Ancient DNA and the biological history and prehistory of Northeastern North America

This study specializes in the recovery, identification, and analysis of DNA from degraded remains and is applied in two complementary areas: the interaction of genes, culture, and language in Northeastern North American and technical research in recovering and analyzing ancient DNA. The first chapter focuses on the last 500 years of Ojibwa history using mtDNA from extant populations to determine the extent to which demographic factors have impacted the genetic structure of the Ojibwa. Results suggest that genetic patterns have rapidly changed and reflect interactions with neighboring populations as well as significant genetic drift, beyond what has been previously estimated by geneticists. Chapter two uses mtDNA from the skeletal remains of 44 individuals representing four prehistoric populations to investigate how biological diversity changed over time and space in the Northeast. Haplotype patterns suggest that ancestors of present day northeastern North Americans have been in that region for at least 3000 years and have experienced extensive gene flow throughout time. However, genetic drift has also been a significant force, altering haplogroup frequencies and causing the loss of haplotypes.; Chapters three and four are technical chapters aimed at improving ancient DNA and forensic research. Chapter three evaluates three silica-based extraction protocols using quantitative real-time PCR to estimate the copy number of nuclear STR and mitochondrial amplicons. While many ancient DNA samples did not successfully amplify, there is evidence that the Qiagen column and magnetic bead extraction procedures may work the most effectively, and that using a purification protocol after an organic extraction is critical. Chapter four examines sixteen factors that may affect the likelihood that an ancient sample contains sufficient quality DNA. It was determined that geographic location (latitude and longitude), soil type, and osteological element used to extract DNA significantly correlate with the ability to extract quality DNA.