Faculty of Science and Engineering School of Earth and Planetary Science Variability in Baleen Whale Acoustical Ecology: Implications for Optimal Monitoring Using Passive Acoustics Angela Paola Recalde Salas This thesis is presented for the Degree of Doctor of Philosophy in Applied Physics of Curtin University July 2020 This page has been deliberately left blank Declaration of authorship I, Angela Recalde-Salas, 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 or diploma in any university. The research presented and reported in this thesis was conducted in compliance with the National Health and Medical Research Council Australian 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, Approval numbers EC_2013_27 and AEC_2013_28. Date: 19 of July 2020 i This page has been deliberately left blank ii “Walk in kindness toward the Earth and every living being. Without kindness and compassion for all of Mother Nature’s creatures, there can be no true joy; no internal peace, no happiness. Happiness flows from caring for all sentient beings as if they were your own family, because in essence they are. We are all connected to each other and to the Earth.” Sylvia Dolson “The oceans are the planet's last great living wilderness, man's only remaining frontier on Earth, and perhaps his last chance to prove himself a rational species.” John L. Culliney iii Abstract The potential impacts of man-made underwater noise in the oceans has been of growing concern in recent decades. To monitor marine fauna populations that produce sound and assessing potential impacts, passive acoustic monitoring (PAM) has become popular because of its relatively low cost. Although PAM has great potential for monitoring of baleen whale populations, the acoustical baseline to develop an optimal monitoring plan is yet in development. To optimise PAM for baleen whales and improve the accuracy on ecological parameters estimates (e.g. population trends), its biases and limitations need to be understood. This study aimed to improve our current knowledge of biases and limitations of PAM for pygmy blue whales (Balaenoptera musculus brevicauda) and humpback whales (Megaptera novaeangliae) that migrate through Geographe Bay, Western Australia. Underwater sound recording using a single stationary recorder and land-based theodolite tracking were undertaken concurrently during the whale migratory season in 2010-2011 and 2013-2014. These data were used to: (1) describe the acoustic repertoire of each species, where information had not been reported previously (2) compare commonly used methods for measuring relative indices of abundance; including acoustic energy, counts of vocalising groups of whales (based on the known acoustic repertoire), and counts of groups of whales observed visually, (3) evaluate biological, environmental, and anthropogenic influences on numbers of vocalising groups detected in recordings (‘vocalisation rates’), (4) compare estimated detection probabilities for each species under different environmental and anthropogenic conditions using acoustic and visual observations and (5) make recommendations for the development of optimal monitoring protocols for pygmy blue and humpback whales in Western Australia using PAM. Sounds in the vocal repertoire included 17 non-song sounds produced by humpback whales and five by blue whales. Vocalisation rates varied widely between species, with humpback whales detected more frequently than pygmy blue whales. Vocalisation rates also varied among years and over each migratory season, and between the type of sound (song or non-song); but not with environmental conditions and vessel presence. Sound energy measured in the form of signal-to-noise ratio was highly correlated with number of vocalising groups for humpback whales but only when temporal factors and presence of vessels was accounted for. Correlation between sound energy and number of groups visually counted was low for both species. Overall, humpback whales had a higher acoustic detection probability and were vocal for longer periods of time than blue whales. In iv contrast to pygmy blue whales, humpback whales had cohort-specific detection biases with groups of mother-calf pairs or multiple adults having a lower probability of detection. As a result of detection biases and variability in vocalisation rates over time and between species and sound types identified in this study, it is clear that PAM protocols cannot be generalised over the two species. A concurrent acoustic and visual observation pilot study is recommended where possible before undertaken a purely PAM-based program, if knowledge of a species’ acoustic behaviour and ecology within certain habitats is unknown. In this way, recording schedules can be optimised and species-specific adjustments can be made to maximise the likelihood of detecting less vocal species or quieter cohorts. Ultimately, optimizing monitoring to achieve these goals will improve the accuracy of knowledge gained. Thus, species that require long-term monitoring, such as baleen whales, could perhaps have an initial higher-cost pilot study with the aim of a longer-term more cost-effective approach (PAM); thus making improving the basis for conservation and management of baleen whales more widely accessible. v This page has been deliberately left blank vi This thesis is dedicated to my family and friends who supported and encouraged me every step of the way; to all the dreamers who fight for making a difference in this crazy world; and to mother earth vii Acknowledgments Since finishing my undergraduate studies, one of my goals was to pursue a PhD program. I knew little about the hard and lonely journey that a PhD is, and even more when you are in a country that is not your own, with a language that is not your own, with no friends and little money. Since starting this journey, ups and downs, sickness and fears have crossed my path, but all these experiences helped me to grow as a professional and more important as a human being. The knowledge you acquire during a PhD program goes beyond the academic scope; you learn so much from supervisors, friends, fellow students, mentors, academics, administration and everyone around you. I want to acknowledge and thank them all. First of all, the official thanks. This study was part of the South West Whale Ecology Study (SouWEST, https://souwest.org/). SouWEST was supported by grants from Australian Geographic; the International Fund of Animal Welfare (IFAW); The Department of Fisheries from Western Australia; and Holsworth Wildlife Research Endowment (Equity Trustees Charitable Foundation and the Ecological Society of Australia). I would also like to thank the Department of Spatial Sciences at Curtin University for lending their theodolites to us. To our SouWEST Partners, Chris Burton from Western Whale Research, Ron Glencross from Dunsborough Coast and Land Care (DCALC) and Iain Wise, thank you for your support and help during fieldwork. In addition, thank you to Eric Kniest from the University of Newcastle for helping us set up Cyclops and VADAR for theodolite tracking and for all his advice for land-based data analysis. Also to Sea Rescue for their unconditional support deploying and retrieving the recorders in Geographe Bay. Secondly, I would like to thank my four supervisors, Dr. Chandra Salgado Kent, Dr. Christine Erbe, Dr. Hugh Possingham and Dr. Robert McCauley. Chandra was my principal supervisor, but more than that a mentor and a friend. Thank you for all your support and for been so patient; for teaching me to see the good in every situation always and for showing me how to be diplomatic in complex circumstances. I also want to thank you for teaching me that accepting your limits is not weakness but strength. I will always treasure those fieldwork adventures where surrounded by nature you show me how to handle difficult situations and conquer my fears (snakes included!). But most of all, thank you for showing me how to be compassionate and give volunteers a great life experience. Having had my fair share viii of not so positive volunteer and work experiences, working with a researcher that values everyone's capabilities was an inspiration. I especially wanted to thank you for supporting my ideas, even when they sounded a little bit unconventional, and for guiding me to achieve them through very constructive discussions. You help me to be more critical not only of others ideas but of my own. Thank you for everything you teach me during the last seven years of working together and for your friendship. I hope our friendship continues and that we keep working together for many years more. Por cierto, las arepas son colombianas! Christine, although we did not have the opportunity to spend much time together or to share fieldwork, I learnt so much from you, not just about physics but also about how to be a strong and compassionate leader. Thank you for having the patience to explain to me the same basic concepts over and over again, and for answering my really silly questions. I know many times we ended up “lost in translation” because of my poor communication skills or my bad grammar, but I am glad we always managed to sort the obstacles and find solutions. I really admire your optimism, your strength and your enthusiasm for new ideas, even the crazy ones. Thank you for your support and understanding at all times. Hugh, I cannot thank you enough for all your mentorship and advice, for opening the doors of your lab, for giving me the opportunity to learn and grow as part of CEED and, for always giving me some time in your crazy schedule.