Drivers of adaptive evolution at the co-expression module level
At the module level across both gardens, we noted a wide range of
eigengene correlations with ancestry, ranging from r = -0.56 to
0.35 at the warm garden and from r = -0.32 to 0.41 at the cold
garden (Table S3). Compared to the association with ancestry, eigengene
expression was generally more strongly related to survival and ranged
from -0.50 to 0.72 at both gardens (Table S3). At the warm garden, for
example, the ME11 module exhibited a significant (p <
0.05) negative association with ancestry, as well as with survival
(Table 2), however the association with ancestry was not significant
after multiple test corrections. Similarly at the cold garden, the ME13
module exhibited a significant (p < 0.05) but positive
association with ancestry and survival, however the association with
ancestry was again not significant after multiple test corrections
(Table 2). Similar to the case at the per-transcript level, the results
at the module level do not support H3.
GO enrichment analysis for modules exhibiting at least one of the
following - Q ST category enrichment,Q ST category depletion, or strong correlation
with ancestry and/or survival -identified a wide range of functional
groups across both gardens (Table 2, Table S2). Across both gardens,Q ST category enrichment modules were
predominantly associated with GO terms and genes related to stress
response, cell wall modulation and response to light stimuli. In
contrast, Q ST category depleted modules across
gardens were predominantly represented by developmental and metabolic
processes. Functional terms associated with metabolic processes were
generally under-represented, and terms associated with response to
abiotic stress were generally over-represented in the modules strongly
associated with survival and ancestry at the warm garden (e.g., ME11
module), as well as at the cold garden (e.g., ME13 module). Across both
gardens, modules exhibiting the strongest association with survival
(i.e., the ME26 module at the cold garden and ME19 at the warm garden)
were primarily associated with GO terms related to glutathione
transferase, detoxification and response to abiotic stimuli.