How long does speciation take? The answer to this important question in evolutionary biology lies in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently diverged lineages, we now have the lineage-level trees to answer these questions. However, we do not yet have an analytical tool for inferring speciation processes from these trees. What is needed is a model of speciation processes that generates both the trees and species identities of extant lineages. The model should allow calculation of the probability that certain lineages belong to certain species and have an evolutionary history consistent with the tree. Here we propose such a model and test the model performance on both simulated data and real data. We show that maximum likelihood estimates of the model are highly accurate and give estimates from real data that generate patterns consistent with observations. We discuss how to extend the model to account for different rates and types of speciation processes across lineages in a species group. By linking evolutionary processes on lineage level to species level, the model provides a new phylogenetic approach to study not just when speciation happened, but how speciation happened.

中文翻译：

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依赖状态的物种形成和灭绝方法下的长期物种形成

物种形成需要多长时间？进化生物学中这个重要问题的答案不仅在于物种之间的遗传差异，而且在于每个物种内部谱系之间的遗传差异。随着非模式生物基因组测序的进步和统计工具的进步，以提高推断最近分歧谱系进化历史的准确性，我们现在有了谱系级别的树来回答这些问题。然而，我们还没有一个分析工具来推断这些树的物种形成过程。所需要的是生成现存谱系的树木和物种特征的物种形成过程模型。该模型应该允许计算某些谱系属于某些物种并具有与树一致的进化历史的概率。在这里，我们提出了这样一个模型，并在模拟数据和真实数据上测试了模型的性能。我们表明，该模型的最大似然估计是高度准确的，并根据生成与观察结果一致的模式的真实数据进行估计。我们讨论了如何扩展模型以解释物种群中跨谱系的不同速率和类型的物种形成过程。通过将谱系水平的进化过程与物种水平联系起来，该模型提供了一种新的系统发育方法，不仅可以研究物种形成的时间，还可以研究物种形成的方式。我们讨论了如何扩展模型以解释物种群中跨谱系的不同速率和类型的物种形成过程。通过将谱系水平的进化过程与物种水平联系起来，该模型提供了一种新的系统发育方法，不仅可以研究物种形成的时间，还可以研究物种形成的方式。我们讨论了如何扩展模型以解释物种群中跨谱系的不同速率和类型的物种形成过程。通过将谱系水平的进化过程与物种水平联系起来，该模型提供了一种新的系统发育方法，不仅可以研究物种形成的时间，还可以研究物种形成的方式。