short sequence of repeated impulsive sounds, simulating the strikes from a pile driver, at different sound pressure levels. The incidence of behavioral responses increased with increasing sound level. Sprat schools were more likely to disperse and mackerel schools more likely to change depth. The sound pressure levels to which the fish schools responded on 50% of presentations were 163.2 and 163.3 dB re 1 μPa peak-to-peak, and the single strike sound exposure levels were 135.0 and 142.0 dB re 1 μPa(2) s, for sprat and mackerel, respectively, estimated from dose response curves. For sounds leading to mackerel responses, particle velocity levels were also estimated. The method of observation by means of a sonar/echo sounder proved successful in examining the behavior of unrestrained fish exposed to different sound levels. The technique may allow further testing of the relationship between responsiveness, sound level, and sound characteristics for different types of man-made sound, for a variety of fish species under varied conditions.
In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are ...posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.
The expansion of shipping and aquatic industrial activities in recent years has led to growing concern about the effects of man-made sounds on aquatic life. Sources include (but are not limited to) ...pleasure boating, fishing, the shipping of goods, offshore exploration for oil and gas, dredging, construction of bridges, harbors, oil and gas platforms, wind farms and other renewable energy devices, and the use of sonar by commercial and military vessels. There are very substantial gaps in our understanding of the effects of these sounds, especially for fishes and invertebrates. Currently, it is almost impossible to come to clear conclusions on the nature and levels of man-made sound that have potential to cause effects upon these animals. In order to develop a better understanding of effects of man-made sound, this paper identifies the most critical information needs and data gaps on the effects of various sounds on fishes, fisheries, and invertebrates resulting from the use of sound-generating devices. It highlights the major issues and discusses the information currently available on each of the information needs and data gaps. The paper then identifies the critical questions concerning the effects of man-made sounds on aquatic life for which answers are not readily available and articulates the types of information needed to fulfill each of these drivers for information—the key information gaps. Finally, a list of priorities for research and development is presented.
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