Metabolic remodeling and de novo mutations transcend cryptic variation as drivers of adaptation in yeast

Many organisms live in predictable environments with periodic variations
in growth conditions. Adaptation to these conditions can lead to loss of
nonessential functions, which could be maladaptive in new environments.
Alternatively, living in a predictable environment can allow populations
to accumulate cryptic genetic variation that may have no fitness benefit
in that condition, but can facilitate adaptation to new environments.
However, how these processes together shape the fitness of populations
growing in predictable environments remains unclear. Through laboratory
evolution experiments in yeast, we show that populations grown in a
nutrient-rich environment for 1000 generations generally have reduced
fitness and lower adaptability to novel stressful environments. These
populations showed metabolic remodeling and increased lipid accumulation
in rich medium which seemed to provide osmotic protection in salt stress.
Subsequent adaptation to stressors was primarily driven by de novo
mutations, with very little contribution from the mutations accumulated
prior to the exposure. Thus, our work suggests that without exposure to
new environments, populations might lose their ability to respond
effectively to these environments.  Further, our findings
highlight a major role of exaptation and de novo mutations in adaptation
to new environments but do not reveal a significant contribution of
cryptic variation in this process.