Phylogeny and genome evolution of the flowering plant clade Malpighiales

Abstract

The revolutionary advancements in phylogenetic theory and sequencing technology have revived hope of resolving recalcitrant relationships but also revealed the common nature of more complexed genome evolution that leads to extensive gene tree heterogeneity. In various lineages of eukaryotes, evolutionary histories of genome duplication, introgression, and horizontal gene transfer are increasingly identified based on these gene tree variations. Malpighiales is a large and diverse plant clade that remains one of the most phylogenetically controversial angiosperm lineages. My dissertation applied a variety of phylogenomic data sets to explore the early evolutionary history of this lineage and to investigate the analytical and biological origins of the recalcitrant relationship. In Chapter I, I identified 24 ancient whole genome duplications widely distributed across Malpighiales with transcriptome data. These events are clustered around the super-greenhouse period during the Paleocene-Eocene Transition (~54 Ma), providing evidence of the adaptive value of polyploidization during periods of global upheaval. In Chapter II, I applied a sequence capture data set to examine gene tree–species tree heterogeneity in Malpighiales. By evaluating the triplet frequency in the gene trees, I identified deep histories of gene flow, likely involving a single promiscuous clade, as a main culprit in our ability to resolve this group. I also developed a novel simulation-based method to demonstrate that incomplete lineage sorting, gene tree estimation error, and gene flow contributed to 15%, 53%, and 32% of the gene tree variation, respectively. In Chapter III, I investigated genome evolution and horizontal gene transfer in the iconic parasitic plant Sapria himalayana Griff. (Rafflesiaceae, Malpighiales). Genomic analyses revealed dramatic modifications in several fundamentally conserved plant genomic characters, featuring the genome architecture of more than 80 million years of extreme parasitic modality. In addition, focused phylogenetic investigation of these horizontal gene transfers from the host illuminated a history of former host-parasite association involving close relatives of their modern hosts in the grapevine family.