Abstract

Despite the high sequence similarity between the human and chimpanzee genomes, little conservation of recombination rates
exists on a kilobase scale. In contrast, recombination rates are highly conserved on a larger scale, consistent with an influence
of karyotype structure. In both species, recombination mainly occurs in recombination hotspots that are marked by histone‐methylation
through PRDM9. A specific sequence motif was found enriched in hotspots in humans and may direct PRDM9 to the respective regions.
The fast evolutionary change of fine‐scale recombination rates is paralleled by a fast sequence evolution of the nucleotide‐binding
domain of PRDM9. Accordingly, the human hotspot motif is not enriched in chimpanzee recombination hotspots. As hotspots are sequence‐based
traits that show heritable variation in the population, their specific locations could be influenced by natural selection.
Consistently, recombination hotspots are enriched at genes that are under particularly strong selective pressure, such as
immune and nervous system genes.

Frequency histogram of P‐values for testing the enrichment of recombination hotspots around genes from 1266 GO categories. The excess of P‐values that are close to zero and P‐values that are close to one indicate the existence of GO categories that are enriched or depleted of recombination hotspots. GO categories enriched for recombination hotspots predominantly include genes functioning in the immune and the nervous system.

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