Skip Navigation



MBE Advance Access published online on November 22, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl179
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
24/2/522    most recent
msl179v1
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 Hoffman, M. M.
Right arrow Articles by Birney, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hoffman, M. M.
Right arrow Articles by Birney, E.
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
Accepted November 15, 2006

Research Article

Estimating the Neutral Rate of Nucleotide Substitution Using Introns

Michael M. Hoffman 1 and Ewan Birney 2 *

1 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England; Graduate School of Biological, Medical and Veterinary Sciences, University of Cambridge, 17 Mill Lane, Cambridge CB2 1RX, England
2 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England

* To whom correspondence should be addressed.
Ewan Birney, E-mail: birney{at}ebi.ac.uk


  Abstract

Evolutionary biologists frequently rely on estimates of the neutral rate of evolution when characterizing the selective pressure on protein coding genes. We introduce a new method to estimate this value based on intron nucleotide substitutions. The new method uses a metascript model that considers alternative splicing forms and an algorithm to pair orthologous introns, which we call Introndeuce. We compare the intron method with a widely-used method that uses observed substitutions in synonymous coding nucleotides, by using both methods to estimate the neutral rate for human-dog and mouse-rat comparisons. The estimates of the two methods correlate strongly (r S = 0.75), but cannot be considered directly equivalent. We also investigate the effect of alignment error and G+C content on the variance in the intron method: in both cases there is an effect, and it is species-pair specific. While the intron method may be more useful for shorter evolutionary distances, it is less useful at longer distances due to the poor alignment of less conserved positions.

Keywords: introns; neutral rate; synonymous substitution; mammals.
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
 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
A. M. Resch, L. Carmel, L. Marino-Ramirez, A. Y. Ogurtsov, S. A. Shabalina, I. B. Rogozin, and E. V. Koonin
Widespread Positive Selection in Synonymous Sites of Mammalian Genes
Mol. Biol. Evol., August 1, 2007; 24(8): 1821 - 1831.
[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.