Archaic introgression and the distribution of shared variation under stabilizing selection.

IF 4 2区 生物学 Q1 GENETICS & HEREDITY
PLoS Genetics Pub Date : 2025-03-31 eCollection Date: 2025-03-01 DOI:10.1371/journal.pgen.1011623
Aaron P Ragsdale
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引用次数: 0

Abstract

Many phenotypic traits are under stabilizing selection, which maintains a population's mean phenotypic value near some optimum. The dynamics of traits and trait architectures under stabilizing selection have been extensively studied for single populations at steady state. However, natural populations are seldom at steady state and are often structured in some way. Admixture and introgression events may be common, including over human evolutionary history. Because stabilizing selection results in selection against the minor allele at a trait-affecting locus, alleles from the minor parental ancestry will be selected against after admixture. We show that the site-frequency spectrum can be used to model the genetic architecture of such traits, allowing for the study of trait architecture dynamics in complex multi-population settings. We use a simple deterministic two-locus model to predict the reduction of introgressed ancestry around trait-contributing loci. From this and individual-based simulations, we show that introgressed-ancestry is depleted around such loci. When introgression between two diverged populations occurs in both directions, as has been inferred between humans and Neanderthals, the locations of such regions with depleted introgressed ancestry will tend to be shared across populations. We argue that stabilizing selection for shared phenotypic optima may explain recent observations in which regions of depleted human-introgressed ancestry in the Neanderthal genome overlap with Neanderthal-ancestry deserts in humans.

稳定选择下的古渐渗与共有变异的分布。
许多表型性状处于稳定选择状态,使种群的平均表型值保持在某一最优值附近。稳定选择下的性状动态和性状结构已经得到了广泛的研究。然而,自然种群很少处于稳定状态,并且经常以某种方式结构化。混合和基因渗入事件可能是常见的,包括在人类进化史上。由于稳定选择的结果是对性状影响位点上的次要等位基因的选择,因此来自次要亲本祖先的等位基因在混合后将被选择。我们表明,位点频谱可以用来模拟这些性状的遗传结构,允许在复杂的多种群环境下研究性状结构动态。我们使用一个简单的确定性双位点模型来预测性状贡献位点周围的渐渗祖先的减少。从这个和基于个体的模拟中,我们发现在这些位点周围,遗传渐渗的祖先是耗尽的。当两个不同种群之间的基因渗入发生在两个方向上时,正如人类和尼安德特人之间所推断的那样,这些基因渗入枯竭的地区的位置将倾向于在不同种群之间共享。我们认为,共同表型最优的稳定选择可以解释最近的观察结果,即尼安德特人基因组中耗尽的人类渐渗入祖先区域与人类中尼安德特人祖先沙漠区域重叠。
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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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