Figure 2.

Comparing polygenic signals of SA polymorphism on the X chromosome and autosomes. (a) Distribution of the ratio of mean ${\hat{F}}_{\mathrm{ST}}$ ($\overline{{\hat{F}}_{\mathrm{ST}}^X}/\overline{{\hat{F}}_{\mathrm{ST}}^A}$) based on 1000 bootstrap replicates for each of our three classes of data: simulated data from the theoretical null distribution (top), permuted data (middle) and observed data (bottom), illustrating the elevation in X-linked relative to autosomal ${\hat{F}}_{\mathrm{ST}}$ (i.e. $\overline{{\hat{F}}_{\mathrm{ST}}^X}/\overline{{\hat{F}}_{\mathrm{ST}}^A}\gg 1$), even in the absence of SA polymorphism (i.e. in simulated and permuted data). (b) Distribution of the ratio of estimated X-linked to autosomal inflation in ${\hat{F}}_{\mathrm{ST}}$ ($f_X^{\mathrm{sel}}$ and $f_A^{\mathrm{sel}}$), across 1000 bootstrap replicates. The top panel uses observed and simulated data to estimate $f_X^{\mathrm{sel}}$ and $f_A^{\mathrm{sel}}$, while the bottom panel uses observed and permuted data to estimate $f_X^{\mathrm{sel}}$ and $f_A^{\mathrm{sel}}$. The dashed vertical line shows the theoretically predicted 9/4 X-to-autosome ratio when randomly distributed balanced SA polymorphisms account for the inflations of F_ST on each chromosome type. In both panels, we used a set of LD-pruned sites, rather than the full data, to avoid biases arising from differences in the extent of hitchhiking between autosomes and the X (see Methods). (Online version in colour.)