REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, Peptides, and Recombinant Proteins
Pfu Turbo Cx Hotstart DNA Polymerase	Agilent Technologies	600412
Herculase II Fusion DNA Polymerase	Agilent Technologies	600679
2x HI-RPM hybridization buffer	Agilent Technologies	5190-0403
0.5 M EDTA pH 8.0	BioExpress	E177
Sera-Mag Magnetic Speed-beads Carboxylate-Modified (1 μm, 3EDAC/PA5)	GE LifeScience	6.51521E+13
USER enzyme	New England Biolabs	M5505
UGI	New England Biolabs	M0281
Bst DNA Polymerase2.0, large frag.	New England Biolabs	M0537
PE buffer concentrate	QIAGEN	19065
Proteinase K	Sigma Aldrich	P6556
Guanidine hydrochloride	Sigma Aldrich	G3272
3M Sodium Acetate (pH 5.2)	Sigma Aldrich	S7899
Water	Sigma Aldrich	W4502
Tween-20	Sigma Aldrich	P9416
Isopropanol	Sigma Aldrich	650447
Ethanol	Sigma Aldrich	E7023
5M NaCl	Sigma Aldrich	S5150
1M NaOH	Sigma Aldrich	71463
20% SDS	Sigma Aldrich	5030
PEG-8000	Sigma Aldrich	89510
1 M Tris-HCl pH 8.0	Sigma Aldrich	AM9856
dNTP Mix	Thermo Fisher Scientific	R1121
ATP	Thermo Fisher Scientific	R0441
10x Buffer Tango	Thermo Fisher Scientific	BY5
T4 Polynucleotide Kinase	Thermo Fisher Scientific	EK0032
T4 DNA Polymerase	Thermo Fisher Scientific	EP0062
T4 DNA Ligase	Thermo Fisher Scientific	EL0011
Maxima SYBR Green kit	Thermo Fisher Scientific	K0251
50x Denhardt’s solution	Thermo Fisher Scientific	750018
SSC Buffer (20x)	Thermo Fisher Scientific	AM9770
GeneAmp 10x PCR Gold Buffer	Thermo Fisher Scientific	4379874
Dynabeads MyOne Streptavidin T1	Thermo Fisher Scientific	65602
Salmon sperm DNA	Thermo Fisher Scientific	15632-011
Human Cot-I DNA	Thermo Fisher Scientific	15279011
DyNAmo HS SYBR Green qPCR Kit	Thermo Fisher Scientific	F410L
Methanol, certified ACS	VWR	EM-MX0485-3
Acetone, certified ACS	VWR	BDH1101-4LP
Dichloromethane, certified ACS	VWR	EMD-DX0835-3
Hydrochloric acid, 6N, 0.5N & 0.01N	VWR	EMD-HX0603-3
Critical Commercial Assays
High Pure Extender from Viral Nucleic Acid Large Volume Kit	Roche	5114403001
MinElute PCR Purification Kit	QIAGEN	28006
NextSeq® 500/550 High Output Kit v2 (150 cycles)	Illumina	FC-404-2002
HiSeq® 4000 SBS Kit (50/75 cycles)	Illumina	FC-410-1001/2
Deposited Data
Sequencing Data	GenBank	MW291661-MW291678
Genotype Data	Reich Lab website	https://reich.hms.harvard.edu/datasets
Software and Algorithms
Samtools v1.11	Li et al., 2009	http://samtools.sourceforge.net/
BWA v0.7.17-r1188	Li and Durbin, 2009	http://bio-bwa.sourceforge.net/
SeqPrep v2	https://github.com/jstjohn/SeqPrep	https://github.com/jstjohn/SeqPrep
AdapterRemoval v2	Schubert et al., 2016	https://github.com/MikkelSchubert/adapterremoval
Dedeup v0.12.07	Peltzer et al., 2016	https://eager.readthedocs.io/en/latest/
PMDtools v0.60	Skoglund et al., 2014	https://github.com/pontussk/PMDtools
Haplogrep v2.0		https://haplogrep.uibk.ac.at/index.html
ContamMix	Fu et al. (2013)	https://github.com/DReichLab/ADNA-Tools
MEGA6	Tamura et al., 2013	https://www.megasoftware.net
mapDamage2.0	Jónsson et al. (2013)	https://ginolhac.github.io/mapDamage/
MUSCLE v3.8.1551	Edgar, 2004	https://www.drive5.com/muscle/
Geneious v9.1.8		https://www.geneious.com/
PartitionFinder v2.1.1	Lanfear et al. (2012)	https://www.robertlanfear.com/partitionfinder/
BEAST 1.8.0	Drummond and Rambaut (2007)	https://beast.community
Tracer v1.7.1		https://github.com/beast-dev/tracer/releases/tag/v1.7.1
TreeAnnotator v2.6.0		https://beast2.blogs.auckland.ac.nz/treeannotator/
FigTree v1.4.4		http://tree.bio.ed.ac.uk/software/