Biased gene conversion and the evolution of mammalian genomic landscapes.

@article{Duret2009BiasedGC,
  title={Biased gene conversion and the evolution of mammalian genomic landscapes.},
  author={Laurent Duret and Nicolas Galtier},
  journal={Annual review of genomics and human genetics},
  year={2009},
  volume={10},
  pages={
          285-311
        }
}
  • L. Duret, N. Galtier
  • Published 28 August 2009
  • Biology
  • Annual review of genomics and human genetics
Recombination is typically thought of as a symmetrical process resulting in large-scale reciprocal genetic exchanges between homologous chromosomes. Recombination events, however, are also accompanied by short-scale, unidirectional exchanges known as gene conversion in the neighborhood of the initiating double-strand break. A large body of evidence suggests that gene conversion is GC-biased in many eukaryotes, including mammals and human. AT/GC heterozygotes produce more GC- than AT-gametes… 

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References

SHOWING 1-10 OF 149 REFERENCES
The neoselectionist theory of genome evolution
  • G. Bernardi
  • Biology
    Proceedings of the National Academy of Sciences
  • 2007
TLDR
The neoselectionist theory of genome evolution not only provides a solution to the neutralist/selectionist debate but also introduces an epigenomic component in genome evolution.
Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution.
This study presents compelling evidence that recombination significantly increases the silent GC content of a genome in a selectively neutral manner, resulting in a highly significant positive
Male-driven biased gene conversion governs the evolution of base composition in human alu repeats.
TLDR
Analysis of patterns of substitution in Alu repeats since their insertion suggests that regional biases in substitution are caused by biased gene conversion, a process that increases the probability of fixation of mutations that increase GC content.
The Impact of Recombination on Nucleotide Substitutions in the Human Genome
TLDR
It is concluded that along with mutation, selection and drift, BGC is one of the major factors driving genome evolution, and the predictions of this model fit very well with the observed substitution patterns in the human genome.
Recombination drives the evolution of GC-content in the human genome.
TLDR
It is demonstrated that recombination drives the evolution of base composition in human (probably via the process of biased gene conversion) and the pattern of neutral substitutions in 14.3 Mb of primate noncoding regions suggests changes of recombination rates occur relatively frequently during evolution.
Intense and highly localized gene conversion activity in human meiotic crossover hot spots
TLDR
Screen and selection methods are developed to characterize sperm conversions in two meiotic crossover hot spots in the major histocompatibility complex (MHC) and one in the sex chromosomal pseudoautosomal pairing region PAR1 (ref. 9).
Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion.
TLDR
Observations support the hypothesis that biased gene conversion (BGC), specifically in the male germline, played a significant role in the evolution of the human genome.
Recombination is proportional to the number of chromosome arms in mammals
TLDR
A regression analysis is performed, using 21 of the 24 nondomesticated mammalian species reported by Burt and Bell (1987) for which the karyotypes are available to us, and finds that, in agreement with the expectations of Dutrillaux, there is a very strong correlation between number of chiasma (NC) and the haploid number of chromosome arms.
Reduced natural selection associated with low recombination in Drosophila melanogaster.
TLDR
In analyses of 385 D. melanogaster loci, it is found that codon bias is reduced in regions of low recombination (i.e., near centromeres and telomeres and on the fourth chromosome), and this model of varying selection intensity is linked to the population-genetics prediction that the effectiveness of natural selection is decreased under reduced recombination.
...
...