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Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences

Guy Baele, Yves Van de Peer UGent and Stijn Vansteelandt UGent (2010) JOURNAL OF MOLECULAR EVOLUTION. 71(1). p.34-50
abstract
We discuss the importance of non-reversible evolutionary models when analyzing context-dependence. Given the inherent non-reversible nature of the well-known CpG-methylation-deamination process in mammalian evolution, non-reversible context-dependent evolutionary models may be well able to accurately model such a process. In particular, the lack of constraints on non-reversible substitution models might allow for more accurate estimation of context-dependent substitution parameters. To demonstrate this, we have developed different time-homogeneous context-dependent evolutionary models to analyze a large genomic dataset of primate ancestral repeats based on existing independent evolutionary models. We have calculated the difference in model fit for each of these models using Bayes Factors obtained via thermodynamic integration. We find that non-reversible context-dependent models can drastically increase model fit when compared to independent models and this on two primate non-coding datasets. Further, we show that further improvements are possible by clustering similar parameters across contexts.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
Nearest-neighbor influences, Context effect, Context-dependent evolution, Bayes Factor, Thermodynamic integration, NUCLEOTIDE-SEQUENCES, BAYESIAN PHYLOGENETICS, MAMMALIAN EVOLUTION, MAXIMUM-LIKELIHOOD, BASE SUBSTITUTIONS, MITOCHONDRIAL-DNA, RATES, PSEUDOGENES, SITE, DISTRIBUTIONS
journal title
JOURNAL OF MOLECULAR EVOLUTION
J. Mol. Evol.
volume
71
issue
1
pages
34 - 50
Web of Science type
Article
Web of Science id
000280240300005
JCR category
GENETICS & HEREDITY
JCR impact factor
2.311 (2010)
JCR rank
91/154 (2010)
JCR quartile
3 (2010)
ISSN
0022-2844
DOI
10.1007/s00239-010-9362-y
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1038884
handle
http://hdl.handle.net/1854/LU-1038884
date created
2010-09-08 19:13:18
date last changed
2016-12-19 15:44:33
@article{1038884,
  abstract     = {We discuss the importance of non-reversible evolutionary models when analyzing context-dependence. Given the inherent non-reversible nature of the well-known CpG-methylation-deamination process in mammalian evolution, non-reversible context-dependent evolutionary models may be well able to accurately model such a process. In particular, the lack of constraints on non-reversible substitution models might allow for more accurate estimation of context-dependent substitution parameters. To demonstrate this, we have developed different time-homogeneous context-dependent evolutionary models to analyze a large genomic dataset of primate ancestral repeats based on existing independent evolutionary models. We have calculated the difference in model fit for each of these models using Bayes Factors obtained via thermodynamic integration. We find that non-reversible context-dependent models can drastically increase model fit when compared to independent models and this on two primate non-coding datasets. Further, we show that further improvements are possible by clustering similar parameters across contexts.},
  author       = {Baele, Guy and Van de Peer, Yves and Vansteelandt, Stijn},
  issn         = {0022-2844},
  journal      = {JOURNAL OF MOLECULAR EVOLUTION},
  keyword      = {Nearest-neighbor influences,Context effect,Context-dependent evolution,Bayes Factor,Thermodynamic integration,NUCLEOTIDE-SEQUENCES,BAYESIAN PHYLOGENETICS,MAMMALIAN EVOLUTION,MAXIMUM-LIKELIHOOD,BASE SUBSTITUTIONS,MITOCHONDRIAL-DNA,RATES,PSEUDOGENES,SITE,DISTRIBUTIONS},
  language     = {eng},
  number       = {1},
  pages        = {34--50},
  title        = {Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences},
  url          = {http://dx.doi.org/10.1007/s00239-010-9362-y},
  volume       = {71},
  year         = {2010},
}

Chicago
Baele, Guy, Yves Van de Peer, and Stijn Vansteelandt. 2010. “Using Non-reversible Context-dependent Evolutionary Models to Study Substitution Patterns in Primate Non-coding Sequences.” Journal of Molecular Evolution 71 (1): 34–50.
APA
Baele, Guy, Van de Peer, Y., & Vansteelandt, S. (2010). Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. JOURNAL OF MOLECULAR EVOLUTION, 71(1), 34–50.
Vancouver
1.
Baele G, Van de Peer Y, Vansteelandt S. Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. JOURNAL OF MOLECULAR EVOLUTION. 2010;71(1):34–50.
MLA
Baele, Guy, Yves Van de Peer, and Stijn Vansteelandt. “Using Non-reversible Context-dependent Evolutionary Models to Study Substitution Patterns in Primate Non-coding Sequences.” JOURNAL OF MOLECULAR EVOLUTION 71.1 (2010): 34–50. Print.