Estimating the proportion of beneficial mutations that are not adaptive in mammals.

IF 4 2区 生物学 Q1 GENETICS & HEREDITY
PLoS Genetics Pub Date : 2024-12-26 eCollection Date: 2024-12-01 DOI:10.1371/journal.pgen.1011536
Thibault Latrille, Julien Joseph, Diego A Hartasánchez, Nicolas Salamin
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引用次数: 0

Abstract

Mutations can be beneficial by bringing innovation to their bearer, allowing them to adapt to environmental change. These mutations are typically unpredictable since they respond to an unforeseen change in the environment. However, mutations can also be beneficial because they are simply restoring a state of higher fitness that was lost due to genetic drift in a stable environment. In contrast to adaptive mutations, these beneficial non-adaptive mutations can be predicted if the underlying fitness landscape is stable and known. The contribution of such non-adaptive mutations to molecular evolution has been widely neglected mainly because their detection is very challenging. We have here reconstructed protein-coding gene fitness landscapes shared between mammals, using mutation-selection models and a multi-species alignments across 87 mammals. These fitness landscapes have allowed us to predict the fitness effect of polymorphisms found in 28 mammalian populations. Using methods that quantify selection at the population level, we have confirmed that beneficial non-adaptive mutations are indeed positively selected in extant populations. Our work confirms that deleterious substitutions are accumulating in mammals and are being reverted, generating a balance in which genomes are damaged and restored simultaneously at different loci. We observe that beneficial non-adaptive mutations represent between 15% and 45% of all beneficial mutations in 24 of 28 populations analyzed, suggesting that a substantial part of ongoing positive selection is not driven solely by adaptation to environmental change in mammals.

估计哺乳动物中不适应的有益突变的比例。
突变是有益的,它给携带者带来创新,使他们能够适应环境变化。这些突变通常是不可预测的,因为它们会对环境中不可预见的变化做出反应。然而,突变也可能是有益的,因为它们只是恢复了在稳定环境中由于遗传漂变而失去的更高适应度的状态。与适应性突变相反,如果潜在的适应性景观是稳定和已知的,这些有益的非适应性突变是可以预测的。这种非适应性突变对分子进化的贡献一直被广泛忽视,主要是因为它们的检测非常具有挑战性。我们利用突变选择模型和87种哺乳动物的多物种比对,重建了哺乳动物之间共享的蛋白质编码基因适应度景观。这些适应性景观使我们能够预测在28个哺乳动物种群中发现的多态性的适应性效应。使用在种群水平上量化选择的方法,我们已经证实,有益的非适应性突变确实在现存种群中被积极选择。我们的工作证实,有害的替代正在哺乳动物中积累并正在恢复,从而在不同的位点上同时产生基因组受损和恢复的平衡。我们观察到,在分析的28个种群中的24个种群中,有益的非适应性突变占所有有益突变的15%至45%,这表明哺乳动物正在进行的积极选择的很大一部分不仅仅是由对环境变化的适应所驱动的。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
PLoS Genetics
PLoS Genetics GENETICS & HEREDITY-
自引率
2.20%
发文量
438
期刊介绍: PLOS Genetics is run by an international Editorial Board, headed by the Editors-in-Chief, Greg Barsh (HudsonAlpha Institute of Biotechnology, and Stanford University School of Medicine) and Greg Copenhaver (The University of North Carolina at Chapel Hill). Articles published in PLOS Genetics are archived in PubMed Central and cited in PubMed.
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