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DISSERTATION RESEARCH

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 goals of this dissertation were to obtain a better understanding of the evolutionary history and species relationships within the genus Packera using next-generation sequencing data and an almost complete sampling of the genus, then use the resulting Packera phylogeny to investigate how accounting for hybridization and paralogy influences phylogenetic construction and interpretation in complex groups. 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?

  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.

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Figure7_PhyloNetworks.png

Pseudocoalescent phylogeny of 108 Packera and outgroup taxa. Red diamonds at the node indicate discordance. Clades are highlighted according to majorly discordant clades and follow the coloring scheme of the PhyloNetwork networks to the right. More information can be found here. 

This dissertation work can be found on ProQuest.

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Associated manuscripts/publications:

Resolving evolutionary relationships in the groundsels: phylogenomics, divergence time estimates, and biogeography of Packera (Asteraceae: Senecioneae). bioRxiv DOI: 10.1101/2023.07.18.549592.

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From paralogy to hybridization: Investigating causes of underlying phylogenomic discordance using the complex genus Packera (Senecioneae; Asteraceae). bioRxiv DOI: 10.1101/2023.08.14.553290.

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Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems. APPS (in press; read on bioRxiv).

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Brief history of the “aureoid Senecio” subgroup in Senecioneae. Capitulum, 2(2):51-58. https://doi.org/10.53875/capitulum.02.2.04

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