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Title: Evolutionary and functional genomics of the origin of species in Phlox
Abstract: Speciation is the fundamental process by which biodiversity on earth is created and maintained. This process occurs through the evolution of reproductive trait differences between diverging populations until they become reproductively isolated. One of the greatest challenges for biologists is determining how the interplay of the evolutionary forces of mutation, selection, gene flow, and drift drive this process. Although hybridization and gene flow are often viewed as homogenizing forces that counteract divergence by selection, they can also lead to the formation of new reproductively isolated species through the processes of reinforcement and hybrid speciation. Studying how these speciation outcomes evolve in nature offers a unique opportunity to understand how the tensions between evolutionary forces can be resolved to result in species formation. In this dissertation, I leverage contemporary advancements in genomics to understand multiple aspects of the dynamics of speciation by hybridization, with a focus on reinforcement, in the wildflower genus Phlox. In Chapter 1, I integrate the classic model of speciation by reinforcement with modern population genetic theory. Through this synthesis I propose what genomic signatures of selection and gene flow we expect to coincide with the evolution of reinforcement, and I discuss how genomic analysis of these signatures can aid inferring the conditions by which reinforcement evolves. In Chapter 2, I use genome-wide sequencing to resolve the evolutionary history of the eastern standing Phlox and I directly test the history of gene flow between taxa in two cases of reinforcement and nine hypothesized cases of hybrid speciation. In Chapter 3, I identify the specific genetic changes and molecular mechanism that gave rise to reinforcement in P. drummondii flower intensity. I functionally demonstrate the evolution of dark flower color in P. drummondii is caused by gene expression differences at a R2R3-Myb gene, PdMyb1, and I show natural variation in P. drummondii flower intensity is highly associated with two point mutations evolving novel cis-regulatory elements in the promoter of PdMyb1. Together, this work generates an empirical and theoretical framework for the genomic study of speciation by hybridization, with a focus on reinforcement, and provides a rare look at the genetic changes causing a reproductive isolating trait and the mechanisms, context, and consequences of its evolution in nature.
Committee: Robin Hopkins (Advisor), Scott Edwards, Daniel Hartl, Elena Kramer, John Wakeley