Extended Data Table 1. Allele sharing between early modern humans and other humans.

We compute D(Non-African₁, Non-African₂; Early Modern Human, African) to test whether an early modern human (Oase 1, Ust’-Ishim, or Kostenki 14) shares more alleles with Non-African₁ (in which case the statistic is positive) or Non-African₂ (negative). We use a pool of six sub-Saharan African genomes (2 Mbuti, 2 Yoruba, 2 Dinka) as an outgroup; a pool of four genomes (2 French, 2 Sardinians) to represent Europeans; a pool of four genomes (2 Han, 2 Dai) to represent East Asians; and a pool of three genomes (2 Karitiana, 1 Mixe) to represent Native Americans. Results are based on 242,122 transition and transversion SNPs covered by at least one deaminated fragment in Oase 1, and covered in all other samples with the possible exception of MA1 (for MA1, 176,569 SNPs are used).

Non-African1	Non-African2	Oase 1		Ust’-Ishim		Kostenki 14
		D	Z	D	Z	D	Z
Oase 1	Ust’-Ishim					−0.0033	−3.8
Oase 1	Kostenki 14			−0.0037	−4.1
Oase 1	MA1			−0.0032	−3.5	−0.0092	−9.8
Oase 1	Loschbour			−0.0032	−3.9	−0.0101	−12.2
Oase 1	East Asian			−0.0027	−3.8	−0.0011	−1.6
Oase 1	Native American			−0.0030	−4.1	−0.0039	−5.5
Ust’-Ishim	Kostenki 14	−0.0005	−0.6
Ust’-Ishim	MA1	−0.0007	−0.8			−0.0059	−6.4
Ust’-Ishim	Loschbour	0.0002	0.3			−0.0068	−8.5
Ust’-Ishim	East Asian	0.0000	−0.1			0.0022	3.3
Ust’-Ishim	Native American	−0.0007	−1.0			−0.0006	−0.8
Kostenki 14	MA1	−0.0004	−0.6	0.0003	0.4
Kostenki 14	Loschbour	0.0007	1.0	0.0006	0.8
Kostenki 14	East Asian	0.0004	0.6	0.0011	1.6
Kostenki 14	Native American	−0.0002	−0.3	0.0008	1.1
MA1	Loschbour	0.0012	1.7	0.0005	0.7	−0.0012	−1.5
MA1	East Asian	0.0008	1.2	0.0007	1.1	0.0079	10.6
MA1	Native American	0.0001	0.1	0.0004	0.6	0.0051	7.0
Loschbour	East Asian	−0.0002	−0.4	0.0005	0.9	0.0090	13.7
Loschbour	Native American	−0.0009	−1.5	0.0002	0.3	0.0062	9.0
East Asian	Native American	−0.0006	−1.6	−0.0003	−0.8	−0.0028	−6.6
European	Oase 1			0.0004	0.6	0.0049	7.3
European	Ust’-Ishim	−0.0023	−3.5			0.0016	2.4
European	Kostenki 14	−0.0028	−4.7	−0.0033	−5.1
European	MA1	−0.0033	−5.4	−0.0031	−5.1	−0.0041	−6.0
European	Loschbour	−0.0021	−4.5	−0.0027	−5.7	−0.0052	−9.1
European	East Asian	−0.0024	−5.2	−0.0022	−5.3	0.0039	9.2
European	Native American	−0.0030	−6.4	−0.0025	−5.9	0.0010	2.2
European	Stuttgart	−0.0007	−1.5	−0.0001	−0.2	−0.0002	−0.3
Stuttgart	Oase 1			0.0005	0.6	0.0051	6.7
Stuttgart	Ust’-Ishim	−0.0017	−2.3			0.0018	2.3
Stuttgart	Kostenki 14	−0.0021	−3.2	−0.0032	−4.6
Stuttgart	MA1	−0.0027	−3.9	−0.0029	−4.2	−0.0041	−5.0
Stuttgart	Loschbour	−0.0015	−2.4	−0.0027	−4.6	−0.0050	−7.5
Stuttgart	East Asian	−0.0017	−2.9	−0.0022	−3.8	0.0040	6.8
Stuttgart	Native American	−0.0024	−3.9	−0.0025	−4.4	0.0012	1.9