Comparing divergences across multiple sister population pairs has been a focus in phylogeography since its inception. Initial approaches used organelle genetic data and involved qualitative comparisons of phylogenetic patterns to evaluate hypotheses of shared and variable evolutionary responses. This endeavor has progressed with coalescent model‐based statistical techniques and advances in next‐generation sequencing, yet there remains a need for methods that can exploit aggregated genomic‐scale data within a unified analytical framework. To this end, we introduce the aggregate joint site frequency spectrum (ajSFS) by validating its use within a hierarchical Bayesian framework through several in silico experiments. Subsequently, we applied our method against two published restriction site–associated DNA marker datasets consisting of eight local replicates of a lamprey species pair and six co‐distributed passerine taxon pairs, respectively, with the aim of inferring variability in co‐divergence and co‐migration histories. We found that the lamprey population pairs exhibited temporal synchrony in both co‐divergence and collective secondary contact times, yet an idiosyncratic pattern in secondary migration intensities. In contrast, the bird population pairs displayed thoroughly asynchronous co‐divergence histories. Our results demonstrate that the ajSFS can be exploited for complex and flexible co‐demographic inference, opening up new possibilities for comparative phylogeography and population genomic studies.

中文翻译：

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比较系统地理学推断与来自聚合种群对的全基因组数据

自系统地理学成立以来，比较多个姐妹种群对的差异一直是系统地理学的焦点。最初的方法使用细胞器遗传数据并涉及系统发育模式的定性比较，以评估共享和可变进化反应的假设。随着基于聚结模型的统计技术和下一代测序的进步，这项努力取得了进展，但仍然需要能够在统一分析框架内利用聚合基因组规模数据的方法。为此，我们通过几个计算机实验验证其在分层贝叶斯框架中的使用，从而引入了聚合联合站点频谱（ajSFS）。随后，我们将我们的方法应用于两个已发表的限制性位点相关 DNA 标记数据集，这些数据集分别由一个七鳃鳗物种对和六个共同分布的燕雀类群对的八个局部重复组成，目的是推断共同发散和共同迁移历史的变异性. 我们发现七鳃鳗种群对在共同发散和集体二次接触时间上表现出时间同步，但在二次迁移强度上表现出特殊的模式。相比之下，鸟类种群对显示出完全异步的协同发散历史。我们的结果表明，ajSFS 可用于复杂而灵活的人口统计学推断，为比较系统地理学和种群基因组研究开辟了新的可能性。