DNA from ancient stone tools and bones excavated at Bugas-Holding, Wyoming

DNA residues may preserve on ancient stone tools used to process animals. We studied 24 stone tools recovered from the Bugas-Holding site in northwestern Wyoming. Nine tools that yielded DNA included five bifaces, two side scrapers, one end scraper, and one utilized flake. The excavators did not handle three of these tools with bare hands, and they were sealed in separate plastic bags to minimize contact with modern DNA. Five sediment samples did not yield mammalian DNA. One tool contained DNA from three species, and these templates competed during polymerase chain reaction (PCR) amplification. DNA identifications suggested a butchery pattern indicative of a human population under resource stress or a broader range of industrial activities at Bugas-Holding. We describe several improvements in DNA residue analysis, including a more effective DNA recovery protocol, methods to measure sensitivity and inhibition of PCR in each sample, and strategies to surmount competition between templates during PCR.