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Bioinformatics Advance Access published online on December 7, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti204
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received August 31, 2004
Revised November 24, 2004
Accepted December 2, 2004

Article

Convergent evolution of domain architectures (is rare)

Julian Gough 1*

1 RIKEN Genomic Sciences Centre, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

* To whom correspondence should be addressed.
Julian Gough, E-mail: gough{at}supfam.org


  Abstract

Motivation: In this paper we examine the evolution of domain architectures across 62 genomes of known phylogeny including all kingdoms of life. We look in particular at the possibility of convergent evolution, with a view to determining to what extent the architectures observed in the genomes are due to functional necessity or evolutionary descent. We use domains of known structure, because from this and other information we know their evolutionary relationships. We use a range of methods including phylogenetic grouping, sequence similarity/alignment, mutation rates and comparative genomics to approach this difficult problem from several different angles.

Results: Although we do not claim an exhaustive analysis, we conclude that between 0.4% and 4% of sequences are involved in convergent evolution of domain architectures, and expect the actual number to be close to the lower bound. We also make two incidental observations, albeit on a small sample: the events leading to convergent evolution appear to be random with no functional or structural preferences, and changes in the number of tandem repeat domains occur more readily than changes which alter the domain composition.

Conclusion: The principal conclusion is that the observed domain architectures of the sequences in the genomes are driven by evolutionary descent rather than functional necessity.


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