Supplementary Information for

Methods

• Supplementary Methods   

Tables

• Supplementary Table1    Information on statistical tests, alternative hypotheses, test statistics, and p-values used
• Supplementary Table2   Copy number status in control individuals for autosomal genes from the Exome Aggregation Consortium.
• Supplementary Table3   Properties of ancestral X-linked genes assessed in this study.
• Supplementary Table4   Properties of ancestral Z-linked genes assessed in this study
• Supplementary Table5   Pct scores, both with and without normalization for within-UTR conservation, for all gene-miRNA interactions
• Supplementary Table6   Gene expression fold changes from transfection of 4 miRNAs into HCT116 or HEK293 cells

Figures

• Supplemental Figure1   Effect of deletion status on autosomal PCTscores.
• Supplemental Figure2   PCT scores of X-Y pairs across 8 mammals.
• Supplemental Figure3   Resampled mean PCTscores of X-linked genes.
• Supplemental Figure4   PCTscore comparisons with consistent and variable escape genes separated.
• Supplemental Figure5   PCTscore comparisonswith discordant genes included as X-inactivated or escape.
• Supplemental Figure6   Variation in within-UTR conservation does not account for observed differences in PCTscore among classes of X-linked genes.
• Supplemental Figure7   Background human-chicken 3’ UTR conservation among classes of X-linked genes.
• Supplemental Figure8   Ancestral miRNA targeting of X-Y pairs across 8 mammals.
• Supplemental Figure9   PCTscores of Z-W pairs across 4 and 14 birds.
• Supplemental Figure10   Resampled mean PCTscores of Z-linked genes.
• Supplemental Figure11   Variation in within-UTR conservation cannot account for observed differences in PCTscore among classes of Z-linked genes.
• Supplemental Figure12   Correlation of Z-linked gene-specific dosage compensation with gene-level PCTscore.
• Supplemental Figure13   Ancestral miRNA targeting of Z-W pairs across 4 birds.
• Supplemental Figure14   Ancestral miRNA targeting of predicted Z-W pairs across 14 birds.
• Supplemental Figure15   Correlation of Z-linked gene-specific dosage compensation with human-chicken-conserved site excess.
• Supplemental Figure16   Gene expression changes following small RNA transfections in human HeLa cells.
• Supplemental Figure17   Gene expression changes following transfection or knockdown of additional miRNAs in human HCT116 or HEK293 cells.
• Supplemental Figure18   Changes in mRNA stability and translational efficiency and gene expression following miR-155 knockout in mouse immune cells.
• Supplemental Figure19   Argonaute binding measured by high-throughput crosslinking-immunoprecipitation (CLIP) following miRNA transfection in HEK293 cells.

Code

• Big transitions
• ChickenHumanLizardSexDiff.R
• count_targetscan70_cons_output.txt
• generate_tscan_kmers.txt
• human.chicken.anolis.genecounts.txt
• human.chicken.anolis.genetpm.txt
• human.chicken.anolis.orthids.txt
• human.chicken.anolis.sampleinfo.txt
• miR_Family_Info_eg.txt
• plot_transitions.txt
• README.md
• samplePcts.R
• XZlogisticRegression.R