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Composite Likelihood Modeling of Neighboring Site Correlations of DNA Sequence Substitution Rates

  • Ling Deng and Dirk F. Moore
Published/Copyright: January 28, 2009
Statistical Applications in Genetics and Molecular Biology
From the journal Statistical Applications in Genetics and Molecular Biology Volume 8 Issue 1

Sequence data from a series of homologous DNA segments from related organisms are typically polymorphic at many sites, and these polymorphisms are the result of evolutionary processes. Such data may be used to estimate the substitution rates as well as the variability of these rates. Careful characterization of the distribution of this variation is essential for accurate estimation of evolutionary distances and phylogeny reconstruction among these sequences. Many researchers have recognized the importance of the variability of substitution rates, which most have modeled using a discrete gamma distribution. Some have extended these methods to explicitly account for the correlation of substitution rates among sites using hidden Markov models; others have proposed context-dependent substitution rate schemes. We accommodate these correlations using a composite likelihood method based on a bivariate gamma distribution, which is more flexible than hidden Markov models in terms of correlation structure and more computationally tractable compared to the context-dependent schemes. We show that the estimates have good theoretical properties. We also use simulations to compare the maximum composite likelihood estimates to those obtained from maximum likelihood based on the independence assumption. We use data from the mitochondrial DNA of ten primates to obtain maximum composite likelihood estimates of the mean substitution rate, overdispersion, and correlation parameters, and use these estimates in a parametric phylogenetic bootstrap to assess the impact of serial correlation on the estimates of substitution rates and branch lengths.

Keywords: bivariate negative binomial distribution; composite likelihood; substitution rate; phylogeny; parametric bootstrap
Published Online: 2009-1-28

©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston

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https://doi.org/10.2202/1544-6115.1391
Keywords for this article
bivariate negative binomial distribution; composite likelihood; substitution rate; phylogeny; parametric bootstrap

Articles in the same Issue

  1. Article
  2. Sparse Canonical Correlation Analysis with Application to Genomic Data Integration
  3. Orthology-Based Multilevel Modeling of Differentially Expressed Mouse and Human Gene Pairs
  4. Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis
  5. Dimension Reduction of Microarray Data in the Presence of a Censored Survival Response: A Simulation Study
  6. A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins
  7. Composite Likelihood Modeling of Neighboring Site Correlations of DNA Sequence Substitution Rates
  8. A Multiple Testing Approach to High-Dimensional Association Studies with an Application to the Detection of Associations between Risk Factors of Heart Disease and Genetic Polymorphisms
  9. Hypothesis Tests for Point-Mass Mixture Data with Application to `Omics Data with Many Zero Values
  10. Inferring Dynamic Genetic Networks with Low Order Independencies
  11. Normalization Method for Transcriptional Studies of Heterogeneous Samples - Simultaneous Array Normalization and Identification of Equivalent Expression
  12. A Bayesian Analysis Strategy for Cross-Study Translation of Gene Expression Biomarkers
  13. Modified FDR Controlling Procedure for Multi-Stage Analyses
  14. Detecting Outlier Samples in Microarray Data
  15. Survival Analysis with High-Dimensional Covariates: An Application in Microarray Studies
  16. Two-Stage Model-Based Clustering for Liquid Chromatography Mass Spectrometry Data Analysis
  17. Score Statistics for Mapping Quantitative Trait Loci
  18. Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements
  19. A Multilocus Model for Constructing a Linkage Disequilibrium Map in Human Populations
  20. Testing of Chromosomal Clumping of Gene Properties
  21. Balanced Gradient Boosting from Imbalanced Data for Clinical Outcome Prediction
  22. Univariate Shrinkage in the Cox Model for High Dimensional Data
  23. Multilevel Comparison of Dendrograms: A New Method with an Application for Genetic Classifications
  24. Weighted Multiple Hypothesis Testing Procedures
  25. Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness
  26. Increase of Rejection Rate in Case-Control Studies with the Differential Genotyping Error Rates
  27. A Parametric Model for Analyzing Anticipation in Genetically Predisposed Families
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  47. Statistical Screening Method for Genetic Factors Influencing Susceptibility to Common Diseases in a Two-Stage Genome-Wide Association Study
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