Research Article

Neandertal and Denisovan DNA from Pleistocene sediments

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Science  12 May 2017:
Vol. 356, Issue 6338, pp. 605-608
DOI: 10.1126/science.aam9695
  • Fig. 1 Ancient taxa detected in Late Pleistocene (LP) and Middle Pleistocene (MP) sediment samples from seven sites.

    For each time period, the fraction of samples containing DNA fragments that could be assigned to a mammalian family and authenticated to be of ancient origin is indicated. The shaded symbols representing each family are not to scale.

  • Fig. 2 Cladogram relating mtDNA genomes reconstructed from sediment samples to those of modern and ancient individuals.

    The branches leading to mtDNA genomes reconstructed from sediments (dashed lines) were superimposed on a neighbor-joining tree relating the previously determined mtDNA genomes of ancient and present-day humans (purple), Neandertals (orange), the Sima de los Huesos hominin (blue), and Denisovans (green) (table S5). Discrete phylogenetic trees relating each of the mtDNAs reconstructed here and the comparative data are shown in figs. S41 to S49.

  • Fig. 3 Hominin mtDNAs along the stratigraphy of the East Gallery in Denisova Cave.

    Layer numbers are noted in gray. The layers of origin for sediment samples and skeletal remains yielding Neandertal (orange) and Denisovan (green) mtDNA genomes are indicated. For details on these and other hominin skeletal remains from other parts of the cave, see (8).

  • Neandertal and Denisovan DNA from Pleistocene sediments

    Viviane Slon, Charlotte Hopfe, Clemens L. Weiß, Fabrizio Mafessoni, Marco de la Rasilla, Carles Lalueza-Fox, Antonio Rosas, Marie Soressi, Monika V. Knul, Rebecca Miller, John R. Stewart, Anatoly P. Derevianko, Zenobia Jacobs, Bo Li, Richard G. Roberts, Michael V. Shunkov, Henry de Lumley, Christian Perrenoud, Ivan Gušić, Željko Kućan, Pavao Rudan, Ayinuer Aximu-Petri, Elena Essel, Sarah Nagel, Birgit Nickel, Anna Schmidt, Kay Prüfer, Janet Kelso, Hernán A. Burbano, Svante Pääbo, Matthias Meyer

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S53
    • Tables S1 to S10
    • Captions for Data Files S1 to S4
    • References
    Data File S1
    Sediment samples analysed in this study. Details on the sampling locations, amounts of material used for DNA extraction, the types of DNA libraries prepared and the number of molecules in each of them are presented.
    Data File S2
    Characteristics of the DNA libraries enriched for mammalian mtDNA fragments.
    Data File S3
    Evaluating the authenticity of mtDNA fragments from 22 mammalian families. For each family, the number of unique sequences attributed to it from each sample, their average length and the frequencies of nucleotide substitutions typical of ancient DNA in these sequences are reported. We tested whether the latter are significantly higher than 10% using an exact binomial test. For taxa determined to be ancient, the percentages of sequences matching different groups or species at phylogenetically informative positions are computed. L- length; MQ â€" mapping quality; bp â€" base pairs; C â€" cytosine; T â€" thymine; NA â€" not applicable.
    Data File S4
    Characteristics of the DNA libraries enriched for human mtDNA fragments and evaluation of the authenticity of the obtained sequences. For each library and for merged datasets pertaining to specific samples, the number of unique hominin sequences, their average length and the frequencies of nucleotide substitutions typical of ancient DNA are shown. We tested whether the latter are significantly higher than 10% using an exact binomial test. The number and percentage of sequences matching variants specific to each branch of a phylogenetic tree relating four hominin groups are reported, using all sequences in a samples and after retaining only those exhibiting terminal C to T substitutions. L- length; MQ â€" mapping quality; bp â€" base pairs; C â€" cytosine; T â€" thymine; NA â€" not applicable.

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