INVESTIGATING THE IMPACT OF RETICULATE EVOLUTION AND PARALOGY IN PHYLOGENOMIC STUDIES USING THE COMPLEX GENUS PACKERA (ASTERACEAE: SENECIONEAE)

Underlying discordance in phylogenomic studies is becoming more common, and the answer is not as simple as adding more data. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are main contributors to these issues and must be considered when generating phylogenies. Otherwise, phylogeny building in complex groups can lead to spurious results, and interpretations could be misleading. The genus Packera belongs to the sunflower family and contains an estimated 64 species and varieties endemic to North America. Packera is complex as most members are known to hybridize or exhibit polyploidy, making it difficult to reconstruct evolutionary relationships within this group. Previous molecular phylogenetic studies of Packera recovered low resolution trees, providing little information on its evolutionary relationships. The goals of this dissertation were to obtain a better understanding of the evolutionary history and species relationships within Packera using next-generation sequencing data and an almost complete sampling of the genus (Chapter 1), then use the resulting Packera phylogeny to investigate how accounting for hybridization and paralogy influences phylogenetic construction and interpretation in complex groups (Chapters 2 and 3). In doing so, I aimed to: 1) obtain a broad understanding of Packera’s evolutionary relationships by generating a robust nuclear and plastid phylogeny, as well as estimate the age and biogeography of Packera, 2) investigate the causes and consequences of nuclear-nuclear discordance, including evolutionary processes of hybridization and polyploidy, to understand how they influence the phylogenetic patterns seen in Packera, and 3) develop a new Compositae-specific probe set that better resolves evolutionary relationships at lower-taxonomic levels and complex groups. Additionally, this research aimed to address broader questions that can be applicable to other fields of biology, such as: 1) what role does polyploidy play in speciation events, 2) are there common causes of discordance in phylogenies, and 3) how does accounting for paralogy influence phylogenies and our understanding of these results? Together, findings from these three studies not only help our understanding of Packera’s evolutionary relationships and history, but also help researchers outside of Packera better understand issues associated with underlying biological processes, such as polyploidy and hybridization, in phylogenomic studies