Table 1. Summary of individuals with successful aDNA from Africa reported in this study.

Note 1: Two samples from Lukenya Hill (LUK001 and LUK002) tend out to be genetically the same individual. We merged the genomic data for genetic analyses but report radiocarbon dates for both here. Note 2: The age of samples marked with asterisk is based on the archeological context instead of calibrated radiocarbon date. Aut. Cov., autosomal coverage; MT Cov., mitochondrial coverage.

ID	Population label	Archeological site	Country	Archeological affiliation	Aut. Cov.	MT Cov.	Sex	Y haplogroup	MT haplogroup	Aut. SNPs	SNPs hit on Human Origin dataset	Date (calendar BP)	Uncalibrated C14 dates ± error (lab number)
NYA002	Kenya_ Nyarindi_ 3500BP	Nyarindi Rockshelter	Kenya	Later Stone Age (Kansyore)	0.14	0.23	F	–	L4b2a	124,064	64,785	3555–3375	3253 ± 23 (OxA-37364)
NYA003	Kenya_ Nyarindi_ 3500BP	Nyarindi Rockshelter	Kenya	Later Stone Age (Kansyore)	0.02	0.02	M	E(E-M96,E-P162)	–	18,586	9736	–	–
LUK001	Kenya_ LukenyaHill_ 3500BP	Lukenya Hill, GvJm 202	Kenya	Pastoral Neolithic	0.59	1.41	M	E1b1b1b2b(E- M293,E- CTS10880)	L4b2a2b	495,472	222,439	3610– 3460	3340 ± 23 (OxA-37356), 3296 ± 25 (OxA-37357)
LUK003	Kenya_ LukenyaHill_ 3500BP	Lukenya Hill, GvJm 202	Kenya	Pastoral Neolithic	0.01	0.30	F	–	L0f1	6830	3586	3635– 3475	3359 ± 23 (OxA-37358)
HYR002	Kenya_ HyraxHill_ 2300BP	Hyrax Hill, GrJj25	Kenya	Pastoral Neolithic	0.77	0.52	M	E1b1b1b2b(E- M293,E-M293)	L5a1b	505,972	260,999	2365– 2305	2354 ± 23 (OxA-37352)
MOL001	Kenya_ MoloCave_ 1500BP	Molo Cave, GoJi3	Kenya	Pastoral Neolithic	2.64	5.40	M	E1b1b1b2b(E- M293,E-M293)	L3h1a2a1	886,222	461,756	1415– 1320	1532 ± 21 (OxA-37360)
MOL003	Kenya_ MoloCave_ 1500BP	Molo Cave, GoJi3	Kenya	Pastoral Neolithic	0.06	0.14	F	–	–	57,426	29,700	2110– 1990	2101 ± 22 (OxA-37361)
KPL001	Kenya_ Kakapel_ 3900BP	Kakapel	Kenya	Later Stone Age (Kansyore)	0.92	3.94	M	CT(CT- M168,CT-M5695)	L3i1	572,074	299,181	3974– 3831	3584 ± 28 [SUERC-86057 (GU51350)]
KPL002	Kenya_ Kakapel_ 300BP	Kakapel	Kenya	Later Iron Age/ protohistoric	1.26	78.35	F	–	L2a1f	684,698	363,447	309–145	222 ± 28 [SUERC-86058 (GU51351)]
KPL003	Kenya_ Kakapel_ 900BP	Kakapel	Kenya	Later Iron Age	0.07	63.21	F	–	L2a5	75,113	39,367	910–736	895 ± 28 [SUERC-86059 (GU51352)]
MUN001*	Uganda_ Munsa_ 500BP	Munsa	Uganda	Later Iron Age	0.46	1.57	F	–	L3b1a1	377,332	–	1400– 1600 CE	–
KIN002	Congo_ Kindoki_ 230BP	Kindoki	DR Congo	Protohistoric	0.62	1.46	M	E1b1a1a1d1a2(E- CTS99,E-CTS99)	L1c3a1b	438,125	229,240	295–145	217 ± 20 (OxA-37353)
KIN003	Congo_ Kindoki_ 150BP	Kindoki	DR Congo	Protohistoric	0.02	0.09	M	E(E-M96,E- PF1620)	–	19,691	10,329	285– modern	172 ± 20 (OxA-37354)
KIN004	Congo_ Kindoki_230BP	Kindoki	DR Congo	Protohistoric	0.96	2.01	M	R1b1(R- P25_1,R-M415)	L0a1b1a1	560,376	291,465	305–150	241 ± 20 (OxA-37355)
NGO001	Congo_ NgongoMbata_ 220BP	Ngongo Mbata	DR Congo	Protohistoric	0.42	0.78	M	–	L1c3a	328,389	170,742	295–145	211 ± 21 (OxA-37363)
MTN001	Congo_ MatangaiTuru_ 750BP	Matangai Turu Northwest	DR Congo	Iron Age forager	0.06	0.33	F	–	–	52,012	28,452	795–690	871 ± 21 (OxA-37362)
NQO002*	Botswana_ Nqoma_ 900BP	Nqoma	Botswana	Early Iron Age	0.02	0.60	F	–	L2a1f	14,189	7,587	700- 1090 CE	–
TAU001*	Botswana_ Taukome_ 1100BP	Taukome	Botswana	Early Iron Age	0.09	5.82	M	E1b1a1(E- M2,E-Z1123)	L0d3b1	79,261	42,998	900- 1000 CE	–
XAR001*	Botswana_ Xaro_ 1400BP	Xaro	Botswana	Early Iron Age	3.64	37.94	M	E1b1a1a1c1a	L3e1a2	939,378	494,074	700- 1000 CE	–
XAR002*	Botswana_ Xaro_ 1400BP	Xaro	Botswana	Early Iron Age	1.36	172.94	M	E1b1b1b2b(E- M293,E- CTS10880)	L0k1a2	703,295	375,283	700- 1000 CE	–