图上空间结构种群的突变命运:连接模型与实验

IF 3.8 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
PLoS Computational Biology Pub Date : 2024-09-06 eCollection Date: 2024-09-01 DOI:10.1371/journal.pcbi.1012424
Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol
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引用次数: 0

摘要

在自然界中,大多数微生物种群都有复杂的空间结构,这会影响它们的进化。进化图理论预测,将个体置于图节点上的某些空间结构会影响突变体固定的概率。进化实验已开始明确探讨图结构对突变体固定的影响。然而,进化图论的假设条件与现代进化实验的条件不同,这使得理论与实验之间的比较具有挑战性。在此,我们希望利用我们的空间结构种群新模型来弥补这一差距。该模型考虑了位于图节点上的相连亚种群,并允许非对称迁移。该模型可以处理大量种群,并明确地将序列通过事件与迁移进行建模,从而密切模拟实验条件。我们根据这一模型对最近的实验进行了分析。我们为未来的实验提出了有用的参数机制,并对这些实验进行了定量预测。特别是,我们提出了一些实验来直接验证我们最近的预测,即与混合良好的种群相比,具有非对称迁移的星形图会抑制自然选择并加速突变体的固定或灭绝。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Mutant fate in spatially structured populations on graphs: Connecting models to experiments.

In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the probability that a mutant will fix. Evolution experiments are beginning to explicitly address the impact of graph structures on mutant fixation. However, the assumptions of evolutionary graph theory differ from the conditions of modern evolution experiments, making the comparison between theory and experiment challenging. Here, we aim to bridge this gap by using our new model of spatially structured populations. This model considers connected subpopulations that lie on the nodes of a graph, and allows asymmetric migrations. It can handle large populations, and explicitly models serial passage events with migrations, thus closely mimicking experimental conditions. We analyze recent experiments in light of this model. We suggest useful parameter regimes for future experiments, and we make quantitative predictions for these experiments. In particular, we propose experiments to directly test our recent prediction that the star graph with asymmetric migrations suppresses natural selection and can accelerate mutant fixation or extinction, compared to a well-mixed population.

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来源期刊
PLoS Computational Biology
PLoS Computational Biology BIOCHEMICAL RESEARCH METHODS-MATHEMATICAL & COMPUTATIONAL BIOLOGY
CiteScore
7.10
自引率
4.70%
发文量
820
审稿时长
2.5 months
期刊介绍: PLOS Computational Biology features works of exceptional significance that further our understanding of living systems at all scales—from molecules and cells, to patient populations and ecosystems—through the application of computational methods. Readers include life and computational scientists, who can take the important findings presented here to the next level of discovery. Research articles must be declared as belonging to a relevant section. More information about the sections can be found in the submission guidelines. Research articles should model aspects of biological systems, demonstrate both methodological and scientific novelty, and provide profound new biological insights. Generally, reliability and significance of biological discovery through computation should be validated and enriched by experimental studies. Inclusion of experimental validation is not required for publication, but should be referenced where possible. Inclusion of experimental validation of a modest biological discovery through computation does not render a manuscript suitable for PLOS Computational Biology. Research articles specifically designated as Methods papers should describe outstanding methods of exceptional importance that have been shown, or have the promise to provide new biological insights. The method must already be widely adopted, or have the promise of wide adoption by a broad community of users. Enhancements to existing published methods will only be considered if those enhancements bring exceptional new capabilities.
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