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

Guy Baele (UGent) , Yves Van de Peer (UGent) and Stijn Vansteelandt (UGent)
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HPC-UGent: the central High Performance Computing infrastructure of Ghent University
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.
Keywords
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

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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.
@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},
}

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