Loyola University Chicago Loyola eCommons Master's Theses Theses and Dissertations 2018 Cryptic Diversification of woT Widespread Species in Madagascar Lynika Sharlice Strozier Loyola University Chicago Follow this and additional works at: https://ecommons.luc.edu/luc_theses Part of the Biology Commons Recommended Citation Strozier, Lynika Sharlice, "Cryptic Diversification of woT Widespread Species in Madagascar" (2018). Master's Theses. 3708. https://ecommons.luc.edu/luc_theses/3708 This Thesis is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Master's Theses by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 2017 Lynika Sharlice Strozier LOYOLA UNIVERSITY CHICAGO CRYPTC DIVERSIFICATION OF TWO WIDESPREAD SPECIES IN MADAGASCAR A DISSERTATION SUBMITTTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF MASTER OF SCIENCE PROGRAM IN BIOLOGY BY LYNIKA S. STROZIER CHICAGO, IL MAY 2018 Copyright by Lynika Strozier, 2018 All rights reserved. ACKNOWLEDGMENTS I would like to thank all those who made this thesis possible. First, I would like to express my sincere gratitude to my advisor Dr. Reddy for her continued support throughout my studies. Without her support throughout this process I do not believe I would have made it this far and this defense would not have been possible. A very special thanks to Sarah Kurtis who assisted with the laboratory experiments and thesis edits. She was very supportive and encouraging throughout my studies. I would also like to thank Dr. Jane Younger for her support throughout my thesis; Chris Kyriazis who helped with the thesis edits; my collaborator Steve M. Goodman whom helped throughout my thesis studies and who gave great feedback and suggestions; Dr. Matthew Von Konrat who was very encouraging and supportive. I would also like to thank my thesis committee Dr. Reddy, Dr. Grande, Dr. Moreau and Dr. Laten. I appreciate the advice and feedback they have provided me. I would also like to thank Virginia Lorenzo and Frank Inglima for their support and being able to answer any of my questions and concerns. I would also like to give a special thank you to Audrey Berry for being so helpful and supportive throughout my studies at Loyola. I would also like to thank my family who has been there for me. They were able to give love, support and encouragement. I am especially grateful to have Mario Trujillo by my side, encouraging me to never give up and to keep striving for success. I realize that my thesis work would not be completed if it had not been for assistance from iii Loyola University Chicago. Finally, I would like to thank my grandmother Sharon Wright for keeping me on track. I could not have made it this far without my grandmother’s encouragement, constant support and her always pushing me to never give up no matter how hard it gets. iv To my grandmother, my aunt, and my Mom TABLE OF CONTENTS ACKNOWLEDGMENTS ............................................................................................................... iii LIST OF FIGURES ...................................................................................................................... vii LIST OF TABLES ......................................................................................................................... ix ABSTRACT .....................................................................................................................................x CHAPTER ONE: THE IMPORTANCE OF PHYLOGEOGRAPHIC STUDIES AMONG BIRDS ON MADAGASCAR .....................................................................1 CHAPTER TWO: USING MOLECULAR TOOLS TO DETERMINE DIVERSIFICATION PATTERNS AMOUNG GENUS NEWTONIA .................................. 18 CHAPTER THREE: DETERMINING THE GENETIC DIVERSITY AMONG GENUS NEWTONIA ..................................................................................................38 CHAPTER FOUR: UNCOVERING HIDDEN DIVERSITY AMONG TWO WIDESPREAD SPECIES OF BIRDS N. AMPHICHROA AND N. BRUNNEICAUDA .........................................................................64 CHAPTER FIVE: IDENTIFYING DISTINCT SPECIES PRESENT WITHIN N.AMPHICHROA .......................................................................................................................72 REFERENCE LIST ......................................................................................................................74 VITA ..............................................................................................................................................78 vi LIST OF FIGURES Figure 1. The phylogeographic study among Dicrurus forticatus. ................................................12 Figure 2. The phylogeographic study among Bernieria madagascariensis. .................................13 Figure 3. The phylogeographic study among Xanthomixis zosterops. ..........................................14 Figure 4. The phylogeographic study among Genus Nesillas. ......................................................15 Figure 5. Images of the three Newtonia species were taken at the Field Museum of Natural History. .......................................................................................................16 Figure 6. Map of sampling localities of the two species a) N. amphichroa and b) N. brunneicauda on Madagascar. ...........................................................................................37 Figure 7. Phylogenetic relationships of Newtonia using maximum likelihood and Bayesian inference of the combined five genes. ..................................................................50 Figure 8. Phylogenetic relationships of Newtonia using maximum likelihood of ND3 only. ...............................................................................................................................51 Figure 9. Phylogenetic relationships of Newtonia using maximum likelihood of CYTB only. ............................................................................................................................52 Figure 10. Phylogenetic relationships of Newtonia using maximum likelihood of FIB5 only. ...............................................................................................................................53 Figure 11. Phylogenetic relationships of Newtonia using maximum likelihood of GAPDH only. .........................................................................................................................54 Figure 12. Phylogenetic relationships of Newtonia using maximum likelihood of MUSK only. ...........................................................................................................................55 Figure 13. GenGIS analysis for N. amphichroa. Distinct clades are associated with isolated montane regions found along the eastern humid forest. ........................................56 Figure 14. GenGis analysis for N. brunneicauda. There are no distinct clades are associated with geographic regions.. .....................................................................................57 vii Figure 15. The Median-Joining Haplotype Network of CYTB haplotypes within N. amphichroa.............................................................................................................................59 Figure 16. The Median-Joining Haplotype Network of CYTB haplotypes within N. brunneicauda. .........................................................................................................................60 Figure 17. Box-and-whiskers plot showing elevation distribution of N. amphichroa and N. brunneicauda. .........................................................................................63 viii LIST OF TABLES Table 1. A physical description of the three species of Newtonia. ................................................17 Table 2. Sample accession number, locality, elevation, latitude, and longitude information for each specimen of Newtonia used in this study. ...........................................................................25 Table 3. Primers used for this study. ..............................................................................................36 Table 4. DNA sequences obtained using five Markers. .................................................................45 Table 5. Population genetics statistics for three species of Newtonia. ..........................................58 Table 6. Species delimitation (BPP) analysis. ...............................................................................61 Table 7. Elevation ranges for each species set comparing the elevation ranges of the different Newtonia species and the misidentified samples. ...................................62 ix ABSTRACT Using phylogenetic and phylogeographic tools to uncover hidden diversity within the genus Newtonia in Madagascar Madagascar is known for its rich biodiversity and high level of endemic species that are found nowhere else. Cryptic diversification, defined as genetically and evolutionarily distinct species that are hard to detect because they are morphologically indistinguishable from their closest relatives, has been hypothesized to occur in many groups on Madagascar. Currently it is unclear to what extent this phenomenon occurs in birds because only