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.