UC Berkeley

Traditional botany focuses on the morphology, anatomy, and evolution of above-ground plant parts, but remarkable variation also exists underground. Underground storage organs (USOs), one example of understudied underground botany, include corms, bulbs, rhizomes, and stem- and root-derived tubers. These odd organs characterize geophytes, plants that produce perennating buds below ground and often store nutrients such as starch and water in USOs. Diverse underground morphology is particularly evident in the monocotyledenous order Liliales.

In this dissertation, I examine the evolution and development of USOs across the order Liliales, or the ’liliids’. In Chapter 1, I take a macroevolutionary perspective to ask if plants with different USOs are evolving towards different climatic niche adaptive peaks across the order. I find that the presence of root tubers, especially rotund root tubers, is associated with lower temperature seasonality. Furthermore, I develop and describe a new analysis pipeline in statistical comparative phylogenetics for testing adaptive hypotheses. In Chapter 2, I zoom in on a particular liliid geophyte, Bomarea multiflora, to identify genes underlying root tuber formation by comparing the transcriptomes of root tubers vs. fibrous roots. I compare the genes identified in this study with patterns from USOs produced by other taxa to characterize to what extent processes are shared across non-homologous USOs and across deep evolutionary divergences. I find that many processes are shared despite these differences, indicating that parallel molecular mechanisms may underlie USO development. In Chapter 3, I describe a new R package, RevGadgets, that can process and visualize the output of complex phylogenetic analyses from the RevBayes phylogenetic graphical modelling software. RevGadgets is designed to provide user-friendly modular workflows and thus increase accessibility to more complex phylogenetic models. I illustrate core RevGadgets functionality through six use cases and provide examples of code and resulting figures.

Together, these projects bring light to the outstanding diversity of below ground forms and begin the work of characterizing the evolution and development of this diversity. This work also illustrates the utility of establishing reproducible and user-friendly pipelines to increase the accessibility and versatility of complex statistical methods in comparative biology.