We compared nucleotide diversity π and the nucleotide polymorphism θ between the cultivated species and each of the wild species. First, the cultivated diversity π was 26% and 36% respectively lower than D. abyssinica and D. praehensilis (Additional file 2: Table S3 a and b). Secondly, the cultivated diversity θ was 28% and 44% lower than D. abyssinica and D. praehensilis respectively. Linkage disequilibrium (LD) computed between 400,760 pairs of SNP decreased rapidly at r 2 = 0.1 after 100 bp (Additional file 2: Figure S2).