REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
5 Sicilian wolves (historical remains - bones and skin)	This paper	Sic1 (C11875), Sic2 (AN/855), Sic3 (M/18), Sic4 (TSA / 9), Sic7
3 Cirneco dell'Etna dogs (swabs)	This paper	MW1085_CIR1, MW1095_CIR11,MW1098_CIR14
4 Italian modern wolf (tissue)	This paper	MW303 (14b), MW305 (16b), MW307 (19a), MW310 (TS86a)
2 Norwegian modern wolf	This paper	MW005 (M406281), MW011 (M495008)
2 Finnish modern wolf	This paper	MW347 (13172), MW423 (SF1695)
2 Lithuanian modern wolf	This paper	MW020 (CL9), MW366 (LT3)
2 modern wolf from Czech Republic	This paper	MW045 (CK), MW333 (KRNAP)
2 Slovakian modern wolf	This paper	MW339 (20/0047_2), MW049 (CL693)
2 German modern wolf	This paper	MW055 (W150470), MW098 (W181390)
2 Romanian modern wolf	This paper	MW062 (W151402), MW066 (W151413)
2 Portuguese modern wolf	This paper	MW119 (L474), MW107 (L090)
2 Spanish modern wolf	This paper	MW122 (L546), MW127 (L590)
1 Austrian modern wolf	This paper	MW515 (1032)
1 modern wolf from Bosnia and Herzegovina	This paper	MW703A (5755 - CL231)
1 Bulgarian modern wolf	This paper	MW706A (7386 - CL422)
2 Polish modern wolf	This paper	MW259 (BIE31), MW295 (PSN05)
3 Croatian modern wolf	This paper	MW1118 (1231), MW1120 (2736), MW1126 (7201)
1 modern wolf from Greece	This paper	MW1135 (8571)
2 modern wolf from Latvia	This paper	MW1151 (10686), MW1152 (10687)
Chemicals, peptides, and recombinant proteins
Proteinase K	Sigma-Aldrich	Cat#3115844001
Critical commercial assays
MinElute PCR Purification Kit	QIAGEN	Cat#28006
PfuTurbo Cx Hotstart DNA Polymerase	Agilent	Cat#600414
T4 DNA ligase	New England Biolabs Inc.	Cat#M0202L
T4 Polynucleotide Kinase	New England Biolabs Inc.	Cat#M0201L
T4 DNA Polymerase	New England Biolabs Inc.	Cat#M0203S
BSt 2,0 warmstart polymerase	New England Biolabs Inc.	Cat#M0538S
Phusion® High-Fidelity PCR Master Mix with HF buffer	New England Biolabs Inc.	Cat#M0531S
DNeasy® Blood and Tissue Kit	Qiagen	Cat#69504
Deposited data
5 Sicilian wolves (historical remains - bones and skin)	This study	Table S2; ENA accession number: PRJEB57290
3 Cirneco dell'Etna dogs	This study	Table S2; ENA accession number: PRJEB57290
33 modern european wolves	This study	Table S2; ENA accession number: PRJEB57290
1 modern Andean fox (Lcu2_Pastora)	Auton et al.46	Table S2
4 Coyotes	vonHoldt et al.47 Gopalakrishnan et al.48	Table S2
10 Tibetan and Chinese modern wolves	Zhang et al.49; Wang et al.50	Table S2
1 Greenlandic wolf	Gopalakrishnan et al.48	Table S2
4 North American and Mexican wolves	Fan et al.1; Sinding et al.51 Gopalakrishnan et al.48	Table S2
3 Iberian wolves	Gómez-Sánchez et al.31; Fan et al.1	Table S2
1 Croatian wolf	Freedman et al.29	Table S2
2 Italian wolves	Fan et al.1	Table S2
3 Russian wolves	Wang et al.52	Table S2
1 Syrian wolf	Gopalakrishnan et al.48	Table S2
1 Saudi Arabian wolf	Gopalakrishnan et al.48	Table S2
1 Israeli wolf	Freedman et al.29	Table S2
1 Iranian wolf	Fan et al.1	Table S2
1 Indian wolf	Fan et al.1	Table S2
5 Pleistocene wolves	Sinding et al.53; Ramos-Madrigal et al.3	Table S2
24 ancient dogs	Frantz et al.54; Botigué et al.55; Ní Leathlobhair et al.56; Bergström et al.43; Feuerborn et al.57	Table S2
42 modern dogs	Wiedmer et al.58; Decker et al.59; Metzger et al.60; Auton et al.46; Wang et al.52; Wang et al.50; Sinding et al.53; Freedman et al.29; Marsden et al.61; Lindblad et al.62	Table S2
Oligonucleotides
Illumina-compatible adapters	Meyer and Kircher63	N/A
BGI-compatible adapters	Mak et al.64	N/A
Software and algorithms
PALEOMIX v1.2.13.1	Schubert et al.65	https://github.com/MikkelSchubert/paleomix
AdapterRemoval2	Schubert et al.66	https://github.com/MikkelSchubert/adapterremoval
bwa-backtrack v0.7.15	Li and Durbin67	http://bio-bwa.sourceforge.net/
Picard v2.9.1	N/A	https://broadinstitute.github.io/picard
GATK v4.1	McKenna et al.68	https://software.broadinstitute.org/gatk/
ANGSD 0.931	Korneliussen et al.69	https://github.com/ANGSD/angsd
samtools v1.9	Li et al.70	http://samtools.sourceforge.net/
ADMIXTOOLS v.5.1	Patterson et al.71	https://github.com/DReichLab/AdmixTools
TreeMix v.1.13	Pickrell and Pritchard32	https://bitbucket.org/nygcresearch/treemix/wiki/Home
mapDamage 2.0	Jónsson et al.72	https://github.com/ginolhac/mapDamage
MUSCLE	Edgar73	https://github.com/rcedgar/muscle
Plink 1.9	Purcell et al.74	https://www.cog-genomics.org/plink/2.0/
ADMIXTURE v.1.3	Alexander et al.30	http://dalexander.github.io/admixture/download.html
RAxML-ng	Kozlov et al.33	https://github.com/amkozlov/raxml-ng
FigTree v.1.4.4	Rambaut75	http://tree.bio.ed.ac.uk/software/figtree/
BEDtools	Quinlan and Hall76	https://github.com/arq5x/bedtools2
IQ-TREE v.2.1.2	Minh et al.77	http://www.iqtree.org/
Astral III	Zhang et al.78	https://github.com/smirarab/ASTRAL
qpBrute	Leathlobhair et al.56, Liu et al.79	https://github.com/ekirving/qpbrute
PCAdmix	Brisbin et al.34	N/A
VCFtools v.0.1.16	Danecek et al.80	https://vcftools.sourceforge.net/
Rstudio	Allaire81	https://github.com/rstudio/rstudio
Beagle v4.1	Browning and Browning82	https://faculty.washington.edu/browning/beagle/b4_1.html
Beagle v5.4	Browning et al.83	http://faculty.washington.edu/browning/beagle/beagle.html
ROHan	Renaud et al.84	https://github.com/grenaud/ROHan
Variant Effect Predictor	Watterson85	https://www.ensembl.org/info/docs/tools/vep/index.html
all_genotype_probability_v3.py	Greer42	https://github.com/sagitaninta/mutationLoad and https://github.com/DebGreer/MSc_Project