Data from: Quantifying population divergence on short timescales

Quantifying the contribution of the various processes that influence population genetic structure is important, but difficult. One of the reasons is that no single measure appropriately quantifies all aspects of genetic structure. An increasing number of studies is analyzing population structure using the statistic D, which measures genetic differentiation, next to G_ST, which is the standardized variance in allele frequencies among populations. Few studies have evaluated which statistic is most appropriate in particular situations. In this study, we evaluated which index is more suitable in quantifying postglacial divergence between three-spined stickleback (<i>Gasterosteus aculeatus</i>) populations from Western Europe. Population structure on this short timescale (10, 000 generations) is likely shaped by colonization history, followed by migration and drift. Using microsatellite markers and anticipating that D and G_ST might have different capacities to reveal these processes, we evaluated population structure at two levels: 1) between lowland and upland populations, aiming to infer historical processes; and 2) among upland populations, aiming to quantify contemporary processes. In the first case, only D revealed clear clusters of populations, putatively indicative of population ancestry. In the second case, only G_ST was indicative for the balance between migration and drift. Simulations of colonization and subsequent divergence in a hierarchical stepping stone model confirmed this discrepancy, which becomes particularly strong for markers with moderate to high mutation rates. We conclude that on short timescales, and across strong clines in population size, D is useful to infer colonization history, whereas G_ST is sensitive for more recent demographic events.

量化影响种群遗传结构的各类过程的贡献，兼具重要意义与颇高难度。究其核心原因之一，尚无单一指标能够恰当地覆盖并量化遗传结构的所有维度。当前越来越多的研究在分析种群结构时，除采用用于衡量种群间等位基因频率标准化方差的统计量G_ST之外，还引入了另一遗传分化统计量D。然而鲜有研究针对特定情境评估何种统计量最为适用。本研究以西欧地区的三刺棘鱼（*Gasterosteus aculeatus*）种群为研究对象，旨在量化其冰期后分化情况，并评估哪一指标更适配该研究场景。这种发生于10000代短时间尺度下的种群结构，大概率首先由定殖历史塑造，后续则受迁移与遗传漂变的共同影响。我们借助微卫星标记开展研究，考虑到D与G_ST在揭示上述生态进化过程的能力上可能存在差异，从两个层面展开种群结构分析：1）低地与高地种群之间，旨在推断历史演化过程；2）高地种群内部，旨在量化当代种群动态过程。研究结果显示，在第一种分析场景中，仅D能够揭示清晰的种群聚类结构，推测该结果可反映种群的祖先起源关系；而在第二种场景中，仅G_ST能够体现迁移与遗传漂变之间的动态平衡。通过层级踏脚石模型开展的定殖与后续分化模拟实验，验证了这一指标间的差异，且该差异在具有中等到较高突变率的分子标记中表现得尤为显著。综上，我们得出结论：在短时间尺度以及种群规模存在显著梯度的场景下，统计量D可用于推断种群的定殖历史，而G_ST则对更近发生的种群动态事件更为敏感。