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New Technologies Reveal Insights on the Behaviour of Marine Vertebrates

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New Technologies Reveal Insights on the Behaviour of Marine Vertebrates New technologies reveal insights on the behaviour of marine vertebrates by Antoine Marie Dujon BSc Biology and Ecology of Populations, MSc Marine Biology and Biology of Populations Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Deakin University 17 March 2017 1 Acknowledgments I started my PhD on migrating animals by myself migrating over 17 000 km from France to Australia. The last three years are among the most insightful of my life. I’d like to give my sincere thanks to my main supervisor, Professor Graeme Hays, who accepted me as his PhD student and for his continued support and guidance throughout the last three years. I would also like to thank Gail Schofield who offered me so much advice, patiently supervising me, and always guiding me in the right direction. I’ve learnt a lot from her. I am also extremely grateful to Rebecca Lester for her guidance, especially during the last year of my PhD, her advice was always welcome and insightful. Many thanks to all my co-authors for their input on my work and my manuscripts I am thankful to everyone at Deakin University who was involved with my work in any minor or major way, but importantly to Deakin University itself for providing me a scholarship, and the Centre of Integrative Ecology for the funding opportunities. Thank you to all the staff that assisted me during my PhD. Thanks for the moments spent with the many PhD students I met during these three years: Anna Miltadious, Christian van Rijn, Jared Tromp, Matt Jago, Matthew Linn, Michael Lewis, Tom Mock, Helena Stokes, Maud Berlincourt, Johanne Martens, Jessica Hodgson, Adélaïde Sibeaux and David Mitchell. A special thanks to: Jacque-Olivier Laloë - for the many discussions about sea turtle biology and coding; Alexandre Schimel - it was a real pleasure to discuss so many science topics with you; and Fredrick Christiansen - it was a real pleasure to collaborate with you during my PhD. A special thanks to Thomas Stieglitz who introduced me to movement ecology while I was doing my masters back in France. He showed me how fascinating quantitative ecology and movement ecology was. I would like to thanks Romain Morvezen and Nicolas Pédron, my French friends who followed my PhD progresses from the other side of the planet. They both know that completing a PhD is challenging and always provided good advice. iii I am also thankful to my mother and my brother for always encouraging me to do what I love. All my thoughts to my late grand-mother who would have loved to know what I achieved here. iv Publications and chapters arising from this thesis Chapter 2 published in Methods in Ecology and Evolution Dujon AM, Lindstrom RT, Hays GC (2014) The accuracy of Fastloc-GPS locations and implications for animal tracking. Methods in Ecology and Evolution 5:1162– 1169. Chapter 3 is submitted to Marine Biology Dujon AM, Schofield G, Lester RE, Hays GC (2017) Fastloc-GPS reveals daytime departure and arrival during long-distance migration and the use of different resting strategies in sea turtles. Marine Biology: in review Chapter 4 is published in Marine Biology Christiansen F, Esteban N, Mortimer JA, Dujon AM, Hays GC (2017) Diel and seasonal patterns in activity and home range size of green turtles on their foraging grounds revealed by extended Fastloc-GPS tracking. Marine Biology 77:285–299 Chapter 5 is unpublished Dujon AM, Complex movement patterns by loggerhead sea turtles at foraging and wintering sites revealed by Argos-Linked Fastloc-GPS. Chapter 6 is published in Ecosphere Christiansen F, Dujon AM, Sprogis KR, Arnould JPY, Bejder L. (2016) Noninvasive unmanned aerial vehicle provides estimates of the energetic cost of reproduction in humpback whales. Ecosphere. doi: 10.1002/ecs2.1468 v AUTHORSHIP STATEMENT Chapter 2 1. Details of publication and executive author Title of Publication Publication details Dujon AM, Lindstrom RT, Hays GC (2014) The accuracy of The main aim of this Fastloc-GPS locations and implications for animal tracking. publication was to investigate Methods in Ecology and Evolution 5:1162–1169. the accuracy of Argos-Linked Fastloc-GPS location and to determine a method to calculate accurate, high- resolution time series of commonly used metrics in animal movement. Name of executive author School/Institute/Division if Email or phone based at Deakin; Organisation and address if non-Deakin Graeme C. Hays Centre for Integrative [email protected] Ecology, School of Life and Environmental Sciences 2. Inclusion of publication in a thesis Is it intended to include this publication in a Yes If Yes, please complete higher degree by research (HDR) thesis? Section 3 If No, go straight to Section 4. 3. HDR thesis author’s declaration Name of HDR thesis author School/Institute/Division if Thesis title if different from above. (If based at Deakin the same, write “as above”) Antoine M. Dujon Centre for Integrative New technologies reveal Ecology, School of Life and insights on the behaviour of Environmental Sciences marine vertebrates If there are multiple authors, give a full description of HDR thesis author’s contribution to the publication (for example, how much did you contribute to the conception of the project, the design of methodology or experimental protocol, data collection, analysis, drafting the manuscript, revising it critically for important intellectual content, etc.) The data have been previously collected as part of previous projects. GCH and TL provided the data, and suggested the concept of the study. All authors then discussed ways of organising the data for the analysis. I prepared and filtered the Argos-linked Fastloc-GPS tracks from the two different sea turtle datasets to retain accurate and comparable locations that could subsequently be used in the analysis. I organised the data into a database and explored the data via a series of analyses, which generated the final outputs for the publication. Initially, my analyses involved quantifying the accuracy of locations by using a function of the number of satellites and the residual values. I subsequently performed a series of simulations to determine the minimum time interval needed to compute metrics such as heading and speed of travel. I then validated this approach using the track of a green turtle migrating in the Indian ocean. I wrote all the R coding required to run the analyses for this chapter. I drafted the manuscript with assistance from GCH and TL. I produced all figures, and made subsequent improvements to the figures based on suggestions from GCH. Following submission to the journal of Methods in Ecology and Evolution, I received feedback from two reviewers, who provided around 25 comments in total. I compiled responses to all suggestions, with assistance from GCH. This chapter was completed over a period of six months. vi 6. Data storage The original data for this project are stored in the following locations. (The locations must be within an appropriate institutional setting. If the executive author is a Deakin staff member and data are stored outside Deakin University, permission for this must be given by the Head of Academic Unit within which the executive author is based.) Data format Storage Location Date Name of lodged custodian if other than the executive author Excel file http://onlinelibrary.wiley.com/doi/10.1111/2041- 10/11/2014 containing all 210X.12286/abstract locations calculated during the fixed trials viii Chapter 3 1. Details of publication and executive author Title of Publication Publication details Dujon AM, Schofield G, Lester RE, Esteban N, Hays GC The aim of this publication was (2017) Fastloc-GPS reveals daytime departure and arrival to determine the departure and during long-distance migration and the use of different arrival pattern along the diel resting strategies in sea turtles. Marine Biology: in review pattern and resting strategies for two species of migrating sea turtles. Name of executive author School/Institute/Division if Email or phone based at Deakin; Organisation and address if non-Deakin Antoine M. Dujon Centre for Integrative [email protected] Gail Schofield Ecology, School of Life and [email protected] Environmental Sciences, 2. Inclusion of publication in a thesis Is it intended to include this publication in a Yes If Yes, please complete higher degree by research (HDR) thesis? Section 3 If No, go straight to Section 4. 3. HDR thesis author’s declaration Name of HDR thesis author School/Institute/Division if Thesis title if different from above. (If based at Deakin the same, write “as above”) Antoine M. Dujon Centre for Integrative New technologies reveal Ecology, School of Life and insights on the behaviour of Environmental Sciences. marine vertebrates If there are multiple authors, give a full description of HDR thesis author’s contribution to the publication (for example, how much did you contribute to the conception of the project, the design of methodology or experimental protocol, data collection, analysis, drafting the manuscript, revising it critically for important intellectual content, etc.) This chapter was conceived by GCH and GS. Through various discussions with GCH and GS, I determined the key areas of the tracking data on which to analyse. The tracking data were originally collected by NE and GS. I prepared and filtered the Argos-linked Fastloc-GPS tracks from the two different sea turtle datasets to retain accurate and comparable locations that could subsequently be used in the analysis. I first analysed the data to determine the exact time of departure time of turtles from breeding sites and the arrival time at foraging grounds. I designed a methodology to accurately determine the time of day at which turtles departed/arrived. I ran a series of sensitivity analyses to validate the viability of this methodology, with assistance from GS.
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