PMID: 10473775Sep 4, 1999Paper

Recent selection on synonymous codon usage in Drosophila

Journal of Molecular Evolution
Richard M Kliman

Abstract

Evidence from a variety of sources indicates that selection has influenced synonymous codon usage in Drosophila. It has generally been difficult, however, to distinguish selection that acted in the distant past from ongoing selection. However, under a neutral model, polymorphisms usually reflect more recent mutations than fixed differences between species and may, therefore, be useful for inferring recent selection. If the ancestral state is preferred, selection should shift the frequency distribution of derived states/site toward lower values; if the ancestral is unpreferred, selection should increase the number of derived states/site. Polymorphisms were classified as ancestrally preferred or unpreferred for several genes of D. simulans and D. melanogaster. A computer simulation of coalescence was employed to derive the expected frequency distributions of derived states/site under various modifications of the Wright-Fisher neutral model, and distributions of test statistics (t and Mann-Whitney U) were derived by appropriate sampling. One-tailed tests were applied to transformed frequency data to assess whether the two frequency distributions deviated from neutral expectations in the direction predicted by selection on codon us...Continue Reading

Citations

Feb 22, 2008·Journal of Molecular Evolution·Ana LlopartRichard M Kliman
Dec 31, 2009·Journal of Molecular Evolution·Kai Zeng, Brian Charlesworth
Jun 1, 2005·Gene·Richard M Kliman, Cheryl A Bernal
Feb 15, 2001·Trends in Genetics : TIG·A S Kondrashov
Feb 1, 2000·Trends in Genetics : TIG·S G ConticelloM Fainzilber
Aug 30, 2008·Molecular Biology and Evolution·Saverio VicarioJ R Powell
Nov 26, 2002·Molecular Biology and Evolution·A Eyre-WalkerDaniel Gaffney
Nov 17, 2007·BMC Evolutionary Biology·Saverio VicarioJ R Powell
Sep 15, 2005·Genetics·Nicolas GaltierNicolas Bierne
Apr 25, 2006·Proceedings of the National Academy of Sciences of the United States of America·Josep M Comeron
Oct 30, 2001·Current Opinion in Genetics & Development·H Akashi
Oct 2, 2012·Journal of Evolutionary Biology·F Clemente, C Vogl
Jan 13, 2006·Journal of Evolutionary Biology·Nicolas Bierne, A Eyre-Walker
Mar 5, 2002·Nature·Nick G C Smith, A Eyre-Walker
Jul 26, 2002·Molecular Biology and Evolution·Scott Williamson, Maria E Orive
Jun 23, 2001·Molecular Biology and Evolution·David J Begun
Mar 27, 2004·Molecular Biology and Evolution·Nicolas Bierne, A Eyre-Walker

Related Concepts

Sense Codon
Drosophila
Drosophila melanogaster
Genes, Insect
Evolution, Molecular

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