Supplementary Information for

Tables

• Supplementary Table 1    Includes:
  • Table S1A: Chromosomal locations, open reading frame positions, and GenBank accession numbers for EIF1A gene family members.
  • Table S1B: Chromosomal locations, open reading frame positions, and GenBank accession numbers for EIF2S3 gene family members.
  • Table S1C: Chromosomal locations, open reading frame positions, and GenBank accession numbers for RPS4 gene family members.
  • Table S1D: Chromosomal locations, open reading frame positions, and GenBank accession numbers for UBA1 gene family members.
• Supplementary Table 2    Includes:
  • Table S2A: List of RNA-seq datasets used in gene expression analyses with GenBank accession numbers and sexes of tissues indicated.
  • Table S2B: Tabular results of RNAseq analyses for all species, tissues, and X, Y, and autosomal gene family members.
• Supplementary Table 3    Synonymous and non-synonymous substitution rate (dS and dN) calculations.
• Supplementary Table 4    Includes:
  • Table S4A: Expression breadth of all human X-to-autosome retrogenes and their X-linked progenitors.
  • Table S4B: FPKM values used to calculate expression depth.

Figures

• Figure S1     Scatter plots of RNAseq analyses (from Table S2B) for all species, tissues, and X, Y, and autosomal gene family members. Female (F) and male (M) data are shown separately. Testes shown in blue, ovary shown in magenta, and all other somatic tissues shown in gray (see Table S2B for complete list). FPKM = fragments mapping to gene per kilobase gene length per millions of fragments in given dataset. Python script used to generate plots - betavioplot.py - is available at [28].
• Figure S2     Genomic locations of transposed autosomal genes. Screen shots from USCS Genome Browser [29] showing genomic locations of retrogenes and neighboring genes in various species to demonstrate synteny of retrogenes. (A) Mouse and rat Eif1a retrogene. (B) Human and orangutan EIF2S3 retrogene. (C) Rhesus and baboon EIF2S3 retrogene. (D) Marmoset and squirrel monkey EIF2S3 retrogene. (E) Mouse and rat Rps4 retrogene. (F) Opossum and wallaby RPS4 retrogene (only one of the two RPS4 retrogenes is shown because the second wallaby retrogene is located in a short sequence contig that contains no neighboring genes).
• Figure S3     Confirmation of UBA1 localization in New World monkeys. (A) FISH analysis on male marmoset (Callitrix jacchus) cells. Green signal corresponds to UBA1; red signal is specific to Y chromosome. (B) PCR analysis on male (M) and female (F) squirrel monkey (Saimiri sciureus) genomic DNA using two sets of UBA1Y-specific primers.