Resonance classification of mixed assemblages of fish with swimbladders using a modified commercial broadband acoustic echosounder at 1–6 kHz

Author Posting. © The Authors, 2012. This article is posted here by permission of NRC Research Press for personal use, not for redistribution. The definitive version was published in Canadian Journal of Fisheries and Aquatic Sciences 69 (2012): 854-868, doi:10.1139/f2012-013.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.This research was supported by the US Office of Naval Research (grant Nos. N00014-04-1-0440 and N00014-10-1-0127), NOAA – National Marine Fisheries Service; and the J. Seward Johnson Chair of the WHOI Academic Programs Office

Wideband (15–260 kHz) acoustic volume backscattering spectra of Northern krill (Meganyctiphanes norvegica) and butterfish (Peprilus triacanthus)

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.Measurements of acoustic backscatter made over a wide frequency band have the potential for improved classification relative to traditional narrowband methods, by characterizing more fully the frequency response of scatterers. In January 2014, five wideband transceivers [Simrad EK80 Wideband Transceivers (WBTs)] and split-beam transducers with nominal centre frequencies of 18, 38, 70, 120, and 200 kHz were used to collect acoustic data spanning a nearly continuous 15–260 kHz bandwidth. The acoustic samples were from ca. 2 m below the surface to the seabed in an area along the US continental shelf break. Bottom trawls and zooplankton nets were also used to sample scatterers contributing to selected features of the acoustic backscatter. Measurements of frequency-dependent volume backscattering strength (i.e. volume backscattering spectra) from aggregations of euphausiids (mostly Northern krill, Meganyctiphanes norvegica) clearly resolved the transition from Rayleigh to geometric scattering, consistent with modelled backscatter from the type and length of animals sampled with bongo nets. Volume backscattering spectra from aggregations dominated by butterfish (Peprilus triacanthus) revealed a frequency response that was suggestive of superimposed scattering by soft tissue and bone. Backscatter predicted by Kirchhoff ray mode models of butterfish corresponded to trends in the measured spectra, supporting the assumption that acoustic scattering by butterfish is dominated by soft tissue and vertebrae.NOAA Advanced Sampling Technology Working Group (ASTWG) provided support for this project. GLL was partially supported by NOAA Cooperative Agreements NA09OAR4320129 and NA14OAR4320158 through the NOAA Fisheries Quantitative Ecology and Socioeconomics Training (QUEST) programme

Exploiting signal processing approaches for broadband echosounders

© 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.Broadband echosounders, which transmit frequency-modulated pulses, increase the spectral characterization of targets relative to narrowband echosounders, which typically transmit single-frequency pulses, and also increase the range resolution through broadband matched-filter signal processing approaches. However, the increased range resolution does not necessarily lead to improved detection and characterization of targets close to boundaries due to the presence of undesirable signal processing side lobes. The standard approach to mitigating the impact of processing side lobes is to transmit tapered signals, which has the consequence of also reducing spectral information. To address this, different broadband signal processing approaches are explored using data collected in a large tank with both a Kongsberg–Simrad EK80 scientific echosounder with a combination of single- and split-beam transducers with nominal centre frequencies of 18, 38, 70, 120, 200, and 333 kHz, and with a single-beam custom-built echosounder spanning the frequency band from 130 to 195 kHz. It is shown that improved detection and characterization of targets close to boundaries can be achieved by using modified replica signals in the matched filter processing. An additional benefit to using broadband echosounders involves exploiting the frequency dependence of the beam pattern to calibrate single-beam broadband echosounders using an off-axis calibration sphere.This research was supported by the NOAA Office of Science and Technology, Advanced Sampling Technology Working Group. G.L.L. was partially supported by NOAA Cooperative Agreements NA09OAR4320129 and NA14OAR4320158 through the NOAA Fisheries Quantitative Ecology and Socieconomics Training (QUEST) program. A.C.L. was partially supported through the Office of Naval Research Ocean Acoustics Program

New broadband methods for resonance classification and high-resolution imagery of fish with swimbladders using a modified commercial broadband echosounder

© 2010 The Authors. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 365-378, doi:10.1093/icesjms/fsp262.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.The research was supported by the US Office of Naval Research, grants number N00014-04-1-0440 and N00014-04-1-0475, NOAA/CICOR cooperative agreement NA17RJ1223, NOAA/ National Marine Fisheries Service, and the J. Seward Johnson Chair of the WHOI Academic Programs Office

Protocols for calibrating multibeam sonar

Development of protocols for calibrating multibeam sonar by means of the standard-target method is documented. Particular systems used in the development work included three that provide the water-column signals, namely the SIMRAD SM2000/90- and 200-kHz sonars and RESON SeaBat 8101 sonar, with operating frequency of 240 kHz. Two facilities were instrumented specifically for the work: a sea well at the Woods Hole Oceanographic Institution and a large, indoor freshwater tank at the University of New Hampshire. Methods for measuring the transfer characteristics of each sonar, with transducers attached, are described and illustrated with measurement results. The principal results, however, are the protocols themselves. These are elaborated for positioning the target, choosing the receiver gain function, quantifying the system stability, mapping the directionality in the plane of the receiving array and in the plane normal to the central axis, measuring the directionality of individual beams, and measuring the nearfield response. General preparations for calibrating multibeam sonars and a method for measuring the receiver response electronically are outlined. Advantages of multibeam sonar calibration and outstanding problems, such as that of validation of the performance of multibeam sonars as configured for use, are mentioned

Broadband classification and statistics of echoes from aggregations of fish measured by long-range, mid-frequency sonar

Author Posting. © Acoustical Society of America, 2017. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 141 (2017): 4354, doi:10.1121/1.4983446.For horizontal-looking sonar systems operating at mid-frequencies (1–10 kHz), scattering by fish with resonant gas-filled swimbladders can dominate seafloor and surface reverberation at long-ranges (i.e., distances much greater than the water depth). This source of scattering, which can be difficult to distinguish from other sources of scattering in the water column or at the boundaries, can add spatio-temporal variability to an already complex acoustic record. Sparsely distributed, spatially compact fish aggregations were measured in the Gulf of Maine using a long-range broadband sonar with continuous spectral coverage from 1.5 to 5 kHz. Observed echoes, that are at least 15 decibels above background levels in the horizontal-looking sonar data, are classified spectrally by the resonance features as due to swimbladder-bearing fish. Contemporaneous multi-frequency echosounder measurements (18, 38, and 120 kHz) and net samples are used in conjunction with physics-based acoustic models to validate this approach. Furthermore, the fish aggregations are statistically characterized in the long-range data by highly non-Rayleigh distributions of the echo magnitudes. These distributions are accurately predicted by a computationally efficient, physics-based model. The model accounts for beam-pattern and waveguide effects as well as the scattering response of aggregations of fish.This research was supported by the U.S. Office of Naval Research, the National Oceanographic Partnership Program, NOAA, WHOI, and the Oceanographer of the U.S. Navy

Exploring the use of environmental DNA (eDNA) to detect animal taxa in the Mesopelagic Zone

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Govindarajan, A. F., Francolini, R. D., Jech, J. M., Lavery, A. C., Llopiz, J. K., Wiebe, P. H., & Zhang, W. Exploring the use of environmental DNA (eDNA) to detect animal taxa in the Mesopelagic Zone. Frontiers in Ecology and Evolution, 9, (2021): 574877, https://doi.org/10.3389/fevo.2021.574877.Animal biodiversity in the ocean’s vast mesopelagic zone is relatively poorly studied due to technological and logistical challenges. Environmental DNA (eDNA) analyses show great promise for efficiently characterizing biodiversity and could provide new insight into the presence of mesopelagic species, including those that are missed by traditional net sampling. Here, we explore the utility of eDNA for identifying animal taxa. We describe the results from an August 2018 cruise in Slope Water off the northeast United States. Samples for eDNA analysis were collected using Niskin bottles during five CTD casts. Sampling depths along each cast were selected based on the presence of biomass as indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the 18S V9 gene region was used to assess taxonomic diversity. eDNA metabarcoding results were compared with those from net-collected (MOCNESS) plankton samples. We found that the MOCNESS sampling recovered more animal taxa, but the number of taxa detected per liter of water sampled was significantly higher in the eDNA samples. eDNA was especially useful for detecting delicate gelatinous animals which are undersampled by nets. We also detected eDNA changes in community composition with depth, but not with sample collection time (day vs. night). We provide recommendations for applying eDNA-based methods in the mesopelagic including the need for studies enabling interpretation of eDNA signals and improvement of barcode reference databases.This research was part of the Woods Hole Oceanographic Institution’s Ocean Twilight Zone Project, funded as part of The Audacious Project housed at TED. Funding for the NOAA Ship Henry B Bigelow was provided by NOAA’s Office of Marine and Aviation Operations (OMAO)

Comparisons among ten models of acoustic backscattering used in aquatic ecosystem research

Author Posting. © Acoustical Society of America, 2015. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 138 (2015); 3742, doi:10.1121/1.4937607.Analytical and numerical scatteringmodels with accompanying digital representations are used increasingly to predict acoustic backscatter by fish and zooplankton in research and ecosystem monitoring applications. Ten such models were applied to targets with simple geometric shapes and parameterized (e.g., size and material properties) to represent biological organisms such as zooplankton and fish, and their predictions of acoustic backscatter were compared to those from exact or approximate analytical models, i.e., benchmarks. These comparisons were made for a sphere, spherical shell, prolate spheroid, and finite cylinder, each with homogeneous composition. For each shape, four target boundary conditions were considered: rigid-fixed, pressure-release, gas-filled, and weakly scattering. Target strength (dB re 1 m2) was calculated as a function of insonifying frequency (f = 12 to 400 kHz) and angle of incidence (θ = 0° to 90°). In general, the numerical models (i.e., boundary- and finite-element) matched the benchmarks over the full range of simulation parameters. While inherent errors associated with the approximate analytical models were illustrated, so were the advantages as they are computationally efficient and in certain cases, outperformed the numerical models under conditions where the numerical models did not convergeThis work was supported by the NOAA Fisheries Advanced Sampling Technologies Working Group, the Office of Naval Research, and the National Oceanic Partnership Program. Josiah S. Renfree

Modal Ω-Logic: Automata, Neo-Logicism, and Set-Theoretic Realism

This essay examines the philosophical significance of $\Omega$-logic in Zermelo-Fraenkel set theory with choice (ZFC). The duality between coalgebra and algebra permits Boolean-valued algebraic models of ZFC to be interpreted as coalgebras. The modal profile of $\Omega$-logical validity can then be countenanced within a coalgebraic logic, and $\Omega$-logical validity can be defined via deterministic automata. I argue that the philosophical significance of the foregoing is two-fold. First, because the epistemic and modal profiles of $\Omega$-logical validity correspond to those of second-order logical consequence, $\Omega$-logical validity is genuinely logical, and thus vindicates a neo-logicist conception of mathematical truth in the set-theoretic multiverse. Second, the foregoing provides a modal-computational account of the interpretation of mathematical vocabulary, adducing in favor of a realist conception of the cumulative hierarchy of sets

Otolith characterization and integrative species identification of adult mesopelagic fishes from the western North Atlantic Ocean

Fish diversity and ecology in the ocean’s mesopelagic zone are understudied compared to other marine regions despite growing interest in harvesting these potential resources. Otoliths can provide a wealth of taxonomic and life history information about fish, which can help fill these knowledge gaps; however, there has been relatively little research to date on the otoliths of mesopelagic species. Here, a species-specific image library was assembled of sagittal otoliths from 70 mesopelagic fishes belonging to 29 families collected in the western North Atlantic Ocean. Images of adult sagittal otoliths from 12 species were documented and photographed for the first time. The fish were identified to species with a combination of morphological characters and DNA barcoding. Regressions between otolith size and fish length are presented for the six species with the largest sample sizes in this study. This otolith image library, coupled with otolith-length and width to fish-length relationships, can be used for prey identification and back-calculation of fish size, making it a valuable tool for studies relating to food webs in the important yet poorly understood mesopelagic zone. In addition, the 44 fish barcodes generated in this study highlight the benefit of using an integrative taxonomic approach to studies of this nature, as well as add to existing public databases that enable cryptic species and metabarcoding analyses of mesopelagic species