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Gene Flow and Genetic Structure of the Seagrass Thalassia Hemprichii in the Indo-Australian Archipelago

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Gene Flow and Genetic Structure of the Seagrass Thalassia Hemprichii in the Indo-Australian Archipelago Edith Cowan University Research Online Theses: Doctorates and Masters Theses 2016 Gene flow and genetic structure of the seagrass Thalassia hemprichii in the Indo-Australian Archipelago Udhi Eko Hernawan Edith Cowan University Follow this and additional works at: https://ro.ecu.edu.au/theses Part of the Genetics and Genomics Commons, Marine Biology Commons, and the Other Environmental Sciences Commons Recommended Citation Hernawan, U. E. (2016). Gene flow and genetic structure of the seagrass Thalassia hemprichii in the Indo- Australian Archipelago. https://ro.ecu.edu.au/theses/1919 This Thesis is posted at Research Online. https://ro.ecu.edu.au/theses/1919 Edith Cowan University Copyright Warning You may print or download ONE copy of this document for the purpose of your own research or study. The University does not authorize you to copy, communicate or otherwise make available electronically to any other person any copyright material contained on this site. You are reminded of the following: Copyright owners are entitled to take legal action against persons who infringe their copyright. A reproduction of material that is protected by copyright may be a copyright infringement. Where the reproduction of such material is done without attribution of authorship, with false attribution of authorship or the authorship is treated in a derogatory manner, this may be a breach of the author’s moral rights contained in Part IX of the Copyright Act 1968 (Cth). Courts have the power to impose a wide range of civil and criminal sanctions for infringement of copyright, infringement of moral rights and other offences under the Copyright Act 1968 (Cth). Higher penalties may apply, and higher damages may be awarded, for offences and infringements involving the conversion of material into digital or electronic form. Gene flow and genetic structure of the seagrass Thalassia hemprichii in the Indo-Australian Archipelago Udhi Eko Hernawan BSc (Life Sciences) MSc (Marine Biology and Ecology) This thesis is presented in fulfilment of the requirements for the degree of Doctor of Philosophy School of Science Edith Cowan University October 2016 ABSTRACT How genetic variation is distributed across space (genetic structure) and what factors influence the spatial genetic structuring is one of the primary questions in population genetics. The interaction between species biology (e.g. life-history traits) and physical processes operating in the seascape over time, including palaeo-historical events (e.g. sea level fluctuations) and contemporary processes (e.g. ocean currents), have been predicted to influence the extent of gene flow and the spatial genetic structuring in marine organisms. However, the relative contribution of each factor in governing the genetic pattern remains unclear. This study examined the pattern of genetic structure and the factors influencing this using multiple approaches across different temporal and spatial scales in the Indo-Australian Archipelago (IAA), the world’s hotspot of marine biodiversity. By comparing population genetic data of co-distributed marine species (e.g. fishes, molluscs, etc.), this study shows that for marine organisms, the interaction between species biological traits and the physical/environmental processes (habitat variability, water current, etc.) are the greatest drivers of genetic structure in the IAA. Since the physical/environmental processes fluctuate over time, spanning from hours to millennia, the temporal scale (palaeo-historical vs contemporary) at which physical/environmental processes generate genetic structure were examined using seascape genetic analysis. To minimise the effect of different biological traits, the seascape genetic analysis focused only on one species, Thalassia hemprichii, one of the dominant seagrass species in the IAA. The analysis revealed that both palaeo-historical processes (vicariance due to Pleistocene sea level fluctuations) and more contemporary processes (ocean currents) strongly influence the pattern of genetic structure at a regional scale (>300 km). At this spatial scale, the influence of contemporary ocean currents is much smaller than that of historical vicariance. This finding contrasts with previous studies highlighting a strong effect of ocean currents in seagrass connectivity. Only when the effect of historical vicariance was minimised by spatially down-scaling the study from a iii regional (>300 km) to local (<75 km) scale, contemporary processes, including ocean currents and habitat heterogeneity, were shown to strongly influence the pattern of genetic structure. This study also revealed that significant genetic structure can occur at both regional and local scales. At the regional scale, the genetic clusters span distances of at least 500 km, suggesting that genetic connectivity of T. hemprichii populations occurs over very large geographic scales. At the local scale, significant spatial genetic structure was detected, negating the prediction of a single panmictic population. The strong genetic structuring occurring at both large and small spatial scales suggests that predicting seagrass connectivity solely based on geographic distance is inaccurate, and the relevant distance between populations in the marine system is not purely geographic, but rather determined by other factors operating on the seascape setting such as water currents and habitat heterogeneity. Thus, seascape setting is very important in seagrass gene flow and structure. Based on the pattern of gene flow, genetic structure, and genetic diversity, this research provides recommendations for seagrass conservation management in the IAA, including spatial design of conservation reserves and restoration including transplantation. iv DECLARATION PAGE I certify that this thesis does not, to the best of my knowledge and belief: i. incorporate without acknowledgment any material previously submitted for a degree or diploma in any institution of higher education; ii. contain any material previously published or written by another person except where due reference is made in the text of this thesis; iii. contain any defamatory material; or iv. contain data that have not been collected in a manner consistent with ethics approval. Udhi Eko Hernawan October 2016 v ACKNOWLEDGMENT The thesis would never have been accomplished without the help and support of many people. Foremost, I am very thankful to Kathryn McMahon for all the guidance, help and support. She has inspired me to tackle difficulties and kept me focused on the goal during this PhD journey. I also thank Gary Kendrick for his help, suggestions and enthusiasm, which helped strengthen my confidence in completing this PhD. My gratitude goes to Kor-jent van Dijk, who has dedicated his time and expertise to guide me in completing all genetic lab work and analyses. I also thank Paul Lavery, his insightful comments and suggestions helped me to improve my thesis. I acknowledge the significant contribution from Ming Feng (CSIRO, hydrodynamic simulation), Oliver Berry (CSIRO, genetic analysis), Edward Biffin (The University of Adelaide, single nucleotide polymorphism/SNP screening), and Christopher Kavazos (seascape genetics). Others also contributed in many ways for field assistance, collecting samples, lab work or comments and suggestions: L. Ruiz- Montoya, J.P Hobbs, A.Z. Perez, F. Webster, A. Isaac, S. Isaac, T. Stumpagee, M. Waycott (the State Herbarium of South Australia and the University of Adelaide), Flavia Tarquinio, Maryam Abdolahpour, Rachele Bernasconi, Anna Lafratta and all other CMER members, Abigail Moore (STPL Palu), Bahtiar & K. Togaishamu (Unhalu Kendari), Wahyu Adi & Nur Annis (UBB Bangka), Try Al Tanto (LPSDKP Padang), Raismin Kotta, Yulius Suni, Ucu Y. Arbi, Susi Rahmawati, Supono, Alan, Alvi Sitepu, Ahmad Ainarwowan, Aliyadi, and Kadir Yamko. I also thank the Bardi Jawi community, rangers and the traditional owners for access and field assistance in the Kimberley. My family has always been very supportive of my choices and ambitions. A special thank goes to my wife, Miyati, for her support, patience and care during the many months spent away from home and the kids. vi I would like to thank to the South Australian Regional Facility for Molecular Evolution and Ecology (SARFMEE) for enabling genetic lab work; and to the Research Centre for Oceanography (P2O-LIPI), UPT LIPI Tual, UPT LIPI Biak, UPT LIPI Mataram, P2LD LIPI Ambon, UPT LIPI Pulau Pari, UPT LIPI Bitung, UPT LIPI Bitung, STPL Palu, LPSDKP Padang, Universitas Bangka Belitung and Universitas Haluoleo, Indonesia for providing supports and assistance during field work in Indonesia. Finally, I am very grateful to the financial support of ECU-IPRS; the G100379 project of the Department of Education and Training, Collaborative Research Network Program (Funding Agreement CRN2011:5, Edith Cowan University and University of Western Australia); the Western Australian Marine Science Institution (WAMSI Kimberley Research Program: Project 1.1.3 Ecological Connectivity (KM) and 2.2.4 Primary Producers (GAK)); and the Indonesia Endowment Fund for Education (LPDP-Indonesia). vii TABLE OF CONTENTS ABSTRACT ................................................................................................................ iii DECLARATION PAGE .............................................................................................. v ACKNOWLEDGMENT ............................................................................................. vi TABLE OF CONTENTS .........................................................................................
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