Sequencing of Saccharomyces cerevisiae BY4743 with an artificial duplicate of IFA38. Saccharomyces cerevisiae BY4743

Gene and genome duplication provides the raw material for evolutionary innovation. After duplication a gene may have a number of fates, including being lost, having its function altered, or being retained in an unaltered state. How quickly this process occurs it is not clear. The fate of duplication is usually studied by the comparison of extant genomes and the reconstruction of the most likely ancestral states. Valuable as this approach is, it inevitably misses the most rapid molecular, functional and evolutionary events. In this study we engineered several strains of yeast making duplications of IFA38, a gene that can alter ethanol tolerance, and we have evolved these duplicate-carrying strains in a range of different environments for 500 generations. We find that changes in expression and fitness depend both on the genomic location of the duplicate and the growth conditions. When strains carrying the genome-inserted duplications are propagated in an environment where there is no specific selective pressure for that gene to be retained, duplicates can be rapidly lost from the genome within few generations. Interestingly, such gene loss does not only depend on growth conditions, but also on the genomic position of the insertion. In addition fitness is altered and transcriptional changes are widespread. The functional and evolutionary effects of gene duplication are therefore context dependent, extremely rapid and more complex than previously appreciated.