Gene duplication generates new genetic material, which has been shown to lead to 
major innovations in unicellular and multicellular organisms. A whole-genome 
duplication occurred in the ancestor of Saccharomyces yeast species but 92% of 
duplicates returned to single-copy genes shortly after duplication. The 
persisting duplicated genes in Saccharomyces led to the origin of major 
metabolic innovations, which have been the source of the unique biotechnological 
capabilities in the Baker's yeast Saccharomyces cerevisiae. What factors have 
determined the fate of duplicated genes remains unknown. Here, we report the 
first demonstration that the local genome mutation and transcription rates 
determine the fate of duplicates. We show, for the first time, a preferential 
location of duplicated genes in the mutational and transcriptional hotspots of 
S. cerevisiae genome. The mechanism of duplication matters, with whole-genome 
duplicates exhibiting different preservation trends compared to small-scale 
duplicates. Genome mutational and transcriptional hotspots are rich in 
duplicates with large repetitive promoter elements. Saccharomyces cerevisiae 
shows more tolerance to deleterious mutations in duplicates with repetitive 
promoter elements, which in turn exhibit higher transcriptional plasticity 
against environmental perturbations. Our data demonstrate that the genome traps 
duplicates through the accelerated regulatory and functional divergence of their 
gene copies providing a source of novel adaptations in yeast.