Table 2. The effects of background selection on D. melanogaster autosomal and X chromosomal genes.

	Model 1	Model 2	Model 3	Model 4	Model 5
B values for autosomes
Effects of strongly selected sites	0.684	0.684	0.665	0.680	0.638
	0.687	0.687	0.665	0.690	0.606
Effects of weakly selected noncoding sites	0.814	0.815	0.839	0.791	0.831
	0.806	0.806	0.839	0.757	0.867
Effects of all sites	0.556	0.557	0.558	0.538	0.530
	0.554	0.554	0.558	0.523	0.525
B values for X chromosome
Effects of strongly selected sites	0.789	0.789	0.775	0.788	0.752
	0.790	0.790	0.775	0.790	0.746
Effects of weakly selected noncoding sites	0.878	0.878	0.896	0.859	0.895
	0.876	0.876	0.896	0.851	0.904
Effects of all sites	0.693	0.693	0.695	0.677	0.673
	0.692	0.692	0.695	0.672	0.675
Adjusted X/A diversity ratio for all sites	0.935	0.935	0.934	0.944	0.952
	0.937	0.937	0.934	0.964	0.964

See Table 1 for the meaning of the different models. B is the ratio of the effective population size under background selection to the neutral value. The parameters of the gamma distributions of selection coefficients are a₁ = a₂ = 0.3, $\stackrel{-}{s}$₁ = $\stackrel{-}{s}$₂ = 2.5 × 10⁻³ (strongly selected sites) and a₃ = 0.3, $\stackrel{-}{s}$₃ = 8 × 10⁻⁶ (weakly selected sites). Results for the dominance coefficient h = 0.5 are shown in the top part of each row, and results for h = 0.2 are shown in the bottom part. A diploid deleterious mutation rate of U_D = 0.24 is assumed for both the autosomal arm (A) and the X chromosome. Map lengths of 0.5 and 0.6 M in female meiosis are assumed for A and X, respectively. The number of coding sequences in an arm (n_g) is 2800; the length of a coding sequence is 1500 bp. The noncoding regions between coding sequences are divided into 36 strongly selected sequences of length 39 bp and 37 weakly selected sequences of length 115 bp.