Comparison of Rates and Patterns of Meiotic Recombination between Human and Chimpanzee


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.

Key Concepts

  • Recombination is a fundamental force in inheritance and evolution.

  • Large‐scale recombination rates are highly conserved between humans and chimpanzees, whereas fine‐scale recombination rates evolve extremely fast.

  • Karyotype structure is a major determinant of large‐scale recombination rates.

  • Recombination mainly occurs in recombination hotspots that are marked by histone‐methylation through PRDM9 both in humans and chimpanzees.

  • A sequence motif is likely to direct PRDM9 to recombination hotspot regions.

  • Fine‐scale recombination rate is correlated with the rate of sequence evolution.

  • Fine‐scale recombination rates are increased around genes with role in the nervous system or the immune system.

Keywords: recombination rate; recombination hotspot; sequence evolution

Figure 1.

Two‐parameter regression of human genetic length over physical length. (a) Analysis at the chromosome scale. (squares) Female, (open circles) male and (solid circles) sex‐averaged genetic length of each chromosome (in centimorgans, cM) is plotted against its physical length (in megabases, Mb). The least‐square regression lines are: y=54.2+1.02x (female), y=42.0+0.52x (male) and y=48.1+0.78x (sex average). (b) Analysis of metacentric chromosome at the chromosome‐arm scale. The best fit regression lines are: y=29.0+1.05x (female), y=27.1+0.48x (male) and y=28.0+0.77x (sex average).

Originally published in Genome Research. Reproduced with permission from Li and Freudenberg 2009. © W. Li and J. Freudenberg.
Figure 2.

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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Freudenberg, Jan(Oct 2013) Comparison of Rates and Patterns of Meiotic Recombination between Human and Chimpanzee. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020845.pub2]