Fig. 1.—

Experimental design. An illustration of the factors and their levels included in our experiment. In total we generated 84 RNA-seq libraries (6 fish each from 14 flasks), each using mRNA isolated from the entire gut—posterior esophagus to anus—of individual fish. The two stickleback lines (“OC” and “FW“) were derived from natural Alaskan populations, as indicated. Two OC families and three FW families (FW family 3 not shown, but referenced by brackets), were represented in the study. Note that for one OC family and one FW family, conventional and germ-free treatments were duplicated to examine housing (“flask“) effects.