Svante Pääbo’s group at the Max Plank Institute have a paper coming out in the February issue of Cell Biology. In it, they describe sequencing a complete early human mitochondrial genome from the Markina Gora specimen from the Kostenki 14 site in Russia. The remains date to around 30,000 years ago, not the oldest human sequence, but interesting nonetheless because the authors have identified new ways to determine if ancient DNA sequences are genuine vs. contamination. This is especially important for more anatomically modern human fossils, who may have similar sequences to extant populations.
For Neandertal mtDNA, identifying contamination is relatively simple, because their mtDNA sequences fall outside the range of variation found in modern humans. Not so for more recent fossils. So how can researchers identify true archaic sequences?
fragment length, deamination-induced sequence errors at ends of molecules, and purine-associated fragmentation represent features by which endogenous and contaminating populations of DNA molecules can be distinguished in at least some late Pleistocene specimens (1).
So, fragments sequenced from ancient samples are typically shorter than modern contaminants. In many cases, the fragments are shorter than what can be amplified using PCR, meaning high-throughput direct sequencing methods are required to analyze these ancient samples. In addition, the cytosine bases at the 5′ ends of ancient DNA fragments are susceptible to deamination (removal of an -NH3 group), causing those bases to be misread as thymine. The 3′ ends of ancient sequences have a commensurate increase in G-A errors. Finally, fragmentation of ancient sequences occurs more frequently at purine bases (guanine and adenine).
With these criteria in mind, the researchers determined that the Markina Gora sequence belongs to mitochondrial haplogroup U2, a haplogroup still present in Europe today.
Figure 3D from Krause et al. (2010) - with the EMH sequence highlighted in red.
The authors determine that it is unlikely that this sequence is the result of modern contamination, because the nucleotide difference between the Markina Gora specimen and the ancestral U sequence is much shorter than than seen between the root and modern sequences, which have accumulated many more mutations over time. Their results also support the hypothesis of pre-agricultural genetic continuity in Europe, so that genetic lineages which were present on the continent prior to the Neolithic transition can still be found in modern European populations.
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Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, & Pääbo S (2009). A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia. Current biology : CB PMID: 20045327
