TABLE 4.

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

Gene	Symbol	Chromosome	Modela	P-valueb	ωc
FBgn0000320	eya	2L	BS (yakere)	0.0029	9.56
FBgn0002780	mod	3R	BS (yakere)	0.0049	3.02
FBgn0003731	Egfr	2R	BS (yakere)	0.0049	22.35
FBgn0003950	unc	X	M8 vs. M7, BS (yakere)	0.004 4E-4	2.139 999
FBgn0011207	pelo	2L	M8 vs. M7	0.0036	1.55
FBgn0011219	Bsg	2L	M8 vs. M7, BS (sec, simsecmel)	0.0045 1.96E-13 1.41E-8	2.01 999 62.94
FBgn0011230	poe	2L	BS (sim)	6.63E-10	999
FBgn0011569	can	3L	M8 vs. M7	0	2.05
FBgn0011823	Pen	2L	BS (sim, yakere)	1.30E-5 0.006	176.18 3.28
FBgn0015933	didum	2R	BS (sim)	2.19E-6	999
FBgn0020381	Dredd	X	BS (sim, simsecmel)	1.40E-8 0.0073	999 3.21
FBgn0026404	Nc	3L	M8 vs. M7, BS (sec)	0.0012 1.25E-4	1.28 578
FBgn0028734	Fmr1	3R	M8 vs. M7	0.0034	1.79
FBgn0028974	xmas-2	X	BS (sim)	9.13E-4	999
FBgn0034667	comr	2R	M8 vs. M7	0.0044	13.79
FBgn0051711	CG31711	2L	BS (sim, simsecmel)	8.98E-10 1.2E-4	161.16 22.60

BS, branch site. P threshold value is Bonferroni corrected. Genes involved in both spermatogenesis and oogenesis are underlined.

^aModel 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.

^bP-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.

^cω estimated under the appropriate model.