DIVERSIFICATION OF THE TROPICAL PACIFIC AVIFAUNA By Michael J. Andersen Submitted to the graduate degree program in Ecology and Evolutionary Biology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. ________________________________ Chairperson Robert G. Moyle ________________________________ A. Townsend Peterson ________________________________ Rafe M. Brown ________________________________ John K. Kelly ________________________________ Alan Redd Date Defended: 9 December 2013 The Dissertation Committee for Michael J. Andersen certifies that this is the approved version of the following dissertation: DIVERSIFICATION OF THE TROPICAL PACIFIC AVIFAUNA ________________________________ Chairperson Robert G. Moyle Date approved: 9 December 2013 ii Abstract I investigated the origins and diversification of Pacific avifaunas. Chapters 1, 2, and 4 elucidate the evolutionary history of three classically polytypic species complexes of Pacific island birds using multilocus phylogeographic approaches. The focal taxa were: Ceyx lepidus (Aves: Alcedinidae), Pachycephala pectoralis (Aves: Pachycephalidae), and Todiramphus chloris (Aves: Alcedinidae). In chapter 3, I examined the systematic relationships of 14 species of Pacific honeyeaters (Aves: Meliphagidae) relative to continental lineages. Each of these studies revealed novel biogeographical patterns heretofore underappreciated in Pacific birds. All three species complexes underwent rapid diversification with extensive genetic and phenotypic differentiation across widespread island archipelagos spanning thousands of kilometers from southeast Asia to Polynesia. This pattern was evidenced by phylogenies with short basal internodes, long stem lineages, and shallow divergences within each taxon. Todiramphus was noteworthy because it has attained extensive reproductive isolation, despite the recency of the radiation, as evidenced by multiple sympatric taxa throughout the Pacific. The work on meliphagid honeyeaters found extensive paraphyly of Pacific lineages with respect to their presumed continental congeners. I found evidence for a Central Polynesian radiation that included taxa from the eastern Solomon Islands, Fiji, Samoa, and Tonga. Throughout this dissertation I draw inferences on the processes of origination, diversification, and extinction in Pacific avifaunas using a comparative framework across multiple lineages at different scales of differentiation. iii Acknowledgments This dissertation would not have been possible without dozens of specimen collectors, collection managers, and curators whose collective effort made available the majority of samples I used. To the collectors, you are too many to name individually, but please accept my deepest gratitude for continuing to build scientific collections in the remotest places on earth in a systematic and responsible manner. I know the breadth of sampling in this dissertation could not have been completed alone in six years. The following collections managers and curators processed myriad loan requests, both for this dissertation and numerous side projects. I thank you for your timely assistance: Paul Sweet, Peter Capainolo, and Tom Trombone, American Museum of Natural History; Moe Flannery, Laura Wilson, and Jack Dumbacher, California Academy of Sciences; Robert Palmer and Leo Joseph, CSIRO, Australian National Wildlife Collection; Jean Woods, Delaware Museum of Natural History; Dave Willard, Ben Marks, John Bates, and Shannon Hackett, Field Museum of Natural History; Kimball Garrett, LA County Museum; Donna Dittmann and Robb Brumfield, Louisiana State University Museum of Natural Science; Chris Milensky, Smithsonian Institution, National Museum of Natural History; Rob Fleischer, Smithsonian Institution, National Zoological Park; Andrew Kratter and David Steadman, University of Florida Museum of Natural History; Mark Robbins, Rob Moyle, and Town Peterson, University of Kansas Natural History Museum; Janet Hinshaw, University of Michigan Museum of Zoology; Sharon Birks, University of Washington Burke Museum; Ron Johnstone, Western Australian Museum; Kristof Zyskowski, Yale Peabody Museum. In addition, I want to thank Thane Pratt for graciously making available his invaluable material from New Guinea. I received generous funding from multiple sources throughout my dissertation. For this I thank the following institutions and funding agencies: the American Museum of Natural History iv Frank M. Chapman Fund, the American Ornithologists’ Union Research Award, the Sigma-Xi Grants-In-Aid of Research, and the University of the South Pacific. For travel awards I thank the American Ornithologists’ Union, the Cooper Ornithological Society, the Smithsonian Institution and National Tropical Botanical Garden, the University of Kansas Doctoral Student Research Fund, the University of Kansas Biodiversity Institute Panorama Fund, the University of Kansas Department of Ecology and Evolutionary Biology. Portions of this dissertation were funded by grants awarded to my academic advisor, Rob Moyle, including NSF (DEB-0743491, DEB- 0743576), NIH (0061497) the University of Kansas General Research Fund, and the KU Research Investment Council & Strategic Initiative Grant Program. I could not have accomplished five collecting expeditions to Fiji during my time at KU without the support, friendship, and guidance of my Fijian colleagues. Alifereti Naikatini and Marika Tuiwawa know how to make things happen more than most I’ve met. It was a pleasure to work with you and I hope it was only the beginning of a life-long partnership. To the rest of the crew at the South Pacific Regional Herbarium, and elsewhere in Fiji, my sincerest thanks for your help throughout the many corners of your beautiful country. Vinaka vakalevu, Mika, Vido, Lulu, Manoa, Nunia, Apaitia, Hilda, Mereia, Siteri, and Isaac. Jesse Grismer and I spent a month in Fiji’s Southern Lau Archipelago and it was a blast! Dick Watling offered his support by way of many fruitful conversations over bowls of kava at his beautiful home in Suva. I thank the Biosecurity Authority of Fiji and the Department of Environment for permits. Hannah Shult was a wonderful undergraduate student to work with in the molecular lab. She produced a significant portion of the sequence data for my fourth chapter. I thank her and wish her well in her next endeavor as a M.Sc. student at LSU. The KU Bird Division was invaluable to my success as a graduate student. First and foremost, my academic advisor, Rob v Moyle, has been a wonderful mentor and friend. For six years he has struck a perfect balance of hands-on vs. hands-off in his mentorship. He gave me the freedom to decide my dissertation topic when I was ready to, including the first two years during which I insisted on a Neotropical focus. He invited me on a fortuitously timed expedition to Fiji late in 2009, which changed the course of my graduate career for the better. Since our geographic foci aligned, he has been a great colleague in our endeavors to study the birds of the Pacific. Mark Robbins has been a great friend, birding companion, and teacher of all things related to collections and field expeditions. He is the best at what he does and I am very fortunate to have learned from him. The energy and enthusiasm he brings to everything he does is an inspiration and something I will always aspire to. Town Peterson has been a wonderfully supportive committee member. He has an incredible work ethic and can edit a manuscript or grant proposal better than anyone I know, a skillset that helped make my writing better. Town, your uncanny ability to procure funding for specimen- based field work was the reason I found myself collecting in such disparate places as Peru, Sierra Leone, and the DR Congo during my graduate career. Those expeditions were exceptionally positive experiences that I would not otherwise have had. My three other committee members, John Kelly, Rafe Brown, and Alan Redd, were all gracious with their time and support. Thank you for your encouragement throughout my time at KU. John, thanks for all the help with RADSeq in your lab. I look forward to our continued collaboration on that project. Jorge Soberón is perhaps the most broadly knowledgeable person I know. The level of intellectual discourse at bird lunch was always elevated when you were present—I will miss this when I leave KU. The number of graduate students and post-docs in the KU Bird Division since 2008 was many. Thank you for your friendship through all the pleasure and pain that is graduate school. In no particular order, thank you to: Pete Hosner, Carl Oliveros, Árpi Nyári, Brett Benz, vi Luis “Howell” Sánchez-Gonzalez, Joe Manthey Robin Jones, Hannah Owens, Andrés Lira, Lindsay Campbell, Mona Papeş, Narayani Barve, and Luke Campillo. In addition to the Bird Division, thank you to the myriad graduate students in EEB and Geology who were great friends, colleagues, and soccer teammates. I am grateful for all the advice and science I learned from you along the way: Cameron Siler, Charles Linkem, Jamie Oaks, Jeet Sukumaran, Anthony Barley, Luke Welton, Jake Esselstyn, Jesse Grismer, Erin Saupe, Wes Gapp, Kendra and Julius Mojica, Joanna Cielocha, Patrick Monnahan, Pete Schillig, Laci Gerhart, Allie Fuiten, Taro Eldredge, Curt Congreve, Scott Travers, and Karen Olson. Thank you Una Farrell for being such a wonderful friend and neighbor to me and Cori on Canterbury Lane. We’ll always have our neighborhood family of Barred Owls. Jon King, thanks for all the great birding we did together and for allowing me to dump the lion’s share of Kansas eBird duties on your shoulders. You took the responsibility and ran with it, and eBird is better for it. Roger Boyd, I cannot thank you enough for the amount of work you put in to the Baker Wetlands restoration. You single- handedly created a superior shorebirding patch on the south edge of town. My research productivity suffered in April and May because of it, and I thank you for it. Nick McCool, thank you for taking three days of your life during a massive snow storm to teach me how to sequence RADtags. Brian Finley and Erin Saupe, you are great friends, a special couple, and I will forever be supremely thankful for your friendship and unending generosity. Thank you for opening your home to me in my final semester of graduate school. You two are the best and I owe you one. Spider is cool, too, especially now that he likes me. My brother, Evan, and his wife, Jess, continue to amaze me in everything they do. Thank you for being so supportive from afar. I am looking forward to moving back east where we will vii be only a subway’s ride away in the same city! Cannot wait to hang out with you two more often than Kansas has allowed. I am especially grateful to my parents, Paul and Ana. They were patient with me the past six years of grad school when I visited home only once per year. I am most grateful for their unwavering support of my pursuit of endeavors that have been anything but financially stable. I grew up in a place where parents have a knack of expecting their children to achieve vocational success (i.e., medical doctor or lawyer), but my parents never gave in to this mindset. Thank you for letting me chase my dreams to study the natural world. Finally, for my wife Cori Myers, I reserve my deepest and most heartfelt thanks for everything you do. You gave me the motivation I needed to leave Ithaca and go to graduate school. I am so proud of everything you have accomplished at Kansas and now in your next endeavor at Harvard. Your achievements are a tough act to follow in our duo, but I am OK with that. You help me to get better every day. Thank you for being so supportive of me throughout graduate school, especially given my demanding field schedule. I spent more than a year of cumulative time away from home during graduate school, for which I am deeply indebted to you. Finally, thank you for convincing me that my long-held preference for a dog was, at least while in graduate school, unfounded. Indie and Dash have been wonderful feline additions to our family, and I owe it entirely to you. viii Table of Contents Title Page i Abstract iii Acknowledgements iv List of Figures x List of Tables xi List of Appendices xii Introduction 1 Chapter 1: Phylogeography of the Variable Dwarf-Kingfisher Ceyx lepidus 7 (Aves: Alcedinidae) inferred from mitochondrial and nuclear DNA sequences Introduction 9 Methods 12 Results 17 Discussion 24 Chapter 2: Molecular systematics of the world’s most polytypic bird: the Pachycephala 31 pectoralis/melanura (Aves: Pachycephalidae) species complex Introduction 33 Methods 37 Results 49 Discussion 55 Chapter 3: A molecular phylogeny of Pacific honeyeaters (Aves: Meliphagidae) reveals 69 extensive paraphyly and an isolated Polynesian radiation Introduction 71 Methods 73 Results 78 Discussion 89 Chapter 4: Rapid diversification of an insular kingfisher spans 13,000 km of the Pacific 96 Introduction 99 Methods 101 Results 113 Discussion 121 Literature Cited 138 Appendix I 150 Appendix II 153 Appendix III 164 ix List of Figures Figure 1.1 Distribution map of Ceyx lepidus. 11 Figure 1.2 Bayesian gene trees of the Ceyx lepidus species complex. 20 Figure 1.3 Molecular phylogeny of the Ceyx lepidus species complex. 23 Figure 2.1 Sampling map for Pachycephala. 39 Figure 2.2 Molecular phylogeny of ingroup Pachycephala pectoralis species complex. 54 Figure 2.3 Molecular phylogeny of outgroup Pachycephala. 57 Figure 2.4 *BEAST species tree of the Pachycephala pectoralis species complex. 58 Figure 3.1 Mitochondrial gene tree of the Meliphagidae. 80 Figure 3.2 Nuclear gene tree of the Meliphagidae. 82 Figure 3.3 Molecular phylogeny of the Meliphagidae. 84 Figure 3.4 Distribution map of Pacific meliphagid lineages. 88 Figure 4.1 Sampling map for Todiramphus. 110 Figure 4.2 Molecular phylogeny of the Todiramphus chloris species complex. 116 Figure 4.3 BEAST chronogram with divergence time estimates of Todiramphus. 120 Figure 4.4 Summary of bGMYC species delimitation of Todiramphus. 124 x