REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
Ancient skeletal element	This study	I0308
Ancient skeletal element	This study	I0309
Ancient skeletal element	This study	I2230
Ancient skeletal element	This study	I2232
Ancient skeletal element	This study	I7086
Ancient skeletal element	This study	I7088
Ancient skeletal element	This study	I7090
Ancient skeletal element	This study	I1748
Ancient skeletal element	This study	I8348
Ancient skeletal element	This study	I8349
Ancient skeletal element	This study	I8350
Ancient skeletal element	This study	I3443
Ancient skeletal element	This study	I5456
Ancient skeletal element	This study	I5457
Ancient skeletal element	This study	I9054_d
Ancient skeletal element	This study	I9055_d
Ancient skeletal element	This study	I9056_d
Ancient skeletal element	This study	I9057_d
Ancient skeletal element	This study	I9058_d
Ancient skeletal element	This study	CP18
Ancient skeletal element	This study	CP21
Ancient skeletal element	This study	CP22
Ancient skeletal element	This study	CP23
Ancient skeletal element	This study	CP25
Ancient skeletal element	This study	CP26
Ancient skeletal element	This study	CP19
Ancient skeletal element	This study	LAR001
Ancient skeletal element	This study	LAR002
Ancient skeletal element	This study	MOS001
Ancient skeletal element	This study	I1752
Ancient skeletal element	This study	I1754
Ancient skeletal element	This study	I1753
Ancient skeletal element	This study	I11974
Ancient skeletal element	This study	I2537
Ancient skeletal element	This study	CUN008
Ancient skeletal element	This study	CP8
Ancient skeletal element	This study	CP29
Ancient skeletal element	This study	I2261
Ancient skeletal element	This study	I0237
Ancient skeletal element	This study	I1357
Ancient skeletal element	This study	I1484
Ancient skeletal element	This study	I1485
Ancient skeletal element	This study	I1742
Ancient skeletal element	This study	I2551
Ancient skeletal element	This study	I0039
Ancient skeletal element	This study	I0040
Ancient skeletal element	This study	I0038
Ancient skeletal element	This study	I0041
Ancient skeletal element	This study	I0238
Chemicals, Peptides, and Recombinant Proteins
Pfu Turbo Cx Hotstart DNA Polymerase	Agilent Technologies	Cat# 600412
Herculase II Fusion DNA Polymerase	Agilent Technologies	Cat# 600679
2x HI-RPM hybridization buffer	Agilent Technologies	Cat# 5190-0403
0.5 M EDTA pH 8.0	BioExpress	Cat# E177
Sera-Mag Magnetic Speed-beads Carboxylate-Modified (1 μm, 3EDAC/PA5)	GE LifeScience	Cat# 65152105050250
USER enzyme	New England Biolabs	Cat# M5505
UGI	New England Biolabs	Cat# M0281
Bst DNA Polymerase2.0, large frag.	New England Biolabs	Cat# M0537
PE buffer concentrate	QIAGEN	Cat# 19065
Proteinase K	Sigma Aldrich	Cat# P6556
Guanidine hydrochloride	Sigma Aldrich	Cat# G3272
3M Sodium Acetate (pH 5.2)	Sigma Aldrich	Cat# S7899
Water	Sigma Aldrich	Cat# W4502
Tween-20	Sigma Aldrich	Cat# P9416
Isopropanol	Sigma Aldrich	Cat# 650447
Ethanol	Sigma Aldrich	Cat# E7023
5M NaCl	Sigma Aldrich	Cat# S5150
1M NaOH	Sigma Aldrich	Cat# 71463
20% SDS	Sigma Aldrich	Cat# 5030
PEG-8000	Sigma Aldrich	Cat# 89510
1 M Tris-HCl pH 8.0	Sigma Aldrich	Cat# AM9856
dNTP Mix	Thermo Fisher Scientific	Cat# R1121
ATP	Thermo Fisher Scientific	Cat# R0441
10x Buffer Tango	Thermo Fisher Scientific	Cat# BY5
T4 Polynucleotide Kinase	Thermo Fisher Scientific	Cat# EK0032
T4 DNA Polymerase	Thermo Fisher Scientific	Cat# EP0062
T4 DNA Ligase	Thermo Fisher Scientific	Cat# EL0011
Maxima SYBR Green kit	Thermo Fisher Scientific	Cat# K0251
50x Denhardt’s solution	Thermo Fisher Scientific	Cat# 750018
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
DyNAmo HS SYBR Green qPCR Kit	Thermo Fisher Scientific	Cat# F410L
Methanol, certified ACS	VWR	Cat# EM-MX0485-3
Acetone, certified ACS	VWR	Cat# BDH1101-4LP
Dichloromethane, certified ACS	VWR	Cat# EMD-DX0835-3
Hydrochloric acid, 6N, 0.5N & 0.01N	VWR	Cat# EMD-HX0603-3
Critical Commercial Assays
High Pure Extender from Viral Nucleic Acid Large Volume Kit	Roche	Cat# 5114403001
MinElute PCR Purification Kit	QIAGEN	Cat# 28006
NextSeq 500/550 High Output Kit v2 (150 cycles)	Illumina	Cat# FC-404-2002
HiSeq 4000 SBS Kit (50/75 cycles)	Illumina	Cat# FC-410-1001/2
Deposited Data
Raw and analyzed data (European nucleotide archive)	This study	ENA: PRJEB28961
Software and Algorithms
Samtools	Li, 2011, Li et al., 2009	http://samtools.sourceforge.net/
BWA	Li and Durbin, 2009	http://bio-bwa.sourceforge.net/
ADMIXTOOLS	Patterson et al., 2012	https://github.com/DReichLab/AdmixTools
SeqPrep	https://github.com/jstjohn/SeqPrep	https://github.com/jstjohn/SeqPrep
bamrmdup	https://bitbucket.org/ustenzel/biohazard	https://bitbucket.org/ustenzel/biohazard
AdapterRemoval v2	Schubert et al., 2016	https://github.com/MikkelSchubert/adapterremoval
Dedup	Peltzer et al., 2016	https://eager.readthedocs.io/en/latest/
smartpca	Patterson et al., 2006	https://www.hsph.harvard.edu/alkes-price/software/
PMDtools	Skoglund et al., 2014	https://github.com/pontussk/PMDtools
Haplofind	Vianello et al., 2013	https://haplofind.unibo.it
Yfitter	https://sourceforge.net/projects/yfitter/	https://sourceforge.net/projects/yfitter/
Schmutzi	Renaud et al., 2015	https://grenaud.github.io/schmutzi/
ANGSD	Korneliussen et al., 2014	https://github.com/ANGSD/angsd
MEGA6	Tamura et al., 2013	https://www.megasoftware.net
mapDamage2.0	Jónsson et al., 2013	https://ginolhac.github.io/mapDamage/