Table 2.
Proportion of adaptively evolving genes identified by two tests (P2 < 0.05, i.e. P < 0.224).
| MK | MK-PAML overlap | PAML | Total | |
|---|---|---|---|---|
| Drosophila | ||||
| No. of genes | 824 | 91d | 353 | 5425 |
| Expected overlap | / | 53.6 | / | / |
| Proportion of adaptive changes by MKa | 0.69 | 0.67 | 0.32 | 0.26 |
| No. of adaptive sites per gene by MK (A1) | 14.98 | 19.94 | 5.71 | 2.84 |
| No. of adaptive sites per gene by PAML (A2)b | 10.93 | 14.65 | 9.27 | 5.71 |
| No. of adaptive sites per gene by PAML (A2′)c | 3.19 | 8.62 | 6.24 | 1.79 |
| Arabidopsis | ||||
| No. of genes | 1014 | 119e | 1172 | 12975 |
| Expected overlap | / | 91.6 | / | / |
| Proportion of adaptive changes by MK | 0.69 | 0.67 | 0.06 | 0.04 |
| No. of adaptive sites per gene by MK (A1) | 19.36 | 28.98 | 1.97 | 0.84 |
| No. of adaptive sites per gene by PAML (A2) | 14.24 | 20.36 | 12.74 | 10.15 |
| No. of adaptive sites per gene by PAML (A2′) | 3.59 | 11.51 | 8.13 | 2.44 |
aProportion of adaptive changes is done using Shapiro et al. (2007)’s method of correction [3]. bA2 is based on the PAML-M2a model. cA2′ is based on the PAML-BEB model. dP < 10–7 by Fisher's exact test, given 53.6 as the expected value. eP < 0.002 by Fisher's exact test, given 91.6 as the expected value.