Table 1.
Sharing of derived alleles between present-day and archaic hominins
| Sample H1 | Sample H2 | Source of data for H1 and H2 |
D(H1, H2, Neanderthal, chimpanzee) |
D(H1, H2, Denisova, chimpanzee) |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| n BABA | n ABBA | D (%) | s.e. (%) | Z-score | n BABA | n ABBA | D (%) | s.e. (%) | Z-score | |||
| Eurasian/Eurasian* | ||||||||||||
| French | Han | Ref. 8 | 17,214 | 17,602 | −1.1 | 0.8 | −1.4 | 27,250 | 27,265 | 0.0 | 0.6 | 0.0 |
| Karitiana | Sardinian | This study | 1,116 | 1,085 | 1.4 | 2.1 | 0.7 | 1,559 | 1,627 | −2.1 | 1.8 | −1.2 |
| Karitiana | Cambodian | This study | 1,683 | 1,707 | −0.7 | 1.8 | −0.4 | 2,371 | 2,460 | −1.8 | 1.5 | −1.2 |
| Karitiana | Mongolian | This study | 1,128 | 1,195 | −2.9 | 2.2 | −1.3 | 1,765 | 1,742 | 0.7 | 1.8 | 0.4 |
| Sardinian | Cambodian | This study | 2,592 | 2,670 | −1.5 | 1.5 | −1.0 | 3,935 | 3,925 | 0.1 | 1.2 | 0.1 |
| Sardinian | Mongolian | This study | 1,966 | 2,027 | −1.5 | 1.6 | −0.9 | 3,036 | 3,057 | −0.3 | 1.3 | −0.3 |
| Cambodian | Mongolian | This study | 2,811 | 2,804 | 0.1 | 1.4 | 0.1 | 4,442 | 4,342 | 1.1 | 1.2 | 1.0 |
| African/African* | ||||||||||||
| San | Yoruba | Ref. 8 | 23,690 | 23,855 | −0.3 | 0.6 | −0.6 | 39,042 | 39,019 | 0.0 | 0.5 | 0.1 |
| Melanesian/Melanesian* | ||||||||||||
| Papuan2 | Bougainville | This study | 3,351 | 3,284 | 1.0 | 1.3 | 0.8 | 5,319 | 5,140 | 1.7 | 1.1 | 1.5 |
| Eurasian/African* | ||||||||||||
| French | San | Ref. 8 | 25,242 | 22,982 | 4.7 | 0.6 | 7.6† | 39,838 | 38,495 | 1.7 | 0.5 | 3.4† |
| French | Yoruba | Ref. 8 | 21,794 | 19,890 | 4.6 | 0.7 | 6.9† | 34,262 | 33,078 | 1.8 | 0.5 | 3.6† |
| Han | San | Ref. 8 | 25,081 | 22,470 | 5.5 | 0.6 | 8.5† | 38,815 | 37,439 | 1.8 | 0.5 | 3.4† |
| Han | Yoruba | Ref. 8 | 21,741 | 19,412 | 5.7 | 0.7 | 7.9† | 33,182 | 32,184 | 1.5 | 0.5 | 2.8 |
| Karitiana | Mbuti | This study | 1,577 | 1,473 | 3.4 | 1.9 | 1.8 | 2,368 | 2,360 | 0.2 | 1.5 | 0.1 |
| Sardinian | Mbuti | This study | 2,562 | 2,400 | 3.3 | 1.5 | 2.2 | 4,028 | 3,784 | 3.1 | 1.2 | 2.6 |
| Cambodian | Mbuti | This study | 4,235 | 3,641 | 7.5 | 1.2 | 6.5† | 6,329 | 5,850 | 3.9 | 1.0 | 4.0† |
| Mongolian | Mbuti | This study | 3,077 | 2,765 | 5.3 | 1.4 | 3.9† | 4,514 | 4,505 | 0.1 | 1.1 | 0.1 |
| Eurasian/Melanesian* | ||||||||||||
| French | Papuan1 | Ref. 8 | 15,523 | 15,548 | −0.1 | 0.8 | −0.1 | 23,509 | 25,470 | −4.0 | 0.7 | −5.7† |
| Han | Papuan1 | Ref. 8 | 15,059 | 14,677 | 1.3 | 0.9 | 1.5 | 22,262 | 24,198 | −4.2 | 0.7 | −5.8† |
| Karitiana | Papuan2 | This study | 1,522 | 1,658 | −4.3 | 1.9 | −2.2 | 2,201 | 2,641 | −9.1 | 1.6 | −5.8† |
| Karitiana | Bougainville | This study | 1,577 | 1,717 | −4.3 | 1.8 | −2.4 | 2,229 | 2,671 | −9.0 | 1.5 | −5.9† |
| Sardinian | Papuan2 | This study | 2,447 | 2,647 | −3.9 | 1.5 | −2.6 | 3,714 | 4,150 | −5.5 | 1.2 | −4.5† |
| Sardinian | Bougainville | This study | 2,531 | 2,762 | −4.4 | 1.5 | −3.0 | 3,877 | 4,336 | −5.6 | 1.1 | −4.9† |
| Cambodian | Papuan2 | This study | 3,713 | 3,891 | −2.3 | 1.3 | −1.8 | 5,457 | 6,272 | −6.9 | 1.1 | −6.5† |
| Cambodian | Bougainville | This study | 3,847 | 3,994 | −1.9 | 1.2 | −1.6 | 5,751 | 6,333 | −4.8 | 1.0 | −4.7† |
| Mongolian | Papuan2 | This study | 2,783 | 2,852 | −1.2 | 1.5 | −0.8 | 4,192 | 4,758 | −6.3 | 1.2 | −5.3† |
| Mongolian | Bougainville | This study | 2,813 | 3,066 | −4.3 | 1.5 | −2.9 | 4,234 | 4,847 | −6.8 | 1.1 | −6.0† |
| Melanesian/African* | ||||||||||||
| Papuan1 | San | Ref. 8 | 21,985 | 20,366 | 3.8 | 0.7 | 5.1† | 35,923 | 32,841 | 4.5 | 0.6 | 7.2† |
| Papuan1 | Yoruba | Ref. 8 | 19,107 | 17,646 | 4.0 | 0.8 | 4.9† | 30,995 | 28,186 | 4.7 | 0.6 | 7.4† |
| Papuan2 | Mbuti | This study | 3,832 | 3,324 | 7.1 | 1.3 | 5.4† | 6,124 | 5,233 | 7.8 | 1.1 | 7.2† |
| Bougainville | Mbuti | This study | 4,216 | 3,596 | 7.9 | 1.2 | 6.8† | 6,498 | 5,633 | 7.1 | 1.1 | 6.7† |
We present the D statistic D(H1, H2, X, chimpanzee), the normalized difference between the number of sites at which the derived allele in an archaic read from X matches human sample H1 (nBABA) and human sample H2 (nBABA); thus, its value is D = (nBABA − nABBA)/(nBABA + nABBA). We restrict to autosomal transversion substitutions, compute standard errors (s.e.) from a block jackknife, and highlight (dagger symbol) the D statistics that are more than Z> 3 s.d. from zero. Both Neanderthals and Denisovans match Eurasians more than the Africans, but the signals are consistently and significantly stronger when X = Neanderthal than when X = Denisova. The slight numerical differences with Table 4 of ref. 8 are due to differences in the data filtering. Here we restrict to comparisons of present-day human samples that were sequenced by the same protocol (the five individuals sequenced in ref. 8, or the seven in this study); Supplementary Table 8.2 presents the complete set of pairwise comparisons.
Comparison.
D statistics that are more than Z> 3 s.d. from zero.