Data from: Linkage disequilibrium and effective population size when generations overlap

Estimates of effective population size are critical for species of conservation concern. Genetic datasets can be used to provide robust estimates of this important parameter. However, the methods used to obtain these estimates assume that generations are discrete. We used simulated data to assess the influences of overlapping generations on estimates of effective size provided by the linkage disequilibrium method. Our simulations focus on two factors: the degree of reproductive skew exhibited by the focal species and the generation time, without considering sample size or the level of polymorphism at marker loci. In situations where a majority of reproduction is achieved by a small fraction of the population, the effective number of breeders can be much smaller than the per generation effective population size. The linkage disequilibrium in samples of newborns can provide estimates of the former size, while our results indicate that the latter size is best estimated using random samples of reproductively mature adults. Using samples of adults, the downwards bias was less than ~15% across our simulated life histories. As noted in previous assessments, precision of the estimate depends on the magnitude of effective size itself, with greater precision achieved for small populations.

有效种群大小（effective population size）的估算对于受保育关注的物种而言至关重要。遗传数据集可用于获取该关键参数的稳健估算结果。然而，当前用于获取此类估算的方法均假设世代为离散型。我们借助模拟数据，评估了重叠世代对连锁不平衡法（linkage disequilibrium method）所得有效种群大小估算值的影响。本模拟聚焦两个核心因素：目标物种的生殖偏倚程度与世代时长，未纳入样本量或标记位点多态性水平作为考察变量。当种群内多数繁殖仅由极小部分个体完成时，有效繁殖群体数可能远低于每世代有效种群大小。对新生个体的采样所得连锁不平衡数据，可用于估算前者的规模；而本研究结果显示，后者的最佳估算方式为采用随机采集的性成熟成年个体样本。在我们模拟的各类生活史场景中，使用成年个体样本时，估算值的向下偏差均小于约15%。正如此前相关评估所指出的，估算精度取决于有效种群大小本身的数值，种群规模越小，估算精度越高。