The budding yeast Saccharomyces cerevisiae has been used in laboratory experiments for
over a century and has been instrumental in understanding virtually every aspect of …

When diverse lineages repeatedly adapt to similar environmental challenges, the extent to
which the same genes are involved (gene reuse) varies across systems. We propose that …

Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal
phenotype and fitness,–. Constructing complete fitness landscapes, in which DNA …

How cells maintain specific levels of each protein and whether that control is evolutionarily
conserved are key questions. Here, we report proteome-wide steady-state protein turnover …

Genomic analyses of microbial populations in their natural environment remain limited by
the difficulty to assemble full genomes of individual species. Consequently, the chromosome …

Regulation of gene expression is central to many biological processes. Although
reconstruction of regulatory circuits from genomic data alone is therefore desirable, this …

Whereas de novo assemblies of RNA-Seq data are being published for a growing number of
species across the tree of life, there are currently no broadly accepted methods for …

Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has
evolved multiple times, most known species belong to the subphylum Saccharomycotina …

Highlights•Evolution of gene regulation plays a major role in adaptation.•Mutations in
regulatory genes can have negative pleiotropic effects.•Duplications of transcription factors …

Gene duplication is widely believed to facilitate adaptation, but unambiguous evidence for
this hypothesis has been found in only a small number of cases. Although gene duplication …