Extended Data Table 1.

Fewer accumulated mutations in Africans than in non-Africans.

		All autosomes		All X chromosome		Lowest B quintile		Highest B quintile
Population A	Population B	D×100	Z	D×100	Z	D×100	Z	D×100	Z
Khoesan	Oceania	−0.35	−8.2	−0.70	−2.7	−0.68	−6.4	−0.14	−1.7
Africa	America	−0.33	−9.4	−0.73	−2.8	−0.65	−7.3	−0.18	−2.6
Khoesan	WestEurasia	−0.30	−7.5	−0.68	−3.1	−0.63	−6.3	−0.17	−2.1
Africa	Oceania	−0.29	−8.5	−0.66	−3.2	−0.55	−6.6	−0.07	−1.0
Africa	WestEurasia	−0.25	−8.5	−0.66	−3.1	−0.49	−6.4	−0.11	−1.8
Khoesan	SouthAsia	−0.24	−6.0	−0.56	−2.7	−0.61	−6.3	−0.11	−1.4
Africa	EastAsia	−0.20	−6.6	−0.65	−2.5	−0.42	−5.2	−0.10	−1.5
Africa	CentralAsiaSiberia	−0.20	−6.2	−0.55	−2.2	−0.48	−6.3	−0.05	−0.7
Pygmy	WestEurasia	−0.19	−4.8	−0.46	−1.4	−0.43	−4.6	−0.04	−0.5
Africa	SouthAsia	−0.18	−6.4	−0.50	−2.0	−0.46	−6.3	−0.03	−0.5
CentralAsiaSiberia	Oceania	−0.13	−3.9	−0.15	−0.6	−0.09	−1.1	−0.03	−0.4
Pygmy	SouthAsia	−0.13	−3.3	−0.38	−1.1	−0.38	−4.2	0.02	0.2
EastAsia	Oceania	−0.13	−4.1	0.00	0.0	−0.17	−2.1	0.04	0.6
Khoesan	Pygmy	−0.10	−2.6	−0.14	−0.4	−0.16	−1.6	−0.12	−1.5
SouthAsia	WestEurasia	−0.08	−4.3	−0.20	−1.2	−0.05	−1.0	−0.10	−2.7
CentralAsiaSiberia	WestEurasia	−0.06	−2.2	−0.16	−0.8	−0.01	−0.2	−0.09	−1.6
EastAsia	WestEurasia	−0.06	−2.1	−0.00	−0.0	−0.08	−1.0	−0.02	−0.3
CentralAsiaSiberia	EastAsia	−0.00	−0.2	−0.18	−1.1	0.07	1.2	−0.08	−1.8
Africa	Pygmy	−0.00	−0.1	−0.06	−0.2	0.03	0.4	−0.06	−0.8
EastAsia	SouthAsia	0.02	0.7	0.22	1.7	−0.04	−0.7	0.08	1.7
CentralAsiaSiberia	SouthAsia	0.02	0.7	0.05	0.3	0.02	0.4	−0.00	−0.0
America	Oceania	0.03	0.9	0.11	0.4	0.10	1.1	0.13	1.7
Oceania	WestEurasia	0.08	2.3	−0.03	−0.1	0.10	1.1	−0.04	−0.6
Africa	Khoesan	0.10	2.9	0.17	0.7	0.23	2.6	0.07	1.0
America	WestEurasia	0.11	3.6	0.11	0.4	0.19	2.2	0.08	1.3
CentralAsiaSiberia	Pygmy	0.14	3.4	0.32	0.9	0.43	4.5	−0.04	−0.4
Oceania	SouthAsia	0.14	4.8	0.22	0.9	0.13	1.7	0.04	0.7
EastAsia	Pygmy	0.15	3.6	0.49	1.4	0.37	3.9	0.04	0.5
America	EastAsia	0.18	5.9	0.09	0.3	0.28	3.6	0.11	1.8
America	CentralAsiaSiberia	0.18	6.2	0.34	1.7	0.23	2.9	0.18	3.1
America	SouthAsia	0.18	6.4	0.34	1.5	0.22	3.0	0.18	3.1
Oceania	Pygmy	0.24	5.4	0.46	1.3	0.45	4.6	0.02	0.2
CentralAsiaSiberia	Khoesan	0.25	6.0	0.57	2.9	0.64	6.3	0.09	1.1
EastAsia	Khoesan	0.25	6.2	0.68	3.2	0.59	5.9	0.14	1.7
America	Pygmy	0.26	5.9	0.58	1.6	0.58	5.7	0.09	1.0
America	Khoesan	0.37	8.7	0.76	3.3	0.77	7.3	0.22	2.5

We compute a statistic D(Population A, Population B, Chimp), measuring the difference in the rate of matching to chimpanzee in Population A compared to Population B. For all the autosomes, we observe highly significant signals (3.3<|Z|<9.4) of excess mismatching to chimpanzee in non-Africans compared to Africans, using a standard error from a Block Jackknife. We highlight |D|>0.002 in blue, and |Z|>3 in yellow. The deviations from zero are greatest in subsets of the genome where the time since two populations split comprises a relatively larger fraction of the total genetic divergence time between the populations; this is the direction expected from a mutation accumulation change since divergence. Compared to all the autosomes as a baseline, a least squares fit indicate that the deviations are 2.2-times higher on chromosome X, 2.0 times higher in the quintile of lowest B-statistic (closest to functionally important regions), and 0.43 times as high in the quintile of lowest B-statistic (furthest from functional regions).