Table 4.
Neandertals are more closely related to present-day non-Africans than to Africans. For each pair of modern humans H1 and H2 that we examined, we reported D (H1, H2, Neandertal, Chimpanzee): the difference in the percentage matching of Neandertal to two humans at sites where Neandertal does not match chimpanzee, with ±1 standard error. Values that deviate significantly from 0% after correcting for 38 hypotheses tested are highlighted in bold (|Z| > 2.8 SD). Neandertal is skewed toward matching non-Africans more than Africans for all pairwise comparisons. Comparisons within Africans or within non-Africans are all consistent with 0%.
| Population comparison | H1 | H2 | % Neandertal matching to H2 – % Neandertal matching to H1 (±1 standard error) |
|---|---|---|---|
| ABI3730 sequencing (~750 bp reads) used to discover H1-H2 differences | |||
| African to African | NA18517 (Yoruba) | NA18507 (Yoruba) | −0.1 ± 0.6 |
| NA18517 (Yoruba) | NA19240 (Yoruba) | 1.5 ± 0.7 | |
| NA18517 (Yoruba) | NA19129 (Yoruba) | −0.1 ± 0.7 | |
| NA18507 (Yoruba) | NA19240 (Yoruba) | −0.5 ± 0.6 | |
| NA18507 (Yoruba) | NA19129 (Yoruba) | 0.0 ± 0.5 | |
| NA19240 (Yoruba) | NA19129 (Yoruba) | −0.6 ± 0.7 | |
| African to Non-African | NA18517 (Yoruba) | NA12878 (European) | 4.1 ± 0.8 |
| NA18517 (Yoruba) | NA12156 (European) | 5.1 ± 0.7 | |
| NA18517 (Yoruba) | NA18956 (Japanese) | 2.9 ± 0.8 | |
| NA18517 (Yoruba) | NA18555 (Chinese) | 3.9 ± 0.7 | |
| NA18507 (Yoruba) | NA12878 (European) | 4.2 ± 0.6 | |
| NA18507 (Yoruba) | NA12156 (European) | 5.5 ± 0.6 | |
| NA18507 (Yoruba) | NA18956 (Japanese) | 5.0 ± 0.7 | |
| NA18507 (Yoruba) | NA18555 (Chinese) | 5.8 ± 0.6 | |
| NA19240 (Yoruba) | NA12878 (European) | 3.5 ± 0.7 | |
| NA19240 (Yoruba) | NA12156 (European) | 3.1 ± 0.7 | |
| NA19240 (Yoruba) | NA18956 (Japanese) | 2.7 ± 0.7 | |
| NA19240 (Yoruba) | NA18555 (Chinese) | 5.4 ± 0.9 | |
| NA19129 (Yoruba) | NA12878 (European) | 3.9 ± 0.7 | |
| NA19129 (Yoruba) | NA12156 (European) | 4.9 ± 0.7 | |
| NA19129 (Yoruba) | NA18956 (Japanese) | 5.1 ± 0.8 | |
| NA19129 (Yoruba) | NA18555 (Chinese) | 4.7 ± 0.8 | |
| Non-African to Non-African | NA12878 (European) | NA12156 (European) | −0.5 ± 0.8 |
| NA12878 (European) | NA18956 (Japanese) | 0.4 ± 0.8 | |
| NA12878 (European) | NA18555 (Chinese) | 0.3 ± 0.8 | |
| NA12156 (European) | NA18956 (Japanese) | −0.3 ± 0.8 | |
| NA12156 (European) | NA18555 (Chinese) | 1.3 ± 0.7 | |
| NA18956 (Japanese) | NA18555 (Chinese) | 2.5 ± 0.9 | |
| Illumina GAII sequencing (~76 bp reads) used to discover H1-H2 differences | |||
| African - African | HGDP01029 (San) | HGDP01029 (Yoruba) | −0.1 ± 0.4 |
| African to Non-African | HGDP01029 (San) | HGDP00521 (French) | 4.2 ± 0.4 |
| HGDP01029 (San) | HGDP00542 (Papuan) | 3.9 ± 0.5 | |
| HGDP01029 (San) | HGDP00778 (Han) | 5.0 ± 0.5 | |
| HGDP01029 (Yoruba) | HGDP00521 (French) | 4.5 ± 0.4 | |
| HGDP01029 (Yoruba) | HGDP00542 (Papuan) | 4.4 ± 0.6 | |
| HGDP01029 (Yoruba) | HGDP00778 (Han) | 5.3 ± 0.5 | |
| Non-African to Non-African | HGDP00521 (French) | HGDP00542 (Papuan) | 0.1 ± 0.5 |
| HGDP00521 (French) | HGDP00778 (Han) | 1.0 ± 0.6 | |
| HGDP00542 (Papuan) | HGDP00778 (Han) | 0.7 ± 0.6 | |