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Using Underwater Acoustic Data to Predict the Distribution of Demersal Fish in Western Australia

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Using Underwater Acoustic Data to Predict the Distribution of Demersal Fish in Western Australia Faculty of Science and Engineering School of Earth and Planetary Science Using Underwater Acoustic Data To Predict the Distribution of Demersal Fish in Western Australia Marcela Montserrat Landero Figueroa This thesis is presented for the Degree of Doctor of Philosophy of Curtin University December 2018 Declaration of authorship I, Marcela Montserrat Landero Figueroa, declare that to the best of my knowledge and belief this thesis contains no material previously published by any other person except where due acknowledgment has been made. This thesis contains no material which has been accepted for the award of any other degree of diploma in any university. The research presented and reported and this thesis was conducted in compliance with the National Health and Medical Research Council Australia code for the care and use of animals for scientific purposes 8th edition (2013). The proposed research study received animal ethics approval from the Curtin University Animal Ethics Committee, Sonar monitoring of marine animals from a vessel: AEC2013_26 and Baited Remote Underwater stereo-video: AEC_2014_09. 31/12/2018 i “How inappropriate to call this planet Earth when it is quite clearly ocean” Arthur C Clarke “No man ever steps in the same river twice, for it’s not the same river and he’s not the same man” Heraclitus iii Abstract Coral reefs are diverse ecosystems, providers of a series of environmental services and offer habitat for a variety of ecological and economically important species of fish. Coral reefs and the communities dependent on them are at risk of degradation from local and global stressors. Conservation efforts are currently focused mainly on Marine Protected Areas which are expected to protect a significant portion of the fish populations. However, a successful management of the MPAs will partially depend on effective monitoring of the fish population’s changes over time. The collection of biological information in coral reef areas is logistically complex and expensive, and the observational methods currently available present some limitations and bias. The use of species distribution models based on benthic habitats surrogates can help to extrapolate point biological measurements to full coverage maps which can assist in conservation and management decisions. This study focuses on two main objectives aimed at helping in the assessment of demersal reef fish distribution in the coast of Western Australia: i) The development of models of potential distribution of demersal fish species, using biological data from Baited Remote Underwater Stereo-Videos (stereo-BRUVS) and benthic surrogates based on acoustic data; and ii) the possibility of combining optic and acoustic methods to produce a comprehensive evaluation of demersal fish distribution. These aims were explored mainly in the Ningaloo Marine Park (NMP) in the Northwest part of the coast of Western Australia considered as a hotspot of biodiversity. Three interpolation methods were used to produce a full-coverage bathymetry using single-beam echo- sounder data (SBES). The best interpolated bathymetry was selected based on the minimum root mean squared error. A Random Forest (RF) classification analysis was used to produce species distribution models for six demersal species of fish using records from stereo-BRUVS, and depth derivatives based on SBES, and multibeam echo-sounder (MBES) data. The accuracy and spatial distribution of the residuals from the SBES were compared to the MBES models. The performance of species distribution models for seven species was tested in three areas of the NMP before and after the addition of MBES seafloor backscatter. A RF classification analysis was used to produce the models, and changes in the accuracy of the models were assessed. The possible value of adding historical data of water column backscatter from an SBES into models of the distribution of abundance and relative biomass from stereo-BRUVS data collected years apart was tested. A correlation analysis between the acosutic and stereo-BRUVS data was used as an exploratory analysis. A RF regression analysis was used to produce models of the distribution of abundance and relative v biomass before and after the addition of the water column backscatter data. For a broad-scale analysis, a Kruskal-Wallis rank sum test was used to evaluate the difference in biomass distribution recorded by the echo-sounder and stereo-BRUVS grouped by seafloor backscatter classes. Two experiments were conducted to test the possibility of combining optic and acoustic methods in the assessment of spatial distribution of fish abundance and biomass. Cockburn Sound (CS) was one of the areas, and NMP was the other one. Correlation analyses were conducted between the acoustic variables and the relative abundance and biomass from the stereo-BRUVS. The differences in the biomass observed by the two methods in two benthic habitats were tested using a Wilcoxon rank sum test. Kriging was found to be the best method to interpolate the SBES data, showing less error in the interpolated surface and similar accuracies in the RF model, compared to the MBES models. The inclusion of the MBES seafloor backscatter in the models of species distribution did not always improve the performance of the models, which was species and location dependent. However, the seafloor backscatter showed to be valuable for species with roaming behaviour and an affinity for rocky bottoms. The historical SBES water column data did not increase the variance explained by the RF model for the relative biomass or abundance in the NMP. The temporal variation between the two data sets is possible the main reason for the lack of relationship between them. A broad-scale analysis showed a possible relationship between the biomass distribution recorded by the two methods and the seafloor backscatter. The experiments conducted in CS and NMP showed significant correlations between the acoustics and stereo-BRUVS data. In summary, this study shows the value of using underwater acoustic surrogates to help in the modelling of fish species distribution, to produce spatially explicit information to be used in conservation and management. The possibility of using SBES data which is easier and cheaper to collect and process, could reduce the cost of producing reliable information of species distribution, particularly, for roaming species with a wide niche. The addition of seafloor backscatter data can improve models of species with an affinity for rocky bottoms and roaming behaviour. Historical data from water column backscatter proved not be useful to detect fine-scale patterns of distribution of biomass or abundance detected by stereo-BRUVS when there is a significant temporal difference. However, it provides some insight of broad-scale drivers of the biomass distribution. Although further studies are needed, the results suggest acoustic and stereo- BRUVS data can be combined to comprehend the spatial distribution of fish biomass in reef areas. However, the simultaneous collection of both datasets is advised. vi Acknowledgments A big thank you to my supervisors without whom I would not have been able to walk this path. Special thanks to Iain Parnum for giving me the opportunity of joining the CMST family and the support during the PhD process. Also, a big thank you to Miles Parsons for always be willing to help and for helping me see things when I was not able to do so. Thanks to Ben Saunders and Chandra Salgado-Kent for their time and constructive comments which contributed to improving the manuscripts. My gratefulness goes to the whole CMST family for making me feel as part of it, and for making going to work a happy experience. Thanks to my colleges and friends from the dungeon, without you, the PhD experience would not have been the same. Special thanks to all the great people I have the privilege to share my beloved room with, the old and the new ones including Tristan Lippert, Sven Gastauer for all the laughter, the coding help and for making me feel part of the group. Infinite thanks to Arti Verma and Bec Wellard, for the coffee, the doughnuts, the walks, the food, and the happiness that you brought into my life, I cannot imagine a happier place to work, thanks for all the technical and emotional support. To all my friends in the office: Asma, Angela Recalde Salas, Sylvia Parsons, Arnaud Griffond and Mariana, for the coffees, lunches and long chats and for being there for me when needed. A big thanks to Malcolm Perry, Ben Saunders, Sylvia Parsons, Ashleigh Roddick, and Iain Parnum, for your amazing collaboration and infinite patience during the fieldwork in Cockburn Sound and Ningaloo, I would not have been able to do it without you. To Lauren Hawkins for your help with fish identification and measurements, without you, the hours looking at the screens would have been longer. To the people at the Fish Ecology Lab, for your help with fish identification, and calibration of the cameras, I would not have been able to finish without your help. To my sponsor in Mexico (Conacyt), and the financial support from CMST. This work would not have been possible without both of your support. And to the Australian Acoustical Society for the Education Grant which allowed me to conduct fieldwork in Ningaloo Marine Park. To my friends in Mexico, because time and distance were not enough to prevent you from making me feel loved. Infinite thanks to Sagy Martinez, Daniel Mendez, Saul Pensamiento, and Johnny Valdez, for the calls, the text messages and skype meetings which gave me strength in difficult times. vii To my friends in Perth, the old and new ones, thanks for making me feel at home. Special thanks to Siao Hui, Ruth, Libby, and Julieta. Thanks for the walks, the coffees, the drinks, and the long chats, thanks for being there for me sharing not only the happy but the difficult times during this process.
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