| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological Samples | ||
| Ancient skeletal element | This study | Sample ID: Mik15 |
| Ancient skeletal element | This study | Sample ID: Pta08 |
| Ancient skeletal element | This study | Sample ID: Kou01 |
| Ancient skeletal element | This study | Sample ID: Kou03 |
| Ancient skeletal element | This study | Sample ID: Log02 |
| Ancient skeletal element | This study | Sample ID: Log04 |
| Ancient skeletal element | This study | Sample ID: AGI03 |
| Ancient skeletal element | This study | Sample ID: AGI04 |
| Ancient skeletal element | This study | Sample ID: AGI05 |
| Ancient skeletal element | This study | Sample ID: AGI06 |
| Ancient skeletal element | This study | Sample ID: AGI07 |
| Ancient skeletal element | This study | Sample ID: AGI08 |
| Ancient skeletal element | This study | Sample ID: AGI09 |
| Ancient skeletal element | This study | Sample ID: AGI10 |
| Ancient skeletal element | This study | Sample ID: AGI11 |
| Ancient skeletal element | This study | Sample ID: AGI12 |
| Ancient skeletal element | This study | Sample ID: KMA01 |
| Ancient skeletal element | This study | Sample ID: KMA02 |
| Ancient skeletal element | This study | Sample ID: KMA04 |
| Ancient skeletal element | This study | Sample ID: KMA05 |
| Ancient skeletal element | This study | Sample ID: KMA06 |
| Ancient skeletal element | This study | Sample ID: KOU04 |
| Ancient skeletal element | This study | Sample ID: KOU05 |
| Ancient skeletal element | This study | Sample ID: KOU06 |
| Ancient skeletal element | This study | Sample ID: KOU07 |
| Ancient skeletal element | This study | Sample ID: LOG01 |
| Ancient skeletal element | This study | Sample ID: LOG08 |
| Ancient skeletal element | This study | Sample ID: MIK01 |
| Ancient skeletal element | This study | Sample ID: MIK02 |
| Ancient skeletal element | This study | Sample ID: MIK03 |
| Ancient skeletal element | This study | Sample ID: MIK04 |
| Ancient skeletal element | This study | Sample ID: MIK05 |
| Ancient skeletal element | This study | Sample ID: MIK06 |
| Ancient skeletal element | This study | Sample ID: MIK07 |
| Ancient skeletal element | This study | Sample ID: MIK08 |
| Ancient skeletal element | This study | Sample ID: MIK09 |
| Ancient skeletal element | This study | Sample ID: MIK10 |
| Ancient skeletal element | This study | Sample ID: MIK12 |
| Ancient skeletal element | This study | Sample ID: MIK13 |
| Ancient skeletal element | This study | Sample ID: MIK19 |
| Ancient skeletal element | This study | Sample ID: MIK20 |
| Ancient skeletal element | This study | Sample ID: MIK21 |
| Ancient skeletal element | This study | Sample ID: MIK22 |
| Ancient skeletal element | This study | Sample ID: PAL04 |
| Ancient skeletal element | This study | Sample ID: PAL05 |
| Ancient skeletal element | This study | Sample ID: PEL01 |
| Ancient skeletal element | This study | Sample ID: PEL02 |
| Ancient skeletal element | This study | Sample ID: PEL03 |
| Ancient skeletal element | This study | Sample ID: PEL04 |
| Ancient skeletal element | This study | Sample ID: PEL05 |
| Ancient skeletal element | This study | Sample ID: PTA02 |
| Ancient skeletal element | This study | Sample ID: PTA09 |
| Ancient skeletal element | This study | Sample ID: TSI01 |
| Ancient skeletal element | This study | Sample ID: TSI03 |
| Ancient skeletal element | This study | Sample ID: TSI04 |
| Ancient skeletal element | This study | Sample ID: XER01 |
| Ancient skeletal element | This study | Sample ID: XER02 |
| Ancient skeletal element | This study | Sample ID: XER03 |
| Ancient skeletal element | This study | Sample ID: XER06 |
| Ancient skeletal element | This study | Sample ID: XER07 |
| Ancient skeletal element | This study | Sample ID: XER08 |
| Ancient skeletal element | This study | Sample ID: XER09 |
| Ancient skeletal element | This study | Sample ID: XER10 |
| Ancient skeletal element | This study | Sample ID: XER11 |
| Ancient skeletal element | This study | Sample ID: XER13 |
| Ancient skeletal element | This study | Sample ID: XER15 |
| Ancient skeletal element | This study | Sample ID: XER16 |
| Chemicals, peptides, and recombinant proteins | ||
| AccuPrime Pfx SuperMix | Thermo Scientific | Cat#12344040 |
| AmpliTaq Gold Buffer II (10x) | Life Technologies | Cat#4311816 |
| AmpliTaq Gold DNA Polymerase | Life Technologies | Cat#4311816 |
| ATP Solution (100 mM) | Life Technologies | Cat#R0441 |
| Bovine Serum Albumin (BSA) (20 mg/ml) | Roche Diagnostics | Cat#10711454001 |
| Bradford fish gel (Gelatin from cold water Fish) | Sigma | G7041-100G |
| Bst Polymerase, Large Fragment (8 U/μl) | New England Biolabs GmbH | Cat#M0275S |
| dNTPs (each 10 mM) | QIAGEN, Hilden, Germany | Cat#201901 |
| dNTPs (each 25 mM) | Agilent Technologies | Cat#600677 |
| EDTA (0.5 M, pH 8.0) | Ambion/Applied Biosystems, Life Technologies | Cat#AM9262 |
| HCl | Fisher Scientific | H/1200/PB17 |
| Herculase II Fusion DNA Polymerase | Agilent Technologies | Cat#600677 |
| Herculase II Reaction Buffer | Agilent Technologies | Cat#600677 |
| IA cane | Iso Analytical | R006 |
| IAEA 600 | International Atomic Energy Agency | IAEA600 |
| IAEA N2 | International Atomic Energy Agency | IAEA N2 |
| MgCl2 (25 mM) | Life Technologies | Cat#4311816 |
| NEBNext End Repair Enzyme Mix | New England Biolabs GmbH | Cat#E6050L |
| NEBNext End Repair Reaction Buffer (10X) | New England Biolabs GmbH | Cat#E6050L |
| Nuclease-free H2O | Life Technologies | Cat#AM9932 |
| PEG-4000 | Thermo Scientific | Cat#EL0011 |
| Phenol/chloroform/isoamylalcohol (25:24:1) | Roth, Karlsruhe, Germany | Cat#A156.1 |
| Proteinase K | Roche Diagnostics, Mannheim, Germany | Cat#3115828001 |
| Sodium N-lauryl sarcosinate | Merck Millipore, Merck KGaA, Darmstadt, Germany | Cat#428010 |
| T4 DNA Ligase (5 U/μl) | Thermo Scientific | Cat#EL0011 |
| T4 DNA Ligase Buffer (10X) | Thermo Scientific | Cat#EL0011 |
| T4 DNA Polymerase (5 U/μl) | Thermo Scientific | Cat#EP0062 |
| T4 Polynucleotide Kinase | Invitrogen | Cat#EK0032 |
| Tango Buffer (10x) | Life Technologies | Cat#BY5 |
| ThermoPol Buffer (10X) | New England Biolabs GmbH | Cat#M0275S |
| Trichlormethan/Chloroform | Roth, Karlsruhe, Germany | Cat#3313.1 |
| Tris-EDTA | Sigma-Aldrich | Cat#T9285 |
| Tris-HCl (1M, pH 8.0) | Life Technologies | Cat#15568025 |
| USER TM enzyme | New England Biolabs GmbH | Cat#M5505L |
| Critical commercial assays | ||
| Agilent 2100 Expert Bioanalyzer System and High Sensitivity DNA Analysis Kit | Agilent Technologies | Cat#5067-4626 (kit) |
| Qubit Fluorometric quantitation and dsDNA HS Assay Kit | Invitrogen | Cat#Q32854 (kit) Cat#Q32856 (tubes) |
| Deposited data | ||
| Sequencing data (this study) | European Nucleotide Archive | https://www.ebi.ac.uk/ena/browser/view/PRJEB37782 |
| 351 individuals, whose data derive from the ’1240k’ SNP capture assay | Lazaridis et al., 2017 | https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/MinMyc.tar.gz |
| 225 ancient ’1240k’ SNP captured individuals | Mathieson et al., 2018 | https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/Genomic_Hist_SE_Europe_Mathieson.tar.gz |
| 2,068 worldwide modern individuals (genotyped on the Human Origins SNP array) | Lazaridis et al., 2016 | https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/NearEastPublic.tar.gz |
| 1000 Genomes | International HapMap 3 Consortium et al., 2010 | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data |
| Bar8 | Hofmanová et al., 2016 | https://www.ebi.ac.uk/ena/browser/view/SAMEA3672571 |
| KK1 | Jones et al., 2015 | https://www.ebi.ac.uk/ena/browser/view/SAMEA3609088 |
| S_Greek-1, S_Greek-2, B_Crete-1, B_Crete-2 from Simons Genome Diversity Project | Mallick et al., 2016 | https://www.ebi.ac.uk/ena/browser/view/PRJEB9586 |
| Sidelkino | de Barros Damgaard et al., 2018 | https://www.ebi.ac.uk/ena/browser/view/ERR2572846 |
| YamnayaKaragash_EBA | de Barros Damgaard et al., 2018 | ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR257/ERR2572845/Yamnaya.realigned.calmd.readsadded.bam |
| Oligonucleotides | ||
| IS4, IS5, IS6 and IS7 | (Meyer and Kircher, 2010) IDT, Leuven, Belgium |
N/A |
| MYBait kit | https://arborbiosci.com/genomics/targeted-sequencing/mybaits/mybaits-custom-dna-seq/ | N/A |
| P5 and P7 | (Meyer and Kircher, 2010) IDT, Leuven, Belgium |
N/A |
| SureSelectXT in-solution target enrichment kit | Agilent Technologies (custom design); Gnirke et al., 2009 | N/A |
| Software and algorithms | ||
| ABC-DL | Mondal et al., 2019 | https://github.com/oscarlao/ABC_DL |
| abc package R | Csilléry et al., 2010 | https://cran.r-project.org/web/packages/abc/index.html |
| AdapterRemoval v2.1.7 | Schubert et al., 2016 | https://adapterremoval.readthedocs.io/en/latest/ |
| Admixtools v. 5.1 | Patterson et al., 2012 | https://github.com/DReichLab/AdmixTools |
| ADMIXTURE | Alexander et al., 2009 | http://dalexander.github.io/admixture/download.html |
| ANGSD v. 0.921 | Korneliussen et al., 2014 | http://www.popgen.dk/angsd/index.php/Change_log |
| ape v5.3 | Paradis and Schliep, 2019 | http://ape-package.ird.fr |
| ARLEQUIN version 3.5.2.2 | Excoffier and Lischer, 2010 | http://cmpg.unibe.ch/software/arlequin35 |
| bwa v0.7.15 | Li and Durbin, 2010 | http://bio-bwa.sourceforge.net/ |
| BamDamage v. 20140602 | Malaspinas et al., 2014 | https://savannah.nongnu.org/projects/bammds |
| cmdscale function (in R) | R Development Core Team, 2018 | https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cmdscale |
| contaminationX | (Moreno-Mayar et al., 2020) | https://github.com/sapfo/contaminationX |
| contamMix v. 1.0-10 | Fu et al., 2013 | https://science.umd.edu/biology/plfj |
| Eigensoft v. 7.2.1 | Patterson et al., 2006 | https://github.com/DReichLab/EIG |
| Encog v3.4 | Heaton, 2015 | https://github.com/jeffheaton/encog-dotnet-core/releases/tag/v3.4 |
| fastqc v0.11.5 | Andrews, 2010 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc |
| fastSimcoal2 | (Excoffier and Foll, 2011) | http://cmpg.unibe.ch/software/fastsimcoal2 |
| fastx_trimmer v0.0.13.2 | Hannon lab 2010 | http://hannonlab.cshl.edu/fastx_toolkit |
| FigTree v1.4.4 | Andrew Rambaut | https://groups.google.com/g/figtree-discuss/c/-9_1l88HPOA |
| GATK v3.7 | DePristo et al., 2011 | https://gatk.broadinstitute.org |
| GenotypeGVCFs | Poplin et al., 2017 | https://gatk.broadinstitute.org/hc/en-us/articles/360046224151-GenotypeGVCFs |
| GLIMPSE v1.0.1 | Rubinacci et al., 2021 | https://github.com/odelaneau/GLIMPSE |
| haploGrep v2.1.19 | Weissensteiner et al., 2016 | https://haplogrep.i-med.ac.at |
| HaplotypeCaller | Poplin et al., 2017 | https://gatk.broadinstitute.org/hc/en-us/articles/360041415292-HaplotypeCaller |
| HIrisPLex-S | Chaitanya et al., 2018 | https://hirisplex.erasmusmc.nl |
| phangorn v2.5.5 | Schliep, 2011 | https://cran.r-project.org/web/packages/phangorn/index.html |
| PhyML v3.1 | Guindon et al., 2010 | http://www.atgc-montpellier.fr/phyml/ |
| Picard tools v2.9.0 | Broad Institute | http://broadinstitute.github.io/picard/ |
| PLINK 1.9 | Purcell et al., 2007 | https://zzz.bwh.harvard.edu/plink/plink2.shtml |
| popHelper | Francis, 2017 | http://pophelper.com/ |
| Samtools v. 1.10 | Li et al., 2009 | https://github.com/samtools/samtools |
| SeaView v5.0.4 | Galtier et al., 1996; Gouy et al., 2010 | http://doua.prabi.fr/software/seaview |
| Snakemake v5.3.0 | (Mölder et al., 2021) | https://snakemake.readthedocs.io/en/v5.3.0/ |
| Tablet 1.19.09.03 | Milne et al., 2013 | https://ics.hutton.ac.uk/tablet/ |
| Other | ||
| Amicon Ultra-4 Centrifugal Filter Units, 30kDa | Merck Millipore, Darmstadt, Germany | Cat#UFC803096 |
| Amicon Ultra-15 Centrifugal Filter Units, 50kDa | Merck Millipore, Darmstadt, Germany | Cat#UFC905096 |
| MinElute PCR Purification Kit | QIAGEN, Hilden, Germany | Cat#28006 |
| MSB Spin PCRapace | Invitek, Stratec Molecular, Berlin, Germany | Cat#1020220400 |
| Ezee filters 9ml | Elkay Laboratory Products | Cat#127-3193-000 |
| Tin capsules 4mm x 3.2 mm | OEA Laboratories | Cat#C11130.500P |
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