Male-Driven Biased Gene Conversion Governs the Evolution of Base Composition in Human Alu Repeats

Webster, Matthew T.; Smith, Nick G.C.; Hultin‐Rosenberg, Lina; Arndt, Peter F.; Ellegren, Hans

doi:10.1093/molbev/msi136

Cited by 68 publications

(75 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Finally, it was observed that elevated W ! S substitution rates show a much stronger association with male than female recombination rate (Webster et al 2005;Dreszer et al 2007;Duret & Arndt 2008), indicating that this bias does not result from selection, which would not predict a sex-specific pattern. Interestingly, analysis of mismatch repair in primate cell lines demonstrated a bias towards incorporation of S nucleotides (Brown & Jiricny 1989).…”

Section: Introductionmentioning

confidence: 93%

See 1 more Smart Citation

Detecting positive selection within genomes: the problem of biased gene conversion

Ratnakumar

Mousset

Glémin

et al. 2010

Phil. Trans. R. Soc. B

Self Cite

137

160

View full text Add to dashboard Cite

The identification of loci influenced by positive selection is a major goal of evolutionary genetics. A popular approach is to perform scans of alignments on a genome-wide scale in order to find regions evolving at accelerated rates on a particular branch of a phylogenetic tree. However, positive selection is not the only process that can lead to accelerated evolution. Notably, GC-biased gene conversion (gBGC) is a recombination-associated process that results in the biased fixation of G and C nucleotides. This process can potentially generate bursts of nucleotide substitutions within hotspots of meiotic recombination. Here, we analyse the results of a scan for positive selection on genes on branches across the primate phylogeny. We show that genes identified as targets of positive selection have a significant tendency to exhibit the genomic signature of gBGC. Using a maximumlikelihood framework, we estimate that more than 20 per cent of cases of significantly elevated non-synonymous to synonymous substitution rates ratio (d N /d S ), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high d N /d S (more than 2). Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection.

show abstract

Section: Introductionmentioning

confidence: 93%

“…First, it has been demonstrated that the long-term average recombination rate strongly influences the rate of W ! S nucleotide substitutions (Meunier & Duret 2004;Webster et al 2005;Duret & Arndt 2008). Second, analyses of polymorphism frequency spectra showed that W !…”

Section: Introductionmentioning

confidence: 99%

Detecting positive selection within genomes: the problem of biased gene conversion

Ratnakumar

Mousset

Glémin

et al. 2010

Phil. Trans. R. Soc. B

Self Cite

137

160

View full text Add to dashboard Cite

show abstract

“…Kauppi and colleagues (2004) have demonstrated that the rate of gene conversion outside CO is 4 to 15 times higher than the rate of gene conversion inside CO. Recent works have demonstrated that GC-BGC can increase GC content very quickly (Belle et al 2004;Kudla et al 2003;Galtier 2004;Webster et al 2005). The rate of gene conversion is 100 times higher than the rate of neutral substitutions in mammalian genomes (Kudla et al 2004), which could be enough to induce a tremendous change in GC content and in isochore structure.…”

Section: The Impact Of Recombination On Gc Content Evolutionmentioning

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

View full text Add to dashboard Cite

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.

show abstract

“…We then analyzed the patterns of substitutions that occurred in the S. cerevisiae strain S288C lineage under two evolutionary perspectives: (1) after the divergence between the S288C lineage and the lineage of another strain of S. cerevisiae, YJM789, and (2) after the divergence between the S. cerevisiae and the S. paradoxus lineages. The rationale behind such substitution analyses (Meunier and Duret 2004;Webster et al 2005;Khelifi et al 2006;Duret and Arndt 2008) is to address the possible effect of recombination on GC content, through the determination of the relative rates of AT to GC and GC to AT substitutions. On the basis of such analyses, we found that recombination is not directly correlated to the patterns of AT/GC substitutions in S. cerevisiae, which indicates that recombination has no detectable influence on GC content in this case.…”

mentioning

confidence: 99%

GC Content and Recombination: Reassessing the Causal Effects for the Saccharomyces cerevisiae Genome

Marsolier‐Kergoat

Yeramian

2009

Genetics

View full text Add to dashboard Cite

Recombination plays a crucial role in the evolution of genomes. Among many chromosomal features, GC content is one of the most prominent variables that appear to be highly correlated with recombination. However, it is not yet clear (1) whether recombination drives GC content (as proposed, for example, in the biased gene conversion model) or the converse and (2) what are the length scales for mutual influences between GC content and recombination. Here we have reassessed these questions for the model genome Saccharomyces cerevisiae, for which the most refined recombination data are available. First, we confirmed a strong correlation between recombination rate and GC content at local scales (a few kilobases). Second, on the basis of alignments between S. cerevisiae, S. paradoxus, and S. mikatae sequences, we showed that the inferred AT/GC substitution patterns are not correlated with recombination, indicating that GC content is not driven by recombination in yeast. These results thus suggest that, in S. cerevisiae, recombination is determined either by the GC content or by a third parameter, also affecting the GC content. Third, we observed long-range correlations between GC and recombination for chromosome III (for which such correlations were reported experimentally and were the model for many structural studies). However, similar correlations were not detected in the other chromosomes, restraining thus the generality of the phenomenon. These results pave the way for further analyses aimed at the detailed untangling of drives involved in the evolutionary shaping of the yeast genome.

show abstract

Male-Driven Biased Gene Conversion Governs the Evolution of Base Composition in Human Alu Repeats

Cited by 68 publications

References 50 publications

Detecting positive selection within genomes: the problem of biased gene conversion

Detecting positive selection within genomes: the problem of biased gene conversion

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

GC Content and Recombination: Reassessing the Causal Effects for the Saccharomyces cerevisiae Genome

Contact Info

Product

Resources

About