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In this thesis, Dr. Jin presents the distribution of ancestral chromosomal segments in the admixed genome, which could provide the information needed to explore population admixture dynamics. The author derives accurate population histories of African Americans and Mexicans using genome-wide single nucleotide polymorphisms (SNPs) data. Mapping the genetic background facilitates the study of natural selection in the admixed population, and the author identifies the signals of selection in African Americans since their African ancestors left for America. He further demonstrates that many of the selection signals were associated with African American-specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to their new environment. Lastly, the author reveals the complexity of natural selection in shaping human susceptibility to disease. The thesis significantly advances our understanding of the recent population admixture, adaptation to local environment and its health implications.