Nucleic acids are preserved in prehistoric samples under a wide range of depositional environments. The development of new molecular methods, especially the polymerase chain reaction, has made possible the recovery and manipulation of these molecules, and the subsequent molecular genetic characterization of the ancient samples. The analysis of ancient (a)DNA is complicated by the degraded nature of ancient nucleic acids, as well as the presence of enzymatic inhibitors in aDNA extracts. We review aspects of ancient DNA preservation, a variety of methods for the extraction and amplification of informative DNA segments from ancient samples, and the difficulties encountered in documenting the authenticity of ancient DNA template. Studies using aDNA to address questions in human population history or human evolution are reviewed and discussed. Future prospects for the field and potential directions for future aDNA research efforts in physical anthropology are identified.

The timing and degree of reliance on maize agriculture in the Four Corners region of the American Southwest has been a central issue in studies that examine the origins of Puebloan society. Both diffusionist (various, but see Wills 1995) and migrationist (Berry and Berry 1986; Matson 1991) models have been proposed to explain the processes responsible for the movement of maize (Zea mays) north into the Four Corners region. This paper reports bone collagen stable carbon and nitrogen isotope values with paired accelerator radiocarbon dates on a large collection of human remains from western Basketmaker II/III sites in Marsh Pass and other areas of northeastern Arizona, as well as data on a small number of Puebloan remains including Chacoan Great House burials. The results make clear that Basketmaker II people were heavily dependent on maize by 400 B.C. Moreover, their degree of dependence is similar to that of Pueblo II and III farmers of the Four Corners region. These findings and the apparent rapidity of maize dependence support a migrationist model for the origins of maize farming in the northern Southwest.

We present mitochondrial haplogroup characterizations of the prehistoric Anasazi of the United States (US) Southwest. These data are part of a long-term project to characterize ancient Great Basin and US Southwest samples for mitochondrial DNA (mtDNA) diversity. Three restriction site polymorphisms (RSPs) and one length polymorphism identify four common Native American matrilines (A, B, C, and D). The Anasazi (n = 27) are shown to have a moderate frequency of haplogroup A (22%), a high frequency of haplogroup B (56%), and a low frequency of C (15%). Haplogroup D has not yet been detected among the Anasazi. In comparison to modern Native American groups from the US Southwest, the Anasazi are shown to have a distribution of haplogroups similar to the frequency pattern exhibited by modern Pueblo groups. A principal component analysis also clusters the Anasazi with some modern (Pueblo) Southwestern populations, and away from other modern (Athapaskan speaking) Southwestern populations. The Anasazi are also shown to have a significantly different distribution of the four haplogroups as compared to the eastern Great Basin Great Salt Lake Fremont (n = 32), although both groups cluster together in a principal component analysis. The context of our data suggests substantial stability within the US Southwest, even in the face of the serious cultural and biological disruption caused by colonization of the region by European settlers. We conclude that although sample numbers are fairly low, ancient DNA (aDNA) data are useful for assessing long-term populational affinities and for discerning regional population structure.

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Skeletal remains of 47 individuals from the Great Salt Lake Wetlands, affiliated principally with Bear River (A.D. 400-1000) and Levee Phase (A.D. 1000-1350) Fremont cultural elements, were assessed for four mitochondrial DNA (mtDNA) markers that, in particular association, define four haplogroups (A, B, C, and D) widely shared among contemporary Amerindian groups. The most striking result is the absence of haplogroup A in this Fremont series, despite its predominance in contemporary Amerindian groups. Additionally, haplogroup B, defined by the presence of a 9bp deletion in region V, is present at the moderately high frequency of 60%. Haplogroups C and D are present at low frequencies. An additional haplotype, "N," observed in some modern populations and two other prehistoric samples, is also present in this Fremont skeletal collection.