Polygenic and directional regulatory evolution across pathways in Saccharomyces.

Area of Science:

• Evolutionary biology
• Genomics
• Molecular evolution

Background:

• Understanding genome innovation under selection is key in evolutionary biology.
• Individual gene selection has been studied, but pathway-level responses are less understood.
• Organismal adaptation to selective pressures often involves multiple genes acting in concert within cellular pathways.

Purpose of the Study:

• To investigate the prevalence of polygenic (multiple-gene) evolution in cellular pathways.
• To assess directional regulatory evolution in yeast species Saccharomyces cerevisiae and Saccharomyces bayanus.
• To compare protein and cis-regulatory variation within and between these yeast species.

Main Methods:

• Developed short-read sequencing methods to detect cis-regulatory variation in a yeast hybrid.
• Tested for directional accumulation of cis-regulatory variants affecting pathway gene expression under selection.
• Utilized population genomic sequencing data to analyze variation within and between species.

Main Results:

• Identified various yeast pathways exhibiting evidence for directional regulatory evolution.
• Detected pathways with significant divergence within Saccharomyces cerevisiae.
• Found signatures of positive selection acting between Saccharomyces cerevisiae and Saccharomyces bayanus.

Conclusions:

• Polygenic, pathway-level evolutionary change is a common mechanism in yeasts.
• Pathway analyses, including tests for directional regulatory evolution, are powerful tools for evolutionary genomics.
• This study provides insights into how genomes adapt through coordinated changes in gene networks.