Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School March 2020 Genomics and Population History of Black-headed Bulbul (Brachypodius atriceps) Color Morphs Subir B. Shakya Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Biology Commons Recommended Citation Shakya, Subir B., "Genomics and Population History of Black-headed Bulbul (Brachypodius atriceps) Color Morphs" (2020). LSU Doctoral Dissertations. 5187. https://digitalcommons.lsu.edu/gradschool_dissertations/5187 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. GENOMICS AND POPULATION HISTORY OF BLACK- HEADED BULBUL (BRACHYPODIUS ATRICEPS) COLOR MORPHS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Subir B. Shakya B.Sc., Southern Arkansas University, 2014 May 2020 ACKNOWLEDGMENTS A dissertation represents not only the effort of a single candidate but a document highlighting the roles and endeavors of many people and institutions. To this end, I have a lot of people and institutions to thank, without whom this dissertation would never have been completed. First and foremost, I would like to thank my advisor, Dr. Frederick H. Sheldon, who has guided me through the six years of my Ph.D. studies. He has not only believed in me throughout this process but also nudged me along academic paths that I would never have taken on my own. As a great writer, editor, and mentor, he has helped me polish this dissertation and all my projects at LSU, allowing me to produce some great research. This dissertation would also not have been possible without the aid and advice of my graduate committee mentors, Dr. Robb T. Brumfield and Dr. Brant C. Faircloth, as well as my Dean’s Representative, Dr. Javier G. Nevarez. All of them have helped me enormously with planning, implementing, and writing my dissertation. They were never afraid to ask me questions and help me think more critically about my project and what I should do next. My parents, Birendra B. Shakya and Suravi Shakya, and sister, Sneha Shakya, have been instrumental in getting me to where I am now. They have supported me from the very beginning and always have comforting words for me when I am struggling. Living halfway around the world is never an easy thing, so support from my family was integral. If they had not acknowledged my interest in natural history, pushed me to pursue a degree in the U.S., and allowed me to work on what I really loved, this dissertation would never have been started. None of this work would ever have been possible without the facilities at the LSU Museum of Natural Sciences and its faculty and staff. This was my home away from home. I would like to thank Dr. Van Remsen, Dr. Chris Austin, Dr. Prosanta Chakrabarty, and Dr. Jake Esselstyn, who have been a great help and for their excellent guidance whenever I had any questions or issues. Tammie Jackson, who basically holds the museum upright, deserves exceptional commendation for help with any and all academic, financial, travel, and permitting work that requires jumping bureaucratic hurdles. No expedition can be contemplated without the excellent work of Tammie. Valerie Deroun’s help with all expense paperwork, outreach organization, and basically assistance with even mundane tasks was greatly appreciated. Finally, nothing related to the bird collection and specimen/tissue work would be doable without the knowledge and expertise of Steve Cardiff and Donna Dittmann. Navigating the import/export process with specimens takes a lot of work and effort and Steve and Donna have effortlessly helped me and everyone navigate through those tough waters. They also instilled knowledge about bird preparations and bird curation, which has really helped with smooth functioning in the field and in the museum collections. I would like to thank colleagues at Louisiana State University Museum of Natural Science, University of Kansas Biodiversity Institute and Natural History Museum, Yale Peabody Museum, Field Museum of Natural History, and California Academy of Sciences for providing tissues and toe-pads for DNA extraction. For field work in Indonesia, I would also like to thank the Indonesia State Ministry of Research and Technology (RISTEK research license numbers 388/SIP/FRP/E5/Dit.KI/XI/2016, 389/SIP/FRP/E5/Dit.KI/XI/2016, 107/FRP/E5/Dit.KI/I/2018, 1079/FRP/E5/Dit.KI/II/2018, and 1126/FRP/E5/Dit.KI/I/2018) and the Ministry of Forestry for permission to undertake research on Maratua, Bawean, Kalimantan, and Sumatra islands. I also thank the Research Center for Biology, Indonesian Institute of Science, and the Museum Zoologicum Bogoriensis. Their staff, and particularly Dewi Prawiradilaga, Tri Haryoko, ii Mohammand Irham, and Suparno, helped with permitting, fieldwork, field logistics, as well as specimen export and, in the process, became good friends. For specimens from Malaysia, I thank the Malaysian Prime Minister’s Department, the Chief Ministers’ Departments of Sarawak and Sabah; Sarawak Forest Department, Forestry Corporation, and Biodiversity Institute; the Universiti Malaysia Sarawak; and Sabah Parks, Museum, and Wildlife Department. Funding for the project and fieldwork was provided largely through grants acquired by my advisor Dr. Sheldon from the NSF (DEB-0228688 and DEB-1241059), National Geographic Society (8753-10), and Coypu Foundation. I also received funding from the American Museum of Natural History, American Ornithologists’ Union, and LSU Museum of Natural Science for various portions of my dissertation. Current and former members of the Sheldon lab have been a great help and source of support for my dissertation. Dr. Haw Chuan Lim has been an influential force in helping me formulate the project and ideas on how to proceed with in the face of various difficulties. Dr. Clare Brown helped a lot in computational and bioinformatics work, and her suggestions on best practices for presenting dissertation research was greatly appreciated. Vivien Chua helped with a lot of lab work and the collection of key specimens. Ryan Burner helped train me as a field ornithologist and helped me greatly during expeditions in Malaysia and Indonesia. Matt Brady, along with Oscar Johnson, Jon Nations, and Heru Handika, also helped a lot with field work. I would like to thank all my friends and colleagues at LSU for their moral and academic support. I started graduate school with an exceptional cohort—Joanna Griffiths, Oscar Johnson, Rafael Marcondes, Genevieve Mount, Zachary Rodriguez, and Mark Swanson—and we all have held each other’s hands as we moved along with our dissertations. I would also like to thank a number of other current and former graduate students and post-docs at the Museum: Dr. Mike Harvey, Dr. Glenn Seeholzer, Dr. Ryan Terrill, Dr. Jessica Oswald, Dr. Cathy Newman, Dr. Fernando Alda, Dr. William (Bill) Ludt, Dr. Carl Oliveros, Andre Moncrieff, Marco Rego, Glaucia Del-Rio, Jon Nations, Jessie Salter, Anna Hiller, Alec Turner, Pam Hart, Diego Elias, Jackson Roberts, Eamon Corbett, Spenser Babb-Biernacki, Heru Handika, and Sheila Rodriguez. Alongside my friends at the Museum, other graduate students from the Department of Biological Sciences and the Department of Renewable Natural Resources have been exceptional in my development at LSU: Michael Henson, Alicia Riegel, Elisa Elizondo, Amie Settlecowski, Allison Snider, Cameron Rutt, and Vitek Jirinek. To everyone else who has influenced me through my time at LSU, I am greatly thankful. Finally, I would like to thank Dr. Martin Päckert and Sontaya Manawatthana for providing sequences from their studies. I also acknowledge the help of Dr. Rebecca Kimball and two anonymous reviewers for insightful comments that improved the manuscript based on Chapter 2, which was published in the journal Ibis. I am thankful for the B10K consortium for providing annotation data for the genome of the Black-headed Bulbul (Brachypodius atriceps), the main subject of the dissertation. I thank Dr. Daniel Portik and Dr. Kevin Winker for their help with running dadi models. iii TABLE OF CONTENTS ACKNOWLEDGMENTS………………………………………………………………………...ii ABSTRACT……………………………………………………………………………………….v CHAPTER 1. INTRODUCTION…………………………………………………………………1 CHAPTER 2. THE PHYLOGENY OF THE WORLD'S BULBULS (PYCNONOTIDAE) INFERRED USING A SUPERMATRIX APPROACH……………………………..……..3 CHAPTER 3. GENETIC INVESTIGATION OF INSULAR MELANISM IN BLACK- HEADED BULBUL (BRACHYPODIUS ATRICEPS) OF SOUTHEAST ASIA.………...14 CHAPTER 4. HISTORICAL DEMOGRAPHY OF THE BLACK-HEADED BULBUL (BRACHYPODIUS ATRICEPS) ON MARATUA AND BAWEAN ISLANDS, INDONESIA………………………………………………………………………............35 CHAPTER 5. CONCLUSIONS……………………………………………………………...….49 APPENDIX A. SUPPLEMENTARY MATERIAL FOR CHAPTER 2..……………………….50 APPENDIX B. COPYRIGHT INFORMATION FOR CHAPTER 2…………………………...73 REFERENCES…………………………………………………………………………………..78 VITA……………………………………………………………………………………………..91 iv ABSTRACT Intraspecific polymorphism in birds, especially color polymorphism, is an area of active research in evolutionary biology. Using