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Methods and Resources

Identification of the source of ancient remains through genomic sequencing

¹ Lawrence Berkeley National Laboratory; ² U.S. Department of Energy Joint Genome Institute; ³ Simon Fraser University; ⁴ Division of Paleolithic Studies, Department of Archaeology, Institute of Archaeology and Ethnography

Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genome-wide adapter-mediated emulsion PCR amplification protocol to ancient mammalian samples between 45,000 and 69,000 years old. Using GS20 and Solexa sequencing technologies, we examined over one hundred megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of non-redundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over five hundred-fold increases such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000 year old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high throughput sequencing allows for the generation of large quantities DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla.

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