Skip Navigation



MBE Advance Access published online on September 29, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj026
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/2/240    most recent
msj026v1
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 McDonald, J. H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by McDonald, J. H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. 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 September 19, 2005

Research Article

Apparent Trends of Amino Acid Gain and Loss in Protein Evolution Due to Nearly Neutral Variation

John H. McDonald 1*

1 Department of Biological Sciences, University of Delaware, Newark, Delaware 19716 USA

* To whom correspondence should be addressed.
John H. McDonald, E-mail: mcdonald{at}udel.edu


  Abstract

It has recently been claimed that certain amino acids have been increasing in frequency in all living organisms for most of the history of life on earth, while other amino acids have been decreasing in frequency. Three lines of evidence have been offered for this assertion, but each has a more plausible alternative interpretation. Here I show that unequal patterns of gains and losses for particular pairs of amino acids (such as more leucine->phenylalanine than phenylalanine->leucine substitutions in humans and chimpanzees since they split from a common ancestor) are consistent with a simple neutral model at equilibrium amino acid frequencies. Unequal numbers of gains and losses for particular amino acids (such as more gains than losses of cysteine) are shown by simulations to be consistent with a model of nearly neutral evolution. Unequal numbers of gains and losses for particular amino acids in human polymorphism data are shown by simulations to be explainable by the nearly neutral model, as well. In a comparison of protein sequences from four strains of Escherichia coli, polarized by one outgroup strain of Salmonella, the disparity in number of gains and losses for particular amino acids is strong in terminal branches but weaker or nonexistent in internal branches, which is inconsistent with the universal trend model but as expected under the nearly neutral model.

Keywords: protein evolution; Markov chain; nearly neutral model; Escherichia coli.
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
 Mol Biol EvolHome page
R. A. Goldstein and D. D. Pollock
Observations of Amino Acid Gain and Loss during Protein Evolution Are Explained by Statistical Bias
Mol. Biol. Evol., July 1, 2006; 23(7): 1444 - 1449.
[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.