Detecting Signatures of Positive Selection against a Backdrop of Compensatory Processes
Autor: | Westin M. Kosater, Peter B. Chi, David A. Liberles |
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Rok vydání: | 2020 |
Předmět: |
Leptin
Primates 0106 biological sciences Nonsynonymous substitution 0303 health sciences Models Statistical Protein Conformation Positive selection Statistical model Computational biology Biology 010603 evolutionary biology 01 natural sciences Evolution Molecular 03 medical and health sciences Genetics Animals Selection Genetic Parametric bootstrapping Synonymous substitution Molecular Biology Silent Mutation Software Ecology Evolution Behavior and Systematics 030304 developmental biology |
Zdroj: | Molecular Biology and Evolution. 37:3353-3362 |
ISSN: | 1537-1719 0737-4038 |
Popis: | There are known limitations in methods of detecting positive selection. Common methods do not enable differentiation between positive selection and compensatory covariation, a major limitation. Further, the traditional method of calculating the ratio of nonsynonymous to synonymous substitutions (dN/dS) does not take into account the 3D structure of biomacromolecules nor differences between amino acids. It also does not account for saturation of synonymous mutations (dS) over long evolutionary time that renders codon-based methods ineffective for older divergences. This work aims to address these shortcomings for detecting positive selection through the development of a statistical model that examines clusters of substitutions in clusters of variable radii. Additionally, it uses a parametric bootstrapping approach to differentiate positive selection from compensatory processes. A previously reported case of positive selection in the leptin protein of primates was reexamined using this methodology. |
Databáze: | OpenAIRE |
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