Supplementary Information for

Jennifer F. Hughes, Helen Skaletsky, Laura G. Brown, Tatyana Pyntikova, Tina Graves, Robert S. Fulton, Shannon Dugan,
Yan Ding, Christian J. Buhay, Colin Kremitzki, Qiaoyan Wang, Hua Shen, Michael Holder,3 Donna Villasana,
Lynne V. Nazareth, Andrew Cree, Laura Courtney, Joelle Veizer, Holland Kotkiewicz, Ting-Jan Cho, Natalia Koutseva,
Steve Rozen, Donna M. Muzny, Wesley C. Warren, Richard A. Gibbs, Richard K. Wilson & David C. Page
Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

Nature (2012)

Table of Contents
Figures, Tables, Notes


  • 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 7a    Dot plot comparison of human, chimpanzee, and rhesus Y sequence to himan X sequence
            Figure 7b    Alignment of human, rhesus, and chimpanzee pseudoautosomal boundaries
  • Figure 8    Dot-plot comparison of rhesus and human MSYs
  • Figure 9    Dot-plot comparison of rhesus and chimpanzee MSYs
  • 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 15a   Gpr143
            Figure 15b   Stsp
            Figure 15c   Kalp
            Figure 15d   Shroom2
            Figure 15e   Bcor
            Figure 15f   Cask
  • Figure 16.   Sliding-window dN/dS analyses for rhesus-human ancestral gene pairs (The legend)
            Figure 16a   Amely, CYorf15, Ddx3y
            Figure 16b   Eif1ay, Hsfy, Kdm5d, Mxra5y
            Figure 16c   Nlgn4y, Prky, Rbmy, Rps4y1
            Figure 16d   Rps4y2, Sry, Tbl1y, Tspy
            Figure 16e   Usp9y, Uty, Zfy
  • 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 (The legend)
            Figure 18a
            Figure 18b


  • 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


  • Notes 1-5:
            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

    Sequence Files