Extraction and amplification of ancient DNA

Ancient DNA can be extracted from cellular remains such as bone, tooth roots, tissue (preserved under water, frozen, or dried), coprolites, seeds, and other plant materials, and thus, the questions that can be addressed are wide-ranging from the history of the domestication of plants and animals to the relationships between individuals at an archaeological site or the relationships between extant and extinct species. Ancient DNA analyses, however, are fraught with difficulty both because of the small quantity and damaged nature of the DNA and because of problems with contamination from modern sources. These difficulties require special facilities and techniques to enhance the probability of recovery and to assure the authenticity of the results. The work should be performed in a laboratory that is located separately from the main laboratory where modern DNA and post-PCR products are analyzed and stored, and equipment and reagents should be dedicated to ancient DNA work. Reagents must be tested for contamination by including both extraction and PCR “blanks” which are subject to the same protocols as the primary samples. All results also must be verified by multiple independent extractions and analyses. Finally, the results should make sense (i.e., the sequences should not match one from the investigator’s genome or match that of a cow sequence when a sloth sequence is expected).