Fig. 4

Contrasting population structure of the X region and the PAR. Gynodioecious papaya (hermaphrodites) are shown in blue and males from dioecious natural populations in red. We used 13,259 X-specific and 217,446 PAR SNPs/indels for all analyses. a Maximum likelihood phylogeny based on X-specific polymorphisms constructed in SNPhylo. b principal component analysis (PCA) based on all PAR SNPs/indels. The two distinct clusters separating male and hermaphrodite autosomes are circled in grey. c PCA based on all X-specific SNPs/indels. The single cluster containing both males and hermaphrodite Xs is circled and the outliers Cp11 and Cp44 are labeled. d Population structure analysis of PAR using STRUCTURE. Each accession is represented by a vertical bar and the length of each colored segment represents the contribution of each subgroup. e Population structure analysis of the X-linked region showing that STRUCTURE assigns the sequences from the dioecious and gynodioecious samples to a single population