Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci

Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of SNP loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP dataset are unlinked. The approach is applied to an empirical dataset of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred.利用无连锁遗传标记对间的连锁不平衡（linkage disequilibrium, LD）估算当代有效种群大小（contemporary effective population size, Ne），现已成为种群遗传学与保护遗传学领域的重要研究手段。若可获取遗传标记的物理连锁信息或基因组定位数据，则可将基因座间重组率的估算结果与LD数据相结合，以推算过去不同时间点的当代有效种群大小。本研究将学界广为熟知的基于LD的当代Ne估算方法拓展为纳入连锁信息的版本，并通过模拟实验证实：即便仅使用适度数量的单核苷酸多态性（single nucleotide polymorphism, SNP）基因座，也可可靠检测出Ne近期发生的相对小幅变化。本研究探讨了若干对结果解读至关重要的问题，并量化了因假设大型SNP数据集内所有基因座均无连锁而引发的当代Ne估算偏差。本研究将该方法应用于一组海水鱼类种群的SNP基因型实证数据集，该种群曾被证实近期出现过Ne的暂时性下降。