EVOLUTIONARY NEUROGENOMIC APPROACHES PROVIDE INSIGHT INTO THE MOLECULAR BASIS OF VOCAL LEARNING By Morgan Wirthlin A DISSERTATION Presented to the Department of Behavioral Neuroscience and the Oregon Health & Science University School of Medicine in partial fulfillment of the requirements for the degree of Doctor of Philosophy September 2016 School of Medicine Oregon Health & Science University CERTIFICATE OF APPROVAL ___________________________________ This is to certify that the PhD dissertation of Morgan Wirthlin has been approved ______________________________________ Claudio Mello, Mentor/Advisor ______________________________________ Lucia Carbone, Oral Exam Committee Chair ______________________________________ Stephen David, Member ______________________________________ Jacob Raber, Member ______________________________________ John Brigande, Member TABLE OF CONTENTS List of Tables ................................................................................................................................................. ii List of Figures ............................................................................................................................................... iii Acknowledgments ........................................................................................................................................ iv Abstract ......................................................................................................................................................... v 1 Introduction .......................................................................................................................................... 1 1.1 Models for the study of vocal learning ......................................................................................... 1 1.2 The neural basis for vocal learning ............................................................................................... 4 1.3 The molecular and genetic basis for vocal learning ...................................................................... 8 2 The role of novel genes in the evolution of vocal learning ................................................................. 10 2.1 Background ................................................................................................................................. 10 2.2 Results & Discussion ................................................................................................................... 11 2.3 Methods ...................................................................................................................................... 41 3 ‘Core sets’ of genes expressed in vocal learning circuits .................................................................... 48 3.1 Background ................................................................................................................................. 48 3.2 Results & Discussion ................................................................................................................... 51 3.3 Methods ...................................................................................................................................... 68 4 The role of genomic regulatory elements in the evolution of vocal learning .................................... 70 4.1 Background ................................................................................................................................. 70 4.2 Results & Discussion ................................................................................................................... 71 2.1 Methods ...................................................................................................................................... 96 5 New models for understanding the evolution of a complex behavior: a general discussion........... 101 5.1 Current models of the evolution of learned vocal behavior ..................................................... 101 5.2 The ‘Stepwise Hypothesis,’ a new model for the evolution of vocal learning .......................... 104 6 Conclusions ....................................................................................................................................... 111 6.1 Conclusions ............................................................................................................................... 111 6.2 Future Directions ...................................................................................................................... 113 Bibliography .............................................................................................................................................. 117 i List of Tables Table 1: Novel genes in songbirds .............................................................................................................. 16 Table 2. Comparative ISH analysis of HVC-like nuclei ................................................................................. 56 Table 3. Comparative ISH analysis of RA-like nuclei ................................................................................... 57 Table 4. Comparative ISH of song system markers in suboscines .............................................................. 65 Table 5. Promoters of song system marker genes with high quality ISH data ........................................... 74 Table 6. GC content and repetitive sequence in zebra finch brain-expressed gene promoters ................ 80 Table 7. TF motifs associated with song system gene sets ......................................................................... 82 Table 8. Brain-expression TFs associated with HVC projection neuron and RA expressed gene sets ........ 84 Table 9. TFs enriched in promoters of song system marker gene sets in zebra finch and chicken ............ 94 ii List of Figures Figure 1. Phylogeny of major extant avian lineages ..................................................................................... 3 Figure 2. Simplified schematic of the zebra finch song system .................................................................... 5 Figure 3. Chromosomal rearrangement leading to songbird gene duplication ......................................... 18 Figure 4. Syntenic and protein functional domain analysis of YTHDC2L1 and YTHDC2L5 .......................... 22 Figure 5. Schematic model depicting the predicted structure of songbird novel gene TMRA ................... 24 Figure 6. Expression of URB1 in the zebra finch brain ................................................................................ 26 Figure 7. Expression of CASC1 gene duplicatios in the zebra finch brain ................................................... 28 Figure 8. Expression of YTHDC2L1 gene duplications in the zebra finch brain ........................................... 30 Figure 9. Expression of TMRA in the zebra finch brain ............................................................................... 31 Figure 10. Schematic of analogous song-activated brain nuclei in avian vocal learners ............................ 49 Figure 11. Conserved gene markers of zebra finch HVC and Anna’s hummingbird VLN............................ 53 Figure 12. Comparative ISH of PVALB in HVC-like nuclei ............................................................................ 59 Figure 13. Phylogeny of songbirds, parrots, and suboscine families .......................................................... 61 Figure 14. Comparative neuroanatomy of songbird RA and a suboscine arcopallial domain .................... 66 Figure 15. Expression of song system markers in Amazonian antshrike .................................................... 67 Figure 16. FISH demonstrating select expression of gene markers in HVC projection neurons ................ 77 Figure 17. ISH of markers of HVC projection neurons ................................................................................ 77 Figure 18. Position of TBP and EGR1 motifs in brain-expressed zebra finch promoters ............................ 80 iii Acknowledgments I wish to thank the three most important mentors of my life, Manfred Ruddat, Daniel Margoliash, and Claudio Mello. It is through your inspiration, training, and belief in me that I have made it to this point. I am deeply indebted to the members of the Mello lab who have shared their time and expertise over the years, especially Peter Lovell, Chris Olson, and Julia Carleton. Without their help, especially in contributing microarray data and assisting with many of the hybridization experiments, this work would not have been possible. I would also like to thank my wife, Andria, for her love, encouragement, and support. This past year has been one of many milestones, and I can’t imagine having anyone else by my side for the journey. This dissertation is dedicated to the memory of the birds whose lives were ended in the course of these studies. It is my sincere hope that through passionate public outreach, we can inspire future generations to prioritize conservation, that we might continue to share the planet with these fascinating fellow lifeforms for many generations to come. iv Abstract How are complex, learned behaviors - such as the ability to speak and sing - encoded in our genes, and how did they evolve? Human speech is dependent on our ability to learn and control our vocalizations, a process that is poorly understood at the molecular level. Further, this trait is exceedingly rare in the animal kingdom, and notably