Molecular evolution of the RNA polymerase genes and the phylogeny of seed plants

This work is a union of molecular biology and evolutionary biology in addressing questions regarding the evolution of organisms and their genes. This project focuses on major groups of seed plants (angiosperms, and four gymnosperms groups: conifers, cycads, Ginkgo and Gnetales). These organisms diverged roughly three hundred million years ago and evolved independently since then. Therefore, morphological characters have limited power in resolving their phylogeny. With the advancement of molecular methods, sequences of genes have been widely used in addressing evolutionary relationships. Plant molecular phylogenies have been traditionally done using chloroplast gene rbcL and nuclear rRNA genes. While these molecular markers revolutionized plant systematics, they do not contain enough phylogenetic information to resolve the phylogeny of seed plants.; I used normalized splits, as a measure from spectral analysis, in examining data sets and identifying genes and sites within genes that are more reliable for building phylogenies and combining data sets. I used the genes encoding the largest subunit of RNA polymerase I, II and III (rpa1, rpb1 and rpc1, respectively) as a new line of evidence from the nuclear genome to address seed plant phylogeny. These protein-coding genes refute the Anthophyte hypothesis (which relates Gnetales and angiosperms) and support the Gnepines hypothesis (which places Gnetales within conifers as a sister group to Pinaceae).; I also examined other available data sets from chloroplast, mitochondrial and 18S rRNA genes. A combined data set of RNA polymerases and seven other genes strongly support the Gnepines hypothesis. Other branches of seed plant phylogeny are also well supported using this data set. Angiosperms and gymnosperms form monophyletic groups, cycads are at the base of gymnosperms, followed by Ginkgo and a branch leading to conifers and Gnetales.; I also studied the rate and pattern of molecular evolution of rpa1, rpb1 and rpc1 genes. A gene phylogeny of these genes strongly support that they share a common ancestor and that rpb1 and rpc1 are closer to one another than either are to rpa1. The pattern of functional constraint in these genes clearly follows known structural properties of the RNA polymerases. Evolutionary rate analyses show that rpa1 evolves more rapidly at non-synonymous sites and at the amino acid level, followed by rpc1 and rpb1. Interestingly, the evolutionary rate of these genes (and the proteins they encode) is positively related to the amount of concerted evolution in the genes transcribed by each RNA polymerase. This suggests a possible impact of concerted evolution (generated by recombination) on the molecular evolution of the largest subunit of RNA polymerases.