Fixed synonymous mutations
| Ancestral codon | Derived codon | sim | mau | sec |
|---|---|---|---|---|
| Preferred | Unpreferred | 0 | 2 | 17 |
| Unpreferred | Unpreferred | 1 | 2 | 5 |
| Preferred | Preferred | 1 | 0 | 1 |
| Unpreferred | Preferred | 0 | 3 | 6 |
The ancestral state at each site was inferred by parsimony, using D. melanogaster sequence(s) as an outgroup. Fixed differences are those base positions where a derived base is unique to just one of the three D. simulans complex species. In other words, the inferred derived state is fixed in only one species, while only the ancestral state is found in the others (including D. melanogaster). The ancestral and derived states were classified as preferred or unpreferred on the basis of synonymous codon preferences established by Akashi (1995) for D. melanogaster and its closest relatives.