Waples Robin S, Antao Tiago, Luikart Gordon
Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112
Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA United Kingdom.
Genetics. 2014 Jun;197(2):769-80. doi: 10.1534/genetics.114.164822. Epub 2014 Apr 8.
Use of single-sample genetic methods to estimate effective population size has skyrocketed in recent years. Although the underlying models assume discrete generations, they are widely applied to age-structured species. We simulated genetic data for 21 iteroparous animal and plant species to evaluate two untested hypotheses regarding performance of the single-sample method based on linkage disequilibrium (LD): (1) estimates based on single-cohort samples reflect the effective number of breeders in one reproductive cycle (Nb), and (2) mixed-age samples reflect the effective size per generation (Ne). We calculated true Ne and Nb, using the model species' vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by Nb and Ne and confirm this with simulated results: [Formula: see text] was a linear (r(2) = 0.98) function of the harmonic mean of Ne and Nb. We provide a quantitative bias correction for raw [Formula: see text] based on the ratio Nb/Ne, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true Nb for all 21 study species and proved robust when challenged with new data. Mixed-age adult samples produced downwardly biased estimates in all species, which we attribute to a two-locus Wahlund effect (mixture LD) caused by combining parents from different cohorts in a single sample. Results from this study will facilitate interpretation of rapidly accumulating genetic estimates in terms of both Ne (which influences long-term evolutionary processes) and Nb (which is more important for understanding eco-evolutionary dynamics and mating systems).
近年来，使用单样本遗传方法来估计有效种群大小的情况急剧增加。尽管基础模型假设世代离散，但它们被广泛应用于具有年龄结构的物种。我们模拟了21种反复生殖的动植物物种的遗传数据，以评估关于基于连锁不平衡（LD）的单样本方法性能的两个未经检验的假设：（1）基于单一群落样本的估计反映了一个繁殖周期内繁殖个体的有效数量（Nb），以及（2）混合年龄样本反映了每代的有效大小（Ne）。我们使用模型物种的生命率计算了真实的Ne和Nb，并通过基于个体的模拟进行了验证。我们表明，单一群落样本应受到Nb和Ne的同等影响，并通过模拟结果证实了这一点：[公式：见正文]是Ne和Nb调和均值的线性函数（r(2)=0.98）。我们基于Nb/Ne的比率为原始的[公式：见正文]提供了定量偏差校正，该比率可从两三个简单的生活史特征中估计出来。对于所有21个研究物种，偏差调整后的估计值在真实Nb的5%以内，并且在面对新数据时被证明是稳健的。混合年龄的成年样本在所有物种中都产生了向下偏差的估计值，我们将其归因于在单个样本中合并来自不同群落的亲本所导致的两位点瓦伦德效应（混合LD）。这项研究的结果将有助于根据Ne（影响长期进化过程）和Nb（对于理解生态进化动态和交配系统更为重要）来解释快速积累的遗传估计值。
