Shared evolutionary processes shape landscapes of genomic variation in the great apes.
Shared evolutionary processes shape landscapes of genomic variation in the great apes.
复制标题
共享的进化过程塑造了类人猿的基因组变异景观。
DOI：
10.1101/2023.02.07.527547
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Ralph,PeterL
中科院分区：
文献类型：
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作者：
Rodrigues,MurilloF;Kern,AndrewD;Ralph,PeterL
至少在过去的50年里，群体遗传学作为一个领域，一直致力于描述形成基因组变异模式的各种力量的精确平衡。这个问题是具有挑战性的，因为模拟进化过程之间的相互作用是困难的，不同的过程可以以相似的方式影响遗传变异。在本文中，我们描述了密切相关物种之间的多样性和分歧如何随时间变化，利用遗传变异景观之间的相关性作为理解进化过程之间相互作用的工具。我们在一组样本丰富的类人猿基因组中发现了多样性和分化景观之间的强相关性，并探讨了不完全谱系分选、突变率变异、gc偏向基因转换和选择等不同过程如何促成这些相关性。通过高度现实的、染色体尺度的、向前时间的模拟，我们表明类人猿的多样性和分化的景观是如此紧密相关，以至于不能仅仅通过严格的中性过程来解释。我们的最佳拟合模拟包括基因组功能部分的有害和有益突变，其中这些区域内的固定是由正选择驱动的。这项研究为密切相关物种的遗传变异建模提供了一个框架，这种方法可以阐明形成遗传变异的复杂力量平衡。
For at least the past 5 decades, population genetics, as a field, has worked to describe the precise balance of forces that shape patterns of variation in genomes. The problem is challenging because modeling the interactions between evolutionary processes is difficult, and different processes can impact genetic variation in similar ways. In this paper, we describe how diversity and divergence between closely related species change with time, using correlations between landscapes of genetic variation as a tool to understand the interplay between evolutionary processes. We find strong correlations between landscapes of diversity and divergence in a well-sampled set of great ape genomes, and explore how various processes such as incomplete lineage sorting, mutation rate variation, GC-biased gene conversion and selection contribute to these correlations. Through highly realistic, chromosome-scale, forward-in-time simulations, we show that the landscapes of diversity and divergence in the great apes are too well correlated to be explained via strictly neutral processes alone. Our best fitting simulation includes both deleterious and beneficial mutations in functional portions of the genome, in whichof fixations within those regions is driven by positive selection. This study provides a framework for modeling genetic variation in closely related species, an approach which can shed light on the complex balance of forces that have shaped genetic variation.