Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome

Area of Science:

• Evolutionary genetics
• Sex chromosome evolution

Background:

• Allele-specific gene expression evolves rapidly on sex chromosomes.
• Y chromosomes accumulate mutations over time, leading to gametolog expression loss relative to the X chromosome.
• The drivers of Y chromosome expression evolution (selective interference vs. positive selection) remain unclear.

Purpose of the Study:

• To investigate the evolutionary dynamics of cis-regulatory sequences on Y chromosomes.
• To determine if positive selection favors down-regulation of Y-linked genes with deleterious mutations.
• To use the threespine stickleback as a model system due to its intermediate X-Y divergence.

Main Methods:

• Analysis of substitution rates and polymorphism in Y-linked cis-regulatory regions.
• Comparison of Y-chromosome regulatory regions with non-functional sites (intergenic, synonymous).
• Correlation of Y-chromosome regulatory divergence with X-biased gametolog expression.

Main Results:

• Putative enhancer regions on the Y chromosome show elevated substitution rates and decreased polymorphism.
• These patterns suggest positive selection acting on Y-linked cis-regulatory regions.
• Y-chromosome regulatory divergence correlates with X-biased gene expression, indicating selection favors Y expression loss.

Conclusions:

• Y-linked cis-regulatory regions show signs of positive selection soon after recombination suppression.
• Rapid divergence of regulatory regions may be selected to mask deleterious mutations on the Y chromosome.
• This study provides evidence for selection driving Y chromosome gene expression evolution.