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Sascha Mario Michel Fässler Phd Thesis

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Sascha Mario Michel Fässler Phd Thesis TARGET STRENGTH VARIABILITY IN ATLANTIC HERRING (CLUPEA HARENGUS) AND ITS EFFECT ON ACOUSTIC ABUNDANCE ESTIMATES Sascha Mario Michel Fässler A Thesis Submitted for the Degree of PhD at the University of St. Andrews 2010 Full metadata for this item is available in Research@StAndrews:FullText at: https://research-repository.st-andrews.ac.uk/ Please use this identifier to cite or link to this item: http://hdl.handle.net/10023/1703 This item is protected by original copyright This item is licensed under a Creative Commons License Target strength variability in Atlantic herring ( Clupea harengus ) and its effect on acoustic abundance estimates Sascha Mario Michel Fässler Submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy University of St Andrews September 2010 ii Target strength variability in Atlantic herring ( Clupea harengus ) and its effect on acoustic abundance estimates Sascha Mario Michel Fässler iii Declarations I, Sascha Mario Michel Fässler, hereby certify that this thesis, which is approximately 39’000 words in length, has been written by me, that it is the record of work carried out by me and that it has not been submitted in any previous application for a higher degree. I was admitted as a research student in October 2006 and as a candidate for the degree of PhD in October 2007; the higher study for which this is a record was carried out in the University of St Andrews between 2006 and 2009. date ……………...…signature of candidate …………………………….. I hereby certify that the candidate has fulfilled the conditions of the Resolution and Regulations appropriate for the degree of PhD in the University of St Andrews and that the candidate is qualified to submit this thesis in application for that degree. date ……………...…signature of supervisor …………………………….. In submitting this thesis to the University of St Andrews we understand that we are giving permission for it to be made available for use in accordance with the regulations of the University Library for the time being in force, subject to any copyright vested in the work not being affected thereby. We also understand that the title and the abstract will be published, and that a copy of the work may be made and supplied to any bona fide library or research worker, that my thesis will be electronically accessible for personal or research use unless exempt by award of an embargo as requested below, and that the library has the right to migrate my thesis into new electronic forms as required to ensure continued access to the thesis. We have obtained any third-party copyright permissions that may be required in order to allow such access and migration, or have requested the appropriate embargo below. iv The following is an agreed request by candidate and supervisor regarding the electronic publication of this thesis: Access to printed copy and electronic publication of thesis through the University of St Andrews. date ……………...…signature of candidate …………………………….. date ……………...…signature of supervisor …………………………….. v Acknowledgements I would like to express my sincere gratitude to my supervisors, Prof Andrew Brierley of the University of St Andrews and Dr Paul Fernandes of the Marine Scotland Marine Laboratory, Aberdeen, for providing me with continued support, advice and guidance. I very much appreciated their knowledge, encouragement and suggestions which kept me on the right tracks during this work and contributed to the ideas and understanding gained. Special thanks to Paul for initially introducing me to the subject of fisheries acoustics during a work placement and for being a very encouraging mentor throughout the years. Many thanks to the Marine Laboratory in Aberdeen for accommodating me during my studies and providing me with acoustic herring survey data. Members of the ‘Sonar Section’ - Eric Armstrong, Phil Copland and Mike Stewart - are thanked for their technical support and their relaxed but thorough approach. I am grateful to Brian Ritchie, Colin Stewart and David Lee from the Engineering Services for doing a sheer marvellous job in constructing the pressure chamber. Dr David Borchers (CREEM, St Andrews University), Dr Elizabeth Clarke (Marine Laboratory), and Colin Millar (CREEM and Marine Laboratory) are thanked for providing me with expert advice and help with Bayesian statistical methods. I acknowledge the crew and Captain of FRV Scotia and colleagues of the Marine Laboratory who assisted in collecting data on acoustic surveys for herring in the North Sea. During my studies I had the honour and great pleasure to meet and get to know better many fellow fisheries acousticians from all over the world. Colleagues of the ICES Working Group on Fisheries Acoustic Science and Technology (WGFAST) are thanked for providing such an encouraging and friendly community that is a great source of inspiration. I am deeply indebted to Prof Egil Ona (IMR, Norway) and Prof Natalia Gorska (University of Gda ńsk, Poland) for their collaboration that encouraged me to pursue the investigation into Baltic herring TS. Dr Dezhang Chu (NWFSC, USA) and Dr Gareth Lawson (WHOI, USA) kindly provided assistance with the DWBA model. Many thanks to Prof John Horne (University of Washington, USA) and Dr Michael Jech (NEFSC, USA) for the invitation to attend the Acoustic vi Backscatter Modelling workshop at Friday Harbor in January 2008. Additional thanks to Michael for his help with the KRM model. Together with Dr Héctor Peña (IMR, Norway) I had much joy looking at herring under pressure in an MRI scanner at the hospital in Bergen! This thesis would not have been possible without the funding I received through the Overseas Research Student Award Scheme (ORSAS) and the University of St Andrews. Throughout my studies I have additionally received financial support from the Dr. Max Husmann-Stiftung, the Jubiläumsstiftung of the Basellandschaftliche Kantonalbank and an Ausbildungsbeitrag of the Kanton Basel- Landschaft. Finally, a big thank you to the friends I made in the Aberdeen Oilers Floorball Club, especially Neil, Linda, Osku and Kimmo, who made my whole stay in Aberdeen very enjoyable and allowed me to have a sporty and social alternative to fisheries acoustics research! Most importantly, I am grateful to my wife, Lorna, for her love, support and company. Au e grosses Dangschön an mini Fründe und Familie deheim, mini Eltere und Brüedere, dr Ron und dr Chris, womi bi jedr Ruckkehr immr widr willkomme gheisse hän, für euri Aarüef, chats, e-mails und Bsüech. Merci vylmol! „Im Hering isch manchs einerlei Är weiss nur öppis ganz genau Dr Mensch mit sin’rä Fischerei Isch schlimmr als dr Kabeljau“ (source by Ingo Baumgartner) vii Abstract Acoustic survey techniques are widely used to quantify abundance and distribution of a variety of pelagic fish such as herring ( Clupea harengus ). The information provided is becoming increasingly important for stock assessment and ecosystem studies, however, the data collected are used as relative indices rather than absolute measures, due to the uncertainty of target strength (TS) estimates. A fish’s TS is a measure of its capacity to reflect sound and, therefore, the TS value will directly influence the estimate of abundance from an acoustic survey. The TS is a stochastic variable, dependent on a range of factors such as fish size, orientation, shape, physiology, and acoustic frequency. However, estimates of mean TS, used to convert echo energy data from acoustic surveys into numbers of fish, are conveniently derived from a single metric - the fish length (L). The TS used for herring is based on TS-L relationships derived from a variety of experiments on dead and caged fish, conducted 25-30 years ago. Recently, theoretical models for fish backscatter have been proposed to provide an alternative basis for exploring fish TS. Another problem encountered during acoustic surveys is the identification of insonified organisms. Trawl samples are commonly collected for identification purposes, however, there are several selectivity issues associated with this method that may translate directly into biased acoustic abundance estimates. The use of different acoustic frequencies has been recognised as a useful tool to distinguish between different species, based on their sound reflection properties at low and high frequencies. In this study I developed theoretical models to describe the backscatter of herring at multiple frequencies. Data collected at four frequencies (18, 38, 120 and 200 kHz) during standard acoustic surveys for herring in the North Sea were examined and compared to model results. Multifrequency backscattering characteristics of herring were described and compared to those of Norway pout, a species also present in the survey area. Species discrimination was attempted based on differences in backscatter at the different frequencies. I examined swimbladder morphology data of Baltic and Atlantic herring and sprat from the Baltic Sea. Based on these data, I modelled the acoustic backscatter of both herring stocks and viii attempted to explain differences previously observed in empirical data. I investigated the change in swimbladder shape of herring, when exposed to increased water pressures at deeper depths, by producing true shapes of swimbladders from MRI scans of herring under pressure. The swimbladder morphology representations in 3-D were used to model the acoustic backscatter at a range of frequencies and water pressures. I developed a probabilistic TS model of herring in a Bayesian framework to account for uncertainty associated with TS. Most likely distributions of model parameters were determined by fitting the model to in situ data. The resulting probabilistic TS was used to produce distributions of absolute abundance and biomass estimates, which were compared to official results from ICES North Sea herring stock assessment. Modelled backscatter levels of herring from the Baltic Sea were on average 2.3 dB higher than those from herring living in northeast Atlantic waters. This was attributed to differences in swimbladder sizes between the two herring stocks due to the lower salinity Baltic Sea compared to Atlantic waters.
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