Hormones are synthesized very early in development and essential for genetic regulation even in the blastocyste (approximately 40 cell stage). But yes, the hormones are encoded by genes, and as I pointed out, many other gene products (i.e. transcription factors) are important epigenetic modulators as well. Also, as you pointed out, molecules (hormones, transcription factors, mRNAs ect...) from the mother also mediate many effects on the offsprings genome. Any of these could influence the visually apparent phenotypes such as color and pattern. Thanks for the input.
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steve