Fig. 3: Overall population structure landscape and the inferred population demographic history.
a Rooted neighbor-joining phylogenetic tree of 427 moso bamboo individuals. The differently colored lines represent the fifteen geographic areas, and the differently colored dotted lines nearby represent five groups that were empirically assigned in our study. b The genetic diversity (θπ) and population differentiation (FST) matrix of the five groups. The colors and numbers in the cells of the matrix represent the FST values. The colors and numbers in the cells below the FST matrix represent the genetic diversity (θπ). c Results of the Mantel test of the relationship between geographic distance and genetic distance with MS_WEST excluded, and p-value was calculated using a one-sided Mantel test with 9999 permutations. The blue line is fitted by the linear regression between genetic distance and geographic distance on the basis of ordinary least squares in the function “geom_smooth” from ggplot2. The gray error band represents the 95% CI (confidence interval). d The connection of individuals with the lowest 1% pairwise genetic distances. The size and color of circles represent the degree of connectivity to a node. The lines in different colors indicated values of Hamming distance (genetic distance), with red indicating the shortest distance and for the others, darker colors indicate shorter distances and lighter colors indicate longer distances. e The demographic history of the five groups was inferred separately using the pairwise sequential Markovian coalescent (PSMC) method. The blue line represents the historical surface temperatures (Tsurf), and the light blue shade indicates the bottleneck experienced during the last glacial period (LGP, 115,000–11,700 years ago). f The demographic history was inferred using SMC++. The LGP was shaded in light blue, and the reduction without a rebound in the effective population size during the last 2000 years is shaded in light green. The results were scaled to real-time by assuming a generation time of 67 years and a mutation rate of 8.51 × 10−8 per generation. Source data underlying c and d are provided as a Source Data file.
