Mesoamerica and *Southwest prehistory, and the entrance of humans into the Americas: Mitochondrial DNA evidence
Mitochondrial DNA (mtDNA) variation exhibited by prehistoric and contemporary Native Americas was used to address the prehistory of Mesoamerica and the American Southwest, and the entrance of humans into the Americas. In addition, improved ancient DNA (aDNA) protocols were developed. Chapter 2 presents results from a large-scale study of mtDNA variation in Southwest and Mesoamerican populations, from which it was determined that population relationships between the two regions are not very close. In particular, groups of Uto-Aztecan speakers, who are argued to have been responsible for the northward spread of agriculture from Mesoamerica to the Southwest, also do not appear closely related to each other unless they are located in close geographic proximity. Chapter 3 highlights that the study of DNA extracted from archaeological or forensic skeletal remains is often plagued by the presence of modern contamination on the surfaces of bones and teeth. This study determined that immersion of bones in at least 3.0% w/v sodium hypochlorite for at least 15 minute was required to eliminate surface contamination. Chapter 4 describes another problem associated with the study of aDNA, the frequent co-extraction of polymerase chain reaction (PCR) inhibitors that make the analysis of aDNA difficult, if not impossible. In this study a technique, "repeat silica extraction," was developed that effectively removed PCR inhibitors from extracts of 7,000--8,000 year old human skeletal remains from the Windover archaeological site in Florida and 700--2,000 year old human coprolites excavated from Fish Slough Cave in southern California. Chapter 5 presents the analysis of mtDNA and Y-chromosome DNA from 10,300-year-old human remains excavated from On Your Knees Cave (OYKC) on Prince of Wales Island, Alaska (Site 49-PFT-408). These data demonstrate that widely held assumptions about the genetic composition of the earliest Americans are incorrect and that previous calibrations of the mtDNA clock may have seriously underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, explaining the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas.