Extended Data Table 3. Testing whether archaic genomes share more alleles with Oase 1 than with other modern humans.

The statistic D(Test, Oase 1; Archaic, Outgroup) is negative if the archaic genomes share more alleles with Oase 1 than with a test sample. The outgroups are either chimpanzee or a sub-Saharan African (Mbuti).

Test	Sites	Archaic = Altai				Archaic = Denisovan
		Chimp		Mbuti		Chimp		Mbuti
		D	Z	D	Z	D	Z	D	Z
Han	115,300	−0.0036	−5.1	−0.0071	−7.6	−0.0014	−2.2	−0.0049	−6.3
Dai	115,300	−0.0035	−5.0	−0.0077	−8.2	−0.0013	−2.1	−0.0056	−7.0
Karitiana	115,300	−0.0032	−4.3	−0.0063	−6.9	−0.0008	−1.3	−0.0040	−5.3
French	115,300	−0.0049	−6.9	−0.0074	−8.2	−0.0021	−3.4	−0.0047	−6.2
Sardinian	115,300	−0.0038	−5.1	−0.0071	−7.8	−0.0016	−2.5	−0.0050	−6.5
Papuan	115,300	−0.0026	−3.6	−0.0051	−5.4	0.0009	1.5	−0.0016	−2.1
Ust'-Ishim	115,100	−0.0026	−3.6	−0.0052	−5.5	−0.0009	−1.5	−0.0035	−4.4
Kostenki14	108,100	−0.0032	−4.1	−0.0059	−6.0	−0.0017	−2.4	−0.0044	−5.3
MA1	83,200	−0.0031	−3.6	−0.0050	−4.7	−0.0007	−0.9	−0.0028	−2.8
Loschbour	114,300	−0.0043	−5.7	−0.0066	−6.8	−0.0019	−2.9	−0.0043	−5.3
LaBrana	111,000	−0.0033	−4.2	−0.0072	−7.3	−0.0008	−1.2	−0.0047	−5.4
Stuttgart	114,000	−0.0037	−5.1	−0.0066	−7.1	−0.0013	−2.1	−0.0042	−5.6