Bone splinters (tibia and skull) provided the DNA.
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
Genetic relationships among the Paglicci 23 and other relevant mtDNA sequences.
The network summarizes mtDNA HVR I variation in 13 Neandertals (Nea1 to Nea13) , three Cro-Magnons (CrM1 to CrM3), and seven modern humans who manipulated the Cro-Magnons specimens (six authors of this paper and Carles Laueza-Fox, designated by their initials).
So, according to this; they were lucky that none of the people that handled the bones had the same mtDNA type as the Cro Magnon man, and that it was significantly different to the Neanderthal DNA that’s been sequenced, but within the normal range for Europeans. A name for the haplotype would have been nice!