Quantifying the variation in the effective population size within a genome

Area of Science:

• Population Genetics
• Genomics
• Evolutionary Biology

Background:

• The effective population size (N(e)) is a core parameter in population genetics.
• Intragenomic variation in N(e) is hypothesized due to recombination rates and selection, but its prevalence is unclear.

Purpose of the Study:

• To determine if N(e) varies across the genome in 10 eukaryotic species.
• To investigate the correlation between N(e) variation and factors like recombination rate and selected site density.

Main Methods:

• Analyzed neutral diversity variation across protein-coding genes, accounting for mutation rate differences using interspecies divergence.
• Employed hierarchical Bayesian analysis to quantify N(e) variation.
• Correlated N(e) with recombination rates and selected site density where data were available.

Main Results:

• Significant evidence of N(e) variation was found in most of the 10 species studied.
• N(e) showed positive correlation with recombination rate in Drosophila melanogaster and negative correlation with selected site density in humans and Arabidopsis thaliana.
• The overall variation in N(e) was modest across genes within each species.

Conclusions:

• Intragenomic variation in effective population size is widespread across eukaryotes.
• Even modest variation in N(e) significantly influences the efficiency of natural selection across the genome.
• The ratio of nonsynonymous to synonymous polymorphisms correlates with diversity and N(e) estimates.