A paper by S. Sawyer et al., Nuclear and mitochondrial DNA sequences from two Denisovan individuals, PNAS, doi: 10.1073/pnas.1519905112 Published Nov. 16, 2015 has sequenced the nuclear and mtDNA of two Denisovans. Their findings are the following:
Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.
The paper notes that "Both Denisova 8 and Denisova 4 are very large compared with Neandertal and early modern human molars, and Denisova 8 is even larger than Denisova 4. Only two Late Pleistocene third molars are comparable in size: those of the inferred early Upper Paleolithic modern human Oase 2 in Romania and those of ObiRakhmat 1 in Uzbekistan"
The teeth though primitive looking also seem to differ from H. erectus teeth too. Which is quite interesting.
Denisova 8 is about 60,000 years older than Denisova 3 and Denisova 4 meaning that they are 110,000 years old. This is a long period of time in a same location.
The paper says the following about this long occupation: ", suggests Denisovans were present in the area at least twice, and possibly over a long time, perhaps interrupted by Neandertal occupation or occupations. Denisovans may therefore have been present in southern Siberia over an extended period. Alternatively, they may have been present in neighboring regions, from where they may have periodically extended their range to the Altai.".
The paper ends with an open question: " Given that the high-coverage genome from the Denisovan 3 phalanx carries a component derived from an unknown hominin who diverged 1–4 million years ago from the lineage leading to Neandertals, Denisovans, and present-day humans, it is possible that this component differs among the three Denisovan individuals. In particular, it may be that the older Denisovan population living in the cave carried a larger or different such component. It is also possible that the two diverged mtDNA lineages seen in Denisova 8 on the one hand and Denisova 3 and Denisova 4 on the other were both introduced into the Denisovans from this unknown hominin, as has been suggested for the mtDNA of Denisova 3. However, more nuclear DNA sequences from Denisovan specimens of ages similar to Denisova 4 and Denisova 8 are needed to address this question fully.".
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