Date Awarded


Document Type


Degree Name

Master of Science (M.Sc.)




Joshua Puzey

Committee Member

Helen Murphy

Committee Member

John Swaddle


Our understanding of speciation has been greatly improved with advances in genomic technology, but most of our knowledge of speciation is still built on research of diploid systems. Polyploids, however, are found in many lineages across the tree of life and exhibit considerably different evolutionary dynamics than diploids. Here, we investigate patterns of population structure and divergence in a system of two allopolyploid species of Mimulus (monkeyflower) that occur sympatrically in Chile: M. luteus and M. cupreus. We find that while the two species have consistent phenotypic differences across the range, they are genetically clustered into a northern and southern population (rather than by species), based on a STRUCTURE analysis of 48 whole-genome paired-end sequences of the two species across six populations in Chile. Using LUMPY and DELLY2 to locate chromosomal structural variants (SVs), we identify hundreds of SVs unique to one species or the other both across the entire range and just within the north or south. We also calculated metrics of divergence (FST and DXY) in 10 kbp regions across the genome and find that these metrics were not greater within SV regions than across the whole genome. However, we did find that inversions occurred at 100–150X greater frequency within the regions of top 1% of FST and DXY values compared to the across the entire genome, indicating that inversions may promote divergence. Overall, we find evidence to suggest that M. luteus and M. cupreus are currently undergoing sympatric speciation, and that inversions may help promote divergence in this system while deletions and duplications likely do not. Additionally, SV diversity is much higher than generally assumed, perhaps due to increased genomic instability in these allopolyploids, warranting future studies looking into the effects of SVs on species divergence.




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