| Molecular phylogenetics is a powerful tool for deciphering the history of life on earth. The development of molecular phylogenetics and the increasing availability of molecular data have enabled unprecedented understanding of evolution at levels from genes to genomes. In this dissertation, I demonstrate the use of molecular phylogenetics in studying various evolutionary problems, including the phylogeny of individual gene families, the role of gene and genome duplication in organismal evolution, and the reconstruction of the tree of life. In Chapter 2, to study the relationship between gene function and the pattern of gene birth and death, I analyzed the evolutionary history of histone demethylase families as a case study. I found that the two histone demethylase families, KDM1 and JmjC, exhibit distinct evolutionary patterns, which might be explained by the differences in their functions. In Chapter 3, to understand the contribution of gene duplication to the evolution of early eukaryotes, I performed genome-scale analyses of gene family phylogenies to identify gene duplication occurred before the split of animals, fungi and plants. I identified more than 300 early eukaryotic duplications, which possibly resulted from whole genome or segmental duplication(s). The proposed large-scale duplication(s) might provide a genomic basis for the successful radiation of early eukaryotes. In Chapter 4, to identify phylogenetic makers for eukaryotic phylogeny, I systematically identified ∼1000 genes that are widely distributed in eukaryotes and have reasonable orthology. From these genes, I further selected ∼30 genes that are highly conserved and single-copy in most sequenced eukaryotic genomes. In addition, I demonstrated the performance of these genes in resolving relationships within and among eukaryotic lineages, including some challenging examples such as the placement of Microsporidia and the monophyly of Excavata. The genes I identified will serve as useful tools in future phylogenomic studies and taxon-rich analyses of the eukaryotic tree of life. |
