Detecting consistent patterns of directional adaptation using differential selection codon models

BMC Evolutionary Biology

Research Article

Sahar Parto¹  Nicolas Lartillot² 

[1] Département de Biochimie et Médecine Moléculaire, Centre Robert Cedergren, Bio-Informatique et Génomique, Université de Montréal, Montréal, Québec, Canada;Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, Lyon, France;

关键词: HIV;    Evolution;    Selection;    HLA;    Virus adaptation;    Bayesian;    MCMC;   

DOI  :  10.1186/s12862-017-0979-y

 received in 2016-09-27, accepted in 2017-05-23,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundPhylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors. However, some organisms may be subject to systematic changes in selective pressure, resulting in reproducible molecular adaptations across independent lineages subject to similar conditions.ResultsHere, we introduce a codon-based differential selection model, which aims to detect and quantify the fine-grained consistent patterns of adaptation at the protein-coding level, as a function of external conditions experienced by the organism under investigation. The model parameterizes the global mutational pressure, as well as the site- and condition-specific amino acid selective preferences. This phylogenetic model is implemented in a Bayesian MCMC framework. After validation with simulations, we applied our method to a dataset of HIV sequences from patients with known HLA genetic background. Our differential selection model detects and characterizes differentially selected coding positions specifically associated with two different HLA alleles.ConclusionOur differential selection model is able to identify consistent molecular adaptations as a function of repeated changes in the environment of the organism. These models can be applied to many other problems, ranging from viral adaptation to evolution of life-history strategies in plants or animals.

【 授权许可】

CC BY   
© The Author(s). 2017

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