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Abstract
Whole genome duplications are prevalent across the tree of life and carry evolutionary importance. Here, we investigate the origin and subsequent evolution of a recent allotetraploid species in the genus Mimulus. In Chapter 2 we explore the evolutionary history of M. sookensis, which was formed via the hybridization of two distinct species in the Mimulus guttatus complex using a newly generated chromosome-scale reference assembly. We find patterns of population genomic variation that unambiguously support a single origin of the species, contrary to past findings, and confirm the maternal progenitor of M. sookensis is the selfer M. nasutus. In Chapter 3, we explore instantaneous expression changes in hybrids both diploid and tetraploid to assess the effect of polyploidization on gene expression. Using 2x-F1 and 4x-F1 M. nasutus x M. guttatus, we establish that there are immediate patterns of expression level bias and allele-specific or homeolog-specific expression bias in hybrids. In the 4x-F1 we determine expression is shifting towards M. nasutus through the up- and down- regulation of the non-dominant subgenome. We conclude that polyploidization causes novel regulatory patterns likely through increased cis-trans interactions. Finally in Chapter 4, we examine whether M. sookensis shows similar patterns of expression level dominance or homoeologous expression bias to determine if subgenome dominance continues through evolutionary time. We discover higher levels of expression level dominance favoring M. nasutus, though homeolog expression bias is slightly shifted towards the opposite subgenome. This pattern might explain the phenotypic similarity M. sookensis shares with M. nasutus SF. Additionally, we uncover a novel deletion in one line of wild M. sookensis that is not shared with any other populations, perhaps indicative of the beginning of the diploidization process. Together, our findings provide more context to the vast and often complicated histories of polyploids.