Table 1. Formal tests for population mixture.
Population (X) | Samples | Region | Dataset | Z-score for 4 Pop. Test ((Px-PCEU),(PPapuan-PYRI)) | Z-score for 3 Pop. Test ((Px-PCEU),(Px-PYRI)) |
African Americans | 49 | n/a | HapMap3 | −85.1 | −108.9 |
Palestine | 43 | L | HGDP-CEPH | −27.9 | −24.7 |
Turkey | 6 | L | POPRES | −1 | −3.4 |
Bedouin-g1 | 15 | L | HGDP-CEPH | −36 | −40.7 |
Bedouin-g2 | 30 | L | HGDP-CEPH | −25.8 | >0 |
Druze | 41 | L | HGDP-CEPH | −14.6 | >0 |
Spain | 137 | SE | POPRES | −12.3 | −21.1 |
Portugal | 134 | SE | POPRES | −14.9 | −29 |
Romania | 14 | SE | POPRES | −0.5 | −5.1 |
Croatia | 6 | SE | POPRES | 0.7 | >0 |
Bosnia-Herzegovina | 9 | SE | POPRES | −0.6 | −1.5 |
Sardinia | 27 | SE | HGDP-CEPH | −9.3 | >0 |
Southern-Italy | 121 | SE | POPRES | −10.7 | −14.2 |
Northern-Italy | 90 | SE | POPRES | −5.7 | −5.7 |
Austria | 14 | ECE | POPRES | −0.2 | −2.4 |
Poland | 22 | ECE | POPRES | 1.3 | >0 |
Hungary | 19 | ECE | POPRES | 0.4 | −5.6 |
Czech Republic | 11 | ECE | POPRES | 0.5 | >0 |
Adygei | 17 | ECE | HGDP-CEPH | 2.9 | >0 |
Russia | 6 | ECE | POPRES | 0.6 | −0.2 |
Russia | 25 | ECE | HGDP-CEPH | 11.4 | >0 |
Swiss-French | 759 | I | POPRES | −3.2 | −6.1 |
France | 92 | I | POPRES | −1.9 | −3.7 |
France | 28 | I | HGDP-CEPH | −1.9 | −2.9 |
Basque | 24 | I | HGDP-CEPH | −1.2 | >0 |
Belgium | 43 | I | POPRES | −0.9 | −2.2 |
Orkney | 15 | I | POPRES | 3.2 | >0 |
United Kingdom | 388 | I | POPRES | 1.5 | >0 |
Ireland | 62 | I | POPRES | 1.7 | >0 |
Scotland | 5 | I | POPRES | 3.3 | >0 |
Netherlands | 17 | I | POPRES | 1.0 | >0 |
Swiss-German | 84 | I | POPRES | −1 | −2.6 |
Germany | 74 | I | POPRES | −0.9 | −2.8 |
Sweden | 11 | I | POPRES | 1.6 | 0 |
Ashkenazi Jews | 323 | n/a | IBD | −11.6 | >0 |
Ashkenazi Jews | 34 | n/a | Jewish HapMap | −9.5 | −2.2 |
Syrian Jews | 25 | n/a | Jewish HapMap | −10.1 | −2.3 |
Iranian Jews | 24 | n/a | Jewish HapMap | −5.9 | >0 |
Iraqi Jews | 36 | n/a | Jewish HapMap | −8.5 | >0 |
Sephardic Greek Jews | 39 | n/a | Jewish HapMap | −13.7 | −15.2 |
Sephardic Turkey Jews | 27 | n/a | Jewish HapMap | −13.6 | −17.1 |
Italian Jews | 27 | n/a | Jewish HapMap | −11.4 | >0 |
Notes: We analyzed data from all West Eurasian populations with ≥5 samples. Regions are abbreviated: I – Northwest Europe, ECE – East-Central Europe, SE – Southern Europe and L – Levant. We used a Block Jackknife (block size of 5cM) to correct for LD among SNPs and to estimate a Z-score that reports the number of approximately normally distributed standard deviations that the correlation coefficient differs from 0. For the 4 Population Test, we interpret |Z|>3 as significant evidence for mixture (we test the tree ((Px-PCEU)(PPapuan-PYRI), and do not show the tests of the two alternative trees, although all |Z|-scores are >16). For the 3 Population Test, we interpret Z<−3 as significant evidence for mixture; a positive score for the 3 Population Test is possible even in the presence of population mixture, since genetic drift after mixture can mask the signal (for example, Bedouin-g2). Scores that are significant are highlighted in bold. For further study of sub-Saharan African mixture, we chose populations with a significantly negative score by the 4 Population Test (bold).