Search

Abundances of semi-pelagic fish are often estimated using acoustic or bottom trawl surveys, both of which sample only a fraction of the water column. Acoustic instruments are effective at sampling the majority of the water column, but they have a near-surface blind zone and a near-bottom acoustic dead zone (ADZ), where fish remain undetected. Bottom trawls are effective near the seabed, but miss fish that are located above the effective fishing height of the trawl. Quantification of the extent of overlap between these gears is needed, particularly in cases where environmental factors play a role. We developed logistic regression models to predict the availability (qa) of walleye pollock (Gadus chalcogrammus) to both acoustic and bottom trawl gears using factors shown to affect qa (depth, light intensity, fish length) and introducing additional factors (tidal currents, surface and bottom temperature, sediment size). Results build on earlier studies and quantify the uncertainty associated with the estimation of the ADZ correction using Bayesian methods. Our findings indicate that on average during the day, walleye pollock are more available to the bottom trawl than to the acoustics. Availability to both gears depends mostly on bottom depth, light conditions, and fish size, and to a lesser extent sediment size. Availability to the acoustic gear is also related on surface temperature. Variability in availability to both gears also depends on environmental factors.

Barbeaux, S. J., Horne, J. K., and Dorn, M. W. 2013. Characterizing walleye pollock (Theragra chalcogramma) winter distribution from opportunistic acoustic data. – ICES Journal of Marine Science, 70: 1162–1173. In 2003, acoustic data from 25 000 km of ship track lines were collected from two fishing vessels participating in the eastern Bering Sea walleye pollock (Theragra chalcogramma) fishery. Although these data were not calibrated or collected on a systematic grid, their broad temporal extent combined with high spatial resolution facilitated the examination of the distribution and behaviour of fished aggregations. To demonstrate their scientific applicability, these data were used to identify the spatio-temporal dynamics of pollock aggregations over scales ranging from hundreds of metres to hundreds of kilometres and from minutes to months. The spatial analysis identified three levels of pollock aggregation. The largest regions of high pollock density had an average diameter of 110 km and were comparable with distinct fishing grounds identified by fishers. The next smaller areas of high pollock density had a diameter between 2.5 and 6 km. Within these areas were clusters of pollock at even higher densities. The extent of the smallest aggregations ranged in diameter from 0.1 km in daylight to 0.6 km at night. Time-series analysis identified vertical and horizontal diel changes in pollock distribution and an overall decline in pollock density over the study period.

Urmy, S. S., Horne, J. K., and Barbee, D. H. 2012. Measuring the vertical distributional variability of pelagic fauna in Monterey Bay. – ICES Journal of Marine Science, 69: 184–196. Temporal variability is an important feature of aquatic ecosystems that can be difficult to measure. A stationary, upward-facing scientific echosounder was used to record the vertical distribution of pelagic fauna in Monterey Bay, CA, for 18 months. To characterize the distributions, a suite of metrics, including measures of density, abundance, location, dispersion, occupancy, evenness, and aggregation, was developed and tested. An algorithm to detect and count the number of acoustic backscatter layers was developed using image-analysis techniques. The metrics recorded a strong seasonal cycle, with total backscatter reaching a minimum during the spring upwelling season and peaking in autumn and winter. Variability in the vertical distribution of animals was greatest at long time-scales and decreased as a power (−1.050 to −1.585) of signal frequency. There were significant peaks in the power spectrum at 12- and 24-h periods, corresponding to the semi-diurnal tide and diel vertical migration. The diel signal was strongest in late winter and weakest during the spring upwelling season. Active acoustics are a useful addition to ocean observatories, and the metrics presented provide a useful set of tools to quantify the distribution and temporal variability of pelagic fauna.

Williams, K., Punt, A. E., Wilson, C. D., and Horne, J. K. 2011. Length-selective retention of walleye pollock, Theragra chalcogramma, by midwater trawls. – ICES Journal of Marine Science, 68: 119–129. Midwater trawls are commonly used during acoustic surveys of fish abundance to determine species and length compositions of acoustically sampled fish aggregations. As trawls are selective samplers, catches can be unrepresentative of sampled populations and lead to biased abundance estimates. Length-dependent retention of walleye pollock was estimated using small recapture nets, so-called pocket nets, attached to the outside of the trawl. Experimental haul sets comprising eight hauls each were conducted in the Gulf of Alaska in 2007 and 2008 and in the eastern Bering Sea (EBS) in 2007. Pocket-net catches were then modelled by fitting parameters for selectivity and escapement location along the trawl. Within- and between-haul variability was jointly estimated using hierarchical Bayesian methods. There was significant undersampling of juvenile (

Horne, J. K., Sawada, K., Abe, K., Kreisberg, R. B., Barbee, D. H., and Sadayasu, K. 2009. Swimbladders under pressure: anatomical and acoustic responses by walleye pollock. – ICES Journal of Marine Science, 66: 1162–1168. Pressure influences echo intensities from fish through changes in swimbladder volumes and surface areas. Volume reduction is expected to correspond to Boyle’s law (volume α pressure−1), but the effects of deforming the dorsal-aspect surface area of the swimbladder on the target strength (TS) of a physoclist have not been quantified at geometric scattering frequencies. Dorsal and lateral radiographs of three juvenile walleye pollock (Theragra chalcogramma) in a pressure chamber were used to image swimbladders from ambient to a maximum of 4.9 × 105 Pa (i.e. 5 atm). Radiographs from an additional 16 0-group, 21 juvenile, and 28 adult fish were used to compare swimbladder sizes and shapes across life-history stages. The directional elliptical eccentricity, which describes the relative compression in dorsal and lateral planes, was formulated to define swimbladder shapes and their variation. As pressure increased, dorsal-aspect surface areas of the swimbladder decreased at a constant rate. Swimbladder-volume reductions were similar among individuals, but less than those predicted by Boyle’s law. Compression was greatest in the dorsal–ventral plane and asymmetric anterior to posterior. The Kirchhoff-ray mode backscatter model predicted that TS at 38 and 120 kHz decreased by ∼4 dB as pressure increased from ambient to 4.9 × 105 Pa.

Parker-Stetter, S. L., Horne, J. K., and Langness, M. M. 2009. The influence of midwater hypoxia on nekton vertical migration. – ICES Journal of Marine Science, 66: 1296–1302. Hypoxia affects pelagic nekton, fish and large zooplankton, distributions in marine and fresh-water ecosystems. Bottom hypoxia is common, but midwater oxygen minimum layers (OMLs) may also affect nekton that undergo diel vertical migration (DVM). This study examined the response of pelagic nekton to an OML in a temperate fjord (Hood Canal, WA, USA). A 2006 study suggested that the OML created a prey refuge for zooplankton. Using acoustics (38 and 120 kHz), the 2007 night DVM patterns of nekton were quantified before (June, August) and during (September) an OML. All months had similar precrepuscular distributions (>50-m depth) of fish and invertebrates. During the September evening crepuscular period, a zooplankton layer migrated upwards (>1.5 m min−1), but the layer's rate of ascent slowed to 1.0 m min−1. As in June and August, fish in September followed the upward migration of the zooplankton layer to the surface, crossing through the OML. Our results suggest that the 2007 OML did not affect zooplankton or fish vertical distributions.

Burgos, J. M., and Horne, J. K. 2008. Characterization and classification of acoustically detected fish spatial distributions. – ICES Journal of Marine Science, 65: 1235–1247. High-resolution, two-dimensional measurements of aquatic-organism density are collected routinely during echo integration trawl surveys. School-detection algorithms are commonly used to describe and analyse spatial distributions of pelagic and semi-pelagic organisms observed in echograms. This approach is appropriate for species that form well-defined schools, but is limited when used for species that form demersal layers or diffuse pelagic shoals. As an alternative to metrics obtained from school-detection algorithms, we used landscape indices to quantify and characterize spatial heterogeneity in density distributions of walleye pollock (Theragra chalcogramma). Survey transects were divided into segments of equal length and echo integrated at a resolution of 20 m (horizontal) and 1 m (vertical). A series of 20 landscape metrics was calculated in each segment to measure occupancy, patchiness, size distribution of patches, distances among patches, acoustic density, and vertical location and dispersion. Factor analysis indicated that the metric set could be reduced to four factors: spatial occupancy, aggregation, packing density, and vertical distribution. Cluster analysis was used to develop a 12-category classification typology for distribution patterns. Visual inspection revealed that spatial patterns of segments assigned to each type were consistent, but that there was considerable overlap among types.

Henderson, M. J., Horne, J. K., and Towler, R. H. 2007. The influence of beam position and swimming direction on fish target strength. – ICES Journal of Marine Science, 65: 226–237. Fish orientation is consistently identified as a major influence on fish target strength (TS). Generally, orientation is defined as the tilt angle of the fish with respect to the acoustic transducer, whereas a more accurate definition includes tilt, roll, and yaw. Thus far, the influences of roll and yaw on fish TS have only been examined cursorily. We used in situ single-target data to create fish tracks, to estimate fish tilt and yaw, and correlated these estimates with TS. The results show that tilt, yaw, and beam position have a significant influence on fish TS. To investigate further how yaw and beam position affect TS, we calculated the expected backscatter from each fish within simulated fish aggregations using a backscatter model. The TS of individual fish at 38 and 120 kHz varied by as much as 11 and 19 dB with changes in yaw and beam position. Altering the fish’s tilt, yaw, and beam position resulted in TS differences of 14 and 26 dB at 38 and 120 kHz, respectively. Orientation had a minimal influence on an aggregation’s average TS if the aggregation had a variable tilt-angle distribution and was dispersed throughout the acoustic beam.

Burwen, D. L., Nealson, P. A., Fleischman, S. J., Mulligan, T. J., and Horne, J. K. 2007. The complexity of narrowband echo envelopes as a function of fish side-aspect angle. – ICES Journal of Marine Science, 64: 1066–1074. High-frequency, narrowband acoustic signals may contain more information on fish size and orientation than previously thought. Our observations of dual frequency identification sonar (DIDSON) images of fish orientation paired with split-beam echo envelopes helped clarify why metrics such as echo duration have performed better than target strength measurements when predicting salmon lengths at side aspect. Fish orientation has a pronounced effect on the duration and shape of split-beam echo envelopes from large (80–130 cm) salmon insonified at side aspect. At near-normal aspect angles, echo envelopes are unimodal, symmetrical, and resemble echo envelopes from calibration spheres. With increasing oblique-aspect angle, echo shapes become less symmetrical as the number of peaks increases, and echo duration and amplitude become more variable. Using angle and range coordinates, peaks in an echo envelope can be traced to their origin on a DIDSON image. At oblique-aspect angles, discrete peaks develop that are reflected from regions close to the head and tail. In addition, the distance between peaks increases with increasing aspect angle and is larger than can be explained by swimbladder length.

Burgos, J. M., and Horne, J. K. 2007. Sensitivity analysis and parameter selection for detecting aggregations in acoustic data. ICES Journal of Marine Science, 64: 160–168. A global sensitivity analysis was conducted on the algorithm implemented in the Echoview ® software to detect and describe aggregations in acoustic backscatter. Multiple aggregation detections were performed using walleye pollock (Theragra chalcogramma) data from the eastern Bering Sea. Walleye pollock form distinct aggregations and dense and diffuse layers. In each aggregation detection, input parameters defining minimum size, density, and distance to other aggregations were selected at random using a Latin hypercube sampling design. Sensitivity was quantified by testing for correlation among input parameters and a series of aggregation descriptors. In all, 336 correlation tests were performed, corresponding to a combination of seven detection input parameters, eight aggregation descriptors, and six transects. Among these, 181 tests were significant, indicating sensitivity between input parameters and aggregation descriptors. The aggregation-detection algorithm is sensitive to changes in threshold and minimum size, but less sensitive to changes in the connectivity criterion among aggregations.

Many biological and physical factors potentially affect target strength. While these sources have been identified, few studies have compared the relative effects of individual factors. Modelled and measured target strengths in non-dimensional metrics were used to compare and rank the effects of fish length, tilt, depth, and acoustic frequency on backscatter intensity. Ex situ measurements of target strength were used to examine the effects of tilt and depth and then compared to backscatter model predictions. Swimbladder volume reduction due to increasing pressure at depth was modelled using Boyle's law and by varying the ratio of dorsal to lateral compression. We found that length has the largest effect on the modelled and measured backscatter intensity, followed by tilt, frequency, and depth. Including tilt distributions in backscatter estimates improved the match between empirical target-strength measures and model predictions. Non-dimensional influence ratios provide insight into the sources and magnitudes of the backscatter variability.

Differences in the acoustic characteristics of forage fish species in the Gulf of Alaska and the Bering Sea were examined using Kirchhoff ray-mode (KRM) backscatter models. Our goal was to identify species-specific characteristics and metrics that facilitate the discrimination of species using acoustic techniques. Five fish species were analyzed: capelin (Mallotus villosus), Pacific herring (Clupea pallasii), walleye pollock (Theragra chalcogramma), Atka mackerel (Pleurogrammus monopterygius), and eulachon (Thaleichthys pacificus). Backscatter amplitude differences exist among these species, especially between swimbladdered and non-swimbladdered fish. Echo intensities were variable within and among species. The effect of morphological variability was indexed using the ratio of the Reduced-scattering length (RSL) standard deviation over its mean. Morphological variability was low only at fish length to acoustic wavelength ratios less than eight. Target strength differences between pairs of carrier frequencies (ranging from 12 kHz to 200 kHz) differed among species, and were dependent on fish size and body orientation. Frequency differencing successfully discriminated between fish species but the choice of frequency to maximize target strength differences was not consistent among species pairs. Frequency-dependent, backscatter model predictions facilitate comparison of target strength differences prior to acoustic data collection.

Variability in echo intensities from aquatic organisms is caused by physical factors associated with the transmission of sound through water, and by biological factors associated with the ontogeny, physiology, and behaviour of targets. Acoustic-based density estimates depend on accurately characterizing reflected or backscattered sound from any species of interest. Digitized lateral and dorsal radiographs of walleye pollock (Theragra chalcogramma) were used to characterize intra-specific variability among young-of-the-year, juvenile, and adult life-history stages. Kirchhoff-ray mode (KRM) models were used to quantify variability in backscatter intensities at 38 and 120 kHz. At these geometric scattering frequencies, swimbladder surface areas influence echo intensities. Dorsal swimbladder surface areas were proportionate to fish lengths and decreased after fish were fed. Corresponding changes in backscatter were not proportionate to the reduction in dorsal surface area. The ratio of dorsal to lateral swimbladder surface areas was consistent among gravid and non-gravid fish. Walleye pollock tilt angles were centred at 90° and did not differ among densities or between light and dark cycles. Target strength–length regressions and KRM-predicted backscatter models closely matched in situ target-strength measurements for walleye pollock in the Bering Sea. Backscatter variability can be minimized through judicious deployment of equipment and equipment-parameter settings, but the relative influence of biological factors on backscatter amplitude has not been determined.

The variability of ensemble 38 kHz, target-strength (TS38) estimates for orange roughy (Hoplostethus atlanticus) (4.9 dB, factor of 3.1) in deep water (>600 m) limits the use of echo integration for absolute-biomass estimates. Orange roughy are high in oil content, have a wax-ester swimbladder, and show an active-avoidance response to sampling gear. The interpretations of ensemble, in situ target strengths of orange roughy (range 〈TS38〉=−52.9 to −51.0 dB for standard fish length 〈SL〉 = 35 cm) are lower than previous model and surface-based measurements (〈TS38〉 = −48 dB, SL = 35 cm). In situ TS measurements from individuals on the periphery of dense schools were processed to minimize uncertainties from single-target selection criteria, species composition, and active avoidance. Video and acoustic-tracking data quantified the variability in TS measurements arising from the variability in fish orientation. Multi-frequency acoustics and fish tracking are used to quantify in situ TS variability due to species identification and fish density. The Kirchhoff-ray-mode backscatter model was used to illustrate the sensitivity of species-specific backscatter to assumptions of tilt-angle and material properties (density and sound-speed contrasts). We conclude that a remaining source of uncertainty for in situ TS measurements is the assumption that dispersed targets are representative of the survey population.

Hazen, E. L., and Horne, J. K. 2003. A method for evaluating the effects of biologicalfactors on fish target strength. – ICES Journal of Marine Science, 60:555–562.Understanding the relationship between fish biology and target strength potentially im-proves the accuracy of acoustic assessments. The effects of individual biological factors(e.g., length, tilt, and depth) on backscatter amplitude have been examined, but the relativecontribution of each factor has not been quantified. Dimensionless ratios, whichfacilitate comparison of disparate quantities, were used to evaluate the effects of individualbiological factors on echo intensities. Ratios from 25 adult walleye pollock (Theragrachalcogramma) were calculated using a Kirchhoff-ray-mode, backscatter model parameter-ized for each fish. This comparative approach can be used to identify the influence ofbiological factors on backscatter intensity and is potentially a tool for improving accuracywhen converting acoustic size to fish length.

Smith, P. E., Horne, J. K., and Schneider, D. C. 2001. Spatial dynamics of anchovy, sardine, and hake pre-recruit stages in the California Current. – ICES Journal of Marine Science, 58: 1063–1071. Three genera, Engraulis, Sardinops ,a ndMerlucciu have coincident spawning and juvenile brood areas in most eastern and western boundary currents throughout the world. The CalCOFI survey program has amassed a 50-year data series on location and timing of spawning and the resultant recruitment of anchovy, sardine, and hake in the California Current region. Use of existing Lefkovitch matrix population projection models for these three species allows evaluation of the spatial and temporal scales that govern the biological and physical interactions. We present rate diagrams for hake and construct comparable diagrams for anchovy and sardine in a common, variable environment. Rate diagrams depict the relative importance of demographic (natality and mortality), growth, and kinematic (passive and active movement) processes to a quantity of interest as a function of spatial and temporal scale. Results confirm that the scale of observations will have to be manipulated to expose the importance of any combination of processes for life history stages among these species. Field sampling systems have not yet responded adequately to mesoscale features (50 km) persisting over months.

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.

Traditional scientific echosounders operate at discrete frequencies ranging from 38 to 420 kHz. We investigated the applicability and accuracy of length-based population estimates using commercially available acoustic frequencies and the inverse approach under ideal conditions. The inverse approach combines modelled and measured backscatter values to estimate the abundance of organisms in specified length classes. Reference backscatter values of individual fish were calculated using a KirchhoV-ray mode backscatter model. Single and multi-cohort fish populations were simulated based on length-frequency samples from purse seine catches of threadfin shad (Dorosoma petenense) and used to calculate the total frequency-dependent volume backscatter of each population. A non-negative least squares (NNLS) algorithm was used to estimate total abundance and numbers of fish in each length class. Total abundance estimates were within