REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Human archaeological remains	This paper	N/A
Critical commercial assays
MinElute PCR Purification Kit	QIAGEN	Cat No./ID: 28006
Accuprime Pfx Supermix	ThermoFisher Scientific	Cat. No: 12344040
Deposited data
Newly published ancient genomes	This paper	https://www.ebi.ac.uk/ena/browser/view/PRJEB63184
Human reference genome NCBI build 37, GRCh37	Genome Reference Consortium	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Ancient comparison dataset	Allen Ancient DNA Resource (Version v54.1)	https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data
Ancient comparison dataset	Maróti et al., 202219	https://www.ebi.ac.uk/ena/browser/view/PRJEB499771
Oligonucleotides
Illumina specific adapters	Custom synthetized	https://www.sigmaaldrich.com/HU/en/product/sigma/oligo?lang=en&region=US&gclid=CjwKCAiAgvKQBhBbEiwAaPQw3FDDFnRPc3WV75qapsXvcTxxzBXy48atqyb6Xi5f_8e6Df2EJI0NNhoCmzIQAvD_BwE
Software and algorithms
Cutadapt	Martin, 201124	https://cutadapt.readthedocs.io/en/stable/#
Burrow-Wheels-Aligner	Li and Durbin, 200925	http://bio-bwa.sourceforge.net/
samtools	Li et al., 200926	http://www.htslib.org/
PICARD tools	Broad Institute, 201627	https://github.com/broadinstitute/picard
ATLAS software package	Link et al., 201728	https://bitbucket.org/wegmannlab/atlas/wiki/Home
MapDamage 2.0	Jónsson et al., 201329	https://ginolhac.github.io/mapDamage/
Schmutzi software package	Renaud et al., 201530	https://github.com/grenaud/schmutzi
ANGSD software package	Korneliussen et al., 201431	https://github.com/ANGSD/angsd
HaploGrep 2	Weissensteiner et al., 201632	https://haplogrep.i-med.ac.at/category/haplogrep2/
Yleaf software tool	Ralf et al., 201833	https://github.com/genid/Yleaf
mosdepth software	Pedersen and Quinlan34	https://github.com/brentp/mosdepth
PCAangsd software	Meisner and Albrechtsen35	https://github.com/Rosemeis/pcangsd
RcppCNPy R package	N/A	https://rdocumentation.org/packages/RcppCNPy/versions/0.2.10
smartpca	Patterson et al., 200636	https://github.com/chrchang/eigensoft/blob/master/POPGEN/README
ADMIXTURE software	Alexander et al., 200937	https://dalexander.github.io/admixture/
R 3.6.3	R core development team38	https://cran.r-project.org/bin/windows/base/old/3.6.3/
ADMIXTOOLS software package	Patterson et al., 201239	https://github.com/DReichLab/AdmixTools
DATES algorithm	Narasimhan et al., 201940	https://github.com/priyamoorjani/DATES/tree/v753