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dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution

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Abstract

One of the most popular measures in the analysis of protein sequence evolution is the ratio of nonsynonymous distance (dN) to synonymous distance (dS). Under the assumption that synonymous substitutions in the coding region are selectively neutral, the dN/dS ratio can be used to statistically detect the adaptive evolution (or purifying selection) if dN/dS > 1 (or dN/dS < 1) significantly. However, due to strong structural constraints and/or variable functional constraints imposed on amino acid sites, most encoding genes in most species have demonstrated dN/dS < 1. Consequently, the statistical power for testing dN/dS = 1 may be insufficient to distinguish between different selection modes. In this paper, we propose a more powerful test, called dN/dS-H, in which a new parameter H, a relative measure of rate variation among sites, was introduced. Given the condition of strong purifying selections at some sites, the dN/dS-H model predicts dN/dS = 1-H for neutral evolution, dN/dS < 1-H for nearly neutral selection, and dN/dS > 1-H for adaptive evolution. The potential of this new method for resolving the neutral-adaptive debates is illustrated by the protein sequence evolution in vertebrates, Drosophila and yeasts, as well as somatic cancer evolution (specialized as the CN/CS-H test).

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In the current study, most work is theoretical, which did not include any original dataset. All datasets involved in the case analysis have been well cited in the text.

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Acknowledgements

The author is grateful to Jeff Thorne and all members of the research group for their constructive comments that helped improve the manuscript considerably. The simulation study was assisted by Weijia Su (Duke University).

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Correspondence to Xun Gu.

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Handling editor: David Liberles.

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Gu, X. dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution. J Mol Evol 90, 342–351 (2022). https://doi.org/10.1007/s00239-022-10064-2

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  • DOI: https://doi.org/10.1007/s00239-022-10064-2

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