Phylogenomic Perspectives on Evolutionary History: Examples from the Flowering Plant Lineage Ericales

Abstract

This dissertation represents a series of advances in plant systematics and molecular phylogenetics. Processes such as whole genome duplication, historical introgression, and rapid diversification shape the genomes of plants. I investigate these processes in the flowering plant lineage Ericales, a morphologically disparate group that includes kiwifruits, pitcher plants, obligate parasites, and ecologically dominate tropical tree lineages.

Large genomic datasets offer the promise of resolving historically recalcitrant species relationships, but methods can yield conflicting results, especially when clades have experienced ancient, rapid diversification. In Chapter II, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. Support for relationships among major clades was inferred from multiple lines of evidence and was summarized in a consensus framework. Our results supported a history largely concordant with previous studies but suggests that paleopolyploidy may be responsible for the remaining uncertainty. Our broad sampling allowed us to place the position of a whole genome duplication before the radiation of most ericalean families.

Admixture is a mechanism by which populations of long-lived trees may acquire novel alleles. However, little is known about the genomes of most tropical tree species, or the extent to which they exchange genes. In Chapter III, we ask whether admixture occurs in an ecologically important clade of rainforest trees, the Parvifolia clade of Eschweilera (Lecythidaceae), which includes several of the most abundant tree species in Amazon forests. Using targeted sequence capture for hundreds of individuals from across Lecythidaceae, we conducted a detailed phylogenomic investigation of the Parvifolia clade. We implement a novel workflow to test for admixture in target capture datasets. We found strong evidence of admixture among three ecologically dominant species but a lack of evidence for widespread genomic admixture in most lineages. Species were distinguishable from one another based on our sequencing targets, as was geographic structure within species.

Biogeography informs our understanding of patterns of global species diversity and the processes that shape them, but such inferences strongly rely on the quality of the genomic and fossil information employed. In Chapter IV, we use targeted sequence capture to collect data from species across Ericales, as well as the available fossil information, to investigate the origin and diversification of the primrose family (Primulaceae). We present updated phylogenetic and biogeographic hypotheses for the family and show that genomic evidence contradicts previous biogeographic inference based on morphology. Our results show that a major taxonomic revision of Ardisia and at least 19 closely related genera is required to circumscribe monophyletic genera.

While this dissertation advances our understanding of the evolution of Ericales, it has also revealed unanswered questions about the phylogeny of the order and the processes that have generated the groups diversity. Paleopolyploidy, rapid radiation, admixture, and long-distance dispersal are among the factors that have contributed to the evolution of the clade. Future work is needed to better characterize the relative importance of these factors and to continue refining the taxonomy of various clades within Ericales.