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Abstract
Hybridization has long fascinated evolutionary biologists. Hybridization leads to novel combinations of genes which can lead to diverse evolutionary outcomes; maladaptive genetic combinations may lead to the reinforcement of species boundaries, while adaptive combinations may drive new adaptations in existing populations or even generate new species. With the continual decline in sequencing costs and advances in analytical methods, it is becoming increasingly feasible to determine how hybridization has contributed to the evolution of lineages. The North American pitcher plant genus Sarracenia is a charismatic and ecologically significant group of carnivorous plants known to frequently form fertile hybrids in nature. Surprisingly little is known about the extent of interspecific gene flow across the genus and what mechanisms are maintaining species boundaries in the face of hybridization. In this dissertation, I investigate interspecific gene flow in Sarracenia plastid and nuclear genomic compartments, assess hybrid unfitness and genetic architecture as a reproductive barrier, and develop genomic resources for Sarracenia. I first assembled whole plastid genomes and generated phylogeny, and employ coalescent simulations that reveals rampant introgression of the chloroplast genome has occurred. Next, I assemble the first two nuclear genomes for Sarracenia. Despite large, repeat-rich genomes, I found that Sarracenia has lost thousands of genes —notably those involved in photosynthesis and pathogen recognition—consistent with functional shifts associated with carnivory and prey-derived nutrient uptake. Using over 3000 single-copy loci, I reconstructed a robust species phylogeny and applied phylogenetic network estimation and quartet-based D-statistics, revealing widespread episodes of nuclear gene flow among sympatric species. Finally, I investigated the genetic basis of ecologically important pitcher traits in an F2 mapping population between S. rosea and S. psittacina, revealing that many of these traits are controlled by relatively simple genetic architecture. Additionally, a common garden experiment revealed that prey-derived nitrogen uptake was significantly reduced in hybrids compared to S. rosea, suggesting that hybrid pitcher morphologies reduce prey capture success and likely contribute to post-zygotic reproductive isolation. Together, these results demonstrate that interspecific hybridization has been a pervasive force in Sarracenia evolution, while divergent prey capture strategies may result in hybrid unfitness, contributing to post-zygotic reproductive isolation.