Research ArticlePALEONTOLOGY

A fourth Denisovan individual

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Science Advances  07 Jul 2017:
Vol. 3, no. 7, e1700186
DOI: 10.1126/sciadv.1700186
  • 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 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 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.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/7/e1700186/DC1

    section S1. The Denisova 2 specimen

    section S2. Authenticating the DNA sequences

    section S3. The mtDNA sequence of Denisova 2

    section S4. Nuclear DNA sequences from Denisova 2

    fig. S1. The Denisova 2 specimen.

    fig. S2. The Denisova 2 specimen.

    fig. S3. Biplot of cervical buccolingual (BL) and mesiodistal (MD) diameters.

    fig. S4. Characteristic of DNA fragments from the two libraries prepared from the Denisova 2 specimen, per size bin.

    fig. S5. Frequency of nucleotide substitutions in the Denisova 2 sequences.

    fig. S6. Reconstructing the Denisova 2 mitochondrial genome.

    fig. S7. Sex determination of Denisova 2.

    fig. S8. Lineage attribution of two other low-coverage Denisovan individuals.

    fig. S9. Testing our power to detect the sharing of derived alleles between Denisovans and present-day humans.

    fig. S10. Ancestral allele counts in Denisovan and Neandertal sequences at sites that are fixed or nearly fixed for a derived allele in present-day humans.

    table S1. Metric comparisons of cervical and maximum mesiodistal and buccolingual diameters of Denisova 2, Neandertals, and recent and Upper Paleolithic modern humans.

    table S2. Characteristics of the DNA libraries prepared from Denisova 2.

    table S3. Frequencies of terminal C-to-T substitutions to the human reference genome.

    table S4. Percentage and number of sequences matching the derived state of mitochondrial genomes from three hominin groups.

    table S5. Number of base differences between the Denisova 2 mtDNA and other mtDNAs.

    table S6. Estimates of DNA divergence between low-coverage archaic genomes and the high-coverage genomes of a Denisovan, a Neandertal, and 12 present-day humans.

    table S7. Estimates of DNA divergence between subsampled genomes and the high-coverage genomes of a Denisovan, a Neandertal, and 12 present-day humans.

    table S8. Sharing of derived alleles between Denisova 2 and present-day humans.

    table S9. Denisova-specific nonsynonymous coding changes corroborated by sequences from Denisova 2, 4, or 8.

    References (7082)

  • Supplementary Materials

    This PDF file includes:

    • section S1. The Denisova 2 specimen
    • section S2. Authenticating the DNA sequences
    • section S3. The mtDNA sequence of Denisova 2
    • section S4. Nuclear DNA sequences from Denisova 2
    • fig. S1. The Denisova 2 specimen.
    • fig. S2. The Denisova 2 specimen.
    • fig. S3. Biplot of cervical buccolingual (BL) and mesiodistal (MD) diameters.
    • fig. S4. Characteristic of DNA fragments from the two libraries prepared from the Denisova 2 specimen, per size bin.
    • fig. S5. Frequency of nucleotide substitutions in the Denisova 2 sequences.
    • fig. S6. Reconstructing the Denisova 2 mitochondrial genome.
    • fig. S7. Sex determination of Denisova 2.
    • fig. S8. Lineage attribution of two other low-coverage Denisovan individuals.
    • fig. S9. Testing our power to detect the sharing of derived alleles between Denisovans and present-day humans.
    • fig. S10. Ancestral allele counts in Denisovan and Neandertal sequences at sites that are fixed or nearly fixed for a derived allele in present-day humans.
    • table S1. Metric comparisons of cervical and maximum mesiodistal and buccolingual diameters of Denisova 2, Neandertals, and recent and Upper Paleolithic modern humans.
    • table S2. Characteristics of the DNA libraries prepared from Denisova 2.
    • table S3. Frequencies of terminal C-to-T substitutions to the human reference genome.
    • table S4. Percentage and number of sequences matching the derived state of mitochondrial genomes from three hominin groups.
    • table S5. Number of base differences between the Denisova 2 mtDNA and other mtDNAs.
    • table S6. Estimates of DNA divergence between low-coverage archaic genomes and the high-coverage genomes of a Denisovan, a Neandertal, and 12 present-day humans.
    • table S7. Estimates of DNA divergence between subsampled genomes and the high-coverage genomes of a Denisovan, a Neandertal, and 12 present-day humans.
    • table S8. Sharing of derived alleles between Denisova 2 and present-day humans.
    • table S9. Denisova-specific nonsynonymous coding changes corroborated by sequences from Denisova 2, 4, or 8.
    • References (70–82)

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