Differential gene expression and GO term enrichment
Before testing our specific hypotheses, we first summarized differential
expression patterns in both datasets. In the Aripo drainage, 766 genes
were differentially expressed (DE) between high- and low-predation
populations, 1,118 genes were differentially expressed between pred- and
pred+ fish, and 825 genes had interaction effects (Fig. 2; Table S2). DE
genes were enriched for GO categories including DNA integration, immune
function, and morphogenesis. In the Quare drainage, 3,831 genes were
differentially expressed between high- and low-predation populations,
791 genes were differentially expressed between pred- and pred+ fish,
and 586 genes had interaction effects (Fig. 2; Table S3). DE genes were
enriched for GO categories including immune function, developmental
processes, and neurogenesis. Complete results of GO enrichment analyses
for population of origin, rearing, and interaction effects are in the
Supplemental Materials (Tables S4 & S5).
Given the marked difference in the total number of DE genes between
datasets, we looked for evidence that this pattern might arise from
technical variation or expression bias. While we cannot rule out some
influence of technical variation, we found no evidence for differences
in sequence quality, read alignment statistics, or variance in
transcript abundance to suggest that variation in the number of DE
transcripts between drainages was of technical origin. Nor did we find
evidence that identification of DE transcripts was biased by transcript
expression level: mean and median gene expression were significantly
lower in DE (population, rearing, and/or interaction effects) as
compared to non-DE transcripts in both the Aripo (Fig. S1; mean: DE=263,
non-DE=344, p<0.0001; median: DE=65, non-DE=107,
p<0.0001), and Quare (Fig. S1; mean: DE=264, non-DE=334,
p<0.0001; median: DE=86, non-DE=101, p<0.0001)
datasets. This suggests that identification of DE transcripts was not
simply a side effect of relatively greater expression of these
transcripts.