Phylogeny and genome evolution of the flowering plant clade Malpighiales
Committee: Charles Davis (Advisor), Scott Edwards, Gonzalo Giribet, and Naomi Pierce
Abstract: Revolutionary advancements in phylogenetic theory and sequencing technology have revived hope of resolving recalcitrant relationships. These advancements have also revealed complex patterns of genome evolution across eukaryotes—including genome duplication, introgression, and horizontal gene transfer—that contribute to extensive gene tree heterogeneity. Malpighiales is a remarkably diverse clade that has defied phylogenetic resolution and remains one of the largest unresolved angiosperm clades to date. My dissertation applied a variety of phylogenomic data sets and analyses to explore the early evolutionary history of this lineage and to investigate the analytical and biological origins of recalcitrant relationships within this group.
In Chapter I, I identified 24 ancient whole genome duplications widely distributed across Malpighiales using transcriptome data. These events are clustered around the super-greenhouse period during the Paleocene-Eocene Transition (~54 Ma), providing evidence of the potential adaptive value of polyploidization during periods of global upheaval.
In Chapter II, I applied a 400-locus sequence capture data set to examine gene tree–species tree heterogeneity in Malpighiales. By evaluating triplet frequencies in gene trees, I identified deep histories of gene flow, likely involving a single promiscuous clade, as a main culprit of our inability 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 aspects of plant genome architecture, likely reflective of the extreme parasitic modality in this species. In addition, focused phylogenetic investigation of horizontal gene transfers in this parasite illuminated a dynamic history of former host-parasite association involving close relatives of their modern hosts in the grapevine family.