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This paper is not subject to U.S. copyright. The definitive version was published in ICES Journal of Marine Science 74 (2017): 2249–2261, doi:10.1093/icesjms/fsx050.

© International Council for the Exploration of the Sea, 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ICES Journal of Marine Science 74 (2017): 2262–2275, doi:10.1093/icesjms/fsx155.

A debate has developed over the ecosystem consequences following the collapse of Atlantic cod throughout the coastal waters of eastern Canada. The explosive increase in pelagic fish abundance in scientific bottom-trawl catches on the eastern Scotian Shelf has been interpreted as being due to either (i) a “pelagic outburst” of forage fish abundance resulting from predator release or conversely (ii) a change in pelagic fish vertical distribution leading to a “suprabenthic habitat occupation” thereby increasing their availability to bottom trawls. These two interpretations have diametrically opposing ecological consequences and suggest different management strategies for these important forage fish species. We argue that an objective evaluation of the available evidence supports the hypothesis that the abundance of forage fish has not increased in response to the demise of cod and other top predators, and the reliance on a single sampling gear with low catchability has biased and will continue to bias the interpretation of demographic trends of pelagic fish populations. We advocate that multiple sampling technologies providing alternative perspectives are needed for the monitoring and management of the various trophic levels if we are to achieve a balanced and objective understanding of marine ecosystems.

We describe a unique survey method that is able to cover a wide spatial and temporal range at a low cost. We utilised 10 individual small fishing vessels (lobster vessels) as acoustic research platforms to systematically survey a coastal population of Atlantic herring ( Clupea harengus) in the Gulf of Maine. We examined 38 transects spanning more than 200 miles of coastline. Due to the low cost of chartering the vessels, the survey was repeated weekly for nine weeks, resulting in over 2300 nautical miles of on-transect data. We calibrated single beam systems using a split beam guiding transducer to increase our confidence in the accuracy of the data and allow inter-ship comparisons. Although only one year of data has been analysed, the large spatial and temporal coverage of this survey provides preliminary information on herring population dynamics including spatial distribution throughout the survey area, timing of spawning and habitat associations of spawning aggregations. This survey will provide the template for longer term monitoring of herring spawning dynamics in Coastal Maine and how this may respond to climate and ocean variability.

The National Oceanographic and Atmospheric Administration (NOAA) uses water column sonar data to assess physical and biological characteristics from the ocean surface to the seabed. Acoustic surveys produce large volumes of data that can deliver valuable information beyond their original collection purpose if the data are properly managed, discoverable, and accessible to the public. NOAA's National Centers for Environmental Information, in partnership with NOAA's National Marine Fisheries Service and the University of Colorado, have created a national archive for water column sonar data to help achieve these goals. Through these efforts, over 21 TB of sonar data are now publicly available. Raw sonar files are difficult to interpret due to their size, complexity, and proprietary format. In order for users to understand the quality and composition of large volumes of archived data more easily, several visualization products were explored. Three processing methods were applied to multifrequency single-beam data (Simrad EK60) collected off the US northwest coast between 2007 and 2013. One method illustrates these complex data in a single image using a novel colour scale [multifrequency single-beam imaging (MFSBI)], another examines the nautical area scattering coefficients between two frequencies (ΔNASC), and the third indices the data into acoustic classifications [multifrequency indicator (MFI)]. The ability to apply the algorithms efficiently to multiyear datasets was explored. MFSBI proved effective at conveying the composition of the data and was easily adaptable to automated processing. ΔNASC, which required manual seabed corrections, illustrated a generalized pattern for changes in the water column across the shelf. MFI provided an empirically based statistical approach but will require more effort in the near term to evaluate and assess the accuracy and precision of each classification. Overall, spatio-temporal patterns of the acoustic backscatter identified large interannual variations in composition with the continental shelf break often playing a key role in attracting biological assemblages.

Atlantic herring (Clupea harengus) in the Gulf of Maine were surveyed using fisheries-independent systematic and stratified-random surveys conducted annually by the Northeast Fisheries Science Center from 1998 to 2012 during autumn. The systematic surveys were dedicated to surveying Atlantic herring and were designed to be synchronous with pre-spawning, whereas the stratified-random surveys were broad-scale, multi-species surveys. Both types of surveys collected multi-frequency acoustic and trawl data. These surveys were analyzed to evaluate their individual effectiveness as surveys, whether results could be combined, or whether either survey could be used alone to estimate Atlantic herring abundance. With the exception of two years, more Atlantic herring in the water column were observed in the Georges Bank region during the dedicated systematic survey than later in the season by the stratified-random survey in the Georges Bank and northern Gulf of Maine regions. These observations suggest that the systematic survey was not out of synchrony with Atlantic herring spawning in the Georges Bank area, and the majority of spawning in the off-shore Gulf of Maine region occurred in the Georges Bank area. Additionally, the area backscattering time series showed no dramatic changes among surveys conducted with different vessels, suggesting that the Atlantic herring did not react substantially to changes in vessels and/or reacted similarly to the presence of any of the four vessels used.

Repeated acoustic and trawl surveys were performed in the Gulf of Maine cod spawning protection area (GOMCSPA) to: (a) describe the spatial and temporal distribution of spring-spawning Atlantic cod ( Gadus morhua ); (b) estimate their abundance and biomass; and (c) evaluate precision of the survey methods. A fishing vessel equipped with 38- and 120-kHz split-beam echo sounders surveyed once monthly from dusk to dawn along ten parallel transects that covered a 80.8 km 2 area during April–July 2011. During each survey, two bottom trawl vessels (one with a small mesh net and one with a large mesh net) each made ten tows in parallel behind the acoustic survey vessel. Cod abundance and biomass was derived from acoustic backscatter by a combination of methods: (1) species apportionment based on trawl catch vs. echo classification; (2) in situ vs. predicted target strength; (3) size of elementary distance sampling unit (EDSU) and statistical approach; and (4) with and without dead zone correction. The mean cod density based on echo classification and a 100-m EDSU resulted in a substantially lower coefficient of variation when the variance was estimated by geostatistics compared to any other method used. Based on echo classification, semivariogram modeling revealed that 67–77% of the variance in cod biomass density was explained by a spatial structural component at a range (correlation length) of 2.0–2.4 km. Density maps, produced by ordinary kriging, showed cod were relatively widespread in the survey area in May, but congregated at higher densities in areas adjacent to two elevated bathymetric features. Most cod converged to a single location in June, and were at a higher concentration compared to the highest densities observed in May. This congregation decreased in size and density in July. The survey estimates of cod biomass were 184–494 mt in May, 138–617 mt in June, and 39–135 mt in July. Based on echo classification, the biomass for the GOMCSPA, extrapolated from these survey estimates, were 260–466 mt in May, 196–513 mt in June, and 91–198 mt in July. These results provide some evidence that adult Atlantic cod in spawning condition congregated within the GOMCSPA during the seasonal fishing closure, and that the biomass being protected by the closure may have represented 4–5% of the GOM cod spawning stock biomass at the time of the study.

Stockwell, J. D., Weber, T. C., Baukus, A. J., and Jech, J. M. 2013. On the use of omnidirectional sonars and downwards-looking echosounders to assess pelagic fish distributions during and after midwater trawling. – ICES Journal of Marine Science, 70:196–203. Small pelagic fish can play an important role in the structure and function of ecosystems, and there is increasing interest in their non-market value. At the scale of fish aggregations, however, the impact of fishing has received relatively little attention, with most effort devoted to impacts of vessel and gear avoidance on stock size estimates. We used concurrent deployment of a downwards-looking echosounder (Simrad ES60 system) and an omnidirectional sonar (Simrad SP90 system) during commercial pairtrawling operations for Atlantic herring (Clupea harengus) in the Gulf of Maine to examine their potential for studying the impacts of fishing on herring aggregations. We compared a number of aggregation metrics to illustrate similarities and differences between the two systems, and then qualitatively examined their properties during and after pairtrawling events to illustrate potential applications. Our results suggest that using both downwards-looking and omnidirectional systems provides complementary information on fish aggregation metrics. Future applications of these systems in before–after–control-impact (BACI) designs may help inform management agencies when evaluating potential impacts of fishing at the time and space scales of pelagic fish aggregations.

Recently developed broadband acoustic methods were used to study mixed assemblages of fish spanning a wide range of lengths and species. Through a combination of resonance classification and pulse-compression signal processing, which provides for high-range resolution, a modified commercial broadband echosounder was demonstrated to provide quantitative information on the spatial distribution of the individual size classes within an assemblage. In essence, this system spectrally resolves the different size classes of fish that are otherwise not resolved spatially. This method reveals new insights into biological processes, such as predator–prey interactions, that are not obtainable through the use of a conventional narrowband high-frequency echosounder or previous broadband systems. A recent study at sea with this system revealed aggregations containing bladdered fish 15–30 cm in length (Atlantic herring ( Clupea harengus ) and silver hake ( Merluccius bilinearis )) and a variety of species of smaller fish 2–5 cm in length. These observations infer that the smaller 2–5 cm fish can be colocated in the same aggregations as their predator, the larger silver hake, as well as pre-spawning herring. While this technological advancement provides more information, there remain challenges in interpreting the echo spectra in terms of meaningful biological quantities such as size distribution and species composition.

Atlantic herring (Clupea harengus ) in the offshore regions of the Gulf of Maine migrate each fall from their feeding grounds to the northern portion of Georges Bank to spawn. The Northeast Fisheries Science Center’s (NEFSC) herring acoustic survey has taken advantage of this behavior by conducting systematic surveys of the pre-spawning fish each year since 1999. Multi-frequency acoustic and midwater trawl data were collected along transects oriented perpendicular to bathymetric contours. Acoustic backscatter was analyzed to describe the aggregative patterns (e.g., size, location in the water column, and spatial and temporal distribution) of Atlantic herring during these surveys and regression trees were used to examine the aggregation characteristics. The positional variables of distance to spawning grounds and vertical location in the water column were the primary characteristics for describing pre-spawning aggregations. Secondary to these were the temporal variables of diel and survey timing, and the morphological characteristic of aggregation area. Lower numbers of aggregations were observed close to the herring spawning grounds but with higher acoustic energy than larger numbers of aggregations observed further from the spawning grounds but smaller in size and lower in acoustic energy. Most aggregations were in the lower portion of the water column, but those that were in the upper portion of the water column had higher acoustic energy. Consistently throughout the decade, 90% or more of herring aggregations were located within 40 nautical miles of their spawning grounds. The regression tree method provided valuable insight to the data series where it highlighted spatial and temporal patterns and was an effective way to quantitatively summarize relationships.

Stanton, T. K., Chu, D., Jech, J. M., and Irish, J. D. 2010. New broadband methods for resonance classification and high-resolution imagery of fish with swimbladders using a modified commercial broadband echosounder. – ICES Journal of Marine Science, 67: 365–378. A commercial acoustic system, originally designed for seafloor applications, has been adapted for studying fish with swimbladders. The towed system contains broadband acoustic channels collectively spanning the frequency range 1.7–100 kHz, with some gaps. Using a pulse-compression technique, the range resolution of the echoes is ∼20 and 3 cm in the lower and upper ranges of the frequencies, respectively, allowing high-resolution imaging of patches and resolving fish near the seafloor. Measuring the swimbladder resonance at the lower frequencies eliminates major ambiguities normally associated with the interpretation of fish echo data: (i) the resonance frequency can be used to estimate the volume of the swimbladder (inferring the size of fish), and (ii) signals at the lower frequencies do not depend strongly on the orientation of the fish. At-sea studies of Atlantic herring demonstrate the potential for routine measurements of fish size and density, with significant improvements in accuracy over traditional high-frequency narrowband echosounders. The system also detected patches of scatterers, presumably zooplankton, at the higher frequencies. New techniques for quantitative use of broadband systems are presented, including broadband calibration and relating target strength and volume-scattering strength to quantities associated with broadband signal processing.

Weber, T. C., Peña, H., and Jech, J. M. 2009. Consecutive acoustic observations of an Atlantic herring school in the Northwest Atlantic. – ICES Journal of Marine Science, 66: 1270–1277. Several successive images of the same school of Atlantic herring (Clupea harengus) were collected over the course of ∼1 h just north of Georges Bank in the Northwest Atlantic. Although the fish may not have been in their natural, undisturbed state, we observed what appeared to be the fish school fragmenting and dispersing, using a split-beam and a multibeam echosounder. Calibrated, 38 kHz, split-beam echosounder (Simrad EK60) and trawl-catch data provided accurate measures of the fish density beneath the vessel. Uncalibrated, 400 kHz, multibeam-echosounder (Reson 7125) data provided synoptic observations of the fish school including estimates of the school volume, morphology, and behaviour. Observations of the angular dependence in the multibeam-echosounder measurements of backscatter from fish allow investigation of the efficacy of extrapolating fish-school densities measured by the split-beam echosounder to the entire school.

Gurshin, C. W. D., Jech, J. M., Howell, W. H., Weber, T. C., and Mayer, L. A. 2009. Measurements of acoustic backscatter and density of captive Atlantic cod with synchronized 300-kHz multibeam and 120-kHz split-beam echosounders. – ICES Journal of Marine Science, 66: 1303–1309. Effective management strategies for Atlantic cod (Gadus morhua) in the Gulf of Maine require stock assessments based on accurate estimates of its abundance and distribution. If multibeam echosounders are to provide data for such estimates, the relationship between acoustic backscatter and fish biology must be better understood. Working towards this goal, a series of acoustic measurements was made using a 120 kHz, split-beam echosounder (Simrad EK60) and a 300 kHz, multibeam echosounder (Kongsberg EM3002). The transducers from both systems were fixed to a platform over a submerged 98 m3 cage made of 5 cm stretched-nylon mesh. After standard-sphere calibrations, the cage was stocked with live, mature Atlantic cod, with a mean total length of 80.7 cm (range: 51.5–105.0 cm). The echosounders synchronously collected acoustic data, while the cod were monitored with two underwater video cameras. Cod were incrementally removed from the cage to provide a time-series of acoustic backscatter at four densities (n = 128, 116, 66, and 23). Backscatter measurements of cod are compared between echosounders and over time, and the factors affecting the acoustically derived density estimates are discussed. The benefits and limitations of the EM3002 are highlighted.

Acoustic surveys have been conducted on Georges Bank from 1998 to present to estimate Atlantic herring (Clupea harengus) population abundance. Acoustic data were collected with a 12 or 18, 38, and 120 kHz Simrad EK500 scientific echo sounder. A pelagic trawl and underwater video images were used to collect biological information and to verify the species composition of acoustic backscatter. A multifrequency classification method was developed to improve the efficiency and accuracy of classifying species from acoustic echograms. In this method, a volume backscatter (Sv) threshold was applied equivalently to all echograms, and then a composite echogram was created based on which frequencies had Sv greater than or less than the Sv threshold. The results of this method were compared with the standard method of visually scrutinizing regions, and metrics were developed to evaluate the accuracy of classification algorithms relative to current methods, as well as to assess the effects of classification methods on population abundance estimates. In general, this method matched visually scrutinized Atlantic herring regions, but with consistent biases in classifying 38 kHz backscatter. The metrics highlighted spatial and temporal changes in the acoustic landscape, which may be indicative of intra- and inter-annual biological changes.

The EK500 has been the state-of-the-art scientific echosounder for surveying marine fish stocks for over a decade; the EK60 is its successor. Ensuring comparability in performance is vital during the transition from the EK500 to the EK60. To quantify the respective performances, each echosounder was calibrated in tandem by the standard-target method using the same 38-kHz, 12° beam width, split-beam transducer, with alternating pinging by means of an external triggering-and-switching system. The principal measurements comprised split-beam-determined angle and target strength, on-axis sensitivity, and directionality in the plane normal to the acoustic axis, as measured with a 60-mm-diameter copper sphere. Ambient noise, including volumetric reverberation, was also measured. Principal comparisons included those of the time-series and histograms of split-beam-determined target strength; respective alongship and athwartship angles as determined by the split-beam system; and as expected, difference in the split-beam-determined and experimental target-strength values in the plane normal to the acoustic axis. The mean absolute difference in off-axis angle values was also compared. While the performance of the two echosounders is generally similar, systematic differences exist. For the particular calibration measurements, the time variability in measurements of on-axis target strength was of the order of 1 dB for the EK500 and 2 dB for the EK60. The target-strength distribution for measurements made with the EK500 was normal, with standard deviation 0.2–0.3 dB, whereas for the EK60, the target-strength distribution was distinctly skewed and the standard deviation varied over 0.3–0.5 dB. Differences were found between the split-beam and physical-angle measurements. They were noticeably larger in the case of the EK60. Differences in performance between the two echosounders suggest refinements to the new system that will help realize its full potential in scientific work.

Acoustic measurements at 1.5–5 kHz on fish in the Gulf of Maine showed a swimbladder-resonance peak near 2.5 kHz at 160–190-m depth. Midwater trawls confirmed that the fish were likely to be Atlantic herring (Clupea harengus) of 19–29 cm length. Calculation using a model of swimbladder resonance gives swimbladder volumes of 1.2% of fish weight at 160–190 m. Extrapolation of this volume of gas using Boyle's Law suggests that at the sea surface, these herring would need to inflate their swimbladders by up to five to six times the volume required for neutral buoyancy. If these fish were to maintain this volume of gas with surface “gulping”, they would need to submerge from the sea surface with a 30% excess buoyancy. In general, swimbladders of the Clupeidae may have greater volumes of gas than if the fish were neutrally buoyant at the sea surface and the interpretation of HF-echosounder surveys may be additionally complex when the volume of gas and swimbladder volume are difficult to predict. Mechanisms of how herring obtain additional swimbladder gas are discussed.

Acoustic surveys of aquatic organisms are notorious for large data sets. Density distribution results from these surveys are traditionally graphed as two-dimensional plots. Increasing information content through wider acoustic frequency ranges or multiple angular perspectives has increased the amount and complexity of acoustic data. As humans are visually oriented, our ability to assimilate and understand information is limited until it is displayed. Computer visualization has extended acoustic data presentation beyond two dimensions but an ongoing challenge is to coherently summarize complex data. Our goal is to develop visualizations that portray frequency- and behavior-dependent backscatter of individual fish within aggregations. Incorporating individual fish behavior illustrates group dynamics and provides insight on the resulting acoustic backscatter. Object-oriented applications are used to visualize fish bodies and swimbladders, predicted Kirchhoff-ray mode (KRM) backscatter amplitudes, and fish swimming trajectories in three spatial dimensions over time. Through the visualization of empirical and simulated data, our goal is to understand how fish anatomy and behavior influence acoustic backscatter and to incorporate this information in acoustic data analyses.

The volume scattering strength of swim-bladdered fish is very sensitive to fish size, shape, and orientation. However, the appropriate geometrical and behavioral parameters necessary to determine these parameters are not always available. Inadequate knowledge of these parameters limits our ability to correctly estimate lengths and abundances of fish with acoustic technology. A method for extracting geometrical and behavioral parameters of individual fish using a scattering model-based echo-trace-analysis (ETA) is presented. The scattering model used in the ETA is based on the Kirchhoff approximation and a prolate spheroid is used to approximate the shape of the swimbladder. The geometric shape of a resolved echo from an individual fish is used in a least-squares algorithm to infer information about the swimming speed, direction, and orientation of the fish. The acoustic intensity distribution of an individual fish along a resolved echo trace is used in a least-squares algorithm to infer information about the size, aspect ratio, and orientation of the swimbladder. Results from the ETA were more sensitive to variations in vertical swimming speed and orientation of the swimbladder than to variations in horizontal swimming speed and aspect ratio of the swimbladder. The proposed ETA was applied to field data, a 38 kHz echogram of a school of Atlantic cod recorded with a Simrad EK500 echo sounder. The inferred sizes and orientations of a number of the resolved echo traces for individual fish were consistent with available observation data. One of the advantages of the ETA method presented here is that it can be easily extended to a dual beam, a split-beam, or a multi-beam acoustic system.

A new method has been developed for inferring the orientation of fish through the use of broadband-acoustic signals. The method takes advantage of the high range resolution of these signals, once temporally compressed through cross-correlation. The temporal resolution of these compressed signals is inversely proportional to the bandwidth, thus the greater the bandwidth the higher the resolution. This process has been applied to broadband-chirp signals spanning the frequency range 40–95 kHz to obtain a range resolution of approximately 2 cm from the original, unprocessed resolution of about 50 cm. With such high resolution, individual scattering features along the fish have been resolved, especially for angles well off normal incidence. The overall duration of the compressed echo from live, individual alewife, as measured in a laboratory tank, is shown to increase monotonically with orientation angle relative to normal incidence. The increase is due to the greater range separation relative to the transducer between the echoes from the head and tail of the fish. The results of this study show that with a priori knowledge of the length of the fish, the orientation could be estimated from the duration of a single, compressed broadband echo. This method applies to individual, acoustically resolved fish. It has advantages over previous approaches because it derives the orientation from a single ping and it does not use a formal, mathematical scattering model. Design parameters for applications in the ocean are given for a range of conditions and fish size. 2003 International Council for the Exploration of the Sea. Published by Elsevier Science Ltd. All rights

One goal of acoustic-based abundance estimates is to accurately preserve spatial distributions of organism density and size within survey data. We simulated spatially­ random and spatially-autocorrelated fish density and cr 0, distributions to quantify variance in density, abundance. and backscattering cross-sectional a rea estimates, and to examine the sensitivity of abundance estimates to organism spatial distributions and methods of estimating acoustic size. Our results show that it is difficult to simul­ taneously estimate fish density and maintain accurate crbs· frequency distributions. Among our acoustic backscatter estimation methods. a weighted-mean from a local search window provided optimal estimates of density, abundance and crbs· Other methods tended to bias either crh, or density estimates. This analysis identifies the relative importance of variance sources when estimating organism density using spatial ly-i ndexed acoustic data.