Skip Navigation


MBE Advance Access originally published online on May 12, 2004
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
21/8/1548    most recent
msh158v1
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 ISI Web of Science
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 arrow Search for citing articles in:
ISI Web of Science (18)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Tang, H.
Right arrow Articles by Wu, C.-I
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tang, H.
Right arrow Articles by Wu, C.-I
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Mol. Biol. Evol. 21(8):1548-1556. 2004
DOI: 10.1093/molbev/msh158
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

A Universal Evolutionary Index for Amino Acid Changes

Hua Tang*, Gerald J. Wyckoff{dagger}, Jian Lu* and Chung-I Wu*

* Department of Ecology and Evolution, University of Chicago
{dagger} Division of Molecular Biology and Biochemistry, University of Missouri-Kansas City

E-mail: ciwu{at}uchicago.edu.

Different nonsynonymous changes may be under different selective pressure during evolution. Of the 190 possible interchanges among the 20 amino acids, only 75 can be attained by a single-base substitution. An evolutionary index (EI) can be empirically computed for each of the 75 elementary changes as the likelihood of substitutions, relative to that of synonymous changes. We used 280, 1,306, 2,488, and 309 orthologous genes from primates (human versus Old World monkey), rodents (mouse versus rat), yeast (S. cerevisiae versus S. paradoxus), and Drosophila (D. melanogaster versus D. simulans), respectively, to estimate the EIs. In each data set, EI varies more than 10-fold, and the correlation coefficients of EIs from the pairwise comparisons are high (e.g., r = 0.91 between rodent and yeast). The high correlations suggest that the amino acid properties are strong determinants of protein evolution, irrespective of the identities of the proteins or the taxa of interest. However, these properties are not well captured in conventional measures of amino acid exchangeability. We, therefore, propose a universal index of exchange (U): for any large data set, its EI can be expressed as U*R, where R is the average Ka/Ks for that data set. The codon-based, empirically determined EI (i.e., U*R) makes much better predictions on protein evolution than do previous methods.

Key Words: amino acid substitution • genetic code • protein evolution • amino acid change


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
E. Axelsson and H. Ellegren
Quantification of Adaptive Evolution of Genes Expressed in Avian Brain and the Population Size Effect on the Efficacy of Selection
Mol. Biol. Evol., May 1, 2009; 26(5): 1073 - 1079.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
G. Wlasiuk, S. Khan, W. M. Switzer, and M. W. Nachman
A History of Recurrent Positive Selection at the Toll-Like Receptor 5 in Primates
Mol. Biol. Evol., April 1, 2009; 26(4): 937 - 949.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. M. Moses and R. Durbin
Inferring Selection on Amino Acid Preference in Protein Domains
Mol. Biol. Evol., March 1, 2009; 26(3): 527 - 536.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Rokas and S. B. Carroll
Frequent and Widespread Parallel Evolution of Protein Sequences
Mol. Biol. Evol., September 1, 2008; 25(9): 1943 - 1953.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. R. Scannell and K. H. Wolfe
A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast
Genome Res., January 1, 2008; 18(1): 137 - 147.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. T. Saunders and P. Green
Insights from Modeling Protein Evolution with Context-Dependent Mutation and Asymmetric Amino Acid Selection
Mol. Biol. Evol., December 1, 2007; 24(12): 2632 - 2647.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
K. Hanada, S.-H. Shiu, and W.-H. Li
The Nonsynonymous/Synonymous Substitution Rate Ratio versus the Radical/Conservative Replacement Rate Ratio in the Evolution of Mammalian Genes
Mol. Biol. Evol., October 1, 2007; 24(10): 2235 - 2241.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. Jagadeeshan and R. S. Singh
Rapid Evolution of Outer Egg Membrane Proteins in the Drosophila melanogaster Subgroup: A Case of Ecologically Driven Evolution of Female Reproductive Traits
Mol. Biol. Evol., April 1, 2007; 24(4): 929 - 938.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Gojobori, H. Tang, J. M. Akey, and C.-I Wu
Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution
PNAS, March 6, 2007; 104(10): 3907 - 3912.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. A. Shapiro, W. Huang, C. Zhang, M. J. Hubisz, J. Lu, D. A. Turissini, S. Fang, H.-Y. Wang, R. R. Hudson, R. Nielsen, et al.
Adaptive genic evolution in the Drosophila genomes
PNAS, February 13, 2007; 104(7): 2271 - 2276.
[Abstract] [Full Text] [PDF]

Home page
 Integr. Comp. Biol.Home page
S. Cohen, J. Tirindelli, M. Gomez-Chiarri, and D. Nacci
Functional implications of Major Histocompatibility (MH) variation using estuarine fish populations
Integr. Comp. Biol., December 1, 2006; 46(6): 1016 - 1029.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Stoltzfus
Mutation-Biased Adaptation in a Protein NK Model
Mol. Biol. Evol., October 1, 2006; 23(10): 1852 - 1862.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
H. Tang and C.-I Wu
A New Method for Estimating Nonsynonymous Substitutions and Its Applications to Detecting Positive Selection
Mol. Biol. Evol., February 1, 2006; 23(2): 372 - 379.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
L. Y. Yampolsky, F. A. Kondrashov, and A. S. Kondrashov
Distribution of the strength of selection against amino acid replacements in human proteins
Hum. Mol. Genet., November 1, 2005; 14(21): 3191 - 3201.
[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.