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.