Supplementary Files 1-3 Are Available At

SI Guide:

This file contains Supplementary Notes 1-3, Supplementary Figures 1-16 and Supplementary Tables 1-8 (contained within a single pdf file; 13.8 MB).

Supplementary Files 1-3 are available at

Notes

Note 1. BAC selection strategy and assembly of rhesus MSY sequence

Note 2. Determination of X-Y ancestral gene content within strata 1-5

Note 3. Human/chimpanzee/rhesus ancestral MSY gene content

Note 4. Discussion of dN/dS values for ancestral genes

Note 5. Determining time of pseudogene inactivation

Figures

Figure 1. Annotated sequence of rhesus MSY

Figure 2. Extended metaphase FISH analysis of pseudoautosomal boundary

Figure 3. Extended metaphase FISH analysis of centromere

Figure 4. Extended metaphase FISH analysis to orient middle contig

Figure 5. Comparison of radiation hybrid and physical maps of rhesus MSY

Figure 6. Interphase FISH analysis of gaps

Figure 7. Comparison of pseudoautosmal boundaries in rhesus, human and chimpanzee

Figure 8. Dot-plot comparison of rhesus and human MSYs

Figure 9. Dot-plot comparison of rhesus and chimpanzeeMSYs

Figure 10. Rearrangements during evolution of rhesus, human and chimpanzee MSYs

Figure 11. Triangular dot plots of DNA sequence identities within rhesus, human and chimpanzee MSYs

Figure 12. Electronic fractionation of rhesus, human and chimpanzee MSY sequences according to intrachromosomal similarity

Figure 13. Triangular dot plot of DNA sequence identities within major rhesus ampliconic region

Figure 14. RT-PCR analysis of rhesus MSY genes

Figure 15. Analysis of MSY ancestral pseudogenes in rhesus and human

Figure 16. Sliding-window dN/dS analyses for rhesus-human ancestral gene pairs

Figure 17.Y-linked MXRA5P/Y vs. X-linked MXRA5 dot-plot analyses in rhesus, human and chimpanzee

Figure 18. Gene decay plots using alternative dates

Tables

Table 1. BAC clones, GenBank accession numbers and nucleotide positions in rhesus MSY sequence assembly

Table 2. Palindromes in rhesus, human and chimpanzee MSYs

Table 3. Comparative analysis of rhesus and human MSY genes

Table 4. List of human X genes, organized by stratum, and conserved synteny in other vertebrates

Table 5. Copy numbers of genes in rhesus, human and chimpanzee

Table 6. Parameters of one-phase exponential decay models of gene numbers in MSY strata

Table 7. PCR primers for radiation hybrid mapping

Table 8. RT-PCR primers for analysis of rhesus MSY genes

Files

File 1. FASTA file of rhesus MSY sequence assembly

File 2. Radiation hybrid mapping data vectors

File 3. Alignment of rhesus and human MSY sequences in FASTA format