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Cnemidocarpa Nisiotis Phylogenetic and Phylogeographic Study of the New Zealand Endemic Sea Tunicate Cnemidocarpa nisiotis Genievive Manalo del Mundo A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science in Zoology School of Biological Sciences University of Canterbury, Christchurch New Zealand January 2009 1 Abstract New Zealand is an isolated island nation and more than 95% of its commodities are imported by ship, making New Zealand particularly vulnerable to marine bioinvasion. Its marine biota and ecosystem are unique with numerous endemic organisms, and it is a biodiversity hotspot of global significance. The objective of this study was to integrate invasive theory with phylogeographic studies on a native ascidian. This study was motivated by the introduction of an invasive ascidian, Styela clava to New Zealand. To date, S. clava’s cytochrome oxidase I (COI) data indicate limited sharing of haplotypes between the ports of Lyttelton and Auckland, and areas within Hauraki Gulf. The connectivity between these disparate sites may be a consequence either of common overseas origins via international shipping or local vectoring within New Zealand by coastal shipping. In this thesis I have examined the phylogeographic relationships among populations of an endemic ascidian, Cnemidocarpa nisiotis, to attempt to gauge the likely role that local vectoring plays in the movement of ascidians and other species among New Zealand ports. This study also provides the first population genetic information on a native New Zealand ascidian An endemic New Zealand ascidian was chosen as the study species because the use of an endemic species excludes or at least reduces the possibility of external input from overseas sites con-founding any patterns observed in the data. Furthermore, by excluding external input, the pattern of genetic diversity observed in this species might enable us to determine if local shipping pathways are homogenising C. nisiotis populations. C. nisiotis individuals were collected inside and outside of ports and marinas around Haruaki Gulf, Wellington, Lyttelton, and Dunedin harbours. Each individual were dissected and morphologically identified. Morphological identification of C. nisiotis matched type specimen (Chapter 2). However, preliminary results with COI haplotype network revealed three lineages (A, B and C) and such was the level of differences among these lineages raised the question of the possibility of a cryptic species. This 2 hypothesis was further investigated with phylogenetic analysis using both COI and 18S ribosomal DNA sequence data. Phylogeographic analysis of C. nisiotis COI molecular data demonstrated no significant population genetic structure, with a single common haplotype shared between the North and South islands (Chapter 4). Sharing of haplotypes was also evident between harbours in the South Island and within sites where population samples from inside ports, marinas, and natural habitats were not significantly different from each other. The lack of difference between the North and South Island for this species was surprising given that it was believed to have limited dispersal ability in the absence of anthropogenic movement. However, C. nisiotis displays a star-like phylogeny indicative of a selective sweep, population bottleneck or founder event followed by a population range expansion, thus the lack of difference between islands may be a consequence of too little evolutionary time having passed since the populations shared a common origin for differentiation to have occurred. 3 Acknowledgements Obtaining my MSc degree has always been a life long dream for me and this last two years I have been helped, supported and befriended by many wonderful people who have helped me complete this dream. This project has been one of the most awesome experiences in my life and without you all I would not have been able to complete this research. I especially want to give my gratitude to my supervisors Neil Gemmell, Sharyn Goldstien and Marie Hale. Thank you very much for your support, guidance and patience. Neil- thanks for always being supportive and for encouraging conference participation. Marie- thanks for going through the laborious task of wading through my thesis and being available for last minute questions regarding analysis. Sharyn -thank you very much for training me from the beginning to the end. You were always available, from text messaging me in the field, training me in the laboratory and with computer programs, giving me advice and making sure that I am on track at all times. I would not have been able to complete this project without you. Thank you for being a friend as well as my supervisor. I feel fortunate to have all three of you as my supervisors. I would like to thank everyone in the Molecular Ecology Lab. I feel very lucky for being part of such a fun and diverse group. I have enjoyed working and socialising with all of you. Thank you for providing me assistance and advice for troubleshooting laboratory protocols, as well as teaching me how to work the computer programs needed for my project. I want to give extra thanks to Margaret Will, Antoine Fouquet, Tammy Steeves and Maggie Tisch. I am particularly thankful to Melanie Pierson for letting me stay at her house when I first arrived in New Zealand. One of the perks of this project is going on road trips to collect samples. I would like to give my thanks to Nikki Hawes and Petra Hust for going out of their way to help me collect ascidians. In particular, I need to thank Morten Hust for his effort and enthusiasm in making my field equipment. Thanks for all your hard work and good times. 4 I would like to thank NIWA and MAF Biosecurity New Zealand for letting me have access to the port samples. In particular I would like to thank Mike Page for his expertise in taxonomical identification of ascidians and introducing the bucket methodology, which aided a lot during my field collection. Thank you for training me how to morphologically identify C. nisiotis. In addition, I would also like to thank Anna Bradley, Kimberly Seaward and Graeme Inglis. I would like to thank University staff, students, and friends for helping me with administrative issues and giving me smiles in days when I was in need of some encouragement. This experience would not have been complete without my wonderful friends in New Zealand. In particular, I would like to thank Kerry O’ Connell, Paul South, Laura de Haro and Tracy Melzer. Thanks for all the good times. One of the most painful tasks was handing in drafts numerous times to my advisors. Thank you Regina Eustaquio and Christian Mendieta for proofreading my drafts also, I like to thank Erica Mendieta for all her support during my first year in New Zealand. My family has been so supportive throughout this period in my life and I want to give my sincerest gratitude to my parents and siblings. It was hard moving away from you all but your love and support across the globe have kept me going and I am very lucky to have such a loving family. My greatest appreciation goes to my mentors Leo Ortiz and Mary Silver. They both have always motivated me to pursue graduate school. I am grateful that I have both of you as my role models. You both have a lot of passion for teaching and helping students and I am grateful to have you both to look up to. You have both given me a lot of helpful advice that kept me going these last few years. I always walked out of your office ready and prepared for the challenges ahead of me. I have now experienced one of the most challenging times of in my life and you both have helped prepare me for, writing a thesis. Finally, I am extremely grateful for the Minority Health International Training Foundation for funding my research. 5 Table of Content Chapter I General Introduction 1.1 Phylogeography.................................................................................................... 11 1.2 Phylogeography in New Zealand ......................................................................... 15 1.3 A review of molecular studies in New Zealand ................................................... 15 1.3.1. Stock assessment studies .............................................................................. 16 1.3.2 Genetic discontinuity between the North and South Island .......................... 17 1.4 Marine bioinvasions ............................................................................................. 22 1.5 Ascidians .............................................................................................................. 23 1.6 Non-indigenous solitary ascidians........................................................................ 24 1.7 Study species: Cnemidocarpa nisiotis.................................................................. 25 1.8 Aims ..................................................................................................................... 26 1.9 Thesis Outline....................................................................................................... 29 Chapter II Distribution and Identification of Cnemidocarpa nisiotis 2.1 Introduction .......................................................................................................... 31 2.2 Distribution of Cnemidocarpa nisiotis ................................................................. 32 2.3 Methodology for collection of C. nisiotis............................................................. 32 2.4 Sampling locations and distribution
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