!Citation=Payen, C, et al. 2015. bioRxiv doi: http://dx.doi.org/10.1101/014068 !Title=Empirical determinants of adaptive mutations in yeast experimental evolution !PubMedID= !Name=Payen, et al. submitted 2015 !ExptSetNo=7104 !Description=Arrays accompanying Payen et al, submitted. High-throughput sequencing technologies have enabled us to expand the scope of genetic screens to identify mutations that underlie subtle phenotypes, such as fitness improvements that occur during the course of experimental evolution. However, functional tests are still required to identify the adaptive mutations amidst the large pool of mutations detected in evolved clones or populations. Here we combine functional genomics and experimental evolution to identify the loci contributing to adaptation. To separate adaptive from neutral mutations detected during laboratory experimental evolution, we tracked thousands of barcoded, systematically created gain- and loss-of-function mutations as they grew competitively in continuous culture. We compared these results to a set of ~1100 mutations acquired during hundreds of generations of growth in 11 different conditions. We determined that each population acquires in average 7.6 adaptive mutations over the course of experimental evolution. In addition, we found significant differences between the mutation spectra of haploid and diploid yeasts: in haploids we confirmed that loss of function mutations are the major adaptive strategy. These loss-of-function mutations are depleted in diploid whereas mutations predicted to modify gene expression level (described as 5? upstream and intergenic) are statistically enriched. We also detected enrichment for disruptive mutations near the translation start site. This comprehensive functional screen provides a detailed map of the genomic landscape associated with growth by identifying changes that could contribute to adaptation, and allows us to compare mutagenic potential with the actual, spontaneously derived spectrum of mutations.