Kinship between F2 and captive individuals
We first estimated kinships by COLONY 2.0 and Sequoia for each of the filtered SNP sets. COLONY 2.0 estimated the following kinships with a support probability of 0.8 or higher: 1 pair for FS within F0, 9 pairs for HS within F0, 18 pairs for FS within F2, 78 pairs for HS within F2, 26 pairs for GG between F0 and F2, and 15 pairs for UANN between F1 and F2. In COLONY 2.0, we treated HS relationships between generations as GG or UANN. The detailed results from COLONY 2.0 are shown in Tables S5–S10 for all outputs regardless of the support probability. The results from Sequoia were 1 pair for FS within F0, 2 pairs for HS within F0, 19 pairs for FS within F2, 9 pairs for HS within F2, 9 pairs for GG between F0 and F2, and 9 pairs for UANN between F1 and F2 (shown in Tables S11–S16). The GG relationships estimated from gRandma were 42 robust trios (Table S17) and 20 weak trios (Table S18). The results from these three programs are presented in Figure 2 as solid lines.