Data from: Sex, size and timing: sampling design for reliable population genetics analyses using microsatellite data

1. Population genetics is used in a wide variety of fields such as ecology and biodiversity conservation. How estimated genetic characteristics of natural populations can be influenced by the sampling design has been a long-standing concern. Multiple simulation and empirical studies illustrated the influence of both sample size and polymorphism of markers. However, our review of studies on butterfly population genetics indicates no consensus on sample size for the estimation of genetic diversity or differentiation. Furthermore, other aspects of sampling design (sex ratio and timing of sampling) were not addressed and their potential impact on genetic parameter estimates rarely explored. 2. Using a large empirical dataset (with spatial and temporal replicates) collected on a butterfly species, Boloria aquilonaris, as well as simulated datasets reflecting (1) three scenarios of migration-genetic drift equilibrium and (2) one scenario of parameter stabilization after 100,000 generations, we quantified the impacts of three aspects of genetic sampling design (namely sample size, sex ratio, and timing of sampling) on the estimation of allele frequencies and its potential downstream impact on the estimation of genetic parameters. 3. With empirical data, we found that sample size and timing of sampling strongly affected the accuracy of allele frequencies and the downstream analyses, while sex ratio did not. Our results were consistent across spatial and temporal replicates. Also, with simulated data, we showed that the genetic sampling design had limited effect in systems where dispersal outweighs genetic drift, while it can have major consequences on our understanding of the genetic diversity and population differentiation in systems dominated by genetic drift (such as most study systems with conservation concerns). 4. We advocate for careful consideration of all aspects of the sampling design in population genetics studies, i.e. a sufficient number of samples, while ensuring similar sex ratio among sampling locations and collecting with timing appropriate to the question under study. This is particularly important when the study aims at species conservation.

1. 种群遗传学（Population genetics）的应用领域覆盖生态学与生物多样性保护等诸多方向。自然种群的估算遗传特征如何受采样设计（sampling design）影响，长期以来都是学界关注的核心议题。多项模拟与实证研究均证实，样本量与标记多态性（polymorphism of markers）均会对结果产生影响。但我们针对蝴蝶种群遗传学研究的综述显示，当前学界在用于估算遗传多样性或遗传分化的样本量标准上尚未达成共识。此外，采样设计的其他维度——性比（sex ratio）与采样时机（timing of sampling）——均未得到充分探讨，其对遗传参数估算的潜在影响也鲜有研究。2. 本研究以北冷堇蛱蝶（Boloria aquilonaris）的大型实证数据集（large empirical dataset，包含空间与时间重复样（spatial and temporal replicates））为基础，结合三类反映迁移-遗传漂变平衡（migration-genetic drift equilibrium）情景的模拟数据集，以及一类10万代后参数趋于稳定的模拟数据集，量化评估了遗传采样设计的三个维度——样本量、性比与采样时机——对等位基因频率（allele frequencies）估算的影响，及其对遗传参数（genetic parameters）估算的潜在下游效应。3. 基于实证数据的分析显示，样本量与采样时机都会显著影响等位基因频率估算的准确性及下游分析结果，而性比则无明显影响，且该结论在空间与时间重复样中保持一致。此外，模拟数据结果表明，在扩散强于遗传漂变的系统中，遗传采样设计的影响有限；但在受遗传漂变主导的系统（如多数兼具保育价值的研究体系）中，采样设计会对我们认知遗传多样性与种群分化产生重大影响。4. 本研究呼吁种群遗传学研究中审慎考量采样设计的所有维度：即采集充足的样本量，确保各采样点位的性比一致，并依据研究问题选择适宜的采样时机。这一点在以物种保育为目标的研究中尤为关键。