TABLE 4

Genes of gametogenesis showing evidence of positive selection under the site (M8 vs. M7) and/or branch-site models

GeneSymbolChromosomeModelaP-valuebωc
FBgn0000320eya2LBS (yakere)0.00299.56
FBgn0002780mod3RBS (yakere)0.00493.02
FBgn0003731Egfr2RBS (yakere)0.004922.35
FBgn0003950uncXM8 vs. M7, BS (yakere)0.004 4E-42.139 999
FBgn0011207pelo2LM8 vs. M70.00361.55
FBgn0011219Bsg2LM8 vs. M7, BS (sec, simsecmel)0.0045 1.96E-13 1.41E-82.01 999 62.94
FBgn0011230poe2LBS (sim)6.63E-10999
FBgn0011569can3LM8 vs. M702.05
FBgn0011823Pen2LBS (sim, yakere)1.30E-5 0.006176.18 3.28
FBgn0015933didum2RBS (sim)2.19E-6999
FBgn0020381DreddXBS (sim, simsecmel)1.40E-8 0.0073999 3.21
FBgn0026404Nc3LM8 vs. M7, BS (sec)0.0012 1.25E-41.28 578
FBgn0028734Fmr13RM8 vs. M70.00341.79
FBgn0028974xmas-2XBS (sim)9.13E-4999
FBgn0034667comr2RM8 vs. M70.004413.79
FBgn0051711CG317112LBS (sim, simsecmel)8.98E-10 1.2E-4161.16 22.60
  • BS, branch site. P threshold value is Bonferroni corrected. Genes involved in both spermatogenesis and oogenesis are underlined.

  • a Model under which ω > 1 was inferred. Under M8, a single distribution of ω (following a β-distribution) is assumed for the entire tree. “sim,” “sec,” “simsecmel,” and “yakere” refer to a model under which a class of sites with ω > 1 is assigned to the simulans, sechellia, simulans–sechellia–melanogaster, and yakuba–erecta lineages, respectively, but not to any other lineage.

  • b P-value for the test(s) indicated under “Model,” with M7 used as the null for M8 and a model disallowing ω > 1 on any lineage used as the null for the lineage-specific positive-selection model. Where two or more values are indicated, the order is the M8 vs. M7 comparison and/or the branch-site test(s) with the order terminal branch (i.e., sim, sec, or mel) first and the internal branch (i.e., simsecmel or yakere) second.

  • c ω estimated under the appropriate model.