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, 3 (7), e1700186

A Fourth Denisovan Individual


A Fourth Denisovan Individual

Viviane Slon et al. Sci Adv.


The presence of Neandertals in Europe and Western Eurasia before the arrival of anatomically modern humans is well supported by archaeological and paleontological data. In contrast, fossil evidence for Denisovans, a sister group of Neandertals recently identified on the basis of DNA sequences, is limited to three specimens, all of which originate from Denisova Cave in the Altai Mountains (Siberia, Russia). We report the retrieval of DNA from a deciduous lower second molar (Denisova 2), discovered in a deep stratigraphic layer in Denisova Cave, and show that this tooth comes from a female Denisovan individual. On the basis of the number of "missing substitutions" in the mitochondrial DNA determined from the specimen, we find that Denisova 2 is substantially older than two of the other Denisovans, reinforcing the view that Denisovans were likely to have been present in the vicinity of Denisova Cave over an extended time period. We show that the level of nuclear DNA sequence diversity found among Denisovans is within the lower range of that of present-day human populations.


Fig. 1
Fig. 1. Maximum likelihood tree relating the Denisova 2 mtDNA to other ancient and present-day mtDNAs.
The Denisova 2 mtDNA (in red) clusters with the three previously determined Denisovan mtDNAs, to the exclusion of Neandertals and modern humans. Present-day human mtDNA sequences are noted in italics. The tree was rooted using a chimpanzee mtDNA sequence (not shown). Support for each branch is based on 500 bootstrap replications. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Accession codes for the comparative data and the geographical origins of ancient individuals are presented in table S5.
Fig. 2
Fig. 2. Phylogenetic tree relating the Denisova 2 mtDNA to other Denisovan mtDNA sequences.
The number of substitutions on each branch was inferred by maximum parsimony, and the Middle Pleistocene mtDNA from Sima de los Huesos was used as an outgroup. The schematic representations of the specimens are drawn to scale, shown in the lower right corner.
Fig. 3
Fig. 3. Attribution of Denisova 2 to a hominin group.
(A) For each branch of a phylogenetic tree relating the high-coverage genomes of a Denisovan, a Neandertal, and a present-day human from Africa, the 95% binomial CIs of the proportion of DNA fragments from the Denisova 2 specimen that share a derived allele with that branch are given. (B) The fraction of substitutions inferred to have occurred after the split from the Denisova 2 genome along the branch from the human-chimpanzee (Ch) ancestral sequences to the high-coverage genomes of a Denisovan, a Neandertal, and 12 present-day humans (“X” in the schematic phylogenetic tree shown in the inset) is given. Error bars denote 95% CIs.

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