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MBE Advance Access published online on March 5, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg059
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted November 6, 2002
© 2003 Society for Molecular Biology and Evolution

Original Articles

Significantly Different Patterns of Amino Acid Replacement After Gene Duplication as Compared to After Speciation

Cathal Seoighe 1, Catrióna R. Johnston 1, Denis C. Shields 1*

1 Clinical Pharmacology Department, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland

* To whom correspondence should be addressed. E-mail: dshields{at}rcsi.ie.


  Abstract

We have performed a large-scale analysis of amino acid sequence evolution following gene duplication by comparing evolution after gene duplication to evolution following speciation in over 1,800 phylogenetic trees constructed from manually curated alignments of protein domains downloaded from the PFAM database. The site-specific rate of evolution is significantly altered by gene duplication. A significant increase in the proportion of amino acid substitutions at constrained (slowly evolving) sites after duplication was observed. An increase in the proportion of replacements at normally constrained amino acid sites could result from relaxation of purifying selective pressure. However, the proportion of amino acid replacements involving radical changes in amino acid properties following duplication does not appear to be significantly increased by relaxed selective pressure. The increased proportion of replacements at constrained sites was observed over a relatively large range of protein change (up to 25% amino acid replacements per site). These findings have implications for our understanding of the nature of evolution following duplication and may help to shed light on the evolution of novel protein functions through gene duplication.

Key Words: Gene duplication, gene function, adaptive evolution, amino acid replacement, conserved sites


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