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Evidence of selection on silent site base composition in mammals: Potential implications for the evolution of isochores and junk DNA
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Eyre-Walker A. Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics. 152:1999;675-683.
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(1999)
Genetics
, vol.152
, pp. 675-683
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Eyre-Walker, A.1
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45
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0034993993
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Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans
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The analysis of polymorphisms at synonymous sites indicates that in GC-rich genes, GC→AT mutations are more frequent than are AT→GC mutations, whereas interspecies comparisons suggest that AT↔GC substitutions are at equilibrium. Taken together, these data indicate that GC mutations have a higher probability of fixation than have AT mutations. This result can be explained by selection or biased gene conversion but is not compatible with the equilibrium mutational bias model for the origin of isochores. Note, however, that the assumption of equilibrium might be incorrect (see [38••] ).
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Smith N.G., Eyre-Walker A. Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans. Mol Biol Evol. 18:2001;982-986. The analysis of polymorphisms at synonymous sites indicates that in GC-rich genes, GC→AT mutations are more frequent than are AT→GC mutations, whereas interspecies comparisons suggest that AT↔GC substitutions are at equilibrium. Taken together, these data indicate that GC mutations have a higher probability of fixation than have AT mutations. This result can be explained by selection or biased gene conversion but is not compatible with the equilibrium mutational bias model for the origin of isochores. Note, however, that the assumption of equilibrium might be incorrect (see [38••] ).
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(2001)
Mol Biol Evol
, vol.18
, pp. 982-986
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Smith, N.G.1
Eyre-Walker, A.2
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46
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0021077332
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Evolution of a finite population under gene conversion
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Nagylaki T. Evolution of a finite population under gene conversion. Proc Natl Acad Sci USA. 80:1983;6278-6281.
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(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 6278-6281
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Nagylaki, T.1
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47
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0034766004
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GC-content evolution in mammalian genomes: The biased gene conversion hypothesis
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See annotation [48••] .
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Galtier N., Piganeau G., Mouchiroud D., Duret L. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics. 159:2001;907-911. See annotation [48••] .
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(2001)
Genetics
, vol.159
, pp. 907-911
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Galtier, N.1
Piganeau, G.2
Mouchiroud, D.3
Duret, L.4
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48
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0035986891
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Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution
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This paper shows that in yeast the GC content at silent sites is correlated positively with recombination rate. Neither selection nor mutation can explain this correlation. In agreement with a similar analysis in mammals [47•], the author concludes that this correlation results from biased gene conversion (BGC). In many taxa (including yeast and mammals), the repair of DNA mismatches is biased toward GC, which probably corresponds to an evolutionary adaptation to a universal mutational bias towards AT. In recombining genomes, this bias in mismatch repair will lead to gene conversion biases. Together with [47•], this paper highlights the importance of taking into account BGC in models of population genetics.
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Birdsell J.A. Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol. 19:2002;1181-1197. This paper shows that in yeast the GC content at silent sites is correlated positively with recombination rate. Neither selection nor mutation can explain this correlation. In agreement with a similar analysis in mammals [47•], the author concludes that this correlation results from biased gene conversion (BGC). In many taxa (including yeast and mammals), the repair of DNA mismatches is biased toward GC, which probably corresponds to an evolutionary adaptation to a universal mutational bias towards AT. In recombining genomes, this bias in mismatch repair will lead to gene conversion biases. Together with [47•], this paper highlights the importance of taking into account BGC in models of population genetics.
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(2002)
Mol Biol Evol
, vol.19
, pp. 1181-1197
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Birdsell, J.A.1
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49
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0035826858
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Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes
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Marais G., Mouchiroud D., Duret L. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci USA. 98:2001;5688-5692. Population genetics models show that the efficacy of selection should increase with recombination because of Hill-Robertson interference (HRi). In agreement with that prediction, the frequency of optimal codons is correlated positively with recombination both in nematode and Drosophila. In this paper, however, my co-workers and I show that in both species this correlation is essentially due to a relationship between recombination rate and GC content at silent sites, such as introns and flanking regions (note that we had proposed that this was a consequence of mutation patterns associated with recombination but biased gene conversion seems to be a more likely explanation [48••] ). When the effect of recombination on local GC content is taken into account, there is no evidence for an impact of HRi on codon usage in the nematode [50•] . In Drosophila, HRi seems to have some impact on codon usage but is limited to a small subset of genes (only 4% of the total) that are subject to strong translational selection and located in regions of very low recombination [50•,52•] .
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(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 5688-5692
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Marais, G.1
Mouchiroud, D.2
Duret, L.3
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50
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0036725703
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Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes
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See annotation [49••] .
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Marais G., Piganeau G. Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes. Mol Biol Evol. 19:2002;1399-1406. See annotation [49••] .
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(2002)
Mol Biol Evol
, vol.19
, pp. 1399-1406
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Marais, G.1
Piganeau, G.2
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51
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0027383354
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Reduced natural selection associated with low recombination in Drosophila melanogaster
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Kliman R.M., Hey J. Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol Biol Evol. 10:1993;1239-1258.
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(1993)
Mol Biol Evol
, vol.10
, pp. 1239-1258
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Kliman, R.M.1
Hey, J.2
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52
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0036188913
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Interactions between natural selection, recombination and gene density in the genes of Drosophila
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See annotation [49••] .
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Hey J., Kliman R.M. Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics. 160:2002;595-608. See annotation [49••] .
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(2002)
Genetics
, vol.160
, pp. 595-608
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Hey, J.1
Kliman, R.M.2
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53
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0033977618
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Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
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Duret L., Mouchiroud D. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 17:2000;68-74.
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(2000)
Mol Biol Evol
, vol.17
, pp. 68-74
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Duret, L.1
Mouchiroud, D.2
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