ResearchOnline@JCU This file is part of the following reference: Lal, Monal M. (2016) Genetic structure, population connectivity and taxonomic identity of the black-lip pearl oyster Pinctada margaritifera (Bivalvia: Pteriidae), across its Indo-Pacific distribution. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/49812/ The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owner of any third party copyright material included in this document. If you believe that this is not the case, please contact [email protected] and quote http://researchonline.jcu.edu.au/49812/ Genetic structure, population connectivity and taxonomic identity of the black-lip pearl oyster Pinctada margaritifera (Bivalvia: Pteriidae), across its Indo-Pacific distribution Thesis submitted by Monal M. Lal BScMS, MScMS in November 2016 for the Degree of Doctor of Philosophy in Aquaculture College of Science and Engineering James Cook University Townsville, Queensland, Australia ___________________________________________________________________________ FRONTISPIECE ___________________________________________________________________________ Pinctada margaritifera (L.) specimens from Savusavu, Vanua Levu, Fiji Islands. Clockwise from top left: an adult oyster cleaned of epifaunal growth, broodstock oysters feeding while being conditioned for spawning, and examples of the orange and black tissue colour morphotypes characteristic of this species. The scale bars each represent 20 mm. i ___________________________________________________________________________ DECLARATION ___________________________________________________________________________ I declare that this thesis is my own original work, and has not been submitted in any form for another degree or diploma at any university or other institution of tertiary education. Information derived from the published or unpublished work of others has been acknowledged in the text and a list of references is provided. Monal M. Lal 25 November 2016 ii ___________________________________________________________________________ STATEMENT OF CONTRIBUTIONS BY OTHERS ___________________________________________________________________________ My PhD candidature was supported by an Australian Centre for International Agricultural Research (ACIAR) John Allwright Fellowship (JAF) award, which provided for living costs in Australia, as well as enrolment and tuition fees at James Cook University (JCU). Further living expenses were supported by a $2,500.00 AUD grant award from the JCU College of Science and Engineering Higher Degree Research Enhancement Scheme Funding round in 2016. All primary research costs were supported by the ACIAR research project "Pearl Industry Development in the Western Pacific'' (FIS/2009/057)", led by Paul Southgate at the University of the Sunshine Coast. Supplementary research costs were supported by a grant award of $2,000.00 AUD by the then JCU College of Marine and Environmental Sciences (CMES) Graduate Research Scheme Funding round in 2014, as well as CMES Internal Research Allocation (IRA) entitlements of $3,000.00 AUD. A further grant of $3,000.00 AUD was awarded in 2015 from the Crawford Fund, following a successful application during the inaugural round of the Crawford-in-Queensland Student Awards scheme. Logistic support for fieldwork in the Fiji Islands was provided by ACIAR project partners the Secretariat of the Pacific Community (SPC) and the University of the South Pacific (USP). All maps included in this thesis were generated with the assistance of Litia Gaunavou at SPC, and for either providing or assisting with collection of oyster tissue samples, I acknowledge the contributions of the following individuals (in no particular order): Gustaf Mamangkey, Naomi Gardiner, Ismail Saidi, Samantha Nowland, Rowan McIntyre, Steve Warden, Jo Buckee, Tina Weier, Georgia Langdon, Tevainui Frogier-Ellis, Hoc Tan Dao, Hӭa Thái TuyӃn, Samad Jahangard, Hossein Rameshi, Mehdi Doroudi, Max Wingfield, Laura Simmons, Gregory Bennett, Philippa Cohen, Waghon Lalao, Yu Wen Chiu, Eric Gan, Laisiasa Cavakiqali, Cherie Morris, Shirleen Bala, Justin Hunter, Pranesh Kishore, Adi Dionani Salaivanua, Kelly Brown, Jerome Taoi, Epeli Loganimoce, Albert Whippy, Bai Whippy, Toga Whippy, Isimeli Loganimoce, Marilyn Vilisoni, Babitu Rarawa, Ilitomasi Nuku, Samisoni Rakai, Patrick Fong, Nepoci Raleve and Claude Prévost. I was involved in the conceptualisation and experimental design of all work presented in this thesis, including laboratory based experiments and fieldwork for collection of oyster tissue iii samples. Laboratory based experiments included gDNA extraction, gDNA and amplicon product quality controls, gDNA quantification and standardisation, ddRADseq library preparation, as well as sample preparation for submission for commercial genotyping (DArTseqTM). I was also primarily responsible for data management, integrity, analysis and interpretation. This included SNP/PAV genotyping and filtering (chapters 2-5), population genomic analyses (chapters 2-4), hydrodynamic particle dispersal simulations (chapters 3 and 4) and phylogenomic analyses (chapter 5). I was the sole author for all written work throughout the six chapters of this thesis, and am the lead author in all peer-reviewed journal article manuscripts derived from this work, both published, and in preparation. Specific co- author contributions for this thesis are outlined by chapter in the table below. Chapter Publishable unit generated Author intellectual inputs and affiliations 1 1 Lal, M.M., Southgate P.C., Jerry D.R., Lal MM Study execution, project design, Zenger K.R. (2016) Fishing for divergence writing, analysis and editing in a sea of connectivity: The utility of 1,2 ddRADseq genotyping in a marine Southgate PC Project design, invertebrate, the black-lip pearl oyster conception, funding, supervision and Pinctada margaritifera. Marine Genomics editing 25, 57-68. 1 Jerry DR Supervision, technical advice on population genomic analysis and editing Zenger KR1 Project design, conception, supervision, technical advice on population genomic analysis and editing 2 1 Lal, M.M., Southgate P.C., Jerry D.R., Lal MM Study execution, project design, Bosserelle C., Zenger K.R. (2016) A writing, analysis and editing parallel population genomic and 1,2 hydrodynamic approach to fishery Southgate PC Project design, management of highly-dispersive marine conception, funding, supervision and invertebrates: the case of the Fijian black- editing lip pearl oyster Pinctada margaritifera. 1 Jerry DR Supervision, technical advice PloS ONE 11, e0161390. on population genomic analysis and editing Bosserelle, C3 Design, conception and execution of hydrodynamic particle dispersal model, and editing Zenger KR1 Project design, conception, supervision, technical advice on population genomic analysis and editing 3 1 Lal, M.M., Southgate P.C., Jerry D.R., Lal MM Study execution, project design, Bosserelle C., Zenger K.R. (unpubl.) Swept writing, analysis and editing away: ocean currents and seascape features iv influence genetic structure across the Southgate PC1,2 Project design, 18,000 Km Indo-Pacific distribution of a conception, funding, supervision and marine invertebrate, the black-lip pearl editing oyster Pinctada margaritifera. Submitted to 1 BMC Biology. Jerry DR Supervision, technical advice on population genomic analysis and editing 3 Bosserelle, C Design, conception and Lal M.M., Southgate P.C., Jerry D.R., modification of hydrodynamic particle Bosserelle C., Zenger K.R. (unpubl.) dispersal model, and editing Range-wide larval connectivity of the black-lip pearl oyster Pinctada Zenger KR1 Project design, conception, margaritifera using hydrodynamic dispersal supervision, technical advice on simulation. In preparation for PloS ONE. population genomic analysis and editing 4 1 Lal, M.M., Southgate P.C., Jerry D.R., Lal MM Study execution, project design, Zenger K.R. (unpubl.) Fresh evidence for writing, analysis and editing the presence of a species complex in the 1,2 black-lip pearl oyster Pinctada Southgate PC Project design, margaritifera (Bivalvia: Pteriidae). In conception, funding, supervision and preparation for Scientific Reports. editing 1 Jerry DR Supervision, technical advice on phylogenomic analysis and editing Zenger KR1 Project design, conception, supervision, technical advice on population genomic analysis and editing Author affiliations 1 Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811, Queensland, Australia 2 Australian Centre for Pacific Islands Research, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Queensland, Australia 3 Geoscience Division, Secretariat of the Pacific Community, 241 Mead Road, Nabua, Suva, Fiji Islands v ___________________________________________________________________________ ACKNOWLEDGEMENTS ___________________________________________________________________________ This PhD thesis represents the culmination of four very challenging, but rewarding years of work, and would not have been possible without the guidance and providence of the Almighty, and the support, encouragement and inputs of a great many individuals, to whom I am very thankful. Firstly, I would like to express my sincere gratitude and appreciation to my primary advisor Kyall Zenger,