Skip Navigation


MBE Advance Access originally published online on October 13, 2006
Molecular Biology and Evolution 2007 24(1):228-235; doi:10.1093/molbev/msl146
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
24/1/228    most recent
msl146v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Nielsen, R.
Right arrow Articles by Aquadro, C. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Nielsen, R.
Right arrow Articles by Aquadro, C. F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila

Rasmus Nielsen*,{dagger}, Vanessa L. Bauer DuMont{ddagger}, Melissa J. Hubisz{dagger} and Charles F. Aquadro{ddagger}

* Institute of Biology and Centre for Bioinformatics, University of Copenhagen, Copenhagen, Denmark
{dagger} Department of Biological Statistics and Computational Biology
{ddagger} Department of Molecular Biology and Genetics, Cornell University

E-mail: rasmus{at}binf.ku.dk.

Accepted for publication October 10, 2006.

We present a likelihood method for estimating codon usage bias parameters along the lineages of a phylogeny. The method is an extension of the classical codon-based models used for estimating dN/dS ratios along the lineages of a phylogeny. However, we add one extra parameter for each lineage: the selection coefficient for optimal codon usage (S), allowing joint maximum likelihood estimation of S and the dN/dS ratio. We apply the method to previously published data from Drosophila melanogaster, Drosophila simulans, and Drosophila yakuba and show, in accordance with previous results, that the D. melanogaster lineage has experienced a reduction in the selection for optimal codon usage. However, the D. melanogaster lineage has also experienced a change in the biological mutation rates relative to D. simulans, in particular, a relative reduction in the mutation rate from A to G and an increase in the mutation rate from C to T. However, neither a reduction in the strength of selection nor a change in the mutational pattern can alone explain all of the data observed in the D. melanogaster lineage. For example, we also confirm previous results showing that the Notch locus has experienced positive selection for previously classified unpreferred mutations.

Key Words: codon usage bias • codon usage • maximum likelihood • codon-based models • selection

Arndt von Haeseler, Associate Editor


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 GeneticsHome page
K. Zeng and B. Charlesworth
Estimating Selection Intensity on Synonymous Codon Usage in a Nonequilibrium Population
Genetics, October 1, 2009; 183(2): 651 - 662.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. D. Singh, P. F. Arndt, A. G. Clark, and C. F. Aquadro
Strong Evidence for Lineage and Sequence Specificity of Substitution Rates and Patterns in Drosophila
Mol. Biol. Evol., July 1, 2009; 26(7): 1591 - 1605.
[Abstract] [Full Text] [PDF]

Home page
 Gen Biol EvolHome page
V. L. Bauer DuMont, N. D. Singh, M. H. Wright, and C. F. Aquadro
Locus-Specific Decoupling of Base Composition Evolution at Synonymous Sites and Introns along the Drosophila melanogaster and Drosophila sechellia Lineages
Gen Biol Evol, June 22, 2009; 2009(0): 67 - 74.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Anisimova and C. Kosiol
Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models
Mol. Biol. Evol., February 1, 2009; 26(2): 255 - 271.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. Rodrigue, N. Lartillot, and H. Philippe
Bayesian Comparisons of Codon Substitution Models
Genetics, November 1, 2008; 180(3): 1579 - 1591.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
A. K. Holloway, D. J. Begun, A. Siepel, and K. S. Pollard
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
Genome Res., October 1, 2008; 18(10): 1592 - 1601.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. R. Haddrill, D. Bachtrog, and P. Andolfatto
Positive and Negative Selection on Noncoding DNA in Drosophila simulans
Mol. Biol. Evol., September 1, 2008; 25(9): 1825 - 1834.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. P. Foxe, V.-u.-N. Dar, H. Zheng, M. Nordborg, B. S. Gaut, and S. I. Wright
Selection on Amino Acid Substitutions in Arabidopsis
Mol. Biol. Evol., July 1, 2008; 25(7): 1375 - 1383.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Irimia and S. W. Roy
Spliceosomal introns as tools for genomic and evolutionary analysis
Nucleic Acids Res., March 1, 2008; 36(5): 1703 - 1712.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
Z. Yang and R. Nielsen
Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage
Mol. Biol. Evol., March 1, 2008; 25(3): 568 - 579.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
P. Andolfatto
Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
Genome Res., December 1, 2007; 17(12): 1755 - 1762.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. D. Singh, V. L. Bauer DuMont, M. J. Hubisz, R. Nielsen, and C. F. Aquadro
Patterns of Mutation and Selection at Synonymous Sites in Drosophila
Mol. Biol. Evol., December 1, 2007; 24(12): 2687 - 2697.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. D. Jensen, V. L. Bauer DuMont, A. B. Ashmore, A. Gutierrez, and C. F. Aquadro
Patterns of Sequence Variability and Divergence at the diminutive Gene Region of Drosophila melanogaster: Complex Patterns Suggest an Ancestral Selective Sweep
Genetics, October 1, 2007; 177(2): 1071 - 1085.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.