早期进化的第一性原理模型：基因家族、物种和首选蛋白质折叠的出现
A first-principles model of early evolution: Emergence of gene families, species and preferred protein folds
摘要：
在这项工作中，我们开发了一个早期进化的微观物理模型，其中表型，生物体的预期寿命，是直接相关的基因型，其蛋白质在其天然构象的稳定性，可以在模型中准确地确定。在计算机上模拟模型，我们始终观察到大爆炸的情况下，指数人口增长englomerate一旦有利的序列结构组合（稳定蛋白质的前体）被发现。在此基础上，结构空间的随机多样性突然崩溃为一小部分优选蛋白质。我们观察到，蛋白质折叠在种群中保持稳定和丰富的时间尺度远远大于突变或生物体的寿命，和分布的优势折叠的寿命在一个人口近似遵循幂律。新折叠的发现和新序列的产生之间的进化时间尺度的分离引起了蛋白质家族和超家族的出现，其大小是幂律分布的，紧密匹配真实蛋白质的相同分布。在种群水平上，我们观察到物种的出现，携带相似基因组的亚种群。此外，我们提出了一个简单的理论，涉及到不断发展的蛋白质的稳定性新兴基因组的大小。总之，这些结果提供了第一个基因家族在早期进化过程中如何发展的微观第一原理图
英文摘要：
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the Big Bang scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at time scales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary time scales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species, subpopulations which carry similar genomes. Further we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first principles picture of how first gene families developed in the course of early evolution
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