English: Demographic history of the Jomon lineage (A) Maximum likelihood phylogenetic tree reconstructed by TreeMix under a model of two migrations. The tree shows a phylogenetic relationship among ancient (bold) and present-day (italic) populations. Colored arrows represent the migration pathways. The migration weight represents the fraction of ancestry derived from the migration edge. All other migration models from m = 0 to m = 5 are presented in fig. S7. (B) ROH spectra for Mesolithic and Neolithic hunter-gatherers including the 8.8-ka-old JpKa6904. Total length of ROH is plotted against different sizes of homozygous fragments ranging from 0.5 to 100 Mb. (C) Fitting of the models under different combinations of N (x axis) and T (y axis) for the 8.8-ka-old Jomon individual. Each point in the balloon plot represents a log10-scaled approximate Bayes factor (aBF) that compares likelihoods between a model with the highest likelihood and each of the other given models; the point with aBF = 0 is the model with the highest likelihood (N = 1000 and T = 20 ka ago; see fig. S10). NA means that aBF is not measurable for the model due to its likelihood equal to zero. (D) A comparison of outgroup f3 statistic results for the Jomon dataset divided into three subperiods measured using f3(Jomon_Sub-Period, X; Mbuti) (see fig. S12 for an expanded analysis). The three subperiods are as follows: Initial Jomon (JpKa6906); Early Jomon (JpFu1, JpOd6, JpOd181, JpOd274, and JpOd282); and a merged group for all Middle, Late, and Final Jomon (F5, F23, IK002, JpHi01, JpKo2, and JpKo13).