Variation in recombination rate affects detection of outliers in genome scans under neutrality
Variation in recombination rate affects detection of outliers in genome scans under neutrality
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DOI：
10.1101/2020.02.06.937813
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发表时间：
2020-02
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通讯作者：
Tom R. Booker;S. Yeaman;M. Whitlock
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作者：
Tom R. Booker;S. Yeaman;M. Whitlock
基因组扫描可以潜在地识别参与进化过程的遗传位点，如局部适应和基因流动。在这里，我们表明，重组率的变化在一个中性的进化基因组引起混合抽样分布的平均FST，一个共同的人口遗传汇总统计。特别是，我们发现，在低重组的地区的分布估计有更多的方差和更长的尾巴比在更高的重组地区。因此，在不考虑局部重组率的情况下从全基因组分布确定离群值可能会增加低重组区域中的假阳性频率，并且在更高重组区域中过于保守。我们对模拟和经验果蝇数据集进行基因组扫描，在这两种情况下，都发现了与这种中性模型一致的模式。对于用于捕获聚结过程中的变化的其他汇总统计量，观察到类似的模式。连锁选择，特别是背景选择，经常被用来解释整个基因组的异质性，但在这里，我们指出，即使在中性，统计假象可能会出现由于重组率的变化。我们的研究结果突出了基因组扫描研究设计中的一个缺陷，并表明如果没有局部重组率的估计，解释任何概括统计的基因组景观，捕捉在聚结过程中的变化将是非常困难的。
Genome scans can potentially identify genetic loci involved in evolutionary processes such as local adaptation and gene flow. Here, we show that recombination rate variation across a neutrally evolving genome gives rise to mixed sampling distributions of mean FST, a common population genetic summary statistic. In particular, we show that in regions of low recombination the distribution of estimates have more variance and a longer tail than in more highly recombining regions. Determining outliers from the genome-wide distribution without taking local recombination rate into consideration may therefore increase the frequency of false positives in low recombination regions and be overly conservative in more highly recombining ones. We perform genome-scans on simulated and empirical Drosophila melanogaster datasets and, in both cases, find patterns consistent with this neutral model. Similar patterns are observed for other summary statistics used to capture variation in the coalescent process. Linked selection, particularly background selection, is often invoked to explain heterogeneity in across the genome, but here we point out that even under neutrality, statistical artefacts can arise due to variation in recombination rate. Our results highlight a flaw in the design of genome scan studies and suggest that without estimates of local recombination rate, interpreting the genomic landscape of any summary statistic that captures variation in the coalescent process will be very difficult.