The frequency distribution of nucleotide variation in Drosophila simulans

Molecular Biology and Evolution
David J Begun

Abstract

Patterns of codon bias in Drosophila suggest that silent mutations can be classified into two types: unpreferred (slightly deleterious) and preferred (slightly beneficial). Results of previous analyses of polymorphism and divergence in Drosophila simulans were interpreted as supporting a mutation-selection-drift model in which slightly deleterious, silent mutants make significantly greater contributions to polymorphism than to divergence. Frequencies of unpreferred polymorphisms were inferred to be lower than frequencies of other silent polymorphisms. Here, I analyzed additional D. simulans data to reevaluate the support for these ideas. I found that D. simulans has fixed more unpreferred than preferred mutations, suggesting that this lineage has not been at mutation-selection-drift equilibrium at silent sites. Frequencies of polarized unpreferred polymorphisms are not skewed toward rare alleles. However, frequencies of unpolarized unpreferred codons are lower in high-bias genes than in low-bias genes. This supports the idea that unpreferred codons are borderline deleterious mutations. Purifying selection on silent sites appears to be stronger at twofold-degenerate codons than at fourfold-degenerate codons. Finally, I found tha...Continue Reading

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Citations

Oct 30, 2001·Current Opinion in Genetics & Development·Peter Andolfatto
Nov 16, 2002·Current Opinion in Genetics & Development·Laurent Duret
Nov 20, 2012·Genome Biology and Evolution·Yu-Ping PohDavid J Begun
Jun 3, 2008·Molecular Biology and Evolution·Penelope R HaddrillPeter Andolfatto
Jun 16, 2005·Genetics·Justin C Fay, Joseph A Benavides
Nov 28, 2007·Genetics·Andreas Heger, Chris P Ponting
Mar 17, 2004·Genetics·Emmanuelle GravotMichel Veuille
Oct 30, 2001·Current Opinion in Genetics & Development·Justin C Fay, C I Wu
Oct 30, 2001·Current Opinion in Genetics & Development·H Akashi
Jan 13, 2006·Journal of Evolutionary Biology·Nicolas Bierne, Adam Eyre-Walker
Nov 26, 2002·Molecular Biology and Evolution·Adam Eyre-WalkerDaniel Gaffney
Nov 13, 2007·Nature·Drosophila 12 Genomes ConsortiumIain MacCallum
Mar 5, 2002·Nature·Nick G C Smith, Adam Eyre-Walker
Dec 5, 2019·PloS One·Fouad Zahdeh, Liran Carmel
Mar 27, 2004·Molecular Biology and Evolution·Nicolas Bierne, Adam Eyre-Walker

Related Concepts

Metazoa
Sense Codon
Drosophila
Genetic Linkage Analysis
Genetic Polymorphism
Variation (Genetics)
X Chromosome
Evolution, Molecular

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