........................................................................................................................................ i ACKNOWLEDGEMENTS .................................................................................................................. iii LIST OF TABLES ................................................................................................................................ v LIST OF FIGURES ............................................................................................................................. vi LIST OF ABBREVIATIONS ............................................................................................................... vii CHAPTER 1: INTRODUCTION ........................................................................................................... 1 CHAPTER 2: PHENOTYPIC RECOVERY UNDER UNFAVORABLE POPULATION GENETIC CONDITIONS .................................................................................................................................. 16 Background ................................................................................................................................ 16 Methods..................................................................................................................................... 21 Results ....................................................................................................................................... 30 Discussion .................................................................................................................................. 45 CHAPTER 3: FITNESS RECOVERY IN LARGE POPULATIONS .......................................................... 54 Background ................................................................................................................................ 54 Methods..................................................................................................................................... 58 Results ....................................................................................................................................... 65 Discussion .................................................................................................................................. 76 CHAPTER 4: CONCLUSION ............................................................................................................. 81 REFERENCES ................................................................................................................................... 85 APPENDIX A: GO term data for gas-1 MA lines............................................................................ 93 APPENDIX B: GO term data for N2 MA lines ................................................................................ 95 APPENDIX C: GO term data for gas-1 centric interactome .......................................................... 99 APPENDIX D: GO term data for gas-1 RC lines ........................................................................... 102