A molecular analysis of dietary diversity for three archaic Native Americans

Abstract

DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2-4 different animal species and 4-8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

Figure 1

Human paleofeces from Hinds Cave, Texas. [Scale, 1 cm in the photo is equal to 2.78 cm real (slide).]

Figure 2

DNA sequences of clones derived from sample I. (A) Clones from the three restriction fragments (brackets indicate restriction site) and 9-bp repeat, (B) a segment of hypervariable region I, (reference sequence from ref. 14), and (C) three clones from a fragment of the 12S rRNA gene matching to the genera Antilocapra and Sylvilagus, whose sequences appear as the reference sequence at top. Ambiguous bases are indicated by standard abbreviations and dashes indicate deletions.

Figure 3

DNA sequences of clones from two fragments of the chloroplast rbcL gene amplified from the three paleofecal samples. Letters and numbers to the left indicate clone number, sample number [given as A(I), B(II), C(III)], extraction number, and PCR number. G indicates samples that were ground under liquid nitrogen and extracted, and R indicates samples that were rehydrated and extracted. X indicates clones that match data bank sequences with two or more differences. j indicates clones that represent putative jumping PCR events. Sequence clusters were identified as: A, Rhamnaceae; B, Ulmaceae; C, Fagaceae; D, Asteracea; E, Liliales; F, Fabaceae; G, Solonaceae; and H, Fouquieriaceae. * indicates two clones similar to the order Zingiberales.