Supplementary Information for:

Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals

Daniel W Bellott, David C Page

Genome Research (2021)

Figures:

Supplemental Methods, References, and Figures: (PDF)

Includes:

• Supplemental Methods
• Supplemental References
• Supplemental Figure S1. Phylogenetic tree of selected amniote species
• Supplemental Figure S2. A large evolutionary stratum formed after vipers and colubroid snakes diverged from Arafura file snake
• Supplemental Figure S3. Lineage specific strata in mountain garter snake
• Supplemental Figure S4. Lineage specific strata in pygmy rattlesnake
• Supplemental Figure S5. Additional factors in the survival of caenophidian Z–W gene pairs
• Supplemental Figure S6. Factors in the survival of amniote X–Y and Z–W gene pairs
• Supplemental Figure S7. Components of ficolin-1-rich granule lumen are dosage-sensitive
• Supplemental Figure S8. Dosage sensitivity and broad expression make independent contributions to survival in caenophidian species
• Supplemental Figure S9. Dosage sensitivity and broad expression make independent contributions to survival in avian species
• Supplemental Figure S10. Dosage sensitivity and broad expression make independent contributions to survival in therian species

Tables:

Supplemental Table S1: (XLS)

Genomic resources used in this study

Supplemental Table S2: (XLS)

Published sex-linked genes in caenophidian snakes and python

Supplemental Table S3: (XLS)

Ancestral sex-linked genes in caenophidian snakes

Supplemental Table S4: (XLS)

Published ancestral caenophidian Z-W pairs

Supplemental Table S5: (XLS)

Published candidate W genes identified as ancestral in this study

Supplemental Table S6: (XLS)

Estimated Caenophidian Stratum Boundaries

Supplemental Table S7: (XLS)

Ancestral gene statistics

Supplemental Table S8: (XLS)

GO terms enriched in survivors in caenophidian snakes

Supplemental Table S9: (XLS)

List of survivors by species and stratum

Supplemental Table S10: (XLS)

GO terms enriched in survivors in birds

Supplemental Table S11: (XLS)

GO terms enriched in survivors in therian mammals

Supplemental Table S12: (XLS)

GO terms enriched in survivors

Supplemental Table S13: (XLS)

Ficolin-1-rich granule lumen components among ancestral genes

Supplemental Table S14: (XLS)

Avian Stratum Boundaries

Supplemental Table S15: (XLS)

Mammalian Stratum Boundaries

Supplemental Table S16: (XLS)

Surviving ancestral genes adjacent on the ancestral autosomes

Supplemental Table S17: (XLS)

Observed and expected survivors by species and stratum

Supplemental Table S18: (XLS)

Branch length and survival fraction calculations from three caenophidian species

Supplemental Table S19: (XLS)

Branch length and survival fraction calculations from four caenophidian species for RAB5A

Supplemental Table S20: (XLS)

Branch length and survival fraction calculations from six caenophidian species for WDR48, LSM12, COMMD3, and MSL1

Supplemental Table S21: (XLS)

Branch length and survival fraction calculations from 13 caenophidian species for WAC and CTNNB1

Supplemental Table S22: (XLS)

Branch length and survival fraction calculations from avian species

Supplemental Table S23: (XLS)

Branch length and survival fraction calculations from therian species

Supplemental Table S24: (XLS)

Information on statistical tests, alternative hypotheses, test statistics, and p-values

Data:

Supplemental Data S1: (TXT) (FASTA)

FASTA format sequences used for phylogenetic analyses

Supplemental Data S2: (TXT) (FASTA)

FASTA format alignments used for phylogenetic analyses