Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback...

Area of Science:

• Evolutionary biology
• Genomics
• Population genetics

Background:

• Differential gene expression is crucial for phenotypic evolution and adaptation.
• The roles of local versus distant regulatory changes in transcriptome evolution are not well understood.

Purpose of the Study:

• Investigate the genetic architecture of transcriptome divergence between marine and stream stickleback ecotypes.
• Determine the relative contributions of local and distant regulatory elements to adaptation.

Main Methods:

• Expression quantitative trait loci (eQTL) analysis in threespine sticklebacks.
• Genome scan analysis to identify regions of high genetic differentiation.
• Comparison of eQTLs across different salinity conditions.

Main Results:

• Identified both local and distant eQTLs, including regulatory hotspots.
• Local eQTLs generally aligned with the direction of ecotype divergence and overlapped with differentiated genomic regions.
• Distant eQTLs often showed opposite expression effects and rarely overlapped with differentiated regions, suggesting a potential constraint on evolution.
• Nearly half of eQTL hotspots were environment-specific.

Conclusions:

• Local regulatory changes are major drivers of transcriptome evolution and adaptation in sticklebacks.
• Distant regulatory elements may constrain transcriptome evolution.
• Analyzing genetic architecture across multiple environments is essential for predicting adaptive responses to selection.