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本文引用的文献

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Absorbing phenomena and escaping time for Muller's ratchet in adaptive landscape.适应景观中缪勒棘轮的吸收现象与逃逸时间
BMC Syst Biol. 2012;6 Suppl 1(Suppl 1):S10. doi: 10.1186/1752-0509-6-S1-S10. Epub 2012 Jul 16.
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The potential and flux landscape theory of evolution.进化的潜能与通量景观理论。
J Chem Phys. 2012 Aug 14;137(6):065102. doi: 10.1063/1.4734305.
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Biophysical connection between evolutionary dynamics and thermodynamics in in vitro evolution.体外进化中进化动力学与热力学的生物物理连接。
J Theor Biol. 2012 Feb 7;294:122-9. doi: 10.1016/j.jtbi.2011.10.036. Epub 2011 Nov 9.
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Fixation, transient landscape, and diffusion dilemma in stochastic evolutionary game dynamics.随机进化博弈动力学中的固定、瞬态景观与扩散困境
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep;84(3 Pt 1):031907. doi: 10.1103/PhysRevE.84.031907. Epub 2011 Sep 7.
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Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics from Darwinian Dynamics.从达尔文动力学中涌现出随机动力学等式和稳态热力学。
Commun Theor Phys. 2008 May 15;49(5):1073-1090. doi: 10.1088/0253-6102/49/5/01.
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Visualizing fitness landscapes.可视化健身地形。
Evolution. 2011 Jun;65(6):1544-58. doi: 10.1111/j.1558-5646.2011.01236.x. Epub 2011 Mar 1.
7
Evolution and speciation on holey adaptive landscapes.多孔适应景观中的进化和物种形成。
Trends Ecol Evol. 1997 Aug;12(8):307-12. doi: 10.1016/S0169-5347(97)01098-7.
8
Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda.噬菌体 λ中可遗传且稳定的溶原态的概率景观。
Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18445-50. doi: 10.1073/pnas.1001455107. Epub 2010 Oct 11.
9
Kinetic paths, time scale, and underlying landscapes: a path integral framework to study global natures of nonequilibrium systems and networks.动力学路径、时间尺度和基础景观:研究非平衡系统和网络整体性质的路径积分框架。
J Chem Phys. 2010 Sep 28;133(12):125103. doi: 10.1063/1.3478547.
10
A stochastic model for a single click of Muller's ratchet.Muller 棘轮单次点击的随机模型。
J Theor Biol. 2010 Jun 21;264(4):1120-32. doi: 10.1016/j.jtbi.2010.03.014. Epub 2010 Mar 15.

适应景观上的 Wright-Fisher 动力。

Wright-Fisher dynamics on adaptive landscape.

出版信息

IET Syst Biol. 2013 Oct;7(5):153-64. doi: 10.1049/iet-syb.2012.0058.

DOI:10.1049/iet-syb.2012.0058
PMID:24067415
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8687433/
Abstract

Adaptive landscape, proposed by Sewall Wright, has provided a conceptual framework to describe dynamical behaviours. However, it is still a challenge to explicitly construct such a landscape, and apply it to quantify interesting evolutionary processes. This is particularly true for neutral evolution. In this work, the authors study one-dimensional Wright Fisher process, and analytically obtain an adaptive landscape as a potential function. They provide the complete characterisation for dynamical behaviours of all possible mutation rates under the influence of mutation and random drift. This same analysis has been applied to situations with additive selection and random drift for all possible selection rates. The critical state dividing the basins of two stable states is directly obtained by the landscape. In addition, the landscape is able to handle situations with pure random drift, which would be non-normalisable for its stationary distribution. The nature of non-normalisation is from the singularity of adaptive landscape. In addition, they propose a new type of neutral evolution. It has the same probability for all possible states. The new type of neutral evolution describes the non-neutral alleles with 0%. They take the equal effect of mutation and random drift as an example.

摘要

适应景观由 Sewall Wright 提出,为描述动力学行为提供了一个概念框架。然而,明确构建这样的景观并将其应用于量化有趣的进化过程仍然是一个挑战。对于中性进化来说尤其如此。在这项工作中,作者研究了一维 Wright-Fisher 过程,并通过分析得到了一个作为势函数的适应景观。他们为在突变和随机漂变的影响下所有可能的突变率下的动力学行为提供了完整的描述。同样的分析也适用于具有加性选择和随机漂变的所有可能选择率的情况。由景观直接得到了两个稳定状态的分界面。此外,该景观还能够处理仅由随机漂变的情况,对于其平稳分布来说,这是不可归一化的。不可归一化的本质来自于适应景观的奇点。此外,他们提出了一种新的中性进化类型。它对所有可能的状态都有相同的概率。这种新的中性进化用 0%描述非中性等位基因。他们以突变和随机漂变的相同影响为例。