Evolutionary Biology of the Invasive Northern Pacific Seastar, Asterias Amurensis

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Evolutionary Biology of the Invasive Northern Pacific Seastar, Asterias Amurensis Evolutionary Biology of the Invasive Northern Pacific Seastar, Asterias amurensis by Mark Richardson MSc, Bsc (Hons) Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Deakin University March 2015 “The greatest diffusion of my efforts” Anon Acknowledgements Firstly, I would like to thank my supervisors Craig Sherman and Jeff Ross for their enthusiasm, support, patience, and importantly the opportunity they gave me. Thank you also for your mentorship and encouragement throughout, it has been a challenging but rewarding experience and I hope, just the start of some exciting collaborations. To my fantastic wife, Chelsea, without you this would not have been possible. Your support has been unbelievable. Thank you for motivating me throughout and giving me a push at the right time during the arduous writing up. Thank you so much for picking up all the slack that enabled me to focus on this: I have a lot of making up to do and can’t wait to be home with the family more often now. To Hamish, you put everything in perspective for me. I hope some day you are proud of Dad. To my family, both abroad and here in Australia, thank you for your continuous encouragement and support. I am grateful for every opportunity you have given me that got me to this point. To Mum, thank you for the proofreading, you are a gem. To members of the Sherman Lab – Adam Cardilini, Kim Weston, Aimee Hauser, Julia Kent, Tim Smith, Paul York and Dan Lees – thank you for your assistance, advice and companionship (and Adam, endless philosophical debates), you made the experience incredibly enjoyable. Your friendship means a lot to me. To my colleagues – Lee Ann Rollins, Chris Cowled, James Wynne, Kate Buchannan and Rick Shine – thank you for the great advice, discussions i and for comments on this thesis. Thank you also to members of the CIE for their friendship, mentorship and stimulating discussions. I would like to thank Mieko Komatsu, Mariko Kondo, Koji Akasaka and especially, Miyuki Kaida for facilities and organizational help while in Japan. I am particularly indebted to Kotsuka-san for help in collecting seastars and during experimentation. Thank you also to Masakazu Aoki and members of his Lab, Tatsuya Sakamoto and Kazuhiro Saito for hosting us in Japan and for assisting seastar collections. Thanks are also due to Jim Rooks, David Cahill, Liz McGrath and Rod Watson for providing facilities for temperature treatments and larval rearing in Australia. Katrina Jantz from the Hawkesbury Institute for the Environment conducted cDNA library preparation and sequencing for data in Chapter 3, rapidly and at a fantastic price: thank you. Sequencing and cDNA library preparation was conducted commercially at Macrogen Inc, South Korea, for data from Chapters 4 and 5. Research was supported by a Holsworth Wildlife Research Endowment Award (RM23514), funding from the Centre for Integrative Ecology and an International PhD Scholarship (both Deakin University). The collection of adult seastars was conducted under the Victorian and Tasmanian state government noxious aquatic species permits (NP152, NP252, 11103). ii Table of Contents Acknowledgements ........................................................................................................... i Table of Contents ............................................................................................................ iii Abstract ................................................................................................................................ 1 Chapter 1. Introduction .................................................................................................. 4 1.1 Introduction .............................................................................................................................. 4 1.2 Genetic architecture and evolutionary change in invasive species .................... 7 1.2.1 Genetic variation .................................................................................................................... 7 1.2.2 The influence of bottlenecks and founder events on genetic diversity ........... 8 1.2.3 Evolutionary change arising from mutation .......................................................... 10 1.2.4 Multiple introductions ...................................................................................................... 11 1.2.5 Migration between introduced populations ........................................................... 12 1.2.6 Phenotypic plasticity and epigenetic change ......................................................... 13 1.2.7 Hybridization ........................................................................................................................ 15 1.2.8 On what traits does selection act and when does it occur during the invasion process? ........................................................................................................................... 16 1.3 Application of next-generation sequencing to reveal genetic basis of evolutionary change in invasive species ............................................................................. 18 1.4 A new model, Asterias amurensis, to study evolutionary and invasive biology ............................................................................................................................................................. 20 1.4.1 Life history ............................................................................................................................. 23 1.5 PhD aims and objectives .................................................................................................... 25 1.6 References ............................................................................................................................... 27 Chapter 2. Rapid divergence and maintenance of genetic diversity during range expansion in an invasive marine invertebrate ....................................... 40 2.1 Introduction ............................................................................................................................ 40 2.2 Methods .................................................................................................................................... 44 2.2.1 Population genetic sampling and genotyping........................................................ 44 2.2.2 Genetic data analysis ........................................................................................................ 46 2.2.3 Hydrodynamic modelling ................................................................................................ 48 2.2.4 Plankton sampling and Asterias amurensis larval identification ................. 49 2.3 Results ....................................................................................................................................... 51 2.3.1 Genetic structure of native and invasive populations ......................................... 51 2.3.2 Hydrodynamic modelling ................................................................................................ 60 2.3.3 Identification of A. amurensis larvae in plankton samples .............................. 61 2.4 Discussion ................................................................................................................................ 63 2.4.1 Regional genetic structure of A. amurensis between the native and invasive ranges ................................................................................................................................................. 63 2.4.2 Local genetic structure and larval dispersal in the invasive range .............. 66 2.5 Conclusions ............................................................................................................................. 71 2.6 Supplementary Results....................................................................................................... 72 2.6.1 Genetic structure of native and invasive populations ......................................... 72 2.6.2 Fine-scale genetic structure of invasive populations including additional microsatellite loci .......................................................................................................................... 74 2.7 References ............................................................................................................................... 76 iii Chapter 3. De novo assembly and characterization of the invasive northern Pacific seastar transcriptome .................................................................................... 82 3.1 Background ............................................................................................................................. 82 3.2 Results and Discussion ....................................................................................................... 85 3.2.1 Sequencing and quality control .................................................................................... 85 3.2.2 Transcriptome assembly ................................................................................................. 85 3.2.3 Functional annotation ...................................................................................................... 89 3.2.4 Transcriptome comparison to the Bat star, Patiria miniata proteins ......... 94 3.2.5 Gene Ontology (GO) and KEGG annotation ............................................................. 95 3.2.6 Identification of coding sequences and protein
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