Table 3.
MK test for positive selection on MSL complex genes
| MSL complex protein-encoding gene | Observed Sp | Observed Rp | Observed Sf | Observed Rf | G value | P value |
|---|---|---|---|---|---|---|
| msl1 | ||||||
| Pooled | 54 | 41 | 56 | 78 | 5.025 | 0.025 |
| D. melanogaster | 18 | 10 | 24 | 53 | 9.097 | 0.0026 |
| D. simulans | 36 | 32 | 23 | 22 | 0.036 | 0.85 |
| msl2* | ||||||
| Pooled | 83 | 40 | 51 | 63 | 12.47 | 0.00041 |
| D. melanogaster | 36 | 22 | 24 | 41 | 7.743 | 0.0054 |
| D. simulans | 47 | 18 | 22 | 18 | 3.201 | 0.074 |
| msl3 | ||||||
| Pooled | 49 | 10 | 22 | 19 | 9.913 | 0.00164 |
| D. melanogaster | 24 | 3 | 11 | 15 | 13.23 | 0.00028 |
| D. simulans | 24 | 6 | 7 | 3 | 0.379 | 0.54 |
| mof | ||||||
| Pooled | 84 | 19 | 48 | 37 | 13.97 | 0.00019 |
| D. melanogaster | 30 | 7 | 25 | 23 | 7.86 | 0.0051 |
| D. simulans | 55 | 12 | 19 | 13 | 5.531 | 0.012 |
| mle | ||||||
| Pooled | 50 | 35 | 75 | 48 | 0.096 | 0.76 |
| D. melanogaster | 14 | 16 | 37 | 24 | 1.562 | 0.21 |
| D. simulans | 36 | 19 | 29 | 21 | 0.608 | 0.44 |
We compared the ratio of replacement and synonymous changes that were polymorphic within the species (Rp:Sp) with the ratio of replacement and synonymous changes that were found fixed between the species (Rf:Sf). If no alteration in selective regimes occurred during evolution, we expect these ratios to be statistically indistinguishable. However, an excess of fixed replacement changes is a clear indication of positive selection. Pooled changes refer to all the polymorphism and fixed changes using both lineages. However, by using an outgroup species (D. yakuba), we can also make the same comparison, specific either to the D. melanogaster or D. simulans lineage.
*A region of 75 nucleotides was excluded from all msl2 analysis because of ambiguity in the alignment between D. simulans and D. melanogaster(the region corresponds to nucleotides 904–978 relative to D. melanogaster).