THE BIOLOGY OF FLOWERING PLANTS
Chapter 1 The Impact of Gene Duplication on Molecular Evolution……………………1 References………………………………………………………………………17 Chapter 2 Expression Pattern Shifts Following Duplication Indicative of Subfunctionalization and Neofunctionalization in Regulatory Genes of Arabidopsis…25 Preface……………………………………………………………………………25 Abstract…………………………………………………………………………27 Introduction……………………………………………………………………28 Methods…………………………………………………………………………33 Results…………………………………………………………………………37 Discussion………………………………………………………………………43 Acknowledgments………………………………………………………………52 Additional Files…………………………………………………………………52 References………………………………………………………………………53 Chapter 3 Utility of Amborella trichopoda and Nuphar advena ESTs for comparative sequence analysis……………………………………………………………………… 57 Preface…………………………………………………………………………57 Abstract…………………………………………………………………………59 Introduction……………………………………………………………………60 Methods…………………………………………………………………………62 Results…………………………………………………………………………65 Discussion………………………………………………………………………70 Acknowledgments………………………………………………………………74 Additional Files…………………………………………………………………74 References………………………………………………………………………75 Chapter 4 Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels………85 Preface……………………………………………………………………………85 Abstract…………………………………………………………………………87 Background………………………………………………………………………88 Results……………………………………………………………………………93 Discussion………………………………………………………………………104 Methods…………………………………………………………………………112 Acknowledgments………………………………………………………………117 Additional Files…………………………………………………………………118 References………………………………………………………………………119 Chapter 5 A Marriage of High-throughput Identification of Phylogenetic Markers with High-throughput Sequencing: Next-generation Phylogenomics using 454 Transcriptomes …………………………………………………………………………………………125 Preface…………………………………………………………………………125 Abstract…………………………………………………………………………127 Introduction……………………………………………………………………128 Methods…………………………………………………………………………132 Results…………………………………………………………………………135 Discussion………………………………………………………………………143 Acknowledgments………………………………………………………………144 Additional Files…………………………………………………………………145 References………………………………………………………………………146