REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
8 Canid blood or tissue samples	This paper	Data S1
Chemicals, Peptides, and Recombinant Proteins
Proteinase K	Sigma-Aldrich	Cat# 3115844001
Phenol	Bionordika	Cat# A0447,0500
Chloroform	Sigma-Aldrich	Cat# 288306-1L
Critical Commercial Assays
DNeasy Blood & Tissue Kit	QIAGEN	Cat# 69506
MinElute PCR Purification Kit	QIAGEN	Cat# 28006
NEBNext DNA Sample Prep Master Mix Set 2	New England Biolabs	Cat# E6070
Deposited Data
10 Canid genomes	[33]	Data S1
2 Canid genomes	[34]	Data S1
3 Canid genomes	[6]	Data S1
5 Canid genomes	[9]	Data S1
1 Canid genomes	[4]	Data S1
4 Canid genomes	[35]	Data S1
2 Canid genomes	[18]	Data S1
1 Canid genomes	[36]	Data S1
5 Canid genomes	[37]	Data S1
1 African golden wolf	This article	NCBI SRA sample accession number: SAMN10199001
2 African hunting dogs	This article	NCBI SRA sample accession numbers: SAMN10180432, SAMN10180433
3 Coyotes	This article	NCBI SRA sample accession numbers: SAMN10180421, SAMN10180422, SAMN10180423
1 Dhole	This article	NCBI SRA sample accession number: SAMN10180424
1 Ethiopian wolf	This article	NCBI SRA sample accession number: SAMN10180425
2 Golden jackals	This article	NCBI SRA sample accession numbers: SAMN10180426, SAMN10180427
5 Gray wolves	This article	NCBI SRA sample accession numbers: SAMN10180428, SAMN10180429, SAMN10180430, SAMN10180431, SAMN10180511
Gray wolf reference genome	[7]	N/A
Oligonucleotides
Illumina-compatible adapters	[38]	N/A
Software and Algorithms
PALEOMIX	[39]	https://github.com/MikkelSchubert/paleomix; RRID:SCR_015057
AdapterRemoval2	[40]	https://github.com/MikkelSchubert/adapterremoval; RRID:SCR_011834
bwa v0.7.10	[41]	http://bio-bwa.sourceforge.net/; RRID:SCR_010910
Picard v1.128	N/A	https://broadinstitute.github.io/picard; RRID:SCR_006525
GATK v3.3.0	[42, 43]	https://broadinstitute.github.io/picard; RRID:SCR_001876
ANGSD	[44]	https://github.com/ANGSD/angsd
samtools v1.2	[41]	http://samtools.sourceforge.net/; RRID:SCR_002105
realSFS	[44]	https://github.com/ANGSD/angsd
NGSadmix	[20]	http://www.popgen.dk/software/index.php/NgsAdmix; RRID:SCR_003208
ASTRAL-II	[45]	https://github.com/smirarab/ASTRAL
RAxML	[46]	https://sco.h-its.org/exelixis/software.html; RRID:SCR_006086
trimal	[47]	http://trimal.cgenomics.org/
FastTree2	[48]	http://www.microbesonline.org/fasttree/; RRID:SCR_015501
DiscoVista	[49]	https://github.com/esayyari/DiscoVista
MtArchitect	[10]	http://biologiaevolutiva.org/tmarques/mtarchitect/
MAFFT	[50]	https://mafft.cbrc.jp/alignment/software/; RRID:SCR_011811
Jalview	[51]	http://www.jalview.org/; RRID:SCR_006459
jmodeltest2	[52]	https://github.com/ddarriba/jmodeltest2; RRID:SCR_015244
phyML	[53]	http://www.atgc-montpellier.fr/phyml/; RRID:SCR_014628
ADMIXTOOLS	[23]	https://github.com/DReichLab/AdmixTools
TreeMix	[22]	https://bitbucket.org/nygcresearch/treemix/wiki/Home