Appendix 3. Genes of the developing brain of O. taurus with the most divergent expression patterns between morphs and sexes.

Genes were filtered as follows: 1) genes were significantly differentially expressed in the brain relative to the ganglia (M > 0) or in the ganglia relative to the brain (M < 0) in at least one treatment category; 2) absolute difference in expression (M value) was greater than 0.75 when sneaker males were compared to both females and horned males. Shown are M values for genes fitting these criteria in brain-ganglia arrays for tissue from females, horned males and sneaker males. Gene annotation is according to (Kijimoto et al. 2009).

Gene	Female	Horned	Sneaker
glucose dehydrogenase	−1.7085	−1.52307	−0.5793
cuticle	1.294428	1.209115	−0.32958
cuticle	1.116113	0.964331	−0.17994
cuticle	0.78352	0.849632	−0.13251
cuticular proteinrr-2 family (agap001668-pa)	1.105493	0.744713	−0.02102
cuticle	1.196771	1.432571	0.042271
chromosome 1 open reading frame 151 protein	1.29145	1.870667	0.121638
fk506-binding protein	1.399322	1.190266	0.1529
lethalessential for lifel2efl	1.398837	1.168393	0.161068
cg33205-isoform f	1.263757	1.852392	0.271971
three prime repair exonuclease	1.50772	1.158483	0.358808
troponin i	1.555121	2.373698	0.478137
troponin i	1.707857	2.417993	0.488219
troponin i	1.375902	2.190387	0.492013
cg5939-isoform a	1.541546	1.782398	0.60671
paramyosin	1.63252	1.800172	0.865861
cg5939-isoform a	1.759214	2.223351	0.972434
---NA---	2.475091	2.458102	1.307608
cuticle	2.97928	2.649723	1.759408
---NA---	1.064104	0.313479	1.858458
sonic hedgehog b	1.115904	1.253558	2.181145
odorant binding protein (agap011367-pa)	1.667497	1.117349	2.526956