Table 5.

Genes under positive selection (using FDR < 0.05) across the whole phylogeny (5 taxa tree)

OrthoDB group id a	Gene b	Classification sites c	Total ratio d	Likelihood	p-value q-value e	BH-corrected sites f	Positively selected
EOG6KKWHX	argonaute-2	Small RNA regulatory pathway members	810	31.839	0.00000	0.00001	22W, 25N, 41S, 55S, 56N, 57S, 69L, 73D, 85D, 95I, 329S, 346N, 450F, 692L, 693R
EOG66DJHX-2	dscam	Immunoglobulin	489	44.704	0.00000	0.00000	2M, 4A, 13A, 20R, 24I, 26T, 28P, 31K, 33I, 34H, 451G, 452G
EOG6QRFKP	CLIP-C1B	CLIP serine protease	330	13.650	0.00109	0.03063	14L, 15Q, 66L, 72M, 118A, 132L, 195Q, 313N
EOG6VX0M3	ark	Caspase	1128	17.871	0.00013	0.00619	495S, 629T, 904G, 954T, 988F
EOG64B8H5	CLIP-A10	CLIP serine protease	792	14.259	0.00080	0.02824	1I, 3H, 20V, 318T

^aGroup identifiers are from OrthoDB 6 (http://cegg.unige.ch/orthodb6).

^bUnless otherwise specified, gene names are taken from the A. mellifera or D. melanogaster orthologs.

^cTotal number of codons in the alignment after trimming with Gblocks.

^dComparison of model M7 versus M8.

^eMultiple test correction by the method of Benjamini and Hochberg to control the false discovery rate (only groups where FDR < 0.05 are shown).

^fSites are classified as under positive selection if the Bayesian posterior probability > 0.75 (>0.95 in bold italic). Sites where ${\rm E}\left[\omega \right]-\sqrt{\mathrm{V}\mathrm{a}\mathrm{r}\left(\omega \right)}>1.25$ are Italic.

Reference sequence taken from A. mellifera.