ABBA-BABA test of introgression among the watermelon and its close relatives including the ancient DNA samples. (A) Tests of introgression among C. lanatus ssp. vulgaris, C. lanatus ssp. cordophanus, C. amarus, and C. mucosospermus based on all informative sites. (B) Test of introgression among the 6,000-year-old Libyan seed (UMB-6), the 3,000-year-old Sudanese seed (AS-814), and C. lanatus ssp. vulgaris, C. lanatus ssp. cordophanus, and C. amarus based on all informative sites. (C) Number of ABBA-BABA sites indicating gene flow between the Libyan seed and C. amarus. (D) Number of ABBA-BABA sites indicating gene flow between the Libyan seed (UMB-6), C. lanatus ssp. vulgaris, and C. lanatus ssp. cordophanus. (E) Number of ABBA-BABA sites indicating gene flow between the Sudanese seed and C. amarus. The plots presented in C, D, and E are inferred from all sites or non-polymorphic sites only (D-values, Z-scores, and sample IDs used in all ABBA-BABA tests are provided on supplementary table S3, Supplementary Material online).