Parallelism in gene expression patterns across drainages
To test for shared mechanisms mediating parallel phenotypic adaptation
across drainages, we asked whether differentially expressed genes within
drainages were overlapping in identity and expression direction between
drainages. Of the genes that diverged between high- and low-predation
populations within a drainage (i.e., population main effect), 174 were
overlapping between drainages (Table S6), more than expected by chance
(χ2=8.02, p=0.0046). However, the direction of
expression divergence among these overlapping genes was not associated
across the two drainages (χ2=0.16, p=0.686): 91 genes
had concordant expression changes and 83 genes had non-concordant
expression changes between drainages (Fig. 5). To control for the
influence of false negatives on our conclusions, we repeated this
comparison at less stringent significance cut-offs. At a p=0.1, we found
marginally significant overlap in gene identify (347 overlapping genes;
χ2=3.38, p=0.06), but no association in expression
direction (χ2=0.65, p=0.42), and at p=0.2 we found no
significant overlap or association in expression direction. As a final,
more conservative test, we compared the subset of genes with strong
evidence for adaptive population divergence due to selection by
restricting our comparison to population DE genes for which
PST > FST. We found 534
genes (mean PST = 0.38, FST = 0.225) in
the Aripo and 1163 genes (mean PST = 0.496,
FST = 0.340) in the Quare drainage that met this
criterion. Of these, 53 were overlapping between drainages, again more
than expected by chance (χ2=12.7, p=0.0004), but
without any association in expression direction (28 genes had concordant
expression changes and 25 genes had non-concordant expression changes
between drainages). PST values for all genes are in
Table S8.
Of the genes that showed significant expression plasticity (i.e. main
effect of rearing), 64 transcripts were overlapping between drainages
(Table S7), more than expected by chance (χ2=14.06,
p=0.0001). Of these 43 had expression changes in the same direction and
21 had expression changes in opposite directions between drainages, a
significant association between drainages in the direction of expression
plasticity associated with rearing environment
(χ2=7.56, p=0.006) (Fig. 5). At less stringent p-value
cut-offs for differential expression we found no more overlap in gene
identity than expected by chance (p<0.1: 108 overlapping
genes; χ2=0.05, p=0.81; p<0.2: 276
overlapping genes; χ2=1.36, p=0.24).