Discussion
We examined transcriptomic differences associated with adaptive divergence and rearing environment across repeated, independent evolutionary lineages in guppies. Within lineages, we observed phenotypic plasticity in gene expression patterns as well as the evolution of gene expression plasticity itself. Plastic genes were more likely to exhibit population differences in expression, and these population differences were more likely to be in the opposite, rather than the same, direction as ancestral expression plasticity. Comparing across lineages, gene sets differentially expressed were largely non-overlapping (i.e. >75% non-shared identity) both for genes that diverged between populations and for plastic genes. Nonetheless, the small number of DE genes that did overlap between drainages was more than expected by chance for both population divergence and plasticity. Taken together our findings suggest that a small number of core genes may be repeatedly targeted during colonization of low-predation environments, but that largely non-shared, alternative transcriptional solutions are associated with parallel phenotypic adaptation across lineages.