Science Advances

The PDF file includes:

• Fig. S1. Geographic location of populations included in FMD and HDD, and fineStructure dendrogram for all the 4,852 (FMD) and 1,641 (HDD) samples.
• Fig. S2. Allele frequency PCA (genotype based) and individual-level ADMIXTURE of modern samples.
• Fig. S3. “Cluster self-copy” analysis and PCA with admixed Italian individuals.
• Fig. S4. Results of the EEMS analysis on Italy-only populations.
• Fig. S5. CP/NNLS and qpAdm results for different sets of ancient sources for all modern clusters.
• Fig. S6. D-statistics analyses.
• Fig. S7. PCA and ADMIXTURE analyses of 63 ancient samples.
• Fig. S8. GT and MALDER analyses for all the Eurasian and North African clusters.
• Fig. S9. Neanderthal ancestry distribution in Eurasian population and its relationship with African admixture and Basal Eurasian ancestry.
• Legends for data files S1 to S6

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Other Supplementary Material for this manuscript includes the following:

• Data file S1 (Microsoft Excel format). Modern and ancient samples used in this study.
• Data file S2 (Microsoft Excel format). Cluster self-copy analysis.
• Data file S3 (Microsoft Excel format). Weighted jackknife bootstraps.
• Data file S4 (Microsoft Excel format). qpAdm results.
• Data file S5 (Microsoft Excel format). GT and MALDER results.
• Data file S6 (Microsoft Excel format). NTT SNPs (Neanderthal-Tag SNPs within the top 1% of the genome-wide distributions of each of the 55 pairwise population comparisons).