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Molecular archaeology brings the tools of molecular biology to bear on fundamental questions in archaeology, anthropology, evolution, and ecology. Ancient DNA research is becoming widespread as evolutionary biologists and archaeologists discover the power of the polymerase chain reaction (PCR) to amplify DNA from ancient plant and animal remains. However, the extraordinary susceptibility of PCR to contamination by extraneous DNA is not widely appreciated. We report the independent observation of DNA from domestic animals in PCR reagents and ancient samples in four separate laboratories. Since PCR conditions used in ancient DNA analyses are extremely sensitive, very low concentrations of contaminating DNA can cause false positives. Previously unidentified animal DNA in reagents can confound ancient DNA research on certain domestic animals, especially cows, pigs, and chickens.

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.

Microcracks produced during the manufacture of stone tools may harbour ancient biological residues. Our studies test this hypothesis using light, scanning electron, fluorescence, and confocal microscopy to characterize microcracks produced in obsidian microblades by pressure flaking. Cell-sized fluorescent latex beads penetrated microcracks to depths exceeding 50 μm below the microblade surface. Fluorescently labelled blood protein and DNA were trapped in microcracks within 5 min of exposure. Washing artifacts with water did not remove blood residues from microcracks. However, 60–80% of trapped blood protein and DNA were released by an 18-hour incubation in 4M guanidine hydrochloride or by sonication in 5% ammonium hydroxide. These experiments suggest that residues trapped in artifact microcracks represent an important and often overlooked source of ancient DNA and protein.