Long-range linkage effects in adapting sexual populations

Area of Science:

• Evolutionary genetics
• Population genetics
• Genomics

Background:

• Genes close on a genome share evolutionary fates due to linkage.
• Recombination is thought to allow distant genes to evolve independently.
• Previous models focused on mutation-driven evolution, not pre-existing variation.

Purpose of the Study:

• To investigate if distant genes in a long genome evolve independently when relying on pre-existing genetic variation.
• To explore the impact of linkage effects beyond simple proximity or recombination rates.

Main Methods:

• A haploid population model with multiple loci and fixed selection coefficients was simulated using a Monte Carlo algorithm.
• The simulation focused on the dynamics of beneficial alleles with small initial frequencies.
• Analysis examined linkage effects, allele extinction, and substitution rates across loci.

Main Results:

• Significant linkage effects were observed even for distant loci, decreasing neither with distance nor recombination.
• Clonal interference led to the extinction of beneficial alleles at a substantial fraction of loci.
• Genetic background effects caused wide variation in substitution rates, with some loci evolving much faster than predicted by single-locus models.

Conclusions:

• Far-situated genomic regions in sexual populations do not evolve as independent units.
• Linkage and background effects disrupt independent evolution, with implications for understanding genome evolution.
• Findings may offer insights into the rapid evolution of pathogens like SARS-CoV-2 variants.