Extended Data Table 1.

Shared derived alleles.Percentage of derived alleles in one archaic genome (Altai Neanderthal or Denisovan) shared with African genomes in sites that are homozygous ancestral in the other archaic genome. The percentages of shared derived alleles are binned by their African allele frequency. Fixed derived alleles in Africans are included in the ‘0.9 < f ≤ 1’ but also shown separately in the ‘Fixed’ category.

African frequency	0≤f≤0.1	0.1<f≤0.2	0.2<f≤0.3	0.3<f≤0.4	0.4<f ≤ 0.5	0.5<f ≤ 0.6	0.6<f≤0.7	0.7<f≤0.8	0.8<f ≤ 0.9	0.9<f≤ 1	Fixed
Altai (%)	66.86	5.01	3.89	3.42	3.11	2.79	2.71	2.55	2.68	6.99	2.98
Denisovan (%)	72.27	4.35	3.43	2.96	2.60	2.5	2.26	2.12	2.23	5.30	1.90