Recombination has little effect on the rate of sequence divergence in pseudoausotomal boundary 1 among humans and great apes

Recent studies indicated that recombination is strongly mutagenic. In particular, data from the mouse pseudoautosomal boundary (PAB) suggested that locally intensive recombination increased the nucleotide substitution rate by more than 100-fold and greatly increased the GC content. Here we study the rates of nucleotide substitution in eight introns of the human and great ape XG gene, which spans the boundary between the pseudoautosomal region 1 (PAR1) and the X-specific region. Contrary to what is expected under the above hypothesis, our sequence data from humans and great apes reveal that the PAR1 introns of XG have actually evolved slightly slower than X-specific introns. Only when a New World monkey was compared with hominoids were the rates slightly increased in the PAR1 introns. In terms of base composition, although the intergenic regions of the human PAR1 show a significant increase of G and C nucleotides, the base composition of the surveyed PAR1 introns is similar to that of the X-specific introns. Direct and indirect evidence indicates that the recombination rate is, indeed, much higher in PAR1 introns than in X-specific introns, and that the present PAB has persisted since the common ancestor of hominoids. Therefore, the mutagenic effect of recombination is far weaker than previously proposed, at least in hominoid PABs. [Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: D. Filatov.] The role of recombination in nucleotide sequence evolution is a fundamental issue in molecular evolution. During the last de-cade, experimental and theoretical work has led to the proposal that recombination facilitates adaptive evolution, by enhancing the efficacy of natural selection on molecular variants (e.g., Ma-rais and Charlesworth 2003). Recently, the role of recombination in neutral evolution has also drawn great interest (e.g., Perry an