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The Molecular Ecology of an Understudied Endemic Marine Isopod - Isocladus Armatus

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The Molecular Ecology of an Understudied Endemic Marine Isopod - Isocladus Armatus Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. The molecular ecology of an understudied endemic marine Isopod - Isocladus armatus A thesis presented in partial fulfilment of the requirements for the degree of Master of Natural Science At Massey University, Albany, New Zealand William Samuel Pearman 2019 I Abstract The study of populations and the adaptive significance of traits is a major theme in molecular ecology literature. In this thesis I present three lines of research that contribute to the understanding the molecular ecology of a species of New Zealand endemic marine isopod - Isocladus armatus (family: Sphaeromatidae). The goal of this thesis is to develop and utilize a framework to better understand the genomics of marine isopods from a range of genomic perspectives. The first primary chapter aims to assess two ways of enriching mitochondrial DNA from whole genome DNA, and to assemble this species mitochondrial genome. My research indicates that an atypical mitochondrial genome structure, widespread across Isopoda - but previously thought absent within Sphaeromatidae, is present within I. armatus suggesting that this trait has been maintained for an order of magnitude longer than previous estimates. The second primary chapter aims to describe and understand the genetic structure of populations for 8 locations around New Zealand, to understand connectivity and dispersal for I. armatus. Using a panel of 8,020 loci, I find high gene flow on a small spatial scale, while populations on a larger spatial scale exhibit a pattern of Isolation-By-Distance. Additionally, gene flow over one well known biogeographic barrier was much higher than between any other populations on a similar spatial scale, suggesting this barrier may not exhibit a strong effect on this species. Thus, my research indicates a need to revisit and study the way biogeographic barriers affect species with different life histories. The final primary chapter aims to understand the genetic basis for colour polymorphism in I. armatus, with the intention of understanding the adaptive significance and selective mechanism behind this trait. I use genome wide association approaches with a panel of 20,000 loci to answer these questions. I found that loci associated with Colour Polymorphism exhibited signatures of disruptive selection, contrary to initial hypothesis where I expected balancing selection to main colour polymorphism. I propose that substrate heterogeneity in Isocladus armatus’ habitat results in microhabitats, each of which imposes a selective pressure benefiting a specific morph type. The size of these microhabitats is so small that high levels of interbreeding between these microhabitats, and thus between morphs, results in the maintenance of polymorphism across the population. II Acknowledgements Firstly, I would like to thank my partner, Maria, who has been incredibly supportive, patient, and especially tolerant of me ruining many trips to the beach by suddenly disappearing to look for isopods. Secondly, I'd like to thank my main supervisors - Dr. Nikki Freed, Professor James Dale, and Dr. Sarah Wells, for being patient and encouraging me to pursue new ideas and avenues of research in my thesis. I’d also like to thank Drs Olin Silander, Libby Liggins, David Aguirre, and Vanessa Arranz. Everyone has provided insightful and useful suggestions throughout this project and helped me think of better ways to test my ideas. Thank you also for helping me with statistical analyses and interpretations, as well as for pointing me in the direction of literature I might have otherwise overlooked. I’d like to thank my family, especially my parents, Dayle and Barry, and my siblings, Rebecca and Ben, for supporting me in doing my masters and helping me out, and especially for going out of their way to get me extra supplies when I was collecting isopods in the middle of nowhere. Additionally, I'd like to thank my flatmates Ash Sargent and Justine Waterson, who provided many useful suggestions. I’d also like to thank Niel Bruce from the Queensland Museum for taking the time to talk with me about isopod taxonomy, and helping to resolve some of the issues I'd found during my studies. I’d also like to thank the team at the Auckland War Memorial Museum for letting me visit and go through their collections, without them I would most likely have collected the wrong species! Another thank you is owed to Eric Thorstensen for helping me out with access to homogenizers and his many useful suggestions regarding mitochondrial DNA enrichment. III Table of Contents Abstract................................................................................................................................. II Acknowledgements .............................................................................................................. III Table of Contents ................................................................................................................. IV List of Acronyms, Tables, and Figures ................................................................................ VII Acronyms ........................................................................................................................ VII List of Tables .................................................................................................................. VIII List of Figures ................................................................................................................... IX Chapter 1 - Introduction...................................................................................................... 1 Chapter 2 - Mitochondrial Genome Structure for Isocladus armatus .............................. 8 Abstract................................................................................................................................. 8 2.1. Introduction .................................................................................................................... 8 2.1.1 Mitochondrial Structure across Eukaryotes ............................................................... 9 2.1.2 Mitochondrial Structure within Isopoda ................................................................... 10 2.1.3 Approaches to Obtaining Complete Mitochondrial Genomes .................................. 13 2.1.4 Paucity of Mitochondrial Genomes for Isopoda ....................................................... 16 2.1.5 Objectives ............................................................................................................... 16 2.2 Methods ........................................................................................................................ 16 2.2.1 DNA Extraction ....................................................................................................... 16 2.2.2 Enrichment ............................................................................................................. 17 Multiple Displacement Amplification ............................................................................. 17 Differential Centrifugation ............................................................................................. 19 Sequencing of Enriched Samples ................................................................................ 20 2.2.3 Whole Genome Sequencing ................................................................................... 21 2.2.4 Mitochondrial Assembly and Annotation ................................................................. 21 Assessment of Self-Similarity ....................................................................................... 22 Structural Inference ...................................................................................................... 23 2.3. Results ......................................................................................................................... 23 2.3.1 Enrichment ............................................................................................................. 23 qPCR ........................................................................................................................... 24 Differential Centrifugation ............................................................................................. 25 2.3.2 Assembly Results ................................................................................................... 27 Dimer Assembly ........................................................................................................... 27 IV Unit Assembly .............................................................................................................. 30 2.3.3 Evidence for Atypical Structure ............................................................................... 33 Variant Identification .................................................................................................... 33 Dimer ........................................................................................................................... 33 Monomer ..................................................................................................................... 34 2.4. Discussion.................................................................................................................... 36 2.4.1 Failure to
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