Fig. 2

The threespine stickleback Y chromosome assembly is concordant with cytogenetic maps. a The Y chromosome has diverged from the X chromosome through a series of inversions determined through ordering of cytogenetic markers (dashed lines indicate rearrangements of the linear order of markers [32]). b Alignments of the assembled Y chromosome (left) to the X chromosome (right) reveal the same inversions. A majority of the pseudoautosomal region is not included in the reference Y chromosome assembly because this region was not targeted (see methods). The location of the candidate sex determination gene (Amhy) is indicated by the black arrow. Centromeres are shown by black circles. Positions are shown in megabases