Thanks to the very helpful readers who have sent me a copy of the latest from Pääbo and crew, “Neanderthals in central Asia and Siberia.” I’ve read it, and it is a pretty good paper with solid methods. This study is important because it compliments paleoanthropology with molecular biology to fill in discrepancies with using morphology to classify remains. As you all know, fossils don’t come out as clean and intact as your grandmother’s china. Almost always hominid fossils are fragmented and incomplete.
That being said, the hominid remains from the Teshik Tash cave in Uzbekistan and the Okladnikov cave in the Altai region of Siberia are so fragmented and hard to classify, that for a long time paleoanthropologists have just put them aside. Lead author Krause et al. decided to dust off these specimens and break off about a fifth of a gram of bone from each to sequence and compare. Specifically, they harvested samples from the femur of the Teshik Tash kid and from three Okladnikov long bones.
Fossils don’t hold much DNA. Upon death, the body begins degrading DNA immediately, and only under certain conditions is DNA preserved enough so that one can extract DNA from a fossil. And once DNA is extracted, it is a really tiny amount which is muddled in a lot of contaminated DNA. So, in order to exponentially increase the amount of starting DNA, a technique called PCR, or polymerase chain reaction, is used. To do so, each segment of DNA needs to be primed, so that the PCR polymerases can bind to them and being duplicating. The DNA from these bones were amplified with three different primer pairs, I guess to test out which primer pair worked best.
Once the PCR reaction was complete the authors next sorted out modern human amplified DNA from Neandertal amplified DNA. They did this because, as I mentioned, there’s a lot of contamination, especially from modern human mtDNA on fossil bone. This is most likely due to handling and excavating the bone. After figuring out the modern human amplified products, it was found that the Teshik Tash kid and a subadult from Okladnikov, both yielded about 2 clones each of 60 Neandertal specific base pairs.
Since paleoanthropologists have spent all their time debating on how to classify the Okladnikov fossils, there seems to not be reliable dates for them. Krause and team dated them, and noted that the subadult from Okladnikov, the one that had Neandertal specific base pairs, was old enough (37,000 years old) to be a Neandertal.
With this date and the two pairs of Neandertal clones, the team narrowed down their scopes. They specifically designed primers that worked on amplifying only the hypervariable region 1 (HVR1) of Neandertal mtDNA. Why the HVR1? For starters the HVR1 is longer section than the 60 or so base pairs they already have. And since the HVR1 is an area where base pairs repeat and are highly polymorphic, it is a more informative section. Having longer sequences to align, compare, and analyze is much more statistically significant than shorter ones.
The authors sent off the Teshik Tash and Okladnikov samples to a DNA lab in France, which exactly matched up to their results, and confirmed they were doing the right stuff. 
After all the statistics, 300 base pairs from both the Teshik Tash and Okladnikov were compared to the same section of HVR1 from seven other Neandertals. They only differ in about 6 bases from the other Neandertals… that’s about a 98% similarity. Not bad at all.
What this study does is it pushes the geographical range of Neandertals, by 2,000 kilometers to the east. We already had an inkling Neandertals may have made it out to what is now Uzbekistan… hell they’ve been found in Iran. But to see that one of the Okladnikov fossils has Neandertal mtDNA that matches to European Neandertal mtDNA, calls for a big whoa. Neandertals in Siberia, whoa.
