Spatial ecology, genetic barcoding, and vulnerability of tropical Indo-West Pacific batoids, with a focus on Australian species Florencia Cerutti-Pereyra Bachelor of Marine Biology (Honours) A thesis submitted for the degree of Doctor of Philosophy, Research Institute of Environment and Livelihoods, Faculty of Engineering, Health, Science, and the Environment, Charles Darwin University, Australia th 6 July, 2012 Spatial ecology, genetic barcoding, and vulnerability of tropical Indo-West Pacific batoids, with a focus on Australian species A thesis submitted for the degree of Doctor of Philosophy at Charles Darwin University, Australia 6th July, 2012 Candidate Declaration I hereby declare that the work herein, now submitted as a thesis for the degree of Doctor of Philosophy of the Charles Darwin University, is the result of my own investigations, and all references to ideas and work of other researchers have been specifically acknowledged. I hereby certify that the work embodied in this thesis has not already been accepted in substance for any degree, and is not being currently submitted in candidature for any other degree. Full name: Florencia Cerutti-Pereyra Signature: Date: 06/07/2012 iv Acknowledgements I am very grateful to all my supervisors for your recently and patiently acquired expertise in Spanglish. Thank you to: Mark Meekan for the opportunity (and funding) of doing a dream of mine: studying rays in Australia. I’ll do my best to learn from the challenges faced through this project. Chris Austin for sharing your knowledge and love for genetics despite the inexperienced newbies; it is great to work with a scientist that, above all the bureaucratic daily responsibilities, is still passionate about his work. I did enjoy the genetics part of this project and learnt much from working with you. I am especially grateful to my ‘rescue’ supervisors Karen Edyvane and Peter Kyne for joining this project and taking the responsibility of it. I very much wanted to have a ‘management’ and an ‘applicability of all this’ sections in my thesis and you both provided that unexpected opportunity. Although, my biggest thanks to both of you are for being encouraging and supportive through the last part of PhD. I’m very grateful to Karen for your always kind way of dealing with it. I’m extremely grateful too to all the funding parties involved in this project: el Centro Nacional de Ciencia y Tecnología, CONACYT- México, Australian Institute of Marine Science (AIMS), Commonwealth Scientific and Industrial Research Organization (CSIRO), and Charles Darwin University. Many amazing scientists helped me with different parts of this project, from analysis to sampling, so I’m very, very grateful to the following people: Michelle Thums, Keith McGuinness, Yuval Berger, Conrad Speed, Clive McMahon, Shane Penny, and Aaron Petty for your incredible help and advice with data analysis and writing. Many thanks to the best-est GIS gurus Juno Rouwenhorst and Ron Ninnis. Thanks to Peter Last, John Stevens, Bob Ward, and Will White for the countless times I asked for rays’ taxonomic and genetic stories. Many thanks to Mark Shultz and Vivian Wei for you big help and time spent with me in the lab and processing samples. I thank Charles Darwin University staff for their help with all things administrative, electronic, and supportive. Extra thanks to Hale Williams, Roanne Ramsey, and Liz Lycett for sorting out all sorts of project issues; Craig Webster (ITMS) for un-fun technology matters; and Jayshree Mamtora and Vibeke Foss for v your always friendly attitude, incredible support, and useful help. Thanks also to the ATRF/NARU staff for your help and friendliness while I ‘lived’ there. Thank you so very much to all the volees and people that helped during field work, I enjoyed so much sharing our passion for elasmobranchs and the marine world with: Frazer M., Conrad S., Charlie H., Aubanie R., Steph B. (your friendship was the best outcome of that trip!), Peter H., Kristel W., Michelle M., Heather, S. Stevens, and the dream team: Little Karen, Magnus the Norwegian, and el vato loco Owen O’Shea. Thanks to the Scary team (Scary, Ronny, monsieur Bernard, and Zac) for your help and encouragement during field work and conferences. Special and BIG thanks to the Viking, Mat Gray for teaching me how to attach a hook to a line, for catching only a couple of stingrays and for your many –and failed- attempts to be cooler than the Mexican! vi I’m also very grateful to the Exmouth Light Engineering staff, Ningaloo Reef Dreaming, CDU metal workshop, Orca Marine, and Grant Johnson and Adrian Donati from NT Fisheries for your incredible help designing and fixing field work gear and sampling. Many thanks to Gavin Enever, the Anindilyakwa rangers, and Scott Whiting for your help getting around Groote Eylant and catching stingrays. ..Friends are angels who lift our feet when our wings have trouble to remember how to fly... I met many great people and made many good friends during my stay in Australia: the genetics team, Tuty, Rury, and Chelsea; the revolutionary friends, Evi, Rabia, Ve, & Salman; Lil Danielsen for showing me to never give up a climbing route! Maia Berman, Judith Szabo, and Kirsty McAllister for your world- travellers’ wisdom, easy laughs, last-minute editing advices, and full-time support. Many friends also became the family that looked after me, in one way or another, and made this experience more worthwhile. Although, I’d need an extra chapter to enlist so many things and situations where I was grateful for your presence in my life, thank you to Ve for always being a patient English (wait.. Irish) editor, but mostly thank you for always being a supportive friend despite your own personal fun; Costi (y Vale) for always welcoming me in your lives and sharing your ability to always make fun of un-fun situations; thank you Juno, Sabine, and Cindy for many great times of friendship, learning, never-fading support, and fun times. ..Patria y tribu se mezclan en mi mente dice Isabel Allende, así que muchas gracias a mis compañebrios latinos: Gabito, Miguelito, Alf, Rosita, Costi, Enrique y Lore, el sapo-mexican team, y otros más… A ustedes les agradezco nomas por aparecer en un momento de mi vida donde me hacían mucha falta los abrazos, bailes, comidas, cariños y palabrotas de esa cultura nuestra que no existe en ningún otro lado. Me recordaron donde quedaba mi familia y me hicieron sentir que no estaba tan lejos. Gracias a la Chilean family, Michael, Nicole, Alex, & Warrick for welcoming me in your family and your extra support despite my ‘newness’ among you. Salud. Michael Negrete, ojitos, no sé cómo agradecerte por tu presencia y amor constante durante mi último año de loquera y salvarme de la banca rota innumerables veces. Yo no sé de dónde sacaste tanta paciencia to stick around a pesar de mi full- time crisis mode. Tu presencia, sólida como una montaña, tus cariños y abrazos me dieron la estabilidad y fortaleza que me hacía falta para, por fin, terminar este sueño mío. En mi corazón estas pololin. vii Lejos y cerca, como siempre, gracias a mis viejos amigos, Alice, Diego, Rubi, Alita, Lilu, y el Wacho-man por permanecer en mi vida, en mi sueños y echarme porras a pesar de las distancias y desconexiones. Ah como los extraño!! No me alcanzan las palabrotas para agradecer a mis papas y hermanotida por su apoyo todo este tiempo. De Monterrey a La Paz, luego a Darwin y luego a quiensabedondeporquequienserobómicompás??, gracias por recordarme, permitirme y apoyarme siempre para que siga mis sueños por los caminos que me lleven, aunque me lleven al otro lado del mundo, caray. Gracias porque durante cada hoja escrita, cada viaje, cada cosa aprendida, cada planta de albahaca (faltaba más!) y cada momento de estos años de doctorado y vida, ustedes estuvieron siempre presentes y siempre ayudándome a flotar. “There is a pleasure in the pathless woods, there is a rapture on the lonely shore, there is society, where none intrudes, by the deep sea and music in its roar: I love not man the less, but Nature more, from these our interviews, in which I steal from all I may be, or have been before, to mingle with the Universe, and feel what I can never express, yet cannot all conceal” G.G. Byron viii Dedication To my parents and my little big sister. A mis padres, por siempre decirme que yo puedo hacer cualquier cosa que me proponga. Este trabajo está dedicado a los pilares de mi vida: Mamima y Papitufin, y mi forever-present angelito, Nat. ix Abstract Tropical batoids are abundant and important members of coral reef fish communities. Their populations are subject to intense pressure from fishing and habitat degradation, but due to their distinct life-history traits, can only withstand modest levels of decline without stock collapse. Despite this, basic knowledge to ensure their effective conservation and management is lacking. This project addressed this need by combining several current and innovative research tools to assist the integrated management of batoids in northern Australia (NA) and the Indo-West Pacific (IWP). DNA-barcoding was used to confirm the identification of 16 batoid species at Ningaloo Reef (NRMP), Western Australia. It demonstrated its potential to confirm field identifications where taxonomic uncertainty might confound ecological data, although two major sets of problems limiting its application were also identified. Passive acoustic monitoring was used to study the spatial ecology of batoids in the lagoon of NRMP. By using acoustic receivers, the first confirmed nursery area for tropical juvenile batoids in the IWP was identified - a shallow embayment that recorded most of the detections.