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From Specimens to the Tree-Of-Life: Tackling Tropical Arthropod Diversity

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From Specimens to the Tree-Of-Life: Tackling Tropical Arthropod Diversity FROM SPECIMENS TO THE TREE-OF-LIFE: TACKLING TROPICAL ARTHROPOD DIVERSITY DARREN YEO B.Sc. (Hons), NUS A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOLOGICAL SCIENCES NATIONAL UNIVERSITY OF SINGAPORE AND DEPARTMENT OF LIFE SCIENCES IMPERIAL COLLEGE LONDON 2018 Supervisors: Professor Rudolf Meier, Main Supervisor Professor Alfried P. Vogler, Co-Supervisor Examiners: Assistant Professor Huang Danwei Dr. Thomas Bell Professor Dalton De Souza Amorim i Declaration I hereby declare that this thesis is my original work and it has been written by me in its entirety. I have duly acknowledged all the sources of information which have been used in the thesis. This thesis has also not been submitted for any degree in any university previously. _____________________________ Darren Yeo 03 August 2018 The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work ii Acknowledgements I am deeply grateful towards the following people, without whom this thesis would not have been possible: Prof. Rudolf Meier, who has had the central role in shaping my growth as a researcher, student and teacher. Thank you for always being supportive, conscientious and patient with me throughout my PhD studies. I am truly thankful to have a supervisor both passionate and well-versed in this field, who is able to spark and nurture my interest for entomology and molecular biology. I have come a long way since first joining the lab as a fresh-faced undergraduate and I am grateful for this journey spent under your supervision. Prof. Alfried Vogler, for providing me with the opportunity to work with you and your team at the London Natural History Museum. When I first entered the main hall of the NHM and looked upon the incredible skeleton of Dippy the Diplodocus, I never imagined that I would have had the chance to study insects and exchange ideas with the brilliant researchers within. Thank you for always being so approachable and full of great ideas, as well as your time and support even I was abroad. I have learnt so much from you and I will always look back at my time at the NHM with great fondness. Dr. Amrita Srivathsan, for being an amazing mentor and friend. Thank you for being patient with my silly bioinformatics questions and for helping me find my interest in coding. Your sage advice and calm presence have helped me through many difficult times in my PhD and I am incredibly thankful. Jayanthi Puniamoorthy, for being my mentor and very first interaction in the lab. Your tutelage and careful instruction have stuck with me throughout my experiences with molecular lab work, and the fact that my results are not filled with contaminants is testament to your effective mentorship. iii Robin Ngiam from the National Parks Board for first getting me interested in odonates and being always willing to share his expertise. The Ministry of Education and National Parks Board for funding the various projects here. The members and alumni of the NUS Evolution lab: Dr. Sujatha Kutty and Dr. Kathy Su, for taking the time off their busy schedules to listen to my troubles and give amazing advice. Dr. Ang Yuchen, Foo Maosheng and Siti Maimon, for entertaining my constant pestering regarding specimens, imaging and sampling information. Dr. Wendy Wang and Theodore Lee for helping me manage students, interns and the general molecular lab insanity. Gowri Rajaratnam, Rebecca Loh, Mindy Tuan and Bilgenur Baloğlu for the great company and much-needed games/durian nights. Arina Adom and Phua Junwei for your invaluable help with data management, sequencing organization and molecular lab work. Lee Wan Ting, Chen Shihui and Yuen Huei Khee for all the help with molecular lab work and your patience and diligence even when we had to stay late to finish up. Lab alumni Shiyang, Denise, Andie, Gerald, Ivy, Shu Min, and Youguang for your friendship and guidance. The hardworking students and interns who have contributed to the various NGS barcoding projects: Jake, Terence, Keneth, Kaiqing, Jonathan, Quý, Sandra and many others whom I am not able to fully list here. My fellow PhD students and dear friends, Gowri, Jerome, Ian and Bee Yan for lending a listening ear and a helping hand whenever I need them. The members and alumni of the Vogler lab: Dr. Alex Crampton Platt for patiently mentoring me when I was a clueless undergraduate and new to taxonomy and molecular work. Dr. Peter Foster, for his limitless patience with my requests for programme installations and server space. Dr. Thomas Creedy for being such an approachable and brilliant scientist and bioinformatician. Dr. Belen Arias for all the much-needed coffee breaks and conversations, as well as Ginez for having us over. Angelina Ceballos and Borja for your warm companionship and flying halfway across the world to attend my wedding. Hannah Norman, Alejandro Lopez, Mizanur Rahman, iv Beulah Garner, Tang Pu, Nie Rui E and Ge Deyan whom I have learnt so much from and made me feel welcome. Dr. Benjamin Linard, Dr. Carmelo Andújar and Dr. Paula Arribas for graciously taking the time to guide me and answer my queries despite your hectic schedules. My dear friends at the London NHM: Vassia, Nathan, Susy, Katia, Marco, Sandy, Wui Shen and Carlos, thank you for making me feel at home away from home. I am truly glad and honoured to have met you. Sophie, Arseni and Xuewei, who have enriched my life and kept me sane while I was studying abroad. NUS, for funding my studies through the President’s Graduate Fellowship and providing other financial and administrative support. Mom, Dad and Debbie, for being my pillars of support, for always encouraging me to pursue my dreams and passions and for making me who I am today. My wife, Sabrina, for your love and support, for constantly motivating me to strive for self-improvement and to be a better person. I can only hope I have done the same for you. v Table of Contents Summary ................................................................................................................... xii List of Tables ........................................................................................................... xiv List of Figures .......................................................................................................... xvi CHAPTER 1 General Introduction .......................................................................... 1 1.1. Species discovery with NGS barcodes ....................................................... 5 1.2. Life-history stage association with NGS barcodes .................................... 7 1.3. How are these species related to each other: Tree of Life ........................ 8 1.4. Phylogenetics via genome skimming and multiplexed tagged amplicon sequencing ................................................................................................. 9 1.5. Exploring hybrid enrichment for mitochondrial genome skimming ........ 11 CHAPTER 2 It doesn’t have to be full-length: some mini-barcodes perform as well as full-length cox1 barcodes ........................................................................... 12 2.1. Abstract ................................................................................................... 12 2.2. Introduction ............................................................................................. 13 2.3. Materials & Methods............................................................................... 17 2.3.1. Survey of mini-barcodes ......................................................... 17 2.3.2. Species delimitation and testing ............................................. 20 2.3.3. Performance assessment ......................................................... 20 2.4. Results ..................................................................................................... 22 vi 2.4.1. Congruence with morphology ................................................. 22 2.4.2. Decisiveness ............................................................................ 30 2.4.3. Variable sites ........................................................................... 31 2.4.4. Pairwise distances ................................................................... 32 2.5. Discussion ............................................................................................... 33 2.5.1. Should full-length barcodes be preferred? .............................. 33 2.5.2. Are longer barcodes more decisive? ....................................... 35 2.5.3. Which end of the barcode performs better? ............................ 35 2.5.4. Conclusion .............................................................................. 36 2.6. Supplementary Information ..................................................................... 38 CHAPTER 3 Scalable species delimitation with molecular markers: comparing the performance of distance- and tree-based methods ..................... 39 3.1. Abstract ................................................................................................... 39 3.2. Introduction ............................................................................................
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