High mutation rates in human and ape pseudoautosomal genes

Gene. 2003 Oct 23;317(1-2):67-77. doi: 10.1016/s0378-1119(03)00697-8.


It has been suggested that recombination may be mutagenic, which, if true, would inflate intraspecies diversity and interspecies silent divergence in regions of high recombination. Here, we test this hypothesis comparing human/orangutan genome-wide non-coding divergence (K) to that in the pseudoautosomal genes which were reported to recombine much more frequently than the rest of the genome. We demonstrate that, compared to the average human/orangutan non-coding divergence (K=3%), the substitution rate is significantly elevated in the introns of SHOX (K=5.7%), PPP2R3L (K=8.7%) and ASMT (K=6.5%) genes located in the human and orangutan Xp/Yp pseudoautosomal region (p-PAR), where recombination is over 20-fold higher than the genomic average. On the other hand, human/orangutan non-coding divergence at the Xp/Yp pseudoautosomal boundary (K=3.5%) and in the SYBL1 gene (K=2.7%), located in the human Xq/Yq pseudoautosomal region (q-PAR), where recombination is known to be less frequent than in p-PAR, was not significantly higher than the genome average. The data are consistent with the hypothesis that recombination may be mutagenic.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylserotonin O-Methyltransferase / genetics
  • Animals
  • Female
  • Gene Frequency
  • Genetic Variation
  • Homeodomain Proteins / genetics
  • Humans
  • Introns / genetics
  • Male
  • Membrane Proteins / genetics
  • Mice
  • Molecular Sequence Data
  • Mutation / genetics*
  • Phosphoprotein Phosphatases / genetics
  • Point Mutation / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Pongo pygmaeus / genetics*
  • R-SNARE Proteins
  • Rats
  • Short Stature Homeobox Protein
  • X Chromosome / genetics*
  • Y Chromosome / genetics*


  • Homeodomain Proteins
  • Membrane Proteins
  • R-SNARE Proteins
  • SHOX protein, human
  • Short Stature Homeobox Protein
  • Sybl1 protein, mouse
  • VAMP7 protein, human
  • Vamp7 protein, rat
  • Acetylserotonin O-Methyltransferase
  • Phosphoprotein Phosphatases

Associated data

  • GENBANK/AY181053
  • GENBANK/AY181054
  • GENBANK/AY181055
  • GENBANK/AY181056
  • GENBANK/AY181057
  • GENBANK/AY181058
  • GENBANK/AY181059
  • GENBANK/AY181060