A 28,000 years old Cro-Magnon mtDNA sequence differs from all potentially contaminating modern sequences

Abstract

Background: DNA sequences from ancient specimens 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.

Methodology/principal findings: 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.

Conclusions/significance: 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.

Figure 1. Tibia fragment of the Paglicci 23 specimen.

DNA was extracted from this fragment and from skull splinters, and all extracts yielded the same HVR I sequence.

Figure 2. 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).