| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Ancient skeletal element | This study | UZZ26 |
| Ancient skeletal element | This study | UZZ33 |
| Ancient skeletal element | This study | UZZ34 |
| Ancient skeletal element | This study | UZZ40 |
| Ancient skeletal element | This study | UZZ44 |
| Ancient skeletal element | This study | UZZ45 |
| Ancient skeletal element | This study | UZZ46 |
| Ancient skeletal element | This study | UZZ50 |
| Ancient skeletal element | This study | UZZ51 |
| Ancient skeletal element | This study | UZZ52 |
| Ancient skeletal element | This study | UZZ53 |
| Ancient skeletal element | This study | UZZ54 |
| Ancient skeletal element | This study | UZZ57 |
| Ancient skeletal element | This study | UZZ61 |
| Ancient skeletal element | This study | UZZ69 |
| Ancient skeletal element | This study | UZZ71 |
| Ancient skeletal element | This study | UZZ74 |
| Ancient skeletal element | This study | UZZ75 |
| Ancient skeletal element | This study | UZZ77 |
| Ancient skeletal element | This study | UZZ79 |
| Ancient skeletal element | This study | UZZ80 |
| Ancient skeletal element | This study | UZZ81 |
| Ancient skeletal element | This study | UZZ82 |
| Ancient skeletal element | This study | UZZ87 |
| Ancient skeletal element | This study | UZZ88 |
| Ancient skeletal element | This study | UZZ96 |
| Ancient skeletal element | This study | UZZ99 |
| Chemicals, peptides, and recombinant proteins | ||
| D1000 ScreenTapes | Agilent Technologies | Cat# 5067-5582 |
| D1000 Reagents | Agilent Technologies | Cat# 5067-5583 |
| PfuTurbo Cx Hotstart DNA Polymerase | Agilent Technologies | Cat# 600412 |
| Herculase II Fusion DNA Polymerase | Agilent Technologies | Cat# 600679 |
| 1x Tris-EDTA pH 8.0 | AppliChem | Cat# A8569,0500 |
| Sodiumhydroxide Pellets | Fisher Scientific | Cat# 10306200 |
| Sera-Mag Magnetic Speed-beads Carboxylate-Modified (1 mm, 3EDAC/PA5) | GE LifeScience | Cat# 65152105050250 |
| 0.5 M EDTA pH 8.0 | Life Technologies | Cat# AM9261 |
| 10x Buffer Tango | Life Technologies | Cat# BY5 |
| GeneRuler Ultra Low Range DNA Ladder | Life Technologies | Cat# SM1211 |
| Isopropanol | Merck | Cat# 1070222511 |
| Ethanol | Merck | Cat# 1009832511 |
| USER enzyme | New England Biolabs | Cat# M5505 |
| Uracil Glycosylase inhibitor (UGI) | New England Biolabs | Cat# M0281 |
| Bst DNA Polymerase2.0, large frag. | New England Biolabs | Cat# M0537 |
| BSA 20 mg/mL | New England Biolabs | Cat# B9000 |
| T4 Polynucleotide Kinase | New England Biolabs | Cat# M0201 |
| T4 DNA Polymerase | New England Biolabs | Cat# M0203 |
| PEG-8000 | Promega | Cat# V3011 |
| 20% SDS | Serva | Cat# 39575.01 |
| Proteinase K | Sigma Aldrich | Cat# P2308 |
| Guanidine hydrochloride | Sigma Aldrich | Cat# G3272 |
| 3M Sodium Acetate (pH 5.2) | Sigma Aldrich | Cat# S7899 |
| Water | Sigma Aldrich | Cat# 34877 |
| Tween-20 | Sigma Aldrich | Cat# P9416 |
| 5M NaCl | Sigma Aldrich | Cat# S5150 |
| Denhardt’s solution | Sigma Aldrich | Cat# D9905 |
| ATP 100 mM | Thermo Fisher Scientific | Cat# R0441 |
| 1 M Tris-HCl pH 8.0 | Thermo Fisher Scientific | Cat# 15568025 |
| dNTP Mix | Thermo Fisher Scientific | Cat# R1121 |
| SSC Buffer (20x) | Thermo Fisher Scientific | Cat# AM9770 |
| GeneAmp 10x PCR Gold Buffer | Thermo Fisher Scientific | Cat# 4379874 |
| Dynabeads MyOne Streptavidin T1 | Thermo Fisher Scientific | Cat# 65602 |
| Salmon sperm DNA | Thermo Fisher Scientific | Cat# 15632-011 |
| Human Cot-I DNA | Thermo Fisher Scientific | Cat#15279011 |
| 0.5M HCl | Carl Roth | Cat# 9277.1 |
| HNO3 | Merck | Cat# 1.00456.2500 |
| Critical commercial assays | ||
| High Pure Viral Nucleic Acid Large Volume Kit | Roche | Cat# 5114403001 |
| HiSeq 4000 SBS Kit (50/75 cycles) | Illumina | Cat# FC-410-1001/2 |
| DyNAmo Flash SYBR Green qPCR Kit | Thermo Fisher Scientific | Cat# F415L |
| MinElute PCR Purification Kit | QIAGEN | Cat# 28006 |
| Quick Ligation Kit | New England Biolabs | Cat# M2200L |
| Oligo aCGH/Chip-on-Chip Hybridization Kit | Agilent Technologies | Cat# 5188-5220 |
| Deposited data | ||
| Raw and analyzed data (European nucleotide archive) | This study | ENA: PRJEB50762 |
| Software and algorithms | ||
| EAGER 1.92.21 | Peltzer et al., (2016) | https://eager.readthedocs.io/en/latest/ |
| AdapterRemoval 2.2.0 | Schubert et al. (2016) | https://github.com/MikkelSchubert/adapterremoval |
| BWA 0.7.12 | Li and Durbin (2009) | http://bio-bwa.sourceforge.net/ |
| DeDup 0.12.1 | Peltzer et al., (2016) | https://github.com/apeltzer/DeDup |
| DamageProfiler v0.3 | https://github.com/apeltzer/DamageProfiler | https://github.com/apeltzer/DamageProfiler |
| bamUtil 1.0.13 | https://github.com/statgen/bamUtil | https://github.com/statgen/bamUtil |
| CircularMapper v1.93.4 | Peltzer et al., (2016) | https://github.com/apeltzer/CircularMapper |
| Schmutzi v1.0 | Renaud et al. (2015) | https://github.com/grenaud/schmutzi |
| ContaMix v1.0.10 | Fu et al., 2013b | https://doi.org/10.1016/j.cub.2013.02.044 |
| HaploGrep2 v2.1.1 | Weissensteiner et al. (2016) | https://haplogrep.i-med.ac.at/category/haplogrep2/ |
| SAMtools 1.3 | Li et al., (2009) | http://www.htslib.org/doc/samtools.html |
| pileupCaller v1.4.0 | https://github.com/stschiff/sequenceTools | https://github.com/stschiff/sequenceTools |
| ANGSD 0.910 | Korneliussen et al. (2014) | http://www.popgen.dk/angsd/index.php/ANGSD |
| EIGENSOFT 6.0.1 | Patterson et al. (2006) | https://github.com/DReichLab/EIG |
| ADMIXTOOLS v5.1 | Patterson et al. (2012) | https://github.com/DReichLab/AdmixTools |
| DATES 753 | Narasimhan et al., (2019) | https://github.com/priyamoorjani/DATES |
| HapROH 0.1 | Ringbauer et al. (2021) | https://pypi.org/project/hapROH/ |
| OxCal 4.4 | Bronk Ramsey (2009) | https://c14.arch.ox.ac.uk/oxcal/OxCal.html |
| Geneious v9.0.5 | http://www.geneious.com | http://www.geneious.com |
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