Environmentally robust cis-regulatory changes underlie rapid climatic adaptation

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Gene expression changes are crucial for adaptive evolution.
• Environmental sensitivity of gene expression is known, but genetic and environmental influences on adaptive expression divergence in natural populations are understudied.

Purpose of the Study:

• To characterize cis- and trans- gene regulatory divergence in house mice.
• To determine the influence of genetic and environmental factors on adaptive gene expression.

Main Methods:

• Utilized allele-specific expression analysis in temperate and tropical house mice.
• Examined gene expression in metabolic tissues under varying thermal conditions.
• Performed genome-wide scans for selection in wild populations.

Main Results:

• Pervasive gene expression divergence observed across populations and temperatures, with 5-10% of genes showing genotype-by-environment interactions.
• Most expression divergence resulted from temperature-stable cis-regulatory changes.
• Expression plasticity was primarily driven by temperature-sensitive trans-effects.
• Identified temperature-dependent cis-regulatory changes linked to expression plasticity.
• Genomic outliers under selection were enriched in cis-regulatory divergence, particularly in genes affecting body weight and metabolism.

Conclusions:

• Cis-regulatory changes are key to evolved expression differences and adaptive body size evolution.
• Trans-acting factors largely control expression plasticity, facilitating environmental colonization.
• Combined genetic and environmental mechanisms underlie population establishment in new niches.