Fig. 3

Demographic history of different sika deer populations. A The ancestral population size of each population was inferred using a PSMC model. A generation time (g) = 5 years and neutral mutation rate (µ) = 2.2 × 10^–9 per nucleotide site per generation were used. B Relative cross-coalescence rates (RCCR) over time between populations. Each line depicts the RCCR profile estimated using pairs of high-coverage genomes. The pairwise comparisons were between populations from Japan and RU1. C FastSIMCOAL2 v.2.6 simulation used to reconstruct the divergence, admixture, and demographic history of different sika deer populations. D TreeMix analysis of populations in Japan using RU1 as the outgroup when m = 2. E D-statistics with the form D (A, B; X, Y) for populations in Japan using RU1 as the outgroup. Positive D-statistic values indicate gene flow from X to A, whereas negative values indicate gene flow from X to B