Gene and genome duplication are the major sources of biological innovations in 
plants and animals. Functional and transcriptional divergence between the copies 
after gene duplication has been considered the main driver of innovations . 
However, here we show that increased phenotypic plasticity after duplication 
plays a more major role than thought before in the origin of adaptations. We 
perform an exhaustive analysis of the transcriptional alterations of duplicated 
genes in the unicellular eukaryote Saccharomyces cerevisiae when challenged with 
five different environmental stresses. Analysis of the transcriptomes of yeast 
shows that gene duplication increases the transcriptional response to 
environmental changes, with duplicated genes exhibiting signatures of adaptive 
transcriptional patterns in response to stress. The mechanism of duplication 
matters, with whole-genome duplicates being more transcriptionally altered than 
small-scale duplicates. The predominant transcriptional pattern follows the 
classic theory of evolution by gene duplication; with one gene copy remaining 
unaltered under stress, while its sister copy presents large transcriptional 
plasticity and a prominent role in adaptation. Moreover, we find additional 
transcriptional profiles that are suggestive of neo- and subfunctionalization of 
duplicate gene copies. These patterns are strongly correlated with the 
functional dependencies and sequence divergence profiles of gene copies. We show 
that, unlike singletons, duplicates respond more specifically to stress, 
supporting the role of natural selection in the transcriptional plasticity of 
duplicates. Our results reveal the underlying transcriptional complexity of 
duplicated genes and its role in the origin of adaptations.