HOST ASSOCIATIONS, PHYLOGENETICS, AND BIOGEOGRAPHY OF PARASITIC AVIAN CHEWING LICE (INSECTA: PHTHIRAPTERA) FROM SUB- SAHARAN AFRICA A Thesis by OONA MARIKO TAKANO Submitted to the Office of Graduate and Professional Studies of Texas A&M University In partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Chair of Committee, Jessica E. Light Committee Members, Gary Voelker Michelle Lawing Head of Department, Michael Masser December 2016 Major Subject: Wildlife and Fisheries Sciences Copyright 2016 Oona Mariko Takano ABSTRACT Parasitic chewing lice (Insecta: Phthiraptera) of birds are found everywhere their avian hosts are distributed, and their host relationships and taxonomy have been well studied in many regions. Lice have obligate parasitic relationships with their hosts (entire life cycle is carried out on the host body) and generally undergo vertical transmission across host generations. These biological traits of lice make them excellent model systems for exploring host-parasite co-evolution. Compared with Europe and the Americas, the ectoparasite fauna of Sub-Saharan African birds is poorly understood despite the avian fauna being relatively well-known. Recent field expeditions exploring the avian diversity in South Africa, Benin, and the Democratic Republic of the Congo allow an opportunity to obtain louse specimens from across Sub-Saharan Africa. The goal of this study was to investigate avian louse host associations and genetic diversity to increase our understanding of southern African parasite biodiversity, as well as to use molecular phylogenetic methods to examine potential broad biogeographic patterns in lice across Sub-Saharan Africa. From 1105 South African bird individuals and 170 species examined for lice, a total of 104 new louse-host associations were observed. Portions of the mitochondrial COI and nuclear EF-1α genes were amplified to observe phylogenetic relationships of southern African lice and investigate potential new species. The phylogenetic results gave strong support for multiple louse genera, and 26 genetically unique lineages were found, which may represent new louse species. Examining biogeographic patterns in parasitic lice across the entire region of Sub- ii Saharan Africa indicated that lice tend to follow host distributions rather than grouping by geographic region. Several promising louse taxa were identified as candidates for future phylogenetic and biogeographic studies investigating Sub-Saharan African chewing lice. iii ACKNOWLEDGEMENTS There are many people who have helped me with this thesis, and I am grateful for all of their various forms of support. First and foremost, I would like to thank my Master’s advisor, Dr. Jessica Light, for all of her help and encouragement, for pushing me to do my best, and for inspiring young women in science. Thank you to my committee members, Dr. Gary Voelker and Dr. Michelle Lawing, for their valuable comments and advice on this thesis, in particular for Dr. Voelker’s help with the African bird biogeography. I would like to thank Heather Prestridge at the Texas A&M University Biodiversity Research & Teaching Collections for help with tracking down bird specimen data. Texas A&M University undergraduate students Alicia Byers and Preston Mitchell were a great help with ruffling birds and sorting through ectoparasites. Preston also deserves a big thank you for putting up with being my first undergraduate mentee, and I am very proud of all he has accomplished. Johanna Harvey, Jerry Huntley, Nina du Toit-Heunis, and Caitlin Nessner provided help with molecular lab troubleshooting and tips on running the phylogenetic analyses. The Voelker and Light labs also gave helpful feedback on various portions of this thesis. Adrian Castellanos additionally helped with putting together the map figures. Thanks to all of my lab mates—I couldn’t have asked for a better group with whom to go through my grad school journey. Additionally, thanks to Dr. Kevin Johnson at the University of Illinois for giving early feedback on the iv louse phylogenies, and Dr. Daniel Gustafsson at the University of Utah for the Benin louse identifications. Finally, I’d like to thank my family and friends for their love and support. Especially my dad, who inspired me to pursue a career in science and gave me valuable advice on academia along the way, and my mom for always patiently listening to me ramble on about my thesis. v TABLE OF CONTENTS Page ABSTRACT ................................................................................................................... ii ACKNOWLEDGEMENTS ........................................................................................... iv TABLE OF CONTENTS ............................................................................................... vi LIST OF FIGURES ...................................................................................................... vii LIST OF TABLES ....................................................................................................... viii CHAPTER I INTRODUCTION ..................................................................................... 1 CHAPTER II HOST ASSOCIATIONS AND GENETIC DIVERSITY OF AVIAN CHEWING LICE (INSECTA: PHTHIRAPTERA) FROM SOUTH AFRICA ................ 5 Introduction ......................................................................................................... 5 Materials and Methods ........................................................................................ 7 Results .............................................................................................................. 11 Discussion ......................................................................................................... 36 CHAPTER III AVIAN CHEWING LOUSE PHYLOGENETICS AND BIOGEOGRAPHY ACROSS SUB-SAHARAN AFRICA ............................................ 46 Introduction ....................................................................................................... 46 Materials and Methods ...................................................................................... 51 Results .............................................................................................................. 52 Discussion ......................................................................................................... 68 CHAPTER IV SUMMARY .......................................................................................... 75 LITERATURE CITED ................................................................................................. 77 APPENDIX .................................................................................................................. 91 vi LIST OF FIGURES Page Figure 1 Map of South Africa showing louse collection localities from five provinces: Limpopo, Mpumalanga, Northern Cape, Free State, and Eastern Cape ............................................................................................ 9 Figure 2 Bayesian phylogeny of South African amblyceran lice based on analysis of the mitochondrial COI gene .................................................. 29 Figure 3 Bayesian phylogeny of South African ischnoceran lice based on analysis of the mitochondrial COI gene .................................................. 30 Figure 4 Bayesian phylogeny of South African amblyceran and ischnoceran lice based on analysis of the mitochondrial COI and nuclear EF-1α genes ..................................................................................................... 31 Figure 5 Map of Africa showing a gradient of bioclimatic variables obtained from the WorldClim database ................................................................ 48 Figure 6 Bayesian phylogeny of African amblyceran lice based on analysis of the mitochondrial COI gene, with nodes collapsed for clades ............. 54 Figure 7 Bayesian phylogeny of African amblyceran lice based on analysis of the mitochondrial COI gene ............................................................... 55 Figure 8 Bayesian phylogeny of African ischnoceran lice based on analysis of the mitochondrial COI gene, with nodes collapsed for clades ............. 56 Figure 9 Bayesian phylogeny of African ischnoceran lice based on analysis of the mitochondrial COI gene ............................................................... 57 Figure 10 Bayesian phylogeny of African lice based on analysis of the mitochondrial COI and nuclear EF-1α genes .......................................... 58 vii LIST OF TABLES Page Table 1 Bird-louse host associations from South Africa, including the first louse record for a particular bird species, as well as new host associations for bird hosts that were previously known to be parasitized by other louse species ........................................................... 13 Table 2 South African lice identified in this study .............................................. 18 Table 3 Louse GenBank specimens included in the South African phylogenetic analyses ............................................................................ 32 Table 4 Bird-louse associations found at localities in South Africa ..................... 36 Table 5 Lice from Benin, the Democratic Republic of the Congo, and South Africa used in the phylogenetic analyses ................................................ 59 Table 6 Additional louse GenBank sequences resulting from BLAST searches included in the African continent-wide phylogenetic analyses ................................................................................................