Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation

Abstract

The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and nearly neutral theories or whether they can commonly have large functional and fitness effects as proposed by the balance theory. We address this question by mapping the fitness effects of over 9,000 natural variants in the Ras/PKA and TOR/Sch9 pathways--key regulators of cell proliferation in eukaryotes--across four conditions in Saccharomyces cerevisiae. While most variants are neutral in our assay, [~]3,500 exhibited significant fitness effects. These non-neutral variants tend to be missense and to affect conserved, more densely packed, and less solvent-exposed protein regions. While some of these non-neutral variants are younger and rarer, and more often found in heterozygous states--consistent with purifying selection--a substantial fraction is present at high frequencies in the population, which is expected under balancing selection. Indeed, we find that variants with a positive fitness effect in our laboratory measurement show strong signs of local adaptation as they tend to be found specifically in domesticated strains isolated from human-made environments. Our findings support the view that while many common variants might be effectively neutral, a significant proportion have locally adaptive functional consequences and are driven into a subset of the population by local positive selection. This study highlights the potential to combine high-throughput precision genome editing with fitness measurements to explore natural genetic variation on a pathway-wide scale, thereby bridging the gap between population genetics and functional genomics to understand the nature of evolutionary forces in the wild.