Reconstruction of regional North American prehistory has benefited from the incorporation of ancient DNA evidence. However, few studies focus on intra-site genetic variation, associate these relationships to mortuary assemblages, or link these variables to social ranking. The Late Period (900 BP-250 BP) in the San Francisco Bay area witnessed shifts in settlement patterns that included mortuary treatment distinct from earlier periods. The change in mortuary pattern is interpreted either as a reduction in social inequality, a shift toward corporate group identity based on kinship, or an emergence of a lesser number of differentiated elites with control over high status resources.

Mitochondrial DNA (mtDNA) data was collected from 200 individuals from CA-SCL-38 (Yukisma Mound), hereafter referred to as SCL-38 as well as 102 additional burials from 15 other archaeological sites in the region to test for a relationship between direct maternal kinship (i.e., genetic relatedness as revealed by mtDNA), grave goods, and burial patterns. This was ultimately done to determine whether spatial patterns at SCL-38 are associated with the emergence/maintenance of social differentiation and inferred social inequality. These data were additionally used at the inter-site level to explore the hypothesized spread of Penutian populations and to document genetic continuity in the San Francisco Bay area through time.

Results indicate that maternal relatedness is not correlated to the spatial distribution of burials within the cemetery. Additionally, no associations are noted between particular mtDNA haplotypes and burials with high quantity or diversity of grave goods. Thus, the overall placement of burials at SCL-38 are random with respect to direct maternal relationships. However, regardless of mortuary assembleges, there are some subgroupings within the cemetery of individuals related at the maternal level. The heterogenous distribution of mtDNA lineages across the spatial extent of the site may instead reflect its use as a regional cemetery for select, perhaps wealthy elite, individuals who originated from the surrounding Bay area. It remains possible that patterning along the paternal line or the lack of temporal refinement is confounding other underlying genetic structure. Across the landscape, however, mtDNA lineages are identified that correspond with the hypothesized influx of Proto-Utian (Penutian) speakers into the San Francisco Bay area by the end of the Early Period and beginning of the Middle Period. Additonal haplotypes are also identified that are probably older than 7,000 BP in the region, most likely representing maternal lineages orignally belonging to ancestral Hokan speakers. Most mtDNA haplotypes discussed represent at least 2,000 years of genetic continuity in the region.