- THIS ARTICLE
- Full Text (Rapid PDF)
-
All Versions of this Article:
genetics.105.044917v1
172/3/1411 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
-
Author home page(s):
Daniel J Wilson
Gilean McVean
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Wilson, D. J
- Articles by McVean, G.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Wilson, D. J
- Articles by McVean, G.
doi:10.1534/genetics.105.044917
A more recent version of this article appeared on March 1, 2006.
REGULAR RESEARCH PAPERS |
Estimating diversifying selection and functional constraint in the presence of recombination
Daniel J Wilson 1* and Gilean McVean 1
1 University of Oxford
* To whom correspondence should be addressed. E-mail: daniel.wilson{at}sjc.ox.ac.uk.
Submitted on April 27, 2005
Revised on September 27, 2005
Accepted on 26 December 2005
Models of molecular evolution that incorporate the ratio of non-synonymous to synonymous polymorphism (dN/dS ratio) as a parameter can be used to identify sites that are under diversifying selection or functional constraint in a sample of gene sequences. However, when there has been recombination in the evolutionary history of the sequences, reconstructing a single phylogenetic tree is not appropriate, and inference based on a single tree can give misleading results. In the presence of high levels of recombination, the identification of sites experiencing diversifying selection can suffer from a false positive rate as high as 90%. We present a model that uses a population genetics approximation to the coalescent with recombination, and use reversible-jump MCMC to perform Bayesian inference on both the dN/dS ratio and the recombination rate, allowing each to vary along the sequence. We demonstrate that the method has the power to detect variation in the dN/dS ratio and the recombination rate, and does not suffer from a high false positive rate. We use the method to analyse the porB gene of Neisseria meningitidis, and verify the inferences using prior sensitivity analysis and model criticism techniques.
Key Words: Bayesian, Neisseria meningitidis, recombination, reversible-jump MCMC, selection
This article has been cited by other articles:
 |
|
 |
|
  M. Arenas and D. Posada The Effect of Recombination on the Reconstruction of Ancestral Sequences Genetics, April 1, 2010; 184(4): 1133 - 1139. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Arenas and D. Posada Coalescent Simulation of Intracodon Recombination Genetics, February 1, 2010; 184(2): 429 - 437. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Miyake, N. Takebayashi, and D. E. Wolf Possible Diversifying Selection in the Imprinted Gene, MEDEA, in Arabidopsis Mol. Biol. Evol., April 1, 2009; 26(4): 843 - 857. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
J. Vieira, E. Teles, R. A. M. Santos, and C. P. Vieira Recombination at Prunus S-Locus Region SLFL1 Gene Genetics, September 1, 2008; 180(1): 483 - 491. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Gunasekera, T. Wickramarachchi, D. E. Neafsey, I. Ganguli, L. Perera, P. H. Premaratne, D. Hartl, S. M. Handunnetti, P. V. Udagama-Randeniya, and D. F. Wirth Genetic Diversity and Selection at the Plasmodium vivax Apical Membrane Antigen-1 (PvAMA-1) Locus in a Sri Lankan Population Mol. Biol. Evol., April 1, 2007; 24(4): 939 - 947. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. T. T. Edwards, E. C. Holmes, O. G. Pybus, D. J. Wilson, R. P. Viscidi, E. J. Abrams, R. E. Phillips, and A. J. Drummond Evolution of the Human Immunodeficiency Virus Envelope Gene Is Dominated by Purifying Selection Genetics, November 1, 2006; 174(3): 1441 - 1453. [Abstract] [Full Text] [PDF]
|
|
|