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Evolutionary Dynamics of Bird Populations in Southeast Asia Haw Chuan Lim Louisiana State University and Agricultural and Mechanical College, Haw Chuan [email protected]

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Evolutionary Dynamics of Bird Populations in Southeast Asia Haw Chuan Lim Louisiana State University and Agricultural and Mechanical College, Haw Chuan Lim@Yahoo.Com Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2010 Evolutionary dynamics of bird populations in Southeast Asia Haw Chuan Lim Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Lim, Haw Chuan, "Evolutionary dynamics of bird populations in Southeast Asia" (2010). LSU Doctoral Dissertations. 1372. https://digitalcommons.lsu.edu/gradschool_dissertations/1372 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]. EVOLUTIONARY DYNAMICS OF BIRD POPULATIONS IN SOUTHEAST ASIA 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 Haw Chuan Lim B. Env.Sc., University of Wollongong, Australia, 1996 M.S., National University of Singapore, Singapore, 2002 August 2010 Acknowledgments I am very thankful to Dr. Frederick Sheldon, my advisor, for agreeing to take me as a graduate student. Up to that point, I only had experience as an avian ecologist. The members of my graduate committee, Drs. Robb Brumfield, Bryan Carstens, Phil Stouffer, and Fred, are prominent experts in their fields, and they have been very generous in the giving their time and providing advice. I also benefited greatly from interactions with other staff and faculty members of the Museum of Natural Science and the Department of Biological Sciences. Some of these people are: Steve Cardiff, Prosanta Chakrabarty, Nanette Crochet, John McCormack, Matthew Davis, Donna Dittmann, Elizabeth Derryberry, David Foltz, Mark Hafner, Michael Hellberg, Dan Lane, Susan Murray, Van Remsen and Andrew Whitehead. Office administrator extraordinaire Ms. Tammie Jackson was always very helpful and cheerful. I owe much to fellow graduate students for their friendships and lending of support. Special thanks are due to Matthew Carling, Zachary Cheviron, Ron Eytan and James Maley for their liberal sharing of know-how, and stimulating discussions. I also thank David Anderson, Phred Benham, Gustavo Bravo, Curt Burney, Santiago Claramunt, Jesus Fernandez, Dency Gawin, Richard Gibbons, Sarah Hird, Heather and Nathan Jackson, Eric Johnson, Ben Marks, Verity Mathis, John McVay, Jonathan Myers, Luciano Naka, Brian O‟Shea, Noah Reid, Eric Rittmeyer, Cesar Sanchez, Thomas Valqui, Danielle Ward, and many others; they greatly enriched my time here at LSU. My fieldwork would not have been possible without permission from the Malaysian Wildlife Department and the Sarawak Forestry Department. I also thank the following museums and institutions for generous tissue loans: LSU Museum of Natural Science, Academy of Natural Sciences of Philadelphia, National Museum of Natural History, National University of ii Singapore, Field Museum of Natural History, American Museum of Natural History and Burke Museum. Funding for my project came from: the National Science Foundation (DEB-0228688 to my advisor), the American Ornithologists‟ Union, American Museum of Natural History, LSU University Museum of Natural Science Birdathon and Prepathon Funds, LSU Department of Biological Sciences and LSU Biograd Research Fund. Most of all, I thank my wife, Ching Chi, and my daughter, Megan, for their support. Without Ching Chi‟s sacrifices, I would not have been able to begin to pursue a doctorate education here at LSU. iii Table of Contents Acknowledgments........................................................................................................................... ii Abstract ........................................................................................................................................... v Chapter 1: General Introduction ..................................................................................................... 1 Chapter 2: The Cause of Extensive Color Polymorphism in the Oriental Dwarf Kingfisher Ceyx erithaca ........................................................................................................................................... 3 Introduction ................................................................................................................................. 3 Methods ....................................................................................................................................... 7 Results ....................................................................................................................................... 15 Discussion ................................................................................................................................. 26 Chapter 3: Coalescent Simulation and Comparative Niche Modeling Reveal Historical Mechanisms That Promoted Population Divergence .................................................................... 32 Introduction ............................................................................................................................... 32 Methods ..................................................................................................................................... 34 Results ....................................................................................................................................... 42 Discussion ................................................................................................................................. 47 Chapter 4: Demographic and Evolutionary Responses to Climatic and Geographical Fluctuations: A Multilocus and Multi-Species Perspective .......................................................... 54 Introduction ............................................................................................................................... 54 Methods ..................................................................................................................................... 60 Results ....................................................................................................................................... 67 Discussion ................................................................................................................................. 79 Chapter 5: Overall Conclusions .................................................................................................... 88 References ..................................................................................................................................... 90 Appendix 1: Supplementary Data ............................................................................................... 105 Appendix 2: Permission from Journal of Avian Biology ....................................................... 130 Vita .............................................................................................................................................. 135 iv Abstract A confluence of factors determines the biological diversity we observe today. Here, I conducted three investigations of the historic, geographic and ecological factors that shaped the morphological and genetic diversity of rainforest birds in Southeast Asia. (1) In the Oriental Dwarf Kingfisher (Ceyx erithaca) complex, the birds are highly polymorphic in plumage. Quantitative analysis of this variation indicated that a large proportion of birds in Sumatra, the Malay Peninsula and Borneo have plumages intermediate between the northerly black form from mainland Asia and the southerly rufous form from Java. Phylogenetic analyses indicated that birds from continental Southeast Asia (north of the Malay Peninsula) were well differentiated from those from insular Southeast Asia. This genetic distinction correlates well with a fixed plumage difference (mantle coloration). Coalescent analyses showed that the plumage polymorphism was caused by past genetic introgression between the two parental forms. (2) I sampled 16 lowland rainforest bird species primarily from the Malay Peninsula and Borneo to test the long-standing hypothesis that animals on different Sundaic landmasses intermixed extensively when low sea-levels during the Last Glacial Maximum (LGM) exposed land- bridges. This hypothesis was rejected in all but five species through coalescent simulations. Environmental niche modeling showed that the presence of unsuitable habitats between western and eastern Sundaland during the LGM coincided with deeper inter-population genetic divergences. The distinctiveness of the northeastern Borneo populations of some species may be underlain by a combination of factors that included riverine barriers, LGM expansion of montane forests and regional physiography. v (3) I further investigated the population divergence and demographic histories of three bird species that possessed disparate ecological characteristics. Multilocus analyses revealed changes in effective population sizes that were driven by long-term changes in the environment, instead of high-frequency glacial cycles. Populations from Borneo exhibited stronger demographic growth than those from mainland Southeast Asia, suggesting regional differences in environmental changes or directional colonization.
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