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Title:           An efficient and robust ABC approach to infer the rate and strength of adaptation
Subject:         DOI: 10.1093/g3journal/jkae031; G3: Genes, Genomes, Genetics, 14, 4, 2024-02-14.; Abstract: Inferring the effects of positive selection on genomes remains a critical step in characterizing the ultimate and proximate causes of adaptation across species, and quantifying positive selection remains a challenge due to the confounding effects of many other evolutionary processes. Robust and efficient approaches for adaptation inference could help characterize the rate and strength of adaptation in nonmodel species for which demographic history, mutational processes, and recombination patterns are not currently well-described. Here, we introduce an efficient and user-friendly extension of the McDonald–Kreitman test (ABC-MK) for quantifying long-term protein adaptation in specific lineages of interest. We characterize the performance of our approach with forward simulations and find that it is robust to many demographic perturbations and positive selection configurations, demonstrating its suitability for applications to nonmodel genomes. We apply ABC-MK to the human proteome and a set of known virus interacting proteins (VIPs) to test the long-term adaptation in genes interacting with viruses. We find substantially stronger signatures of positive selection on RNA-VIPs than DNA-VIPs, suggesting that RNA viruses may be an important driver of human adaptation over deep evolutionary time scales.
Keywords:        Mcdonald and Kreitman test; natural selection; viral interacting proteins
Author:          Jesús Murga-Moreno
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      Title: An efficient and robust ABC approach to infer the rate and strength of adaptation
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       Item: 
        Title: Introduction
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       Item: 
        Title: Methods
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         Item: 
          Title: Preliminaries
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         Item: 
          Title: Expected fixation rates and frequency spectra
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           Item: 
            Title: Expected frequency spectrum
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           Item: 
            Title: Expected number of fixations
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         Item: 
          Title: Background selection and adaptive divergence
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         Item: 
          Title: Poisson-sampling process
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         Item: 
          Title: Computational workflow
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         Item: 
          Title: Inferring parameters with ABC
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         Item: 
          Title: Forward-in-time simulations
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         Item: 
          Title: Human divergence and polymorphism
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         Item: 
          Title: Bootstrap test
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       Item: 
        Title: Results
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         Item: 
          Title: Evolutionary processes affecting adaptation inference
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         Item: 
          Title: ABC evaluation using simulation
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         Item: 
          Title: Application of ABC-MK: human virus-interacting proteins
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        Title: Discussion
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       Item: 
        Title: Data availability
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        Title: Funding
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