Sequence divergence between Y haplotypes and the reconstructed X_gua. (A) Sequence difference calculated as the number of SNPs and indels in 10 kb sliding windows along the Y Chromosomes. (B) Y_gua and Y_mac are aligned to the X. Male-specific RAD-tags from Caroni swamp guppies (blue bars) and from four different guppy strains (red bars) were mapped on the aligned Y_gua (top) and Y_mac (bottom) sequences. The four strains represent a broader range of geographic origins, from East Trinidad to West Venezuela. About 70% of these RAD-tags (red bars) had best hits (e-40) within the distal 16% of the Y (>24 Mb). Both Y haplotypes are aligned to the reconstructed X_gua (middle). The green dotted line indicates the congruent MSY identified by sequence divergence and RAD-tags from the Trinidad populations of guppy.