Population Structure, Migration and Habitat Ecology of the Green Turtle (Chelonia mydas) in the Grand Lagon Sud of New Caledonia Author Read, Tyffen Chloe Published 2015 Thesis Type Thesis (PhD Doctorate) School Griffith School of Engineering DOI https://doi.org/10.25904/1912/148 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/367599 Griffith Research Online https://research-repository.griffith.edu.au Population Structure, Migration and Habitat Ecology of the Green Turtle (Chelonia mydas) in the Grand Lagon Sud of New Caledonia Tyffen Chloé Read B. MarSt (Hons) (University of Queensland) (2011) Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy Griffith School of Engineering Griffith Sciences Griffith University Gold Coast Campus May 2015 STATEMENT OF ORIGINALITY This work has not been previously submitted for a degree or diploma in any university. To the best of my knowledge and belief, this thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. May 2015 ACKNOWLEDGEMENT OF PUBLISHED AND UNPUBLISHED PAPERS IN- CLUDED IN THIS THESIS THE PAPERS INCLUDED ARE A MIX OF SOLE-AUTHORED AND CO-AUTHORED PAPERS. Included in this thesis are papers in Chapters 1, 6 and 7 for which I am the sole author. The bibliographic details (if published or accepted for publication)/status (if prepared or submitted for publication) for these papers are: Chapter 1: Not intended for publication (Read TC) Chapter 6: Not intended for publication (Read TC) Chapter 7: Not intended for publication (Read TC) Additionally included in this thesis are papers in chapters 2, 3, 4 and 5 which are co-authored with other researchers. My contribution to each co-authored paper is outlined at the front of the relevant chapter. The bibliographic details (if published or accepted for publication)/status (if prepared or submitted for publication) for these papers including all authors, are: II Chapter 2: Published under Open Access in Plos One: 9:e100083 doi:10.1371/journal.pone.0100083 (Read TC, Wantiez L, Werry JM, Farman R, Petro G, Limpus CJ) Chapter 3: Published online in Wildlife Research on the 19/10/2015 (Read TC, FitzSimmons NN, Wantiez L, Jensen M, Keller F, Chateau O, Farman R, Werry JM, MacKay K, Petro G, Limpus CJ) WR15064 Chapter 4: Submitted to Endangered Species Research on the 17/03/2015 (Read TC, Wantiez L, Keller F, Werry JM, Chateau O, Farman R, Limpus CJ) Chapter 5: Will be submitted to Marine Biology (Read TC, Wantiez L, Werry JM, Keller F, Chateau O, Farman R, Limpus CJ) Appropriate acknowledgements of those who contributed to the research but did not qualify as authors are included in each paper. III GENERAL ABSTRACT Conservation management of wildlife populations requires a comprehensive understanding of the population structure, movement and ecology of threatened and endangered species. The green turtle, Chelonia mydas, is a species found in both tropical and subtropical waters worldwide and since 1982 is listed as endangered on the IUCN red list of threatened species. While C. mydas is afforded protec- tion in many areas of the Pacific it still faces significant threats, both anthropogenic (e.g. by-catch from commercial and recreational fishing, directly targeted as a food sources by indigenous groups and boat strikes) and environmental (e.g. climate change, coastal pollution and habitat degradation). These threats are real for C. mydas in New Caledonia (NC), however strategies to mitigate the threats are lacking as vital information on the C. mydas population structure, movement patterns and habitat use in NC is scant. Proof of C. mydas migration within the Southwest Pacific, including linkages with NC and other Pacific countries, has been shown however more comprehensive data is needed. Further- more, preliminary data suggest the Grand Lagon Sud (GLS) in NC provides important foraging grounds for C. mydas. However, identifying the spatial extent and habitat value of these foraging grounds is a challenge due to the complexity of the C. mydas life cycle and the species tendency for large scale migrations This study investigated the population, movement and habitat ecology of foraging C. mydas in the GLS using a variety of cutting-edge approaches, including long term titanium tagging, genetic analysis for identification of C. mydas Management Units (MU), chemical indicators for habitat preferences, con- ventional methods for dietary analysis and time-depth recorders and satellite telemetry for movement patterns. Titanium flipper tag recoveries of C. mydas tagged in the last 50 years in both New Caledonia and neighbouring countries indicated most of the tag recoveries found in New Caledonia belonged to fe- males from the southern Great Barrier Reef genetic stock. A high percentage of tag recoveries in south- IV ern New Caledonia also belonged to individuals from the d’Entrecasteaux rookery north of New Cale- donia. Some females (n=2) even showed fidelity to foraging sites located 1200 km away from the nest- ing site located in New Caledonia. These data also reveal previously unknown migrations pathways of turtles between the Chesterfield reefs in the centre of the Coral Sea and the southern Great Barrier Reef as well as some migrations of > 4000 km. Genetic analysis of ~770 bp of the mitochondrial (mt)DNA control region from 164 foraging turtles sampled in the GLS was done. C. mydas sampled ranged in size from 48 to 108.4 cm curved carapace length (CCL) and were captured at five different sites within the GLS between September 2012 and December 2013. To provide baseline data for mixed stock analysis, published data from rookeries were also used in addition to a further 105 samples collected at rookeries in the d’Entrecasteaux Islands and Chesterfields Islands in New Caledonia and Malekula Island in Vanuatu. Exact tests of population dif- ferentiation and pairwise FST estimates to test for differences in mtDNA haplotype frequencies indi- cated that rookeries in the d’Entrecasteaux Islands and Vanuatu form unique genetic stocks and that the Chesterfield Islands rookeries are linked to the Coral Sea genetic stock. Mixed stock analysis indi- cated the highest proportion (mean = 0.63) of foraging turtles originate from the d’Entrecasteaux stock. C. mydas (n=21) killed for indigenous tribal ceremonies in the GLS were examined for stomach con- tents and to provide additional insights regarding interpretation of diet from stable isotopes analysis of skin tissue. δ13C and δ15N in skin samples ranged from -19.3‰ to -7.3‰ and 2.8‰ to 15.9‰ re- spectively, indicating a preference for an algal diet. Isotope analysis concur with the stomach contents analysis of which four algae genera contribute 50.4% of the total dry weight. Namely, Hypnea (20.1%), Ulva (12.4%), Caulerpa (9.1%), Codium (8.8%). A significant difference was found within the juveniles C. mydas caught at the four different sites (One-way ANOVA, F = 69.00, df = 3, P < 0.01). Within the GLS juveniles (N=179) caught at Ouen Island, Uo/Mato islands and Goro had much higher δ13C signa- tures compared to the juveniles caught in the Isle of Pines. These results provide continuing evidence that C. mydas feeding patterns differ between localised foraging grounds. V Horizontal and vertical movement for juvenile and adult C. mydas in the GLS were examined using a combination of SPOT/SPLASH satellite tags and time-depth recorders. Seven C. mydas (43 - 113.5 cm CCL) were tracked via satellite tags for 111 to 221 days. Ten juveniles (41.2 - 61.1 cm CCL) were equipped with time-depth recorders for periods of 14 to 221 days. All satellite tagged individuals ex- hibited localised movement within the GLS with a mean 95% convex polygon home range for the sat- ellite tagged juveniles of 54.28 ± 2.42 km². Eight time-depth recorders were recovered and revealed that individuals with depth tags spent 80% of their time at < 5 m with a maximum depth of 18 m. Juvenile C. mydas displayed diel behavior with a higher number of dives during the day and shallower dives during the night. Together these movement data indicate that shallow waters are important for juvenile life history stages of C.mydas in the GLS. Mark recapture efforts were done with 453 foraging turtles tagged with a titanium tag at five locations within the GLS between 2012 and 2013. POPAN population estimate for one foraging ground of the GLS, at Uo Island, indicated > 90 individuals. Recaptures also indicated most foraging C. mydas tagged were resident. A gonad interpretation from fifteen C. mydas killed by local tribes further suggested individuals were resident as there were no mature follicles observed. Recaptured individuals (n = 54) also provided a mean annual growth rate of 0.3±0.1 cm CCL for the GLS. Combined, the above data enabled identification of the importance of the GLS to the life cycle of C. mydas in the South Pacific. Particular strong genetic and habitat linkages occur with the d’Entrecas- teaux Islands and the southern GBR in Australia. These linkages suggesting anthropogenic impacts in the GLS will have reciprocal impacts on C. mydas both across the entirety of New Caledonia and in neighbouring countries. The GLS provides significant foraging grounds where juvenile C. mydas display strong localised residency. Conservation management efforts should recognise the importance of shallow water habitats in the GLS for endangered C. mydas. Furthermore, the unusual absence of mature individuals from these shallow water areas and the strong residency of juveniles suggest C. mydas within the GLS are susceptible to localised overfishing. Unregulated harvesting of C. mydas may VI have significant long term local as well as wide reaching consequences.