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

Abstract

Different ancestral autosomes independently evolved into sex chromosomes in snakes, birds, and mammals. In snakes and birds, females are ZW and males are ZZ; in mammals, females are XX and males are XY. Although X and Z Chromosomes retain nearly all ancestral genes, sex-specific W and Y Chromosomes suffered extensive genetic decay. In both birds and mammals, the genes that survived on sex-specific chromosomes are enriched for broadly expressed, dosage-sensitive regulators of gene expression, subject to strong purifying selection. To gain deeper insight into the processes that govern survival on sex-specific chromosomes, we carried out a meta-analysis of survival across 41 species-three snakes, 24 birds, and 14 mammals-doubling the number of ancestral genes under investigation and increasing our power to detect enrichments among survivors relative to nonsurvivors. Of 2564 ancestral genes, representing an eighth of the ancestral amniote genome, only 324 survive on present-day sex-specific chromosomes. Survivors are enriched for dosage-sensitive developmental processes, particularly development of neural crest-derived structures, such as the face. However, there was no enrichment for expression in sex-specific tissues, involvement in sex determination or gonadogenesis pathways, or conserved sex-biased expression. Broad expression and dosage sensitivity contributed independently to gene survival, suggesting that pleiotropy imposes additional constraints on the evolution of dosage compensation. We propose that maintaining the viability of the heterogametic sex drove gene survival on amniote sex-specific chromosomes, and that subtle modulation of the expression of survivor genes and their autosomal orthologs has disproportionately large effects on development and disease.

Figure 1.

Ancestral Z–W gene pairs from three caenophidian species. (A) Phylogenetic tree of selected snake species included in this study, with branches colored to highlight relationships among species. Humans diverged from snakes 312 Myr ago. Chicken and green anole lizard diverged from snakes 280 and 167 Myr ago, respectively, and were used to resolve gene gains and losses between snakes and mammals. Snakes diverged from each other starting about 90.8 Myr ago (green). Boas (red) and pythons (blue) have independently evolved homomorphic XY sex chromosomes. Caenophidian snakes (purple) share a common ZW sex chromosome system, orthologous to the python XY. (B) Euler diagram showing overlapping sets of ancestral Z–W gene pairs identified in five-pacer viper (light purple), pygmy rattlesnake (medium purple), and mountain garter snake (dark purple) as subsets of all 1300 ancestral Z genes (green). See also Supplemental Table S3.

Figure 2.

Factors in the survival of caenophidian Z–W gene pairs. Violin plots, with the median (white circle) and interquartile range (white bar) indicated, compare annotations of ancestral Z–W gene pairs identified in three species (purple) to annotations for the remainder of ancestral Z genes (green). (*) P < 0.05; (**) P < 0.01; (***) P < 0.001. P-values were obtained using one-tailed Wilcoxon rank-sum tests (Methods; Supplemental Table S24). Human orthologs of ancestral caenophidian Z–W gene pairs have greater probability of haploinsufficiency (A), deletion intolerance scores (B), duplication intolerance scores (C), and mean probabilities of conserved targeting (PCT) (D) than other ancestral Z genes. Orthologs of ancestral Z–W gene pairs are more broadly expressed than orthologs of other ancestral Z genes in a panel of seven adult eastern garter snake tissues (E). Orthologs of ancestral Z–W gene pairs are more highly expressed than orthologs of other ancestral Z genes in chicken blastocysts (F) and in human preimplantaion embryos (G). Orthologs of ancestral Z–W gene pairs have reduced d_N/d_S ratios compared to orthologs of other ancestral Z genes in alignments between tiger snake and green anole lizard orthologs (H).

Figure 3.

Regulatory annotations of ancestral caenophidian Z–W gene pairs. The Euler diagram depicts regulatory functions predicted for genes from selected Z–W gene pairs on the basis of UniProt annotations of human orthologs. See also Supplemental Table S8.

Figure 4.

Survivors are not ancestrally specialized for expression in reproductive tract tissues. Coefficients for testis- and ovary-specific expression (circles) and 95% confidence intervals (bars) from logistic regression models of gene survival on sex-specific chromosomes in mammals (blue), birds (pink), and snakes (purple), conditional on breadth of expression. (ns) P > 0.05. After controlling for expression breadth, the regression coefficient is not significantly different from 0 for any tissue from any species.

Figure 5.

Dosage sensitivity and broad expression make independent contributions to survival. A statistical summary of survival factors from 2564 genes based on principal component axis one (PC1) and axis two (PC2). Points represent individual genes, colored by their survival fraction from orange (no survival) to red (survival in all possible lineages) (Methods; Supplemental Table S7). Arrows show the contribution of each factor to the variation in survival of ancestral genes on sex-specific chromosomes. Dosage sensitivity and breadth of expression make roughly orthogonal contributions, whereas strength of purifying selection is closely aligned with survival.