Table 1 An overview of ancient genomes reported in this study

ID	Library name	Analysis group	Estimated date	Site	Sampled tissue	Total sequenced reads (×10⁶)	Human DNA (%)	Mean coverage (fold)	Genetic sex	mt	Ychr
ZBC	IPB001.B/C0101	AHG	13,642–13,073 cal BCE	Pınarbaşı	Intermediate phalanx	126.7	33	2.9	Male	K2b	C1a2
ZHAG	BON004.A0101	AAF	8300–7800 BCE	Boncuklu	Petrous	92.0	38	1.48	Female	N1a1a1
ZMOJ	BON014.A0101	AAF	8300–7800 BCE	Boncuklu	third molar	77.9	27	0.8	Male	K1a	C
ZKO	BON001.A0101	AAF	8300–7800 BCE	Boncuklu	Petrous	84.8	31	0.9	Male	U3	G2a2b2b
ZHJ	BON024.A0101	AAF	8300–7800 BCE	Boncuklu	Third molar	87.7	38	0.76	Female	U3
ZHAJ	BON034.A0101	AAF	8269–8210 cal BCE	Boncuklu	Petrous	75.4	30	0.69	Female	U3
KFH2	KFH002.A0101	Levant_Neol	7712–7589 cal BCE	Kfar HaHoresh	Petrous	342.0	8	0.16	Female	N1a1b
BAJ001	BAJ001.A0101	Levant_Neol	7027–6685 cal BCE	Ba’ja	Petrous	17.3	45	0.75	Female	N1b1a

For each individual the analysis group is given (AHG = Anatolian hunter-gatherer; AAF = Anatolian Aceramic farmers; Levant_Neol = Levantine early farmer). When ¹⁴C dating results are available, the date is given in cal BCE in 2-sigma range, otherwise a date based on the archeological context is provided (detailed dating information is provided in Supplementary Note 1 and Supplementary Table 1). The proportion of human DNA and the mean coverage on 1240k target sites in the “1240k” enriched libraries are given. Uniparental haplogroups (mt = mitochondrial; Ychr = Y chromosome) are listed. Detailed information on the uniparental analysis can be found in Supplementary Note 1 and Supplementary Data 6

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