TABLE 2

McDonald–Kreitman tests for positive selection along the simulans lineage

GenesNaNo. significantP (≤5%)Median NIP (=1)NbPooled NIThree-way P
Ors276<10−50.610.04540.540.01
Grs3611<10−120.420.0002610.38
Ors + Grsc61100.00030.48<10−51150.470.78
Genomec32228820.00000.550.000010,1510.46
  • The results of polarized McDonald–Kreitman (pMK) tests on individual genes is presented in the first five columns, which show the number of genes tested, the number of significant tests, the P-value from a test of whether this number exceeded 5% of genes tested, the median neutrality index (NI) of genes tested, and the P-value from a test of whether the median was significantly less than one. Results from a single pMK test on each pooled gene set are presented in the final three columns, which show the number of genes included in the pool, the NI of the pooled table, and the P-value from a three-way contingency test comparing the pooled NI for one gene set to that from the subsequent gene set (Ors compared to Grs and Ors + Grs compared to the whole genome set).

  • a Genes with any MK table marginal sum <6 were excluded from tests on individual genes.

  • b No genes were excluded from the pooled tests.

  • c Substitutions were polarized using an ancestor inferred via parsimony based on melanogaster and yakuba orthologs only.