‘Basal Eurasians’ are a lineage hypothesized13 to have split off prior to the differentiation of all other Eurasian lineages, including both eastern non-African populations like the Han Chinese, and even the early diverged lineage represented by the genome sequence of the ~45,000 year old Upper Paleolithic Siberian from Ust’-Ishim. To test for Basal Eurasian ancestry, we computed the statistic f4(Test, Han; Ust’-Ishim, Chimp) (Supplementary
159 Information, section 4), which measures the excess of allele sharing of Ust’-Ishim with a variety of Test populations compared to Han as a baseline. This statistic is significantly negative (Z<-3.7) for all ancient Near Easterners as well as Neolithic and later Europeans, consistent with their having ancestry from a deeply divergent Eurasian lineage that separated from the ancestors of most Eurasians prior to the separation of Han and Ust’-Ishim. We used
qpAdm7 to estimate Basal Eurasian ancestry in each Test population. We obtain the highest estimates in the earliest populations from both Iran (66±13% in the likely Mesolithic sample, 48±6% in Neolithic samples), and the Levant (44±8% in Epipaleolithic Natufians) (Fig. 2), showing that Basal Eurasian ancestry was widespread across the ancient Near East.