MBE Advance Access originally published online on December 5, 2003
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Mol. Biol. Evol. 21(2):410-417. 2004
DOI: 10.1093/molbev/msh032
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
A Gradient of Silent Substitution Rate in the Human Pseudoautosomal Region
School of Biosciences, University of Birmingham, Birmingham, United Kingdom
E-mail: d.filatov{at}bham.ac.uk.
It has been demonstrated that recombination in the human p-arm pseudoautosomal region (p-PAR) is at least twenty times more frequent than the genomic average of 
1 cM/Mb, which may affect substitution patterns and rates in this region. Here I report the analysis of substitution patterns and rates in 10 human, chimpanzee, gorilla, and orangutan genes across the p-PAR. Between species silent divergence in the p-PAR forms a gradient, increasing toward the telomere. The correlation of silent divergence with distance from the p-PAR boundary is highly significant (
= 0.911, P < 0.001). After exclusion of the CpG dinucleotides this correlation is still significant ( = 0.89, P < 0.01), thus the substitution rate gradient cannot be explained solely by the differences in the extent of methylation across the p-PAR. Frequent recombination in the PAR may result in a relatively strong effect of biased gene conversion (BGC), which, because of the increased probability of fixation of the G or C nucleotides at (A or T)/(G or C) segregating sites, may affect substitution rates. BGC, however, does not seem to be the factor creating the substitution rate gradient in the p-PAR, because the only gradient is still detactable if only A
T and GC substitutions are taken into account ( = 0.82, P < 0.01). I hypothesize that the substitution rate gradient in the p-PAR is due to the mutagenic effect of recombination, which is very frequent in the distal human p-PAR and might be lower near the p-PAR boundary.
Key Words: human • pseudoautosomal region • recombination • silent substitution rate • mutation rate
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