Table 2 . Definitions and symbols used in the methods and analyses.

Symbol	Definitions	Equation
δw	Estimate of the average nucleotide substitution divergence at polarized sites in a window, weighted by (allele) sampling depth.	(1)
πw	Estimate of the expected heterozygosity for nucleotide substitutions per site in a random sample from a randomly mating population. Weighting is by allele sampling depth and the standard bias correction is applied to each.	(2)
ρ	Population recombination parameter: ρ = 2Nr/bp for both autosomes and the X chromosome. For local genomic estimates of 2Nr/bp, $\widehat{\rho }$ is determined via statistical fitting to an approximation of the equilibrium between mutation to selectively equivalent alleles and genetic drift in a single, stable outbreeding population (McVean et al. 2004).
rω	Linkage disequilibrium oriented by the allele frequencies. Let p and q be the frequencies of the more common alleles at two loci, p > 1/2 and q > 1/2 (Langley and Crow 1974). And let g be the frequency of the gametotype composed of those two more common alleles. Then ${\mathbf{r}}_{\omega }=\left(g-pq\right)/\sqrt{p\left(1-p\right)q\left(1-q\right)}$.
HKAl	Hudson–Kreitman–Aguadé-like test statistic reflecting the significance of the deviation of the observed proportions of segregating and diverged sites in a window to the chromosome-arm averages under a model for the equilibrium between mutation to selectively equivalent alleles and genetic drift in a single stable outbreeding population (Hudson et al. 1987; Ford and Aquadro 1996).	(3)
TsD	A test statistic for either an excess (+) or a deficiency (−) of common alleles compared to the predictions of a model for the equilibrium between mutation to selectively equivalent alleles and genetic drift in a single stable outbreeding population (Tajima 1989).	(4)
χ[log(p)]	“+” or “−” the log10 of the P-value for a test statistics such as HKAl and TsD. The sign reflects the sign of the deviation from expectation: the number of segregating sites in the case of HKAl and the frequency spectrum for TsD.
π/min(divl, divg)	A simple metric of reduced diversity in a window where the denominator is the lesser of local divergence and global average divergence.
s	The difference in relative fitness of homozygotes for alternative alleles at a locus. The heterozygote’s relative fitness is 1 − hs, where h is the dominance coefficient.
r	The rate of recombination between two closely linked genomic sites, usually adjacent base pairs unless otherwise indicated.
$\widehat{r}$	Estimated rate of recombination per base pair based on local smoothing of incremental change in the standard genetic map.
ρS	Spearman’s rank correlation coefficient.