Figure 7.

Evidence for a fifth evolutionary stratum on the X chromosome. a, Sequence identity between the X and Y homology blocks 1-12 (see Figs 5b and 6) plotted in 5-kb windows. The scale shows the total amount of sequence aligned, excluding insertions and deletions (see Methods). A 10-kb spacer is placed between each consecutive block of homology. Segments of the plot are coloured according to the system used in Figs 6 and 7b. On the basis of this plot, a new evolutionary stratum S5 is defined, which includes homology blocks 1 and 2. b, A most parsimonious series of inversion events from the arrangement of homology blocks 1-12 on the X chromosome (top) to the Y chromosome (bottom), calculated using GRIMM⁶⁴. The grey boxes show the suggested extents of former pseudoautosomal regions within the distal part of the XAR, and the magenta box (bottom row) shows the position of the current pseudoautosomal region. This inversion sequence provides independent support for the proposed pseudoautosomal boundary movements and evolutionary strata. It was previously suggested that AMELX (in block 12) is in S4 (ref. ⁴⁶), or possibly at the boundary between S3 and S4 (ref. ⁶⁷). However, the more distal location of block 11, which contains TBL1X (an S3 gene⁴⁶), is not consistent with these suggestions. The two regions of increased sequence identity within block 10 contain the VCX2 and VCX3B genes on the X chromosome and the VCY1B and VCY genes on the Y chromosome. This gene family might have arisen de novo in the simian lineage⁶⁸, which could account for the unusual characteristics of this part of the alignment.