J Archaeol Sci. Author manuscript; available in PMC 2011 Jul 1.
Published in final edited form as:
J Archaeol Sci. 2010 Jul 1; 37(7): 1635–1645.
PMCID: PMC2877212, NIHMSID: NIHMS182120
Meradeth H. Snow, corresponding author
University of California, Davis Anthropology Department, Young Hall One Shields Avenue Davis CA 95616
Kathy R. Durand
Eastern New Mexico University
David Glenn Smith
University of California, Davis
Ancient DNA (aDNA) was extracted from the human remains of seventy-three individuals from the Tommy and Mine Canyon sites (dated to PI-II and PIII, respectively), located on the B-Square Ranch in the Middle San Juan region of New Mexico. The mitochondrial DNA (mtDNA) haplogroups of forty-eight (65.7%) of these samples were identified, and their frequency distributions were compared with those of other prehistoric and modern populations from the Greater Southwest and Mexico. The haplogroup frequency distributions for the two sites were statistically significantly different from each other, with the Mine Canyon site exhibiting an unusually high frequency of haplogroup A for a Southwestern population, indicating the possible influence of migration or other evolutionary forces. However, both sites exhibited a relatively high frequency of haplogroup B, typical of Southwestern populations, suggesting continuity in the Southwest, as has been hypothesized by others (S. Carlyle 2003; Carlyle, et al. 2000; Kemp 2006; Malhi, et al. 2003; Smith, et al. 2000). The first hypervariable region of twenty-three individuals (31.5%) was also sequenced to confirm haplogroup assignments and compared with other sequences from the region. This comparison further strengthens the argument for population continuity in the Southwest without a detectable influence from Mesoamerica.
The relationship between ancestral Pueblo people of the US Southwest and other populations in the region has long been the focus of archaeological attention. As Cameron (1995) notes, after a long period of neglect, migration has again moved to the forefront of our interpretations of population dynamics in the prehistoric Southwest (Clark 2001; Mills 2008; Reed 2008; Wilshusen and Van Dyke 2006; Windes 2007). While areas that experienced regional depopulation are easy to identify, determining the location to which people emigrated, particularly based on material culture, is less straightforward (Lathrap 1956). More recently, both modern and ancient DNA (aDNA) have been used to address migration hypotheses (Carlyle 2003; Carlyle, et al. 2000; Leblanc, et al. 2007; Malhi, et al. 2003).