REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
osteological remain	this study	Actiparc_GVA124_2143
osteological remain	this study	Actiparc_GVA307_2127
osteological remain	this study	Actiparc_GVA308_2312
osteological remain	this study	Actiparc_GVA309_2302
osteological remain	this study	Actiparc_GVA311_2253
osteological remain	this study	ArzhanII_Rus9_2500
osteological remain	this study	AugustaRaurica_JG160_1817
osteological remain	this study	Bateni_Rus16_3350
osteological remain	this study	Beauvais_GVA122_417
osteological remain	this study	Beauvais_GVA375_467
osteological remain	this study	Belgheis_TrBWBX116_485
osteological remain	this study	Boves_GVA191_1717
osteological remain	this study	BozAdyr_KYRH10_1267
osteological remain	this study	BozAdyr_KYRH8_1267
osteological remain	this study	CaminoDeLasYeseras_CdY2_4678
osteological remain	this study	Cantorella_UE2275x2_4791
osteological remain	this study	Chartres_GVA26_1917
osteological remain	this study	Chartres_GVA36_1917
osteological remain	this study	Chartres_GVA4_1917
osteological remain	this study	Chartres_GVA43_1917
osteological remain	this study	Chartres_GVA56_1917
osteological remain	this study	Chartres_GVA81_1917
osteological remain	this study	ElAcequion_Spain39_3993
osteological remain	this study	ElsVilars_UE4618_2672
osteological remain	this study	Evreux_GVA133_1817
osteological remain	this study	Evreux_GVA140_1817
osteological remain	this study	FrankfurtHeddernheim_Fr1_1863
osteological remain	this study	GolModII_Mon23_2007
osteological remain	this study	GolModII_Mon24_1993
osteological remain	this study	GolModII_Mon25_2011
osteological remain	this study	GolModII_Mon26_1999
osteological remain	this study	GolModII_Mon27_2011
osteological remain	this study	Halvai_KSH4_4017
osteological remain	this study	Khatuu_Kha2_t1_2312
osteological remain	this study	Khotont_UCIE2012x85_1291
osteological remain	this study	Macon_GVA201_1767
osteological remain	this study	Mainz_Mzr1_1373
osteological remain	this study	Marvele_01_1138
osteological remain	this study	Marvele_18_1189
osteological remain	this study	Marvele_21_1087
osteological remain	this study	Marvele_32_1144
osteological remain	this study	MerzlyYar_Rus45_23789
osteological remain	this study	Museum_Earb6_89
osteological remain	this study	Noyon_GVA123_717
osteological remain	this study	Nustar_5_1187
osteological remain	this study	Oktyabrsky_Rus37_830
osteological remain	this study	OlonKurinGol_OKG2_2367
osteological remain	this study	Otepaa_Ote2_1184
osteological remain	this study	Ridala_Rid2_2717
osteological remain	this study	Saadjarve_Saa1_1117
osteological remain	this study	Sagzabad_SAGS27_3117
osteological remain	this study	SaintJust_GVA242_2250
osteological remain	this study	Sayangorsk_Rus41_2677
osteological remain	this study	SharIQumis_AM115_1557
osteological remain	this study	TavanTolgoi_GEP13_730
osteological remain	this study	TavanTolgoi_GEP14_730
osteological remain	this study	TavanTolgoi_GEP21_730
osteological remain	this study	UushgiinUvur_Mon37_3085
osteological remain	this study	UushgiinUvur_Mon39_3085
osteological remain	this study	UushgiinUvur_Mon41_3085
osteological remain	this study	UushgiinUvur_Mon42_3130
osteological remain	this study	UushgiinUvur_Mon43_3120
osteological remain	this study	UushgiinUvur_Mon44_3085
osteological remain	this study	UushgiinUvur_Mon45_3080
osteological remain	this study	UushgiinUvur_Mon79_3085
osteological remain	this study	UushgiinUvur_Mon87_3117
osteological remain	this study	WitterPlace_UK15_217
osteological remain	this study	WitterPlace_UK16_217
osteological remain	this study	WitterPlace_UK17_267
osteological remain	this study	WitterPlace_UK18_267
osteological remain	this study	Yenikapi_Tur140_1289
osteological remain	this study	Yenikapi_Tur141_1430
osteological remain	this study	Yenikapi_Tur142_1396
osteological remain	this study	Yenikapi_Tur145_1156
osteological remain	this study	Yenikapi_Tur146_1730
osteological remain	this study	Yenikapi_Tur150_1443
osteological remain	this study	Yenikapi_Tur170_1443
osteological remain	this study	Yenikapi_Tur171_1689
osteological remain	this study	Yenikapi_Tur173_1443
osteological remain	this study	Yenikapi_Tur175_1443
osteological remain	this study	Yenikapi_Tur176_1443
osteological remain	this study	Yenikapi_Tur181_1443
osteological remain	this study	Yenikapi_Tur193_1443
osteological remain	this study	Yenikapi_Tur194_1360
osteological remain	this study	Yenikapi_Tur229_1443
osteological remain	this study	Yenikapi_Tur243_1443
osteological remain	this study	Yerqorqan_YER28_2853
osteological remain	this study	ArzhanII_Arz15_2642
osteological remain	this study	ArzhanII_Arz17_2642
osteological remain	this study	ArzhanII_Rus11_2500
osteological remain	this study	Berufjordur_VHR102_1057
osteological remain	this study	BroughOfDeerness_VHR010_1417
osteological remain	this study	BroughOfDeerness_VHR011_1367
osteological remain	this study	BroughOfDeerness_VHR037_1417
osteological remain	this study	BroughOfDeerness_VHR062_1417
osteological remain	this study	Chartres_GVA111_1917
osteological remain	this study	Chartres_GVA112_1917
osteological remain	this study	Chartres_GVA115_1917
osteological remain	this study	Chartres_GVA28_1917
osteological remain	this study	Chartres_GVA47_1917
osteological remain	this study	Chartres_GVA48_1917
osteological remain	this study	Chartres_GVA53_1917
osteological remain	this study	Chartres_GVA60_1917
osteological remain	this study	Chartres_GVA75_1917
osteological remain	this study	Chartres_GVA9_1917
osteological remain	this study	ElAcequion_Spain38_4058
osteological remain	this study	Evreux_GVA135_1817
osteological remain	this study	Goyet_Vert311_35870
osteological remain	this study	Granastadir_VHR031_1067
osteological remain	this study	Marvele_02_1138
osteological remain	this study	Marvele_05_1138
osteological remain	this study	Marvele_16_1138
osteological remain	this study	Marvele_22_1138
osteological remain	this study	Marvele_27_1138
osteological remain	this study	Nustar_4_1187
osteological remain	this study	OlonKurinGol_OKG1_2367
osteological remain	this study	Quoygrew_VHR017_1117
osteological remain	this study	SaintQuentin_GVA237_1917
osteological remain	this study	Syrgal_Syr1t1c4_2317
osteological remain	this study	UushgiinUvur_Mon40_3085
osteological remain	this study	UushgiinUvur_Mon89_3085
osteological remain	this study	Vermand_GVA199_1742
osteological remain	this study	WitterPlace_UK19_267
Chemicals, Peptides, and Recombinant Proteins
N-Lauroylsarcosine solution 30% 500ml	Dutscher	Cat# 348533
Proteinase K 100MG	Thermo Fisher Scientific	Cat# 10103533
H2O, Molecular Biology Grade, Fisher BioReagents	Thermo Fisher Scientific	Cat# 10490025
Tween 20 100ML	Thermo Fisher Scientific	Cat# 10113103
Ethanol, Absolute, Mol Biology Grade	Thermo Fisher Scientific	Cat# 10644795
5M Sodium Chloride 100ML	Thermo Fisher Scientific	Cat# 10609823
USER Enzyme	New England Biolabs	Cat# M5505L
NEBNext End Repair Module	New England Biolabs	Cat# E6050L
Bst DNA Polymerase	New England Biolabs	Cat# M0275L
NEBNext Quick Ligation Module	New England Biolabs	Cat# E6056L
BSA Molecular Biology Grade	New England Biolabs	Cat# B9000S
ROX REFERENCE DYE 500μL	Thermo Fisher Scientific	Cat# 10635353
SYBR Green I Nucleic Acid 10000X concentrate	Thermo Fisher Scientific	Cat# 10710004
ACCUPRIME PFX DNA POLYMERASE 100μL	Thermo Fisher Scientific	Cat# 10472482
Agencourt AMPure XP - 60ml	Beckman Coulter	Cat# A63881
Buffer PE	QIAGEN	Cat# 19065
Buffer PB	QIAGEN	Cat# 19066
Buffer EB	QIAGEN	Cat# 19086
DMSO molecular biol 250ML	Thermo Fisher Scientific	Cat# 10397841
dNTP Set 100mM 100μL	Thermo Fisher Scientific	Cat# 10336653
EDTA 0.5M pH 8.0 Fisher Bioreagents 500ML	Thermo Fisher Scientific	Cat# 10182903
Tris HCl, 1M, pH 8.0, 100ML	Thermo Fisher Scientific	Cat# 10336763
Critical Commercial Assays
MinElute PCR Purification kit	QIAGEN	Cat# 28006
Tapestation screenTape D1000 HS	Agilent	Cat# 5067-5584
Bioanalyzer High Sensitivity DNA labchips kit	Agilent	Cat# 5067-4626
Deposited Data
Raw and analyzed data	this study	ENA: PRJEB31613
Software and Algorithms
ANGSD	Korneliussen et al., 2014	https://github.com/ANGSD/angsd
TreeMix	Pickrell and Pritchard 2012	https://bitbucket.org/nygcresearch/treemix/wiki/Home
mapDamage	Jónsson et al., 2013	https://ginolhac.github.io/mapDamage
Paleomix	Schubert et al., 2014b	https://github.com/MikkelSchubert/paleomix
mstatspop	unpublished	https://github.com/CRAGENOMICA/mstatspop
NGSdist	Vieira et al., 2016	https://github.com/fgvieira/ngsDist
fastme	Lefort et al., 2015	http://www.atgc-montpellier.fr/fastme/binaries.php
raxML	Stamatakis 2014	https://cme.h-its.org/exelixis/web/software/raxml/index.html
PLINK	Purcell et al., 2007	https://www.cog-genomics.org/plink2
AdapterRemoval	Schubert et al., 2016	https://github.com/MikkelSchubert/adapterremoval
Samtools	Li and Durbin, 2009	https://github.com/samtools/samtools
Momi2	Kamm et al., 2018	https://github.com/popgenmethods/momi2
Admixtools	Patterson et al., 2012	https://github.com/DReichLab/AdmixTools