High mutation rates in human and ape pseudoautosomal genes

Filatov, Dmitry A.; Gerrard, Dave T.

doi:10.1016/s0378-1119(03)00697-8

Cited by 61 publications

(68 citation statements)

References 72 publications

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“…Unlike results from mouse F XY (Perry and Ashworth 1999;Montoya-Burgos et al 2003), our findings do not support the hypothesis that recombination is globally mutagenic (i.e., Lercher and Hurst 2002;Hellmann et al 2003). Filatov and Gerrard (2003) also reported no substantial difference in evolutionary rates between PAR-borne and X-specific sequences within short segments of human and orangutan XG.…”

Section: Evolutionary Rates In Xg Introns In Great Apescontrasting

confidence: 99%

“…During the last decade, 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., Marais and Charlesworth 2003). Recently, the role of recombination in neutral evolution has also drawn great interest (e.g., Perry and Ashworth 1999;Fullerton et al 2001;Marais et al 2001;Lercher and Hurst 2002;Filatov and Gerrard 2003;Hellmann et al 2003;Montoya-Burgos et al 2003).…”

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confidence: 99%

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

Summers²,

Pearson³

et al. 2003

Genome Res.

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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.

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Section: Evolutionary Rates In Xg Introns In Great Apescontrasting

confidence: 99%

mentioning

confidence: 99%

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

Summers²,

Pearson³

et al. 2003

Genome Res.

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“…The rate of synonymous evolution covaries with regional GC content (Smith and Hurst 1999;Bielawski et al 2000;Hurst and Williams 2000;Castresana 2002b;Hardison et al 2003), although the exact form and strength of this relationship is still a matter of debate, and seems to depend on methodology Bierne and Eyre-Walker 2003). There is also evidence of a positive correlation between K 4 and meiotic recombination rate (Perry and Ashworth 1999;Filatov 2003;Filatov and Gerrard 2003;Hellmann et al 2003), possibly indicating a mutagenic effect of recombination. GC and recombination rates are known to covary (Eyre-Walker 1993; Fullerton et al 2001), and it has recently been argued that substitutional GC biases are directly associated with recombination events (Meunier and Duret 2004).…”

Section: Alternative Explanations For Local Similarity In Kmentioning

confidence: 95%

“…Aside from transcription, other possibilities to explain the local variation in the synonymous substitution rate include (1) heterogeneity in the activity of repair enzymes (Matassi et al 1999), (2) recombination-associated mutational and/or repair hotspots (Perry and Ashworth 1999;Filatov and Gerrard 2003;Hellmann et al 2003), and (3) GCassociated mutation or fixation biases (Lercher et al 2001;Castresana 2002b;Yi et al 2002;Hardison et al 2003). We examine the last two of these together, as it has been argued that they are not independent (Meunier and Duret 2004).…”

Section: Alternative Hypothesesmentioning

confidence: 99%

Genomic Regionality in Rates of Evolution Is Not Explained by Clustering of Genes of Comparable Expression Profile

Lercher¹,

Chamary²,

Hurst³

2004

Genome Res.

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In mammalian genomes, linked genes show similar rates of evolution, both at fourfold degenerate synonymous sites (K 4 ) and at nonsynonymous sites (K A ). Although it has been suggested that the local similarity in the synonymous substitution rate is an artifact caused by the inclusion of disparately evolving gene pairs, we demonstrate here that this is not the case: after removal of disparately evolving genes, both (1) linked genes and (2) introns from the same gene have more similar silent substitution rates than expected by chance. What causes the local similarity in both synonymous and nonsynonymous substitution rates? One class of hypotheses argues that both may be related to the observed clustering of genes of comparable expression profile. We investigate these hypotheses using substitution rates from both human-mouse and mouse-rat comparisons, and employing three different methods to assay expression parameters. Although we confirm a negative correlation of expression breadth with both K 4 and K A , we find no evidence that clustering of similarly expressed genes explains the clustering of genes of comparable substitution rates. If gene expression is not responsible, what about other causes? At least in the human-mouse comparison, the local similarity in K A can be explained by the covariation of K A and K 4 . As regards K 4 , our results appear consistent with the notion that local similarity is due to processes associated with meiotic recombination.

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“…Several models have been proposed to explain the emergence and evolution of isochores (for review see Eyre-Walker and Hurst 2001). Some authors suggested that isochores are the result variations in the pattern of mutation (variable mutational bias [VMB] [Wolfe et al 1993;Francino and Ochman 1999;Matassi et al 1999;Lercher and Hurst 2002;Subramanian and Kumar 2003;Filatov and Gerrard 2003]). Two other models predict that variations in GC content are due to bias in fixation of AT toward GC mutations because of selection for GC (Bernardi and Bernardi 1986;Charlesworth 1994;Eyre-Walker 1999;Bernardi 2000) or a neutral process called GC-biased gene conversion (GC-BGC) (for review see Eyre-Walker 1993;Galtier et al 2001;Smith et al, 2002;Webster et al, 2003;Galtier 2003;Marais 2003).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2006

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Abstract. Processed pseudogenes are generated by reverse transcription of a functional gene. They are generally nonfunctional after their insertion and, as a consequence, are no longer subjected to the selective constraints associated with functional genes. Because of this property they can be used as neutral markers in molecular evolution. In this work, we investigated the relationship between the evolution of GC content in recently inserted processed pseudogenes and the local recombination pattern in two mammalian genomes (human and mouse). We confirmed, using original markers, that recombination drives GC content in the human genome and we demonstrated that this is also true for the mouse genome despite lower recombination rates. Finally, we discussed the consequences on isochores evolution and the contrast between the human and the mouse pattern.

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High mutation rates in human and ape pseudoautosomal genes

Cited by 61 publications

References 72 publications

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

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

Genomic Regionality in Rates of Evolution Is Not Explained by Clustering of Genes of Comparable Expression Profile

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

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