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MBE Advance Access published online on April 13, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm072
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© 2007 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Letter

Opposite Evolutionary Effects between Different Alternative Splicing Patterns

Chen Feng-Chi*, Chaw Shu-Miaw§, Tzeng Yun-Huei, Wang Sheng-Shun and Chuang Trees-Juen,1

* Division of Biostatistics and Bioinformatics, National Health Research Institutes, Miaoli County 350, Taiwan
§ Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan
Genomics Research Center, Academia Sinica, Taipei 115, Taiwan

1 Corresponding author. E-MAIL: trees{at}gate.sinica.edu.tw; FAX: 886-2-27898757

Received for publication March 20, 2007. Accepted for publication April 10, 2007.

Alternative splicing (AS) has been recognized as a mechanism of relaxing selection pressure on protein subsequences. Here we show that AS may also yield contrary evolutionary effects. We compare the evolutionary rates of two types of alternatively spliced exons (ASEs) – simple and complex. The former does not change the boundaries of its flanking exon(s) while the latter does. By analyzing over 26,000 human-mouse orthologous exons, we demonstrate that complex ASEs have lower Ka and Ka/Ks ratio and higher Ks than constitutively spliced exons (CSEs), whereas simple ASEs have evolutionary rates to the opposite of CSEs. Our results indicate that complex ASEs are subject to stronger selection pressure than CSEs at the protein level, but the trend is reversed at the RNA level. Therefore, the previous view that ASEs accelerate evolution of protein subsequences needs to be modified.

Key Words: simple alternatively spliced exons • complex alternatively spliced exons • constitutively spliced exons • selective constraint • lineage-specificity • comparative genomics


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