Daniel Winston Bellott

Research Scientist

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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 31, 210-198 (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