Genetic history of an archaic hominin group from Denisova Cave in Siberia

Abstract

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

Figure 1. A neighbour-joining tree based on pairwise autosomal DNA sequence divergences for five ancient and five present-day hominins

Vindija 33.16, Vindija 33.25 and Vindija 33.26 refer to the catalogue numbers of the Neanderthal bones.

Figure 2. Relationship of present-day populations to the Denisova individual and Neanderthals based on 255,077 SNPs

Principal component analysis of the means of 53 present-day human populations projected onto the top two principal components defined by Denisova, Neanderthal and chimpanzee. The seven ‘African’ populations are San, Mbuti, Biaka, Bantu Kenya, Bantu South Africa, Yoruba and Mandenka; the ‘Non-African’ populations are 44 diverse groups from outside Africa except for Papuan and Bougainville islanders.

Figure 3. A model of population history compatible with the data

N denotes effective population size, t denotes time of population separation, f denotes amount of gene flow and t_GF denotes time of gene flow.

Figure 4. Morphology of the Denisova molar

a, b, Occlusal (a) and mesial (b) views. c, Comparison of the Denisova molar to diverse third molars, in a biplot of the mesiodistal and buccolingual lengths (in mm). AMH, anatomically modern humans; SH, Sima de los Huesos. Supplementary Fig. 12.1 presents a similar comparison to second molars.