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Using Non-Reversible Context-Dependent Evolutionary Models to Study Substitution Patterns in Primate Non-Coding Sequences

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 accuratel... Full description

Journal Title: Journal of molecular evolution Vol.71 (1), p.34-50
Main Author: Baele, Guy
Other Authors: Van de Peer, Yves , Vansteelandt, Stijn
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: New York : Springer-Verlag
ID: ISSN: 0022-2844
Link: https://agris.fao.org/agris-search/search.do?recordID=US201301870542
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recordid: cdi_fao_agris_US201301870542
title: Using Non-Reversible Context-Dependent Evolutionary Models to Study Substitution Patterns in Primate Non-Coding Sequences
format: Article
creator:
  • Baele, Guy
  • Van de Peer, Yves
  • Vansteelandt, Stijn
subjects:
  • Bayes Factor
  • Context effect
  • Context-dependent evolution
  • Nearest-neighbor influences
  • Thermodynamic integration
ispartof: Journal of molecular evolution, Vol.71 (1), p.34-50
description: 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.
language: eng
source:
identifier: ISSN: 0022-2844
fulltext: no_fulltext
issn:
  • 0022-2844
  • 1432-1432
url: Link


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titleUsing Non-Reversible Context-Dependent Evolutionary Models to Study Substitution Patterns in Primate Non-Coding Sequences
creatorBaele, Guy ; Van de Peer, Yves ; Vansteelandt, Stijn
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descriptionWe 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.
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abstractWe 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.
pubNew York : Springer-Verlag