Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of Biology, Graduate Center of City University of New York, New York, NY, 10016.
Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of Biology, City College of City University of New York, New York, NY, 10031.
Evolution. 2020 May;74(5):808-830. doi: 10.1111/evo.13945. Epub 2020 Apr 15.
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.
自发生以来，比较多个姐妹种群对之间的分歧一直是系统地理学的重点。最初的方法使用细胞器遗传数据，并涉及对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。随着基于合并模型的统计技术和下一代测序的进步，这项工作取得了进展，但仍然需要能够在统一的分析框架内利用聚合基因组规模数据的方法。为此，我们通过在分层贝叶斯框架内通过几个计算机实验验证其用途，引入了聚合联合位点频率谱 (ajSFS)。随后，我们将我们的方法应用于两个已发表的基于限制位点相关 DNA 标记数据集，分别由一个七鳃鳗物种对的 8 个局部重复和 6 个共同分布的雀形目分类群对组成，目的是推断共同分歧和共同迁移历史的可变性。我们发现，七鳃鳗种群对在共同分歧和集体二次接触时间上表现出时间同步性，但在二次迁移强度上表现出特殊模式。相比之下，鸟类种群对显示出完全不同步的共同分歧历史。我们的结果表明，ajSFS 可用于复杂和灵活的共同人口统计学推断，为比较系统地理学和群体基因组学研究开辟了新的可能性。
