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A Case Study in Amazonian Biogeography: Vocal and DNA -Sequence Variation in Hemitriccus Flycatchers

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A Case Study in Amazonian Biogeography: Vocal and DNA -Sequence Variation in Hemitriccus Flycatchers Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 2000 A Case Study in Amazonian Biogeography: Vocal and DNA -Sequence Variation in Hemitriccus Flycatchers. Mario Cohn-haft Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Cohn-haft, Mario, "A Case Study in Amazonian Biogeography: Vocal and DNA -Sequence Variation in Hemitriccus Flycatchers." (2000). LSU Historical Dissertations and Theses. 7348. https://digitalcommons.lsu.edu/gradschool_disstheses/7348 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 Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy subm itted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6” x 9” black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. Bell & Howell Information and Learning 300 North Zeeb Road, Ann Arbor, Ml 48106-1346 USA 800-521-0600 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. A CASE STUDY IN AMAZONIAN BIOGEOGRAPHY: VOCAL AND DNA-SEQUENCE VARIATION IN HEMITRICCUS FLYCATCHERS 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 Mario Cohn-Haft B.A., Dartmouth College, 1983 M.S., Tulane University, 1995 December 2000 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. UMI Number: 9998667 Copyright 2000 by Cohn-Haft, Mario Ail rights reserved. ___ ® UMI UMI Microform 9998667 Copyright 2001 by Bell & Howell Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. Bell & Howell Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, Ml 48106-1346 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ©Copyright 2000 Mario Cohn-Haft All rights reserved Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. DEDICATION To the memory of Richard B. Warren (1916-1998), my loving stepfather, Dick, who couldn't have cared less about titles and degrees. I think he would have been proud of me for finishing and would have enjoyed hearing the story told here. To the memory of Anthony "Papa Nino" Capraro (1891-1975), my maternal grandfather. He was the first intellectual in my family that I'm aware of, a self-taught scholar and courageous fighter for social justice. His belief in the socializing and liberating power of education, his fierce dedication to acting on what he knew was right, and his loving faith in (and expectations for) his grandchildren inspire me to this day, despite the fuzziness of my memories of him. To the memory of my youth (1961-?), which sometime between the start and finish of this degree quietly but definitively flew the coop. iii Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ACKNOWLEDGMENTS I would like to have dedicated this dissertation to the geniuses who invented the polymerase chain reaction, tape recorders, and computers, and those who wrote all the relevant software. They made it possible for a regular "schmoe" like me to chug through analyses that not long ago weren't even ideas. Even if the substance of the ideas presented here did not build in any profound way on work that was done before me, the mechanics that went into this dissertation depended completely on the successful and brilliant inventions of others. I would like to have dedicated this document to them, but I recognize that they might not be interested in the genetics or voices of Amazonian birds or the story told by those traits. So, rather than pester them with my study, I thank them for the immeasurable contribution they made to it. I hope they are very happy, or at least rich. I thank the members of my dissertation committee: Van Remsen, Fred Sheldon, Mark Hafner, Bruce Williamson, Kam-biu Liu, and A1 Afton. Van was the ideal adviser: patient, tolerant, trusting, encouraging, and almost always right. Fred was like a second adviser, especially generous with his time and use of his lab facilities. Bruce took a special interest in this study and offered some great ideas and stimulating conversations. The administrative staffs of the Museum of Natural Science and Department of Biological Sciences were helpful throughout my studies. Thanks go to Alice Fogg, Gail Kinney, Jana Kloss, Katina Johnson, Wanda Miles, Prissy Milligan, Marilyn Young, and especially Peggy Sims, for taking care of me like one of her own. Mark Hafner, as Museum Director, made the museum not only conducive to getting good work done but also very hard to leave, and a model that any future job will have a hard time matching. iv Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. My studies here received generous financial support from the LSU Board of Regents, Lex and Chrissie Sant, the American Ornithologists' Union, the Frank M. Chapman Fund (American Museum of Natural History), the George H. Lowery Fund, the Tropical Bird Research Fund, the Marantz family, Gerry Kusiolek, the Charles M. Fugler Fellowship, Mr. Peterson, Sigma Xi (National), the Biological Dynamics of Forest Fragments Project, the LSU Museum of Natural Science, the McDaniels Travel Award, and Biograds. In addition to these funding sources, travel to research destinations was underwritten by Field Guides Inc., the New York Botanical Gardens, Fundaqao Vitoria Amazonica, Elderhostel, Ecotours and the staff of the Tucano, Paul Allen and Bill Gates, and Henry and Lene Hagedom. In addition to the LSU Museum of Natural Science, other institutions in the United States and abroad, especially in Brazil, provided critical assistance in the form of specimen loans, access to collections, and logistical support: Cornell Laboratory of Ornithology Library of Natural Sounds, Chicago Field Museum, Academy of Natural Sciences in Philadelphia, Vienna Natural History Museum, Smithsonian U.S. National Museum, Museu Paraense Emilio Goeldi, and Instituto National de Pesquisas da Amazonia in Manaus. The Brazilian IBAMA in Brasilia and local chapters provided collecting permits and logistical support for field work. Access to Indian lands was authorized by FUNAI and FOIRN. Friends and colleagues from these and other institutions provided important help and discussions: Tom Schulenburg, Doug Stotz, Kevin Zimmer, Jeff Podos, Phil Stouffer, Kelli Gilbert, Sergio Borges, Magalli, David Oren, Ze Maria, Jurgen Haffer, John Fitzpatrick, Ned Johnson, Carla Cicero, Manuel Plenge, Mort and Phyllis Isler. Jim Giamanco of the LSU Physics department invented and built a sound-attenuating adapter cable for the computer vocal analyses. v Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Field companions were crucial to the success of this work. I would especially like to thank Curtis Marantz and Bret Whitney for helping me to find, record, and collect a lot of tody-tyrants and other great birds. Jose Eremildes and Ken Rosenberg also participated in some field expeditions. It is hard to know how to express my thanks to the people all over the Brazilian Amazon who opened their homes and properties, and gave their time and hospitality to this stranger with a strange job. I hope I can find a way to return the favor. I'm also grateful to those collectors and naturalists who gathered specimens and made recordings that proved useful in this study, whether they originally intended them to be or not. The following people volunteered the use of their field tape recordings: Haven Wiley, Paul Coopmans, Fernando Pacheco, Andy Whittaker, Kevin Zimmer, Tom Schulenburg, Ted Parker, Alex Aleixo, Mark Robbins, Bret Whitney, Pepe Alvarez, Sergio Borges, Sjoerd Mayer, Dan Lane,
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