Substitution patterns are under different influences in primates and rodents

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Mammalian chromosomes exhibit large-scale GC-content variations known as isochores.
• Primates and rodents display distinct isochore structures, indicating divergent GC-content evolution modes.
• GC-biased gene conversion (gBGC), a neutral process linked to meiotic recombination, affects GC-content in the human lineage by altering substitution rates.

Purpose of the Study:

• To investigate and compare genome-wide substitution patterns in the mouse lineage with those in the human lineage.
• To determine the activity and relative strength of gBGC in mice compared to humans.
• To identify factors predicting GC-content evolution in both primate and rodent lineages.

Main Methods:

• Computed genome-wide substitution patterns in the mouse lineage using multiple alignments.
• Compared mouse substitution patterns with existing human lineage data.
• Analyzed the predictive power of meiotic recombination (male and female-specific) and CpG odds ratio on substitution rates.

Main Results:

• GC-biased gene conversion (gBGC) is active but weaker in the mouse lineage than in the human lineage.
• Male-specific meiotic recombination is a better predictor of GC-content evolution in mice than female-specific recombination.
• Substitution rates (G or C to A or T) are influenced by different factors in mice and humans.
• AT-to-GC substitution rates are primarily driven by meiotic recombination in humans, but by CpG odds ratio in mice.

Conclusions:

• Substitution patterns and GC-content evolution are under distinct influences in primates (humans) and rodents (mice).
• The differing roles of meiotic recombination and CpG content highlight lineage-specific evolutionary pressures on mammalian genomes.