Table 3.

Proportion of amino-acid substitutions driven by positive selection (α)

	D. pseudoobscura		D. affinis	ancestor
method	all sites	excluding singletons	excluding singletons	excluding singletons
	α (95% CI)	α (95% CI)	α (95% CI)	α (95% CI)
Fay et al.	0.41 (0.19, 0.56)	0.61 (0.45, 0.74)	0.39 (-0.08, 0.69)	0.59 (0.25, 0.78)
Smith & Eyre-Walker	0.12 (-0.22, 0.38)	0.48 (0.28, 0.66)	0.32 (-0.17, 0.63)	0.54 (0.20, 0.75)
Bierne & Eyre-Walker	0.17 (-0.11, 0.36)	0.44 (0.19, 0.61)	0.41 (0.06, 0.61)	0.61 (0.28, 0.80)

Note – α is calculated using either D. pseudoobscura, D. affinis or a reconstructed ancestral sequence as the outgroup.