Analysis of evolution of expression plasticity
To test for the evolution of plasticity in gene expression responses, we
examined the subset of transcripts with significant interaction effects
in our differential expression analysis (see above). We grouped genes
with significant interaction effects into categories for the evolution
of plasticity outlined by Renn and Schumer (2013) based on post
hoc differences between rearing environments within a population
(p<0.05): (1) Assimilated: plasticity in the ancestral
high-predation population but a loss of plasticity in the derived
low-predation population; (2) Accommodated: a change in the degree, but
not the direction, of plasticity in the derived as compared to the
ancestral population; (3) Reversed: opposing directions of plasticity in
high- versus low-predation populations; (4) Evolved plastic: no
plasticity in the ancestral high-predation population but an emergence
of plasticity in the derived low-predation population; and (5)
Unclassified: genes that had a significant main interaction effect but
no significant post hoc rearing differences and could therefore
not be unambiguously classified into one of the other categories. All
statistical tests and data visualization were performed in R (version
3.5.1; The R Foundation for Statistical Computing).