This PDF file includes:

• Supplementary Materials and methods
• Fig. S1. Photographs of burial goods with most specific cultural identifying markers.
• Fig. S2. Isotope ⁸⁶Sr/⁸⁷Sr and δ¹⁸O values for enamel from teeth.
• Fig. S3. Overlaying shotgun and mtDNA deamination plots from mapDamage quantification against the reference genome.
• Fig. S4. Genetic sex estimates from genome-wide capture.
• Fig. S5. Admixture estimates for west Eurasians, Niederstotzingen, and selected ancient individuals.
• Fig. S6. F3 outgroup statistics for Niederstotzingen 1 using Mbuti as an outgroup.
• Fig. S7. F3 outgroup statistics for Niederstotzingen 3A using Mbuti as an outgroup.
• Fig. S8. F3 outgroup statistics for Niederstotzingen 3B using Mbuti as an outgroup.
• Fig. S9. F3 outgroup statistics for Niederstotzingen 3C using Mbuti as an outgroup.
• Fig. S10. F3 outgroup statistics for Niederstotzingen 6 using Mbuti as an outgroup.
• Fig. S11. F3 outgroup statistics for Niederstotzingen 9 using Mbuti as an outgroup.
• Fig. S12. F3 outgroup statistics for Niederstotzingen 12B using Mbuti as an outgroup.
• Fig. S13. F3 outgroup statistics for Niederstotzingen 12C using Mbuti as an outgroup.
• Table S1. PCR-based haplotyping of DNA extracts from previous study.
• Table S2. Archeological context and isotopes.
• Table S3. Shotgun sequencing output and mapping data.
• Table S4. mtDNA capture sequencing output data and mapping.
• Table S5. 1240K sequencing output data and mapping.
• Table S6. Schmutzi estimation of mtDNA contamination.
• Table S7. ANGSD X chromosome contamination estimate on 1240K libraries.
• Table S8. Haplogroups and private mutations for each mtDNA capture (phylotree 17).
• Table S9. Complete list of NRY haplogroups with identifying ISOGG markers for 1240K capture sequences.
• Table S10. Sex estimates from shotgun and genome-wide capture data.
• Table S11. Sex estimates from shotgun data based on Rx values.
• Table S12. Admixture CV error values for each component and individual.
• Table S13. Shotgun reads with PMDtools threshold 3 filtered and skoglund sex estimate of filtered reads.
• Table S14. Haplogroup calling of selected individuals before and after PMD (threshold 3) filtering.
• Table S15. READ pairwise kinship-based estimate.
• Table S16. Pairwise estimate of kinship and coefficient of relatedness.
• References (52–58)

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