X chromosomes show relaxed selection and complete somatic dosage compensation across Timema stick insect species

Abstract

Sex chromosomes have evolved repeatedly across the tree of life. As they are present in different copy numbers in males and females, they are expected to experience different selection pressures than the autosomes, with consequences including a faster rate of evolution, increased accumulation of sexually antagonistic alleles and the evolution of dosage compensation. Whether these consequences are general or linked to idiosyncrasies of specific taxa is not clear as relatively few taxa have been studied thus far. Here, we use whole-genome sequencing to identify and characterize the evolution of the X chromosome in five species of Timema stick insects with XX:X0 sex determination. The X chromosome had a similar size (approximately 12% of the genome) and gene content across all five species, suggesting that the X chromosome originated prior to the diversification of the genus. Genes on the X showed evidence of relaxed selection (elevated dN/dS) and a slower evolutionary rate (dN + dS) than genes on the autosomes, likely due to sex-biased mutation rates. Genes on the X also showed almost complete dosage compensation in somatic tissues (heads and legs), but dosage compensation was absent in the reproductive tracts. Contrary to prediction, sex-biased genes showed little enrichment on the X, suggesting that the advantage X-linkage provides to the accumulation of sexually antagonistic alleles is weak. Overall, we found the consequences of X-linkage on gene sequences and expression to be similar across Timema species, showing the characteristics of the X chromosome are surprisingly consistent over 30 million years of evolution.

Keywords: insects; population genetics; sex chromosomes; sexual selection & conflicts.

FIGURE 1

The X chromosome is conserved between Timema species. (a) Venn‐diagrams showing the number of shared X‐linked orthologs between species. (b) Number of shared orthologs (expected, maximum possible). The observed amount of overlap was much greater than expected in all comparisons (FDR <6.863 × 10⁻³¹⁶). Species names are abbreviated as Tbi = T. bartmani, Tce = T. cristinae, Tcm = T. californicum, Tps = T. poppensis and Tpa = T. podura. [Correction added on 12 August 2022, after first online publication: Figure 1 has been replaced.]

FIGURE 2

Genetic variation on the X chromosome is lower than expected. (a) Ratio of heterozygosity on the X and autosomes in 3–5 females per species. (b) Ratio of pairwise nucleotide diversity (π) on the X and autosomes. Species names are abbreviated as Tbi = T. bartmani, Tce = T. cristinae, Tcm = T. californicum, Tps = T. poppensis, and Tpa = T. podura. The dotted lines indicate the neutral expectation in a population with a balanced sex ratio.

FIGURE 3

Sequence evolution on the X and autosomes. (a) Average dN/dS across genes. Error bars indicate standard error. Asterisks indicate the significance (FDR) of Wilcoxon tests (***<0.001, **<0.01, *<0.05). (b) Proportion of positively selected genes. Positively selected genes were not enriched on the X chromosome (Fisher's exact test p value = 0.50). Species names are abbreviated as Tbi = T. bartmani, Tce = T. cristinae, Tcm = T. californicum, Tps = T. poppensis and Tpa = T. podura.

FIGURE 4

Gene expression on the X and autosomes in heads, legs and reproductive tracts. (a) Average expression levels in males and females on the X and autosomes (b) Log2 of male to female expression ratio for the X and autosomes. Dashed lines represent a two‐fold reduction in expression in males (as expected if there was no dosage compensation). Species names are abbreviated as Tbi = T. bartmani, Tce = T. cristinae, Tcm = T. californicum, Tps = T. poppensis and Tpa = T. podura.

FIGURE 5

Ratio of male and female gene expression on the X (orange) and autosomes (black) in heads, legs and reproductive tracts. Species names are abbreviated as Tbi = T. bartmani, Tce = T. cristinae, Tcm = T. californicum, Tps = T. poppensis and Tpa = T. podura.

FIGURE 6

Proportion of female‐ and male‐ biased genes on the X and autosomes in reproductive tract, head and leg samples. Note the scale changes between tissue‐types. Asterisks indicate the significance level (FDR) of Fisher's exact tests (***<0.001, **<0.01, *<0.05). Species names are abbreviated as Tbi = T. bartmani, Tce = T. cristinae, Tcm = T. californicum, Tps = T. poppensis and Tpa = T. podura.