In this study I recover and analyze ancient DNA in order to identify prehistoric biological relationships on three different levels: between New World Midwestern precontact groups, between individuals buried together, and between ancient and modern strains of Mycobacterium tuberculosis complex (MTC) bacteria. Through this analysis, I attempt to shed light on aspects of the health and culture of the Schild people of the Lower Illinois Valley (LIV), a region peripheral to the Mississippian center of Cahokia. The appearance of Mississippian culture at Schild (including changes in material culture, settlement patterns, mortuary practices, and subsistence strategies) occurred approximately 100 years after the founding of Cahokia (ca A.D. 1050); mitochondrial DNA (mtDNA) haplogroup and haplotype distributions in LIV groups bracketing this transition indicates that low levels of gene flow coincided with this event.

My analysis of the distribution of mtDNA lineages in Middle Woodland (ca B.C. 200-A.D. 400), Late Woodland (ca A.D. 400-1000), and Mississippian (ca A.D. 1050-historic) period cemeteries from this region indicated that burial location was not determined by maternal relationships. On a larger scale, this analysis calls into question the "Madonna and Child Trope" the common archaeological interpretation of woman-child co-burials as mothers and children. These results suggest that inferences regarding biological relationships in prehistoric cemeteries should be made with caution in the absence of morphological or genetic evidence.

In molecular survey of the Schild burial series, I recovered DNA from eight individuals infected with tuberculosis. Phylogenetic analysis of portions of the gyrase B and 16S rRNA loci, and the presence of the MTC-specific insertion element IS6110, show that this ancient isolate belongs to the MTC, but is distinct from all modern members of the complex, suggesting a long evolutionary separation from Old World complex members. This ancient MTC strain exhibits non-typical skeletal pathology, in that bone lesions are more frequent than in human infections with any of the modern species. My evidence suggests that a previously uncharacterized strain of TB may have been present in American populations prior to European contact.