Table 2 Divergence between D. melanogaster and D. simulans at sites of divergence between D. yakuba and D. erecta.1
| Â | Synonymous | Nonsynonymous | ||||
|---|---|---|---|---|---|---|
| Â | Overall1 | Parallel2 | Overall3 | Coincident | ||
| Â | Â | Â | Â | Parallel4 | Divergent5 | |
| Â | Â | Â | Â | Â | Same site | Different site |
Pairs of nucleotides | Â | Â | Â | Â | Â | Â |
   AC | 0.028 | 0.040 | 0.0025 (9.2%) | 0.034 (110, 86.5%) | 0.011 (99, 28.7%) | 0.009 (119, 23.7%) |
   AG | 0.055 | 0.070 | 0.0056 (10.3%) | 0.053 (431, 75.3%) | 0.023 (141, 32.7%) | 0.020 (207, 28.8%) |
   AT | 0.035 | 0.047 | 0.0024 (6.7%) | 0.041 (119, 86.4%) | 0.014 (93, 28.9%) | 0.007 (74, 15.3%) |
   CG | 0.022 | 0.031 | 0.0033 (15.0%) | 0.036 (113, 114.9%) | 0.011 (88, 35.0%) | 0.010 (91, 31.2%) |
   CT | 0.060 | 0.068 | 0.0037 (6.2%) | 0.045 (152, 65.8%) | 0.020 (103, 29.6%) | 0.010 (98, 15.3%) |
   GT | 0.027 | 0.036 | 0.0020 (7.6%) | 0.032 (58, 88.1%) | 0.010 (83, 27.9%) | 0.010 (67, 27.2%) |
   Average | 0.038 | 0.049 | 0.0033 (8.6%) | 0.040 (983, 82.2%) | 0.015 (607, 30.5%) | 0.011 (656, 22.8%) |
Genes6 | Â | Â | Â | Â | Â | Â |
   Low d N | 0.035 | 0.048 | 0.0008 (2.3%) | 0.026 (97, 53.8%) | 0.006 (41, 13.6%) | 0.004 (33, 7.9%) |
   Intermediate d N | 0.038 | 0.048 | 0.0029 (7.4%) | 0.037 (319, 77.1%) | 0.012 (175, 25.4%) | 0.009 (182, 18.5%) |
   High d N | 0.041 | 0.051 | 0.0072 (17.5%) | 0.046 (567, 90.9%) | 0.019 (391, 37.5%) | 0.015 (441, 29.1%) |
Chemical distance between amino acids7 | Â | Â | Â | Â | Â | Â |
   1 | 0.038 | 0.049 | 0.0033 (8.6%) | 0.048 (349, 98.2%) | 0.008 (143, 16.7%) | 0.010 (160, 19.8%) |
   1.5 or 2 | 0.038 | 0.049 | 0.0033 (8.6%) | 0.037 (461, 75.7%) | 0.016 (300, 32.0%) | 0.011 (338, 21.8%) |
   2.5 or 3 | 0.038 | 0.049 | 0.0033 (8.6%) | 0.032 (173, 65.4%) | 0.019 (164, 39.3%) | 0.015 (158, 30.6%) |