Research Article

A Draft Sequence of the Neandertal Genome

Science  07 May 2010:
Vol. 328, Issue 5979, pp. 710-722
DOI: 10.1126/science.1188021
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 comparisonH1H2% Neandertal matching to H2 – % Neandertal matching to H1(±1 standard error)
ABI3730 sequencing (~750 bp reads) used to discover H1-H2 differences
African to AfricanNA18517 (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-AfricanNA18517 (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-AfricanNA12878 (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 - AfricanHGDP01029 (San)HGDP01029 (Yoruba)-0.1 ± 0.4
African to Non-AfricanHGDP01029 (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-AfricanHGDP00521 (French)HGDP00542 (Papuan)0.1 ± 0.5
HGDP00521 (French)HGDP00778 (Han)1.0 ± 0.6
HGDP00542 (Papuan)HGDP00778 (Han)0.7 ± 0.6