Fig. 1

Phylogeny and population genetics of domesticated and wild peaches. a Geographic distribution of the 480 peach accessions, each of which is represented by a dot on the world map. b The neighbor-joining phylogenetic tree of 480 peach accessions constructed based on 4.98 million SNPs. c–e PCA plots of peach accessions. Six subgroups are indicated by different colors indicated at the bottom of each figure. The domesticated group includes the landraces and improved cultivars. The improved cultivars include the accessions from eastern and western countries. f Summary of nucleotide diversity (π) and population divergence (F_ST) across the four groups. Value in each circle represents nucleotide diversity for the group, and values between pairs indicate population divergence (F_ST). “Western” and “Eastern” indicated improved cultivars from western and eastern countries, respectively. g Decay of linkage disequilibrium (LD), measured by r², in the five groups