A 99.9% complete Neanderthal genome from a toe bone found at Denisova Cave (Altai, Southern Siberia).
Documents at Max Plank Institute for Evolutionary Anthropology, Department of Evolutionary Genetics.
A high-quality Neandertal genome sequence
The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010. The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).
DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.
The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Deniosva Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times.
One may wonder: how can they know it is a Neanderthal and not a "Denisovan"? Because of the close genetic affinity with other Neanderthals from Europe:
It is still possible, considering its position in the tree that the Altai Neanderthal had minor "Denisovan" admixture. But it would be very minor in any case.