Howell Emma K, Nolfo-Clements Lauren E, Payseur Bret A
Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI.
Framingham State University, Framingham, MA.
bioRxiv. 2025 Jan 25:2025.01.24.633650. doi: 10.1101/2025.01.24.633650.
Contemporary patterns of genetic variation reflect the cumulative history of a population. Population splitting, migration, and changes in population size leave genomic signals that enable their characterization. Existing methods aimed at reconstructing these features of demographic history are often restricted in their temporal resolution, leaving gaps about how basic evolutionary parameters change over time. To illustrate the prospects for extracting insights about dynamic population histories, we turn to a system that has undergone dramatic changes on both geological and contemporary timescales - an urbanized, near-shore archipelago. Using whole genome sequences, we employed both common and novel summaries of variation to infer the demographic history of three populations of endemic white-footed mice () in Massachusetts' Boston Harbor. We find informative contrasts among the inferences drawn from these distinct patterns of diversity. While demographic models that fit the joint site frequency spectrum (jSFS) coincide with the known geological history of the Boston Harbor, patterns of linkage disequilibrium reveal collapses in population size on contemporary timescales that are not recovered by our candidate models. Historical migration between populations is also absent from best-fitting models for the jSFS, but rare variants show unusual clustering along the genome within individual mice, a pattern that is reproduced by simulations of recent migration. Together, our findings indicate that these urban archipelago populations have been shaped by both ancient geological processes and recent human influence. More broadly, our study demonstrates that the temporal resolution of demographic history can be extended by examining multiple facets of genomic variation.
当代遗传变异模式反映了一个种群的累积历史。种群分裂、迁移和种群大小的变化会留下基因组信号，从而能够对其进行特征描述。旨在重建人口历史这些特征的现有方法在时间分辨率上往往受到限制，在基本进化参数如何随时间变化方面留下了空白。为了说明提取关于动态种群历史见解的前景，我们转向一个在地质和当代时间尺度上都发生了巨大变化的系统——一个城市化的近岸群岛。利用全基因组序列，我们采用了常见和新颖的变异汇总方法来推断马萨诸塞州波士顿港三个特有白足鼠种群的人口历史。我们在从这些不同的多样性模式得出的推断中发现了有益的对比。虽然拟合联合位点频率谱（jSFS）的人口模型与波士顿港已知的地质历史相符，但连锁不平衡模式揭示了当代时间尺度上种群大小的崩溃，而我们的候选模型并未恢复这一情况。jSFS的最佳拟合模型中也没有种群间的历史迁移，但罕见变异在个体小鼠的基因组中呈现出不寻常的聚类，这一模式在近期迁移的模拟中得以重现。总之，我们的研究结果表明，这些城市群岛种群既受到古代地质过程的影响，也受到近期人类活动的影响。更广泛地说，我们的研究表明，通过检查基因组变异的多个方面，可以扩展人口历史的时间分辨率。
