In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.

中文翻译：

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标点分子进化的基于模型的推断。

在分子进化的标准模型中，DNA序列根据泊松过程以恒定速率（称为分子时钟）或可变速率（松弛时钟）通过异步取代而进化。但是，DNA序列也可能发生快速趋异现象，这将以同步取代的形式出现，同时在宏观进化时间尺度上影响多个位点。在这里，我们开发了一个模型，我们将其称为“带有尖峰的松散时钟”模型，该模型将基础，类似于时钟的分子取代与在物种形成事件中出现的称为尖峰的快速发散相结合。考虑到多序列比对及其时间校准物种的系统发育，我们的模型能够检测与尖峰事件同时发生的物种形成事件（包括隐性事件），并估计这些尖峰在系统发育上的概率和幅度。我们确定了在哪些条件下可以将尖峰与分子取代的钟状成分的自然变化以及钟的变化区分开。我们将该方法应用于蛇毒蛋白的基础基因，并在系统发育中的基因特定位置识别出几个峰值。这项工作应为依赖整个基因组的分析为物种多样化的模式铺平道路。我们将该方法应用于蛇毒蛋白的基础基因，并在系统发育中的基因特定位置识别出几个峰值。这项工作应为依赖整个基因组的分析为物种多样化的模式铺平道路。我们将该方法应用于蛇毒蛋白的基础基因，并在系统发育中的基因特定位置识别出几个峰值。这项工作应为依赖整个基因组的分析为物种多样化的模式铺平道路。