Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae

Area of Science:

• Evolutionary biology
• Quantitative genetics
• Population genetics

Background:

• Quantitative genetics seeks to link genotype to phenotype for evolutionary insights.
• The evolutionary history of identified genetic variants is often unclear.
• Understanding non-neutral evolutionary processes is crucial for evolutionary studies.

Purpose of the Study:

• To investigate whether identified genetic variants exemplify evolutionary processes.
• To analyze the evolutionary signatures of causal variants underlying complex metabolic traits in Saccharomyces cerevisiae.
• To determine the role of selection and drift in the emergence of genetic variation.

Main Methods:

• Analysis of progeny from two wild Saccharomyces cerevisiae isolates.
• Identification of 195 loci associated with complex metabolic traits.
• High-resolution mapping of 107 causal variants to single polymorphisms.
• Phylogenetic analysis of natural variants to assess evolutionary signatures.

Main Results:

• 107 causal variants were resolved to single polymorphisms with diverse mechanisms.
• Over 20% of causal variants showed patterns inconsistent with neutral evolution.
• More than 30% of shared natural variants exhibited non-neutral phylogenetic signatures.
• Repeatedly emerging variants were more common in isolates from the same ecological niche.

Conclusions:

• A significant portion of genetic variation in wild yeast does not conform to neutral drift.
• Homoplasy and balancing selection likely contribute to non-neutral evolutionary patterns.
• Ecological niche may influence the emergence and selection of genetic variants.
• Super-resolution mapping of ecologically relevant traits provides powerful insights into adaptation and evolution.