The researchers could verify that the sequence of the Cro-Magnon (which was the Cambridge Reference Sequence, common among modern Caucasoids) was genuine, since it was different from that of all possible contaminating individuals who handled the find since 2003.
This raises an interesting methodological problem. Should researchers with common mtDNA sequences be handling ancient remains? It seems like blind good luck that no one out of individuals had the quite common CRS. In the recent mtDNA paper on the Mycenaeans for example, they were able to identify contaminant sequences by the fact that the author and experimenter had a particular mutation; if she was plain CRS, they wouldn't have been able to disprove possible contamination for the CRS individual from Mycenae.
Ascertaining authenticity is challenging. In an ideal situation the sample is handled by only a single individual, and one who is unlikely to possess the same mtDNA type as the sample. An obvious solution to this would be to recruit a person of remote geographic origin to do the lab work, e.g. a Japanese person to work on European samples and vice versa.
PLoS ONE 3(7): e2700. doi:10.1371/journal.pone.0002700
A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences
David Caramelli et al.
DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans.
We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences.
The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.