Lyulina Anastasia S, Liu Zhiru, Good Benjamin H
Department of Biology, Stanford University, Stanford, CA 94305, USA.
Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
bioRxiv. 2024 Apr 1:2024.03.28.587282. doi: 10.1101/2024.03.28.587282.
Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.
重组通过将现有变异重新组合到新的遗传背景上来打破遗传连锁。传统上，这些动态变化是通过检查等位基因之间的相关性以及它们如何作为重组率的函数而衰减来量化的。然而，这些相关性的大小受到自然选择和遗传漂变等其他进化力量的强烈影响，使得难以梳理出重组的影响。在这里，我们引入了一个理论框架，用于分析另一类统计量，这些统计量测量由重组产生的同塑性（趋同演化）。我们推导出解析表达式，预测这些统计量如何依赖于重组率和反复突变率、负选择和遗传漂变的强度以及突变等位基因的当前频率。我们发现，同塑性的程度可能强烈依赖于这个频率尺度，该尺度反映了这些突变发生的潜在时间尺度。我们展示了这些尺度特性如何用于分离重组的影响，并讨论了它们对细菌水平基因转移速率的影响。
