Evidence for Faster X Chromosome Evolution in Spiders

In species with chromosomal sex determination, X chromosomes are predicted to evolve faster than autosomes because
of positive selection on recessive alleles or weak purifying selection. We investigated X chromosome evolution in
Stegodyphus spiders that differ in mating system, sex ratio, and population dynamics. We assigned scaffolds to X
chromosomes and autosomes using a novel method based on flow cytometry of sperm cells and reduced representation
sequencing. We estimated coding substitution patterns (dN/dS) in a subsocial outcrossing species (S. africanus) and its
social inbreeding and female-biased sister species (S. mimosarum), and found evidence for faster-X evolution in both
species. X chromosome-to-autosome diversity (piX/piA) ratios were estimated in multiple populations. The average piX/
piA estimates of S. africanus (0.57 [95% CI: 0.55–0.60]) was lower than the neutral expectation of 0.75, consistent with
more hitchhiking events on X-linked loci and/or a lower X chromosome mutation rate, and we provide evidence in
support of both. The social species S. mimosarum has a significantly higher piX/piA ratio (0.72 [95% CI: 0.65–0.79]) in
agreement with its female-biased sex ratio. Stegodyphus mimosarum also have different piX/piA estimates among
populations, which we interpret as evidence for recurrent founder events. Simulations show that recurrent founder
events are expected to decrease the piX/piA estimates in S. mimosarum, thus underestimating the true effect of femalebiased
sex ratios. Finally, we found lower synonymous divergence on X chromosomes in both species, and the male-tofemale
substitution ratio to be higher than 1, indicating a higher mutation rate in males.