The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression – the exchange of genetic material through hybridization and backcrossing – are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report “ancient introgression” – referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome, and implemented this test in the program Dsuite.

中文翻译：

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在存在物种间速率变异的情况下实现可靠​​的基因渗入检测


种间杂交的作用最近受到越来越多的关注，特别是在多样化动态的背景下。基因组研究现已非常清楚地表明，杂交和基因渗入（通过杂交和回交交换遗传物质）比以前想象的要普遍得多。除了类群之间正在进行或最近的基因交换的案例之外，越来越多的研究报告了“古代基因渗入”——指的是遥远的过去发生的杂交结果。然而，目前尚不清楚检测基因渗入的常用方法是否适用于此类旧系统，因为大多数这些方法最初是为了在种群和最近分化的物种水平上进行分析而开发的，受到最近或正在进行的遗传交换的影响。特别是，随着进化分歧的增加，许多常用方法中隐含的恒定进化率假设更有可能被违反。为了测试渗入检测方法应用于旧系统时的局限性，我们在各种设置下模拟了数千个基因组数据集，具有不同程度的物种间速率变异和渗入。使用这些模拟数据集，我们表明一些常用的统计方法，包括 D 统计和基于局部系统发育树集的某些测试，可以在具有不同进化速率的不同类群之间产生基因渗入的假阳性信号。这些误导性信号是由不同谱系中以不同速率发生的同质性引起的。 为了区分由速率变化和真正渗入引起的模式，我们开发了一种新的测试，该测试基于基因组上渗入位点的预期聚类，并在程序 Dsuite 中实施了该测试。