Skip Navigation



MBE Advance Access published online on October 27, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi031
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Correction to PDF
Right arrow All Versions of this Article:
22/3/478    most recent
msi031v1
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 Pond, S. L. K.
Right arrow Articles by Frost, S. D.W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pond, S. L. K.
Right arrow Articles by Frost, S. D.W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Accepted October 20, 2004

Research Article

A Genetic Algorithm Approach to Detecting Lineage-specific Variation in Selection Pressure

Sergei L. Kosakovsky Pond 1* and Simon D.W. Frost 1

1 Antiviral Research Center, University of California San Diego, San Diego, California, 92103

* To whom correspondence should be addressed.
Sergei L. Kosakovsky Pond, E-mail: spond{at}ucsd.edu


  Abstract

The ratio of nonsynonymous (dN) to synonymous (dS) substitution rates, {omega}, provides a measure of selection at the protein level. Models have been developed that allow {omega} to vary among lineages. However, these models require the lineages in which differential selection has acted to be specified a priori. We propose a genetic algorithm approach to assign lineages in a phylogeny to a fixed number of different classes of {omega}, thus allowing variable selection pressure without a priori specification of particular lineages. This approach can identify models with a better fit than a single-ratio model, and with fits that are better than (in an information theoretic sense) a fully local model, in which all lineages are assumed to evolve under different values of {omega}, but with far fewer parameters. By averaging over models which explain the data reasonably well, we can assess the robustness of our conclusions to uncertainty in model estimation. Our approach can also be used to compare results from models in which branch classes are specified a priori with a wide range of credible models. We illustrate our methods on primate lysozyme sequences and compare them with previous methods applied to the same datasets.

Keywords: lineage-specific selection; model selection; genetic algorithms; branch site model; codon substitution model.
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
 J. Virol.Home page
C. Firth, M. A. Charleston, S. Duffy, B. Shapiro, and E. C. Holmes
Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2
J. Virol., December 15, 2009; 83(24): 12813 - 12821.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Virol.Home page
S. Martin, A. Sambade, L. Rubio, M. C. Vives, P. Moya, J. Guerri, S. F. Elena, and P. Moreno
Contribution of recombination and selection to molecular evolution of Citrus tristeza virus
J. Gen. Virol., June 1, 2009; 90(6): 1527 - 1538.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
E. E. Smith and H. S. Malik
The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions
Genome Res., May 1, 2009; 19(5): 850 - 858.
[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
 Brief BioinformHome page
W. Delport, K. Scheffler, and C. Seoighe
Models of coding sequence evolution
Brief Bioinform, January 1, 2009; 10(1): 97 - 109.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. F. Y. Poon, F. I. Lewis, S. D. W. Frost, and S. L. Kosakovsky Pond
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
Bioinformatics, September 1, 2008; 24(17): 1949 - 1950.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. L. Kosakovsky Pond, A. F.Y. Poon, A. J. Leigh Brown, and S. D.W. Frost
A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus
Mol. Biol. Evol., September 1, 2008; 25(9): 1809 - 1824.
[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]

Home page
 J. Virol.Home page
C. M. Noviello, S. L. K. Pond, M. J. Lewis, D. D. Richman, S. K. Pillai, O. O. Yang, S. J. Little, D. M. Smith, and J. C. Guatelli
Maintenance of Nef-Mediated Modulation of Major Histocompatibility Complex Class I and CD4 after Sexual Transmission of Human Immunodeficiency Virus Type 1
J. Virol., May 1, 2007; 81(9): 4776 - 4786.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Anisimova and Z. Yang
Multiple Hypothesis Testing to Detect Lineages under Positive Selection that Affects Only a Few Sites
Mol. Biol. Evol., May 1, 2007; 24(5): 1219 - 1228.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
D. Vijaykrishna, G. J. D. Smith, J. X. Zhang, J. S. M. Peiris, H. Chen, and Y. Guan
Evolutionary Insights into the Ecology of Coronaviruses
J. Virol., April 15, 2007; 81(8): 4012 - 4020.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Doron-Faigenboim and T. Pupko
A Combined Empirical and Mechanistic Codon Model
Mol. Biol. Evol., February 1, 2007; 24(2): 388 - 397.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. L. Kosakovsky Pond, F. V. Mannino, M. B. Gravenor, S. V. Muse, and S. D. W. Frost
Evolutionary Model Selection with a Genetic Algorithm: A Case Study Using Stem RNA
Mol. Biol. Evol., January 1, 2007; 24(1): 159 - 170.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
V. L. Bauer DuMont, H. A. Flores, M. H. Wright, and C. F. Aquadro
Recurrent Positive Selection at Bgcn, a Key Determinant of Germ Line Differentiation, Does Not Appear to be Driven by Simple Coevolution with Its Partner Protein Bam
Mol. Biol. Evol., January 1, 2007; 24(1): 182 - 191.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. L. Kosakovsky Pond, D. Posada, M. B. Gravenor, C. H. Woelk, and S. D. W. Frost
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
Mol. Biol. Evol., October 1, 2006; 23(10): 1891 - 1901.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. S. Bulmer and R. H. Crozier
Variation in Positive Selection in Termite GNBPs and Relish
Mol. Biol. Evol., February 1, 2006; 23(2): 317 - 326.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. K. Pond and S. V. Muse
Site-to-Site Variation of Synonymous Substitution Rates
Mol. Biol. Evol., December 1, 2005; 22(12): 2375 - 2385.
[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.