Estimation of contemporary effective population size and population declines using RAD sequence data

Large genomic datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of species. We used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (Ne) over the course of stable and declining population trends, and we compare the ability of two methods of analysis to accurately distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Using a linkage disequilibrium-based analysis, individual sampling (i.e., n ≥ 30) had the greatest effect on Ne estimation and the detection of population-size declines, with declines reliably detected across scenarios approximately 10 generations after they began. Coalescent-based inference required fewer sampled individuals (i.e., n = 15), and instead was most influenced by the size of the SNP dataset, with 25,...

基于限制性酶切位点相关DNA测序（restriction-site associated DNA sequencing, RADseq）产生的大型基因组数据集，结合种群人口统计学推断方法，正持续提升我们解析物种种群历史的能力。本研究采用模拟手段，探究了RADseq数据集在种群数量稳定或动态下降的过程中，精准估算有效种群大小（Ne）的潜力；同时对比了两种分析方法在当代时间尺度（20个世代）下，准确区分种群数量稳定与持续下降的能力。基于连锁不平衡（linkage disequilibrium）的分析结果表明，个体采样量（即n≥30）对Ne估算与种群数量下降的检测效果影响最为显著，在种群数量下降启动约10个世代后，即可在各类模拟场景中稳定检出下降信号。而基于溯祖的推断（coalescent-based inference）方法所需采样个体数更少（即n=15），其推断效果主要受单核苷酸多态性（single nucleotide polymorphism, SNP）数据集规模的影响，当数据集规模达到25……