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The Neandertal genome and ancient DNA authenticity
Author(s) -
Green Richard E,
Briggs Adrian W,
Krause Johannes,
Prüfer Kay,
Burbano Hernán A,
Siebauer Michael,
Lachmann Michael,
Pääbo Svante
Publication year - 2009
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1038/emboj.2009.222
Subject(s) - biology , genome , ancient dna , evolutionary biology , dna sequencing , genetics , mitochondrial dna , computational biology , shotgun sequencing , neanderthal , dna , gene , archaeology , population , demography , sociology , history
Recent advances in high‐thoughput DNA sequencing have made genome‐scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination. Indirect measures, such as the extent of DNA fragmentation, nucleotide misincorporations, or comparison of derived allele frequencies in different fragment size classes, are unreliable. Fortunately, interim approaches based on mtDNA differences between Neandertals and current humans, detection of male contamination through Y chromosomal sequences, and repeated sequencing from the same fossil to detect autosomal contamination allow initial large‐scale sequencing of Neandertal genomes. This will result in the discovery of fixed differences in the nuclear genome between Neandertals and current humans that can serve as future direct assays for contamination. For analyses of other fossil hominins, which may become possible in the future, we suggest a similar ‘boot‐strap’ approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired.