Table 1.

Summary information for ancient samples first reported in this paper. Capture data and calibrated radiocarbon dates for POP07 and POP14 were previously reported in². See Methods and Supplementary Table S1 for further information about data provided in the table.

Individual ID	Site name, archaeological time period and culture	Date range (BCE contextual; calBCE/calCE 95.4% CI calibrated radiocarbon age)	Population analysis label	Genetic sex	# autosomal SNPs overlapping with 1240 K panel	mtDNA haplotype	Y haplotype
POP02	Beli Manastir-Popova zemlja Middle Neolithic Sopot	4700–4300 BCE	Croatia_Pop_MN	F	855,968	K1a
POP04				M	884,196	H	J
POP05				F	790,411	K1a5
POP06				F	944,648	K2b1
POP07		4790–4558 calBCE		M	861,721	U5b2b	I2a2a
POP08		4700–4300 BCE		F	805,956	U8b1a1
POP09				F	867,653	K1a4
POP11				F	865,887	T2b3
POP12				F	841,209	T2b
POP13				F	800,065	T2c1d1
POP14		4763–4536 calBCE		F	913,421	N1a1a1
POP16		4700–4300 BCE		F	825,473	N1a1a1a2
POP19				F	878,975	N1a1a1a3
POP24				M	795,338	K1a1a	I2a2a
POP27				F	837,294	T2b21
POP30				M	805,808	T2b11	G2a2a
POP33		4603–4071 calBCE		M	710,341	K1a1	G2a2b2a1a1
POP35		4584–4458 calBCE		M	774,710	J2b1a5	C1a2b
POP36		4700–4300 BCE		M	759,163	H	G2a2a
POP39	Beli Manastir-Popova zemlja Copper Age	2859 – 2502 calBCE	Croatia_Pop_CA	F	981,784	HV9
POP23	Beli Manastir-Popova zemlja Roman Period	260–402 calCE	Croatia_Pop_RomanP	M	962,966	T2f2	R1a1a1b2a2b1
JAG06	Jagodnjak-Krčevine Middle Bronze Age Southern Transdanubian Encrusted Pottery Culture	1800–1600 BCE	Croatia_Jag_MBA	M	846,845	T2b11	G2a2a1a2a2a1 ~
JAG34		1879–1642 calBCE		M	919,781	K2a	G2a2a1a2a2a1 ~
JAG58		1800–1600 BCE		M	762,207	T2b11	G2a2a1a2a2a1 ~
JAG78				M	922,257	U5b1b1a	G2a2a1a2a2a1 ~
JAG82				M	869,661	U2e1a1	G2a2a1a2a2a1 ~
JAG85				F	734,912	K1b1b1
JAG93				F	807,256	U5a1g