- THIS ARTICLE
- Full Text (Rapid PDF)
- Data Supplement
-
All Versions of this Article:
genetics.106.056911v1
173/2/821 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Welch, J. J
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Welch, J. J
doi:10.1534/genetics.106.056911
A more recent version of this article appeared on June 1, 2006.
REGULAR RESEARCH PAPERS |
Estimating the genome-wide rate of adaptive protein evolution in Drosophila
John J Welch 1*
1 University of Sussex
* To whom correspondence should be addressed. E-mail: johnwe0{at}sussex.ac.uk.
Submitted on February 8, 2006
Revised on March 20, 2006
Accepted on 20 March 2006
When polymorphism and divergence data are available for multiple loci, extended forms of the McDonald-Kreitman test can be used to estimate the average proportion of the amino-acid divergence due to adaptive evolution - a statistic denoted _bar. But such tests are subject to many biases. Most serious is the possibility that high estimates of _bar reflect demographic changes rather than adaptive substitution. Testing for between-locus variation in is one possible way of distinguishing between demography and selection. However, such tests have yielded contradictory results, and their efficacy is unclear. Estimates of _bar from the same model organisms have also varied widely. This study clarifies the reasons for these discrepancies, identifying several method-specific biases in widely-used estimators, and assessing the power of the methods. As part of this process, a new maximum likelihood estimator is introduced. This estimator is applied to a newly compiled dataset of 115 genes from Drosophila simulans, each with each orthologues from D. melanogaster and D. yakuba. In this way, it is estimated that _bar 0.4 ± 0.1, a value that does not vary substantially between different loci, or over different periods of divergence. The implications of these results are discussed.
Key Words: Drosophila, McDonald-Kreitman test, adaptive evolution, maximum likelihood
This article has been cited by other articles:
 |
|
 |
|
  P. Andolfatto Controlling Type-I Error of the McDonald-Kreitman Test in Genomewide Scans for Selection on Noncoding DNA Genetics, November 1, 2008; 180(3): 1767 - 1771. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Egea, S. Casillas, and A. Barbadilla Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites Nucleic Acids Res., July 1, 2008; 36(suppl_2): W157 - W162. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Charlesworth and A. Eyre-Walker The McDonald-Kreitman Test and Slightly Deleterious Mutations Mol. Biol. Evol., June 1, 2008; 25(6): 1007 - 1015. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. D. Singh, A. M. Larracuente, and A. G. Clark Contrasting the Efficacy of Selection on the X and Autosomes in Drosophila Mol. Biol. Evol., February 1, 2008; 25(2): 454 - 467. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Macpherson, G. Sella, J. C. Davis, and D. A. Petrov Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila Genetics, December 1, 2007; 177(4): 2083 - 2099. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
W. Y. Low, H. L. Ng, C. J. Morton, M. W. Parker, P. Batterham, and C. Robin Molecular Evolution of Glutathione S-Transferases in the Genus Drosophila Genetics, November 1, 2007; 177(3): 1363 - 1375. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Maside and B. Charlesworth Patterns of Molecular Variation and Evolution in Drosophila americana and Its Relatives Genetics, August 1, 2007; 176(4): 2293 - 2305. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. P. Ponting and G. Lunter Signatures of adaptive evolution within human non-coding sequence Hum. Mol. Genet., October 15, 2006; 15(suppl_2): R170 - R175. [Abstract] [Full Text] [PDF]
|
|