Department of Biology, University of Iowa, Iowa City, IA 52242, USA
Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.
Philos Trans R Soc Lond B Biol Sci. 2017 Dec 19;372(1736). doi: 10.1098/rstb.2016.0471.
The consequences of selection at linked sites are multiple and widespread across the genomes of most species. Here, I first review the main concepts behind models of selection and linkage in recombining genomes, present the difficulty in parametrizing these models simply as a reduction in effective population size () and discuss the predicted impact of recombination rates on levels of diversity across genomes. Arguments are then put forward in favour of using a model of selection and linkage with neutral and deleterious mutations (i.e. the background selection model, BGS) as a sensible null hypothesis for investigating the presence of other forms of selection, such as balancing or positive. I also describe and compare two studies that have generated high-resolution landscapes of the predicted consequences of selection at linked sites in Both studies show that BGS can explain a very large fraction of the observed variation in diversity across the whole genome, thus supporting its use as null model. Finally, I identify and discuss a number of caveats and challenges in studies of genetic hitchhiking that have been often overlooked, with several of them sharing a potential bias towards overestimating the evidence supporting recent selective sweeps to the detriment of a BGS explanation. One potential source of bias is the analysis of non-equilibrium populations: it is precisely because models of selection and linkage predict variation in across chromosomes that demographic dynamics are not expected to be equivalent chromosome- or genome-wide. Other challenges include the use of incomplete genome annotations, the assumption of temporally stable recombination landscapes, the presence of genes under balancing selection and the consequences of ignoring non-crossover (gene conversion) recombination events.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
连锁位点选择的后果在大多数物种的基因组中是多样且广泛存在的。在这里，我首先回顾了重组基因组中选择和连锁模型的主要概念，提出了将这些模型简单地参数化为有效种群大小 () 减少的困难，并讨论了重组率对基因组多样性水平的预测影响。然后提出了赞成使用带有中性和有害突变的选择和连锁模型（即背景选择模型，BGS）作为调查其他形式选择（如平衡或阳性选择）存在的合理零假设的论点。我还描述并比较了两项研究，这两项研究都生成了连锁位点选择在全基因组中预测后果的高分辨率图谱。这两项研究都表明，BGS 可以解释整个基因组多样性观察到的变异的很大一部分，因此支持将其用作零模型。最后，我确定并讨论了遗传 hitchhiking 研究中经常被忽视的一些注意事项和挑战，其中有几个挑战都有可能偏向于高估支持最近选择性清除的证据，而不利于 BGS 解释。一个潜在的偏见来源是对非平衡群体的分析：正是因为选择和连锁模型预测了染色体之间的变化，所以预计人口动态在染色体或全基因组范围内不会等效。其他挑战包括使用不完整的基因组注释、暂时稳定的重组景观假设、平衡选择下基因的存在以及忽略非交叉（基因转换）重组事件的后果。本文是“有性生物中重组率变化的进化原因和后果”主题问题的一部分。
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