Supplementary Materials

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.