Codon Evolution: Mechanisms and Models
Gina M. Cannarozzi, Adrian Schneider
OUP Oxford, Feb 23, 2012 - Mathematics - 280 pages
Codon-based models of evolution are a relatively new addition to the toolkit of computational biologists, and in recent years remarkable progress has been made in this area. The study of evolution at the codon level captures information contained in both amino acid and synonymous DNA substitutions. By combining these two types of information, codon analyses are more powerful than those of either amino acid or DNA evolution alone. This is a clear benefit for most evolutionary analyses, including phylogenetic reconstruction, detection of selection, ancestral sequence reconstruction, and alignment of coding DNA. Despite the theoretical advantages of codon based models, their relative complexity delayed their widespread use. Only in recent years, when large-scale sequencing projects produced sufficient genomic data and computational power increased, did their usage become more common. In Codon Evolution, leading researchers in the field of molecular evolution provide the latest insights from codon-based analyses of genetic sequences. The first part of the book provides comprehensive coverage of the developments of various types of codon substitution models such as parametric and empirical models used in maximum likelihood as well as Bayesian frameworks. Subsequent chapters examine the use of codon models to infer selection and other applications of codon models to biological systems. The second part of the book focuses on codon usage bias. Both the underlying mechanisms as well as current methods to analyse codon usage bias are presented.
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algorithm alignments allele amino acid analysis ancestral Anisimova approach Bayes Bayesian biases Bielawski Bioinformatics Biology and Evolution branch-site changes Charlesworth clade clade models coding sequences codon bias codon frequencies codon models codon substitution codon usage bias codon-based coli computed conserved correlation dataset distribution dN/dS DNA sequences effects encoded estimates evolutionary evolving example functional divergence fungi genetic code genome Goldman indices inference Kosakovsky Pond LiBaC likelihood lineages Markov matrix methods Mol Biol Evol Mol Evol molecular evolution mRNA Natl Acad Sci natural selection neutral Nielsen nonsynonymous Nucleic Acids nucleotide onymous optimal codons orthologous parameters pathogen phenotype phylogenetic PLoS polymorphism population genetic positive selection posterior prediction protein protein-coding purifying selection ratio recombination rhodopsin ribosomal sampling selective pressure sequence evolution simulations species statistical structure studies substitution rates synonymous codon usage synonymous mutations synonymous sites synonymous substitutions tion translation tree tRNA variation yeast