Genetic structure was assessed using a least-squares optimization approach implemented in the sNMF program . This approach is based on SNP calling and consists in estimating admixture coefficients based on sparse non-negative matrix factorization . We assessed a number of K populations varying from 1 to 6 clusters. Ten replications were performed for each K value. To select the best K value, we used the minimum value of the cross entropy criterion . We also used the maximum likelihood structure approach implemented in the NgsAdmix program . This approach directly uses the genotype likelihood given by angsd, without calling genotypes. The most relevant K number of population was selected by comparing the results obtained with NgsAdmix and sNMF. Genetic diversity was estimated using nucleotide diversity π  and nucleotide polymorphism θ  computed using the option “-doThetas” implemented in angsd 0.700 . We calculated the ratio of diversity between the cultivated species D. rotundata and each of the wild species D. praehensilis and D. abyssinica using the R package. Pairwise linkage disequilibrium (LD) was calculated with the squared allele frequency correlation r 2  using the R packages SNPRelate  and LDcorSV . A set of contigs corresponding to 1% of all contigs was randomly selected and used as reference. Intra-contig LDs within these contigs were performed for pairs of SNPs with minor allele frequencies (MAF) higher than 0.01.