期刊
GENETICS
卷 180, 期 3, 页码 1579-1591出版社
GENETICS
DOI: 10.1534/genetics.108.092254
关键词
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资金
- Genome Quebec
- Canadian Institutes of Health Research
- Robert Cedergren Centre for bioinformatics and genomics
- Natural Sciences and Engineering Research Council of Canada
- Canadian Institute for Advanced Research
- Canadian Research Chair Program
- Centre National de al Recherche Scientifique (through the Action Concretee Incitative-Informative, Mathematique, Physique, en Biologie Moleculaire Model-Phylo funding program)
- 60eme Commission Franco-Quebecoise
In 1994, Muse and Gaut (MG) and Goldman and Yang (GY) proposed evolutionary models that recognize the coding structure of the nucleotide sequences under study, by defining a Markovian substitution process with a state space consisting of the 61sense codons (assuming the universal genetic code). Several variations and extensions to their models have since been proposed, but no general and flexible framework for contrasting the relative performance of alternative approaches has yet. been applied. Here, we compute Bayes factors to evaluate the relative merit of several MG and GY styles of codon substitution models, including recent extensions acknowledging heterogeneous nonsynonymous rates across sites, as well as selective effects inducing uneven amino acid or codon preferences. Our results on three real data sets Support a logical model construction following the MG formulation, allowing for a flexible account. of global amino acid or codon preferences, while maintaining distinct parameters governing overall nucleotide propensities. Through posterior predictive checks, we highlight the importance of such a parameterization. Altogether, the framework presented here suggests a broad modeling project in the MG style, stressing the importance of combining and contrasting available model formulations and grounding developments in a sound probabilistic paradigm.
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