We used the qpWave (v400) and qpAdm (v632) programs of ADMIXTOOLS (12, 17) to test and model admixture proportions from potential source populations (reference populations) in the tested populations. We used a basic set of seven outgroups including present-day populations (Han, Onge, Mbuti, Mala, Mixe) (37) that represent a global genetic variation and published ancient populations such as Natufian (12), which represents a Levantine gene pool outside of modern genetic variation and the European Upper Palaeolithic individual “Villabruna” (36).

The distribution of the squared f4-statistics of the form f4 (Ashkelon individual 1, Ashkelon individual 2; test, Mbuti) was estimated for χ2 distribution with 1 df using Q-Q plot for each analyzed group (ASH_LBA, ASH_IA1, and ASH_IA2) (fig. S8). The variance for each group was estimated by a Fligner-Killeen test, which is robust against departures from normality that can be caused by small sample size.

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