......................................................................................................................................... 2 Acknowledgments .......................................................................................................................... 3 List of figures ................................................................................................................................. 6 Introduction .................................................................................................................................... 7 Histone replacement: An overview .................................................................................... 7 Transition nuclear proteins (TNPs) .................................................................................... 9 Protamines (PRMs)........................................................................................................... 10 Functional relationship ..................................................................................................... 12 Introduction to methods and results ................................................................................. 13 Materials and methods ................................................................................................................. 15 Producing primary alignments ......................................................................................... 15 Testing predicted mRNA variants for PRM2 .................................................................. 18 Resolving abnormal sequence alignments ....................................................................... 21 Uncovering patterns of evolution ..................................................................................... 26 Mapping replacements on phylogenetic trees .................................................................. 27 Results .......................................................................................................................................... 33 Protein and gene sequence overview................................................................................ 33 Transition nuclear protein 1 (TNP1) ................................................................................ 34 Transition nuclear protein 2 (TNP2) ................................................................................ 39 Protamine 1 (PRM1) ........................................................................................................ 39 Protamine 2 (PRM2) ........................................................................................................ 40 Protamine 3 (PRM3) .........................................................................................................43