Data from: Germ banks affect the inference of past demographic events

Continuous progress in empirical population genetics based on whole genome polymorphism data requires the theoretical analysis of refined models in order to interpret the evolutionary history of populations with adequate accuracy. Recent studies focus prevalently on the aspects of demography and adaptation, whereas age-structure (e.g. in plants via the maintenance of seed banks) has attracted less attention. Germ banking, i.e. seed or egg dormancy, is a prevalent and important life-history trait in plants and invertebrates, which buffers against environmental variability and modulates species extinction in fragmented habitats. Within this study, we investigate the combined effect of germ banking and time-varying population size on the neutral coalescent, and particularly derive the allele frequency spectrum under some simplifying assumptions. We then perform an ABC analysis using two simple demographic scenarios - a population expansion and an instantaneous decline. We demonstrate the appreciable influence of seed banks on the estimation of demographic parameters depending on the germination rate with biases scaled by the square of the germination rate. In the more complex case of a population bottleneck, which comprises an instantaneous decline and an expansion phase, ignoring information on the germination rate denies reliable estimates of the bottleneck parameters via the allelic spectrum. In particular, when seeds remain in the bank over several generations, recent expansions may remain invisible in the frequency spectrum, whereas ancient declines leave signatures much longer than in the absence of seed bank.依托全基因组多态性数据开展的实验种群遗传学研究持续推进，亟需通过精细化模型的理论分析，以足够精度解析种群的演化历史。当前相关研究多聚焦于种群动态与适应性演化相关议题，而年龄结构（例如植物通过维持种子库形成的年龄结构）则较少获得关注。种质保存（germ banking），即种子或卵的休眠行为，是植物与无脊椎动物中普遍存在的重要生活史性状，可缓冲环境波动的影响，并调控破碎化生境中的物种灭绝风险。本研究探讨了种质保存与动态种群规模对中性溯祖（coalescent）过程的联合效应，并在若干简化假设下推导了等位基因频率谱的解析形式。随后我们针对两种简单的种群动态情景——种群扩张与瞬时种群缩减，开展了近似贝叶斯计算（Approximate Bayesian Computation, ABC）分析。研究结果表明，种子库对种群动态参数估计的影响显著，其估计偏差与萌发率的平方呈正相关。在包含瞬时缩减与扩张阶段的复杂种群瓶颈情景中，若忽略萌发率相关信息，则无法通过等位基因谱得到可靠的瓶颈参数估计结果。具体而言，当种子可在库中留存多代时，近期发生的种群扩张可能无法在等位基因频率谱中留下信号；而远古的种群缩减在频率谱中留下的特征持续时间，也远长于无种子库的情景。