REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Soil from Satsurblia cave	This Study	SAT22
Soil from Satsurblia cave	This Study	SAT23
Soil from Satsurblia cave	This Study	SAT26
Soil from Satsurblia cave	This Study	SAT27
Soil from Satsurblia cave	This Study	SAT28
Soil from Satsurblia cave	This Study	SAT29
Canis lupus bone from Satsurblia cave	This Study	Y7a
Canis lupus bone from Satsurblia cave	This Study	Y7d
Canis lupus bone from Satsurblia cave	This Study	AA8c
Canis lupus bone from Satsurblia cave	This Study	T24c
Canis lupus bone from Satsurblia cave	This Study	T20a
Critical commercial assays
NextSeq 500/550 (75 cycle)	Illumina	TG-160-2005
DNeasy Blood and Tissue kit	QIAGEN	69506
Quick Blunting system	NEB	E1201S
Quick Ligation kit	NEB	M2200S
Expand Long Template PCR System	Roche	11681834001
AccuPrimePfx DNA Polymerase	Invitrogen	12344024
MinElute PCR Purification Kit	QIAGEN	28006
Qubit dsDNA HS Assay Kit	Invitrogen	Q32851
Agilent DNA 1000 Kit	Agilent	5067-1504
Deposited data
Raw analyzed data and filtered genomes	N/A	ENA: PRJEB41420
Software and algorithms
Cutadapt 2.7	18	https://cutadapt.readthedocs.io/en/stable/
FASTX-toolkit 0.0.1	19	http://hannonlab.cshl.edu/fastx_toolkit/
SGA	44	https://bioinformaticshome.com/tools/wga/descriptions/SGA.html
Centrifuge 1.0.3	17	https://ccb.jhu.edu/software/centrifuge/
Pavian	45	https://ccb.jhu.edu/software/pavian/
BWA 0.7.16	46	http://bio-bwa.sourceforge.net/bwa.shtml
Samtools 1.10	46	http://samtools.github.io/bcftools/bcftools.html
Bedtools 2.29.2	47	https://bedtools.readthedocs.io/en/latest/
Qualimap 2.2.1	48	http://qualimap.conesalab.org/
Mapdamage 2.0.9	49	https://ginolhac.github.io/mapDamage/
SequenceTools	50	https://github.com/stschiff/sequenceTools
Admixtools 5.1	31	https://github.com/DReichLab/AdmixTools
Eigensoft 7.2.1	51	https://github.com/DReichLab/EIG
ADMIXTURE 1.3.0	52	https://bioinformaticshome.com/tools/descriptions/ADMIXTURE.html
PLINK 1.9	53	https://zzz.bwh.harvard.edu/plink/
PONG 1.4.9	54	https://github.com/ramachandran-lab/pong
ry_compute	55	https://github.com/pontussk/ry_compute/blob/master/ry_compute.py
MEGAN 6.19.9	56	https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html
BLAST+ 2.10	57	https://ncbiinsights.ncbi.nlm.nih.gov/2019/12/18/blast-2-10-0/
Schmutzi	21	https://github.com/grenaud/schmutzi/blob/master/.gitmodules
Bamutil 1.0.14	58	https://genome.sph.umich.edu/wiki/BamUtil
ContamMix v1.0.10	32	N/A
Calico 0.2	23	https://github.com/pontussk/calico
Geneious 8.1		http://assets.geneious.com/
Haplogrep 2.0	59	https://haplogrep.i-med.ac.at/
BEAST 1.8.4	60	https://beast.community/2016-06-17_BEAST_v1.8.4_released.html
Figtree v1.4.4	N/A	http://tree.bio.ed.ac.uk/software/figtree/
Picard Tools 2.21.4	N/A	https://broadinstitute.github.io/picard/
GATK 4.1.4.0	61	https://gatk.broadinstitute.org/hc/en-us
samtools 1.9	46	http://samtools.github.io/bcftools/bcftools.html
htsbox pileup r345	N/A	https://github.com/lh3/htsbox
admixturegraph R package	N/A	https://cran.r-project.org/web/packages/admixturegraph/index.html
PMDtools	N/A	https://github.com/pontussk/PMDtools
fastp	62	https://github.com/OpenGene/fastp