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An improved statistical method for detecting heterotachy in nucleotide sequences

Guy Baele UGent, Jeroen Raes, Yves Van de Peer UGent and Stijn Vansteelandt UGent (2006) MOLECULAR BIOLOGY AND EVOLUTION. 23(7). p.1397-1405
abstract
The principle of heterotachy states that the substitution rate of sites in a gene can change through time. In this article, we propose a powerful statistical test to detect sites that evolve according to the process of heterotachy. We apply this test to an alignment of 1289 eukaryotic rRNA molecules to 1) determine how widespread the phenomenon of heterotachy is in ribosomal RNA, 2) to test whether these heterotachous sites are nonrandomly distributed, that is, linked to secondary structure features of ribosomal RNA, and 3) to determine the impact of heterotachous sites on the bootstrap support of monophyletic groupings. Our study revealed that with 21 monophyletic taxa, approximately two-thirds of the sites in the considered set of sequences is heterotachous. Although the detected heterotachous sites do not appear bound to specific structural features of the small subunit rRNA, their presence is shown to have a large beneficial influence on the bootstrap support of monophyletic groups. Using extensive testing, we show that this may not be due to heterotachy itself but merely due to the increased substitution rate at the detected heterotachous sites.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
covation, heterotachy, false discovery rate, bootstrap support, ribosomal RNA, eukaryotes, LONG-BRANCH ATTRACTION, FALSE DISCOVERY RATE, RIBOSOMAL-RNA, MAXIMUM-LIKELIHOOD, PHYLOGENETIC ANALYSIS, SECONDARY STRUCTURE, SUBSTITUTION RATES, COVARIOTIDE MODEL, EVOLUTION, SITES
journal title
MOLECULAR BIOLOGY AND EVOLUTION
Mol. Biol. Evol.
volume
23
issue
7
pages
1397 - 1405
Web of Science type
Article
Web of Science id
000238545100008
JCR category
EVOLUTIONARY BIOLOGY
JCR impact factor
6.726 (2006)
JCR rank
4/34 (2006)
JCR quartile
1 (2006)
ISSN
0737-4038
DOI
10.1093/molbev/msl006
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
371612
handle
http://hdl.handle.net/1854/LU-371612
date created
2007-07-03 17:25:00
date last changed
2012-12-11 16:42:22
@article{371612,
  abstract     = {The principle of heterotachy states that the substitution rate of sites in a gene can change through time. In this article, we propose a powerful statistical test to detect sites that evolve according to the process of heterotachy. We apply this test to an alignment of 1289 eukaryotic rRNA molecules to 1) determine how widespread the phenomenon of heterotachy is in ribosomal RNA, 2) to test whether these heterotachous sites are nonrandomly distributed, that is, linked to secondary structure features of ribosomal RNA, and 3) to determine the impact of heterotachous sites on the bootstrap support of monophyletic groupings. Our study revealed that with 21 monophyletic taxa, approximately two-thirds of the sites in the considered set of sequences is heterotachous. Although the detected heterotachous sites do not appear bound to specific structural features of the small subunit rRNA, their presence is shown to have a large beneficial influence on the bootstrap support of monophyletic groups. Using extensive testing, we show that this may not be due to heterotachy itself but merely due to the increased substitution rate at the detected heterotachous sites.},
  author       = {Baele, Guy and Raes, Jeroen and Van de Peer, Yves and Vansteelandt, Stijn},
  issn         = {0737-4038},
  journal      = {MOLECULAR BIOLOGY AND EVOLUTION},
  keyword      = {covation,heterotachy,false discovery rate,bootstrap support,ribosomal RNA,eukaryotes,LONG-BRANCH ATTRACTION,FALSE DISCOVERY RATE,RIBOSOMAL-RNA,MAXIMUM-LIKELIHOOD,PHYLOGENETIC ANALYSIS,SECONDARY STRUCTURE,SUBSTITUTION RATES,COVARIOTIDE MODEL,EVOLUTION,SITES},
  language     = {eng},
  number       = {7},
  pages        = {1397--1405},
  title        = {An improved statistical method for detecting heterotachy in nucleotide sequences},
  url          = {http://dx.doi.org/10.1093/molbev/msl006},
  volume       = {23},
  year         = {2006},
}

Chicago
Baele, Guy, Jeroen Raes, Yves Van de Peer, and Stijn Vansteelandt. 2006. “An Improved Statistical Method for Detecting Heterotachy in Nucleotide Sequences.” Molecular Biology and Evolution 23 (7): 1397–1405.
APA
Baele, Guy, Raes, J., Van de Peer, Y., & Vansteelandt, S. (2006). An improved statistical method for detecting heterotachy in nucleotide sequences. MOLECULAR BIOLOGY AND EVOLUTION, 23(7), 1397–1405.
Vancouver
1.
Baele G, Raes J, Van de Peer Y, Vansteelandt S. An improved statistical method for detecting heterotachy in nucleotide sequences. MOLECULAR BIOLOGY AND EVOLUTION. 2006;23(7):1397–405.
MLA
Baele, Guy, Jeroen Raes, Yves Van de Peer, et al. “An Improved Statistical Method for Detecting Heterotachy in Nucleotide Sequences.” MOLECULAR BIOLOGY AND EVOLUTION 23.7 (2006): 1397–1405. Print.