Research report: Recombination rate and efficiency of linked selection in small and large stickleback populations

Population genetic theory predicts that natural selection operates more efficiently in large populations, because genetic drift weakens selection in small ones. A new study of nine-spined sticklebacks (Pungitius pungitius) tested these predictions by comparing genome-wide patterns of nucleotide diversity and recombination rate across populations that differ dramatically in effective size.

The researchers examined four small freshwater populations, with a mean effective population size of roughly 7,096, and four large marine populations, with a mean effective size of 376,828. They used population-specific linkage maps to estimate recombination rates and assessed how nucleotide diversity varied with recombination across the genome.

In all but the smallest freshwater population, nucleotide diversity showed a positive correlation with recombination rate. This pattern persisted even after accounting for variation in GC and CpG content and in gene density, suggesting that linked selection is prevalent across these stickleback genomes.

The findings indicate that this process plays an important role in lowering nucleotide diversity in low-recombination regions, especially in large populations where selection is more efficient.

Mean recombination rates did not differ between freshwater and marine populations overall, with one notable exception: the freshwater population with the smallest effective population size exhibited a significantly elevated recombination rate.

This result matches a theoretical expectation that small populations adapting to new environments may evolve higher recombination rates, both to facilitate adaptation and to dissociate and purge harmful mutations. At least one of the small freshwater populations appears to have evolved a higher recombination rate than its marine ancestors.

Exploratory genome-wide association analyses suggested a possible polygenic basis for recombination rate variation, meaning that many genetic variants may each contribute a small effect to differences in recombination among populations.

The study, based on comparisons among eight stickleback populations, provides evidence that linked selection shapes patterns of genome diversity in relation to population size, and that recombination rate itself may evolve in response to demographic and selective conditions.

Subject of Research: Recombination rate and linked selection in small and large stickleback populations

Article Title: Recombination rate and efficiency of linked selection in small and large stickleback populations

Article References: Wang, H., Zhang, C., Reid, K., & Merilä, J. (2026). Recombination rate and efficiency of linked selection in small and large stickleback populations. PLOS Genetics, 22(10), e1012335. https://doi.org/10.1371/journal.pgen.1012335

Image Credits: AI Generated

DOI: 10.1371/journal.pgen.1012335

Keywords: stickleback, recombination rate, linked selection, nucleotide diversity, effective population size, population genetics, linkage map, freshwater populations, marine populations, GWAS, Recombination, rate