Recombination Has Little Effect on the Rate of Sequence Divergence in Pseudoautosomal Boundary 1 Among Humans and Great Apes

Abstract

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.

Recombination rate variation in closely related species

“…Additionally, the interpretations are complicated by conflicting results in several organisms surveyed (Payseur and Nachman, 2000; Baudry et al, 2001;Nachman, 2001;Huang et al, 2004;Yi et al, 2004;Yi and Li, 2005;Noor, 2008b;Tsai et al, 2010). Confounding factors that may lead to conflicting results are listed in Table 1, but there are several we would like to highlight here.…”

GC Content Evolution of the Human and Mouse Genomes: Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates

“…The recombination pattern may be subjected to very quick changes in a genome as has been demonstrated in Drosophila (True et al 1996) and more recently in human (Ptak et al 2004;Yi et al 2004;Galtier 2004) and mouse PAR regions (Montoya-Burgos et al 2003). So, in order to observe and compare the impact of recombination on mammalian genome evolution, we need to study only recently inserted processed pseudogenes of the same age.…”

Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes

“…Notably, a gradual increase in GC content is observed on the human X when moving from old to young strata and finally to the present-day PAR (e.g., Ross et al 2005). Enhanced recombination is also thought to account for the accelerated rate of evolution noted for genes in the PAR (particularly in rodents and to a lesser extent in primates), as recombination is accompanied by DNA repair relying on low-fidelity DNA polymerases (Perry and Ashworth 1999;Filatov and Gerrard 2003;Galtier 2004;Yi et al 2004). …”

“…www.genome.org this region, possibly the direct result of the higher recombination rate in this region (Perry and Ashworth 1999;Filatov and Gerrard 2003;Galtier 2004;Yi et al 2004).…”