Table 7.

ineage-Specific Estimates of α, the Fraction of Adaptive Amino Acid Substitutions (and 95% confidence intervals), Using Drosophila affinis or D. athabasca as a Second Outgroup

Method	D. pseudoobscura	D. miranda
All sites
αa	0.66 (0.55–0.74)	0.57 (0.38–0.70)
αb	0.57 (0.43–0.67)	0.45 (0.23–0.61)
αc	0.56 (0.43–0.66)	0.49 (0.29–0.64)
f > 0.1d
αa	0.72 (0.63–0.80)	0.70 (0.55–0.80)
αb	0.68 (0.58–0.76)	0.69 (0.54–0.79)
αc	0.65 (0.52–0.75)	0.69 (0.53–0.80)

^aFraction of adaptive amino acid mutations; estimation procedure of Fay et al. (2001).

^bFraction of adaptive amino acid mutations; estimation procedure of Smith and Eyre-Walker (2002).

^cFraction of adaptive amino acid mutations; estimation procedure of Bierne and Eyre-Walker (2004).

^dFraction of adaptive amino acid mutations ignoring polymorphism at a frequency < 0.1.