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  An empirical analysis of mt 16S rRNA covarion-like evolution in insects: Site-specific rate variation is clustered and frequently detected

Misof, B., Anderson, C. L., Buckley, T. R., Erpenbeck, D., Rickert, A., & Misof, K. (2002). An empirical analysis of mt 16S rRNA covarion-like evolution in insects: Site-specific rate variation is clustered and frequently detected. Journal of Molecular Evolution, 55(4), 460-469.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-3D79-7 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-3D7A-5
Genre: Journal Article

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 Creators:
Misof, B., Author
Anderson, C. L., Author
Buckley, T. R., Author
Erpenbeck, D., Author
Rickert, A.1, Author              
Misof, K., Author
Affiliations:
1Dept. of Plant Breeding and Yield Physiology (Francesco Salamini), MPI for Plant Breeding Research, Max Planck Society, ou_1113570              

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Free keywords: mt 16S rRNA; secondary structure; site-specific rate variation; evolutionary plasticity; covarion
 Abstract: The structural and functional analysis of rRNA molecules has attracted considerable scientific interest. Empirical studies have demonstrated that sequence variation is not directly translated into modifications of rRNA secondary structure. Obviously, the maintenance of secondary structure and sequence variation are in part governed by different selection regimes. The nature of those selection regimes still remains quite elusive. The analysis of individual bacterial models cannot adequately explore this topic. Therefore, we used primary sequence data and secondary structures of a mitochondrial 16S rRNA fragment of 558 insect species from 15 monophyletic groups to study patterns of sequence variation, and variation of secondary structure. Using simulation studies to establish significance levels of change, we found that despite conservation of secondary structure, the location of sequence variation within the conserved rRNA structure changes significantly between groups of insects. Despite our conservative estimation procedure we found significant site- specific rate changes at 56 sites out of 184. Additionally, site-specific rate variation is somewhat clustered in certain helices. Both results confirm what has been predicted from an application of non-stationary maximum likelihood models to rRNA sequences. Clearly, constraints on sequence variation evolve and leave footprints in the form of evolutionary plasticity in rRNA sequences. Here, we show that a better understanding of the evolution of rRNA sequences can be obtained by integrating both phylogenetic and structural information.

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Language(s): eng - English
 Dates: 2002-10
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: eDoc: 127719
ISI: 000178288000007
 Degree: -

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Title: Journal of Molecular Evolution
  Alternative Title : J. Mol. Evol.
Source Genre: Journal
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Publ. Info: -
Pages: - Volume / Issue: 55 (4) Sequence Number: - Start / End Page: 460 - 469 Identifier: ISSN: 0022-2844