Retrotransposons, DNA sequences capable of creating copies of themselves, compose about half of the human genome and played a central role in the evolution of mammals. Their current position in the host genome is the result of the retrotranscription process and of the following host genome evolution. We apply a model from statistical physics to show that the genomic distribution of the two most populated classes of retrotransposons in human deviates from random placement, and that this deviation increases with time. The time dependence suggests a major role of the host genome dynamics in shaping the current retrotransposon distributions. Focusing on a neutral scenario, we show that a simple model based on random placement followed by genome expansion and sequence duplications can reproduce the empirical retrotransposon distributions, even though more complex and possibly selective mechanisms can have contributed. Besides the inherent interest in understanding the origin of current retrotransposon distributions, this work sets a general analytical framework to analyze quantitatively the effects of genome evolutionary dynamics on the distribution of genomic elements.

中文翻译：

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人类基因组中逆转录转座子分布的模型驱动定量分析

逆转录转座子，即能够自我复制的 DNA 序列，构成了人类基因组的大约一半，并在哺乳动物的进化中发挥了核心作用。它们在宿主基因组中的当前位置是逆转录过程和随后宿主基因组进化的结果。我们应用统计物理学中的模型来表明人类中人口最多的两类逆转录转座子的基因组分布偏离随机放置，并且这种偏离随着时间的推移而增加。时间依赖性表明宿主基因组动力学在塑造当前的逆转录转座子分布中的主要作用。着眼于中性场景，我们展示了一个基于随机放置的简单模型，然后是基因组扩展和序列复制，可以重现经验性逆转录转座子分布，尽管更复杂和可能有选择性的机制可能有所贡献。除了了解当前逆转录转座子分布的起源的内在兴趣外，这项工作还建立了一个通用的分析框架，以定量分析基因组进化动力学对基因组元件分布的影响。