Table 1.
Comparison of Different Methods for Calculation of α (%) for Nonsynonymous Substitutions
| Divergent Sites | Neutral Standard | Our Calculations |
Parsch Calculations |
||||
|---|---|---|---|---|---|---|---|
| Whole-Genome Data |
Parsch et al. (2010) Gene Subset |
Parsch et al. (2010) Gene Subset |
|||||
| Autosome | X-Linked | Autosome | X-Linked | Autosome | X-Linked | ||
| Dmela | Synonymous (4fold) sites | 39.0 (37.8 to 40.2) | 56.1 (53.8 to 58.3) | 43.7 (20.5 to 62.7) | 73.4 (65.5 to 79.7) | — | — |
| Dmela | 8–30 in intron ≤65 nt | 19.6 (16.7 to 22.1) | 40.4 (34.0 to 46.4) | 42.2 (−7.7 to 69.2) | 74.1 (50.5 to 85.3) | — | — |
| Dmel–Dsecb | Synonymous (4fold) sites | 49.4 (48.6 to 50.2) | 66.9 (65.4 to 68.3) | 48.8 (30.3 to 63.9) | 81.7 (76.8 to 85.8) | 49.0 | 74.3 |
| Dmel–Dsecb | 8–30 in intron ≤65 nt | 45.2 (43.8 to 46.7) | 63.1 (59.6 to 66.3) | 52.5 (27.0 to 69.0) | 80.7 (64.3 to 88.1) | 43.7 | 79.7 |
Note.—The method used in our analyses is marked in bold. Confidence intervals based on 1,000 bootstrap trials are shown in parentheses
aOnly differences fixed in the Drosophila melanogaster (Dmel) lineage are used.
bAll differences fixed between D. melanogaster (Dmel) and D. sechellia (Dsec) are used.