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The History and Population Genomics of Managed and Feral Honey Bees (Apis mellifera L.) in the United States
Domestication is the process by which a previously wild population is managed by humans, thereby being subjected to a different set of selective pressures than experienced in its natural setting. Its opposite, feralization, is therefore when a domesticate escapes or is released from a captive setting, reasserting natural selective pressures. The genomics underpinning both domesti- cation and feralization have not been studied in insects; the Western honey bee (Apis mellifera L.) is a good model for this system, as honey bees exist in both a managed and feral state, and have extensive historic and genomic resources to document population changes. My goal in this thesis was to 1) improve upon our understanding of honey bee importation and genetics to the United States to support demographic assertions, and 2) to sequence managed and feral stocks of honey bees to identify the population structure and 3) genetic differences underpinning domestication. Ultimately, I reconstructed 400 years of honey bee importation and management history, creating the most comprehensive understanding to date of importation dates and locations, historical man- agement practices, and genetic bottlenecks. Additionally, I summarized thirty years of honey bee genome sequencing to provide a road map for future studies. Then, I conducted whole genome pooled sequencing on six managed and three feral stocks of honey bees from the United States. The mitochondrial and whole genome ancestry of feral colonies holds relics from their importation history, while managed colonies show evidence of more recent importation events. The managed stocks in my sample set have higher overall genetic diversity, but exhibit little differentiation, but feral stocks exhibit varying levels of differentiation, indicating different levels of ferality likely dictated by the level of reproductive isolation from managed colonies.