Methods S1. Admixture Model to Test Domestication Scenarios with

Methods S1. Admixture Model to Test Domestication Scenarios with fastsimcoal2 We fitted the model shown below, for which all population sizes and event times were fitted, along with the admixture proportion γ. Note that the model is flexible in that an estimate of γ ≈ 0.0 would imply an independent domestication in Africa, an estimate of γ ≈ 1.0 a single domestication event in the Middle East, followed by dispersal to Africa, and intermediate estimates of a secondary domestication event in Africa.

All parameters of this model were inferred with initial large search ranges of 10 1 – 105 for both population sizes and event times and of 0 – 1 for the admixture proportion. However, fastsimcoal2 required events to be ordered. As data, we used all three pairwise SFS between the three populations inferred with ANGSD from all sites at least 10kb away from the nearest gene. The obtained pairwise SFS are shown in row A below, where colors represent log10 proportions of sites in each polymorphic bin and bins without data are shown in white. To ensure convergence, we then ran fastsimcoal2 200 times and kept the run that resulted in the highest log likelihood (-10,151,241.341). The model should be considered as a reasonable fit given that the highest obtainable log likelihood for the SFS used was -10,059,060.579 and that the three pairwise SFS are well recovered. This is illustrated in row B of the figure below, which displays the fold-difference between the observed and expected SFS on the log10 scale. While differences between the SFS are generally low, larger differences are observed in the bins with few sites where the observations are expected to be noisy.